value: Coiled-coil and C2 domain-containing protein 2A

value: Component of the tectonic-like complex, a complex localized at the transition zone of primary cilia and acting as a barrier that prevents diffusion of transmembrane proteins between the cilia and plasma membranes. Required for ciliogenesis and sonic hedgehog/SHH signaling (By similarity)

value: Part of the tectonic-like complex (also named B9 complex)

commentType: SUBUNIT

value: Localizes at the transition zone, a region between the basal body and the ciliary axoneme

value: Cytoplasm

value: Cytoplasm, cytoskeleton, cilium basal body

commentType: ALTERNATIVE PRODUCTS

value: Strongly expressed in prostate, pancreas, kidney, lung, liver, retina, kidney, fetal brain and fetal kidney. Lower expression in spleen, small intestine, colon, skeletal muscle, ovary, thymus and heart

value: At Carnagie stage 13 (CS13, after 4 weeks of development) and CS14 CC2D2A is ubiquitously expressed, with a distinct signal in the spinal cord and limb buds. At CS17 CC2D2A continue to be widely expressedin particular throughout the central nervous system (CNS), lung, and digestive tract epithelia. At CS22 expression continues to be intense within the CNS, where strong and specific expression is observed in the eye and in external granular layer of cerebellum. CC2D2A expression is also observed in the costal perichondrium

commentType: DISEASE

diseaseId: Meckel syndrome 6

description: A disorder characterized by a combination of renal cysts and variably associated features including developmental anomalies of the central nervous system (typically encephalocele), hepatic ductal dysplasia and cysts, and polydactyly.

database: MIM

value: The disease is caused by variants affecting the gene represented in this entry

diseaseId: Joubert syndrome 9

description: A disorder presenting with cerebellar ataxia, oculomotor apraxia, hypotonia, neonatal breathing abnormalities and psychomotor delay. Neuroradiologically, it is characterized by cerebellar vermian hypoplasia/aplasia, thickened and reoriented superior cerebellar peduncles, and an abnormally large interpeduncular fossa, giving the appearance of a molar tooth on transaxial slices (molar tooth sign). Additional variable features include retinal dystrophy and renal disease.

diseaseId: COACH syndrome 2

description: A form of COACH syndrome, a disorder characterized by cerebellar vermis hypoplasia, developmental delay, impaired intellectual development, ataxia, and hepatic fibrosis. Patients present the molar tooth sign, a midbrain-hindbrain malformation pathognomonic for Joubert syndrome and related disorders. Other features, such as coloboma and renal cysts, may be variable. COACH2 inheritance is autosomal recessive.

diseaseId: Retinitis pigmentosa 93

description: A form of retinitis pigmentosa, a retinal dystrophy belonging to the group of pigmentary retinopathies. Retinitis pigmentosa is characterized by retinal pigment deposits visible on fundus examination and primary loss of rod photoreceptor cells followed by secondary loss of cone photoreceptors. Patients typically have night vision blindness and loss of midperipheral visual field. RP93 is an autosomal recessive, mild to moderate form, with onset in the second or third decade of life.

sequenceCautionType: Miscellaneous discrepancy

note: Contaminating sequence. Potential poly-A sequence.

note: Aberrant splicing.

description: Coiled-coil and C2 domain-containing protein 2A

description: Disordered

description: Disordered

description: Disordered

type: Compositional bias

description: Basic and acidic residues

description: Basic residues

description: Basic and acidic residues

description: Basic and acidic residues

description: Acidic residues

description: Polar residues

description: in isoform 2

description: in isoform 3

description: in isoform 4

description: in isoform 4

description: in isoform 3

description: in isoform 2

description: in JBTS9; uncertain significance; dbSNP:rs186264635

description: in dbSNP:rs16892095

description: in JBTS9; benign; dbSNP:rs144439937

description: in JBTS9; dbSNP:rs754221308

description: in dbSNP:rs16892134

description: in dbSNP:rs190698163

description: in dbSNP:rs537906621

description: in JBTS9; dbSNP:rs199768782

description: in dbSNP:rs751256652

description: in RP93; dbSNP:rs200707391

description: in JBTS9; dbSNP:rs863225173

description: in JBTS9; dbSNP:rs863225169

description: in MKS6 and JBTS9; dbSNP:rs386833752

description: in COACH2 and JBTS9; dbSNP:rs267606709

description: in JBTS9; dbSNP:rs118204051

description: in JBTS9; dbSNP:rs1473532901

description: in JBTS9; dbSNP:rs863225170

description: in JBTS9; dbSNP:rs386833755

description: in JBTS9; dbSNP:rs779823379

description: in JBTS9; dbSNP:rs754586025

description: in JBTS9; uncertain significance; dbSNP:rs763486732

description: in MKS6; uncertain significance

description: in JBTS9; dbSNP:rs863225168

description: in JBTS9; digenic inheritance; the patient also carries mutation C-360 in CEP41; dbSNP:rs387907058

description: in MKS6; uncertain significance; dbSNP:rs780673487

description: in MKS6; uncertain significance

description: in JBTS9; dbSNP:rs1478902342

description: in JBTS9 and COACH2; dbSNP:rs118204052

description: in JBTS9; dbSNP:rs763425007

description: in JBTS9; dbSNP:rs201502401

description: in JBTS9

description: in Ref. 5; AAI03711

authors:
Tallila J.
Jakkula E.
Peltonen L.
Salonen R.
Kestilae M.

title: Identification of CC2D2A as a Meckel syndrome gene adds an important piece to the ciliopathy puzzle.

referencePositions:
NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1)
FUNCTION
INVOLVEMENT IN MKS6

authors:
Nagase T.
Kikuno R.
Ishikawa K.
Hirosawa M.
Ohara O.

title: Prediction of the coding sequences of unidentified human genes. XVI. The complete sequences of 150 new cDNA clones from brain which code for large proteins in vitro.

referencePositions: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2)

authors:
Hillier L.W.
Graves T.A.
Fulton R.S.
Fulton L.A.
Pepin K.H.
Minx P.
Wagner-McPherson C.
Layman D.
Wylie K.
Sekhon M.
Becker M.C.
Fewell G.A.
Delehaunty K.D.
Miner T.L.
Nash W.E.
Kremitzki C.
Oddy L.
Du H.
Sun H.
Bradshaw-Cordum H.
Ali J.
Carter J.
Cordes M.
Harris A.
Isak A.
van Brunt A.
Nguyen C.
Du F.
Courtney L.
Kalicki J.
Ozersky P.
Abbott S.
Armstrong J.
Belter E.A.
Caruso L.
Cedroni M.
Cotton M.
Davidson T.
Desai A.
Elliott G.
Erb T.
Fronick C.
Gaige T.
Haakenson W.
Haglund K.
Holmes A.
Harkins R.
Kim K.
Kruchowski S.S.
Strong C.M.
Grewal N.
Goyea E.
Hou S.
Levy A.
Martinka S.
Mead K.
McLellan M.D.
Meyer R.
Randall-Maher J.
Tomlinson C.
Dauphin-Kohlberg S.
Kozlowicz-Reilly A.
Shah N.
Swearengen-Shahid S.
Snider J.
Strong J.T.
Thompson J.
Yoakum M.
Leonard S.
Pearman C.
Trani L.
Radionenko M.
Waligorski J.E.
Wang C.
Rock S.M.
Tin-Wollam A.-M.
Maupin R.
Latreille P.
Wendl M.C.
Yang S.-P.
Pohl C.
Wallis J.W.
Spieth J.
Bieri T.A.
Berkowicz N.
Nelson J.O.
Osborne J.
Ding L.
Meyer R.
Sabo A.
Shotland Y.
Sinha P.
Wohldmann P.E.
Cook L.L.
Hickenbotham M.T.
Eldred J.
Williams D.
Jones T.A.
She X.
Ciccarelli F.D.
Izaurralde E.
Taylor J.
Schmutz J.
Myers R.M.
Cox D.R.
Huang X.
McPherson J.D.
Mardis E.R.
Clifton S.W.
Warren W.C.
Chinwalla A.T.
Eddy S.R.
Marra M.A.
Ovcharenko I.
Furey T.S.
Miller W.
Eichler E.E.
Bork P.
Suyama M.
Torrents D.
Waterston R.H.
Wilson R.K.

title: Generation and annotation of the DNA sequences of human chromosomes 2 and 4.

referencePositions: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]

authors:
Mural R.J.
Istrail S.
Sutton G.
Florea L.
Halpern A.L.
Mobarry C.M.
Lippert R.
Walenz B.
Shatkay H.
Dew I.
Miller J.R.
Flanigan M.J.
Edwards N.J.
Bolanos R.
Fasulo D.
Halldorsson B.V.
Hannenhalli S.
Turner R.
Yooseph S.
Lu F.
Nusskern D.R.
Shue B.C.
Zheng X.H.
Zhong F.
Delcher A.L.
Huson D.H.
Kravitz S.A.
Mouchard L.
Reinert K.
Remington K.A.
Clark A.G.
Waterman M.S.
Eichler E.E.
Adams M.D.
Hunkapiller M.W.
Myers E.W.
Venter J.C.

title: The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC).

referencePositions: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORMS 3 AND 4)

referencePositions: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 1-527 (ISOFORM 2)

authors:
Ota T.
Suzuki Y.
Nishikawa T.
Otsuki T.
Sugiyama T.
Irie R.
Wakamatsu A.
Hayashi K.
Sato H.
Nagai K.
Kimura K.
Makita H.
Sekine M.
Obayashi M.
Nishi T.
Shibahara T.
Tanaka T.
Ishii S.
Yamamoto J.
Saito K.
Kawai Y.
Isono Y.
Nakamura Y.
Nagahari K.
Murakami K.
Yasuda T.
Iwayanagi T.
Wagatsuma M.
Shiratori A.
Sudo H.
Hosoiri T.
Kaku Y.
Kodaira H.
Kondo H.
Sugawara M.
Takahashi M.
Kanda K.
Yokoi T.
Furuya T.
Kikkawa E.
Omura Y.
Abe K.
Kamihara K.
Katsuta N.
Sato K.
Tanikawa M.
Yamazaki M.
Ninomiya K.
Ishibashi T.
Yamashita H.
Murakawa K.
Fujimori K.
Tanai H.
Kimata M.
Watanabe M.
Hiraoka S.
Chiba Y.
Ishida S.
Ono Y.
Takiguchi S.
Watanabe S.
Yosida M.
Hotuta T.
Kusano J.
Kanehori K.
Takahashi-Fujii A.
Hara H.
Tanase T.-O.
Nomura Y.
Togiya S.
Komai F.
Hara R.
Takeuchi K.
Arita M.
Imose N.
Musashino K.
Yuuki H.
Oshima A.
Sasaki N.
Aotsuka S.
Yoshikawa Y.
Matsunawa H.
Ichihara T.
Shiohata N.
Sano S.
Moriya S.
Momiyama H.
Satoh N.
Takami S.
Terashima Y.
Suzuki O.
Nakagawa S.
Senoh A.
Mizoguchi H.
Goto Y.
Shimizu F.
Wakebe H.
Hishigaki H.
Watanabe T.
Sugiyama A.
Takemoto M.
Kawakami B.
Yamazaki M.
Watanabe K.
Kumagai A.
Itakura S.
Fukuzumi Y.
Fujimori Y.
Komiyama M.
Tashiro H.
Tanigami A.
Fujiwara T.
Ono T.
Yamada K.
Fujii Y.
Ozaki K.
Hirao M.
Ohmori Y.
Kawabata A.
Hikiji T.
Kobatake N.
Inagaki H.
Ikema Y.
Okamoto S.
Okitani R.
Kawakami T.
Noguchi S.
Itoh T.
Shigeta K.
Senba T.
Matsumura K.
Nakajima Y.
Mizuno T.
Morinaga M.
Sasaki M.
Togashi T.
Oyama M.
Hata H.
Watanabe M.
Komatsu T.
Mizushima-Sugano J.
Satoh T.
Shirai Y.
Takahashi Y.
Nakagawa K.
Okumura K.
Nagase T.
Nomura N.
Kikuchi H.
Masuho Y.
Yamashita R.
Nakai K.
Yada T.
Nakamura Y.
Ohara O.
Isogai T.
Sugano S.

title: Complete sequencing and characterization of 21,243 full-length human cDNAs.

referencePositions: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 283-1620 (ISOFORMS 1/2)

authors:
Noor A.
Windpassinger C.
Patel M.
Stachowiak B.
Mikhailov A.
Azam M.
Irfan M.
Siddiqui Z.K.
Naeem F.
Paterson A.D.
Lutfullah M.
Vincent J.B.
Ayub M.

title: CC2D2A, encoding a coiled-coil and C2 domain protein, causes autosomal-recessive mental retardation with retinitis pigmentosa.

referencePositions:
TISSUE SPECIFICITY
SUBCELLULAR LOCATION
INVOLVEMENT IN JBTS9

authors:
Noor A.
Windpassinger C.
Patel M.
Stachowiak B.
Mikhailov A.
Azam M.
Irfan M.
Paterson A.D.
Lutufullah M.
Doherty D.
Vincent J.B.
Ayub M.

authors:
Mougou-Zerelli S.
Thomas S.
Szenker E.
Audollent S.
Elkhartoufi N.
Babarit C.
Romano S.
Salomon R.
Amiel J.
Esculpavit C.
Gonzales M.
Escudier E.
Leheup B.
Loget P.
Odent S.
Roume J.
Gerard M.
Delezoide A.-L.
Khung S.
Patrier S.
Cordier M.-P.
Bouvier R.
Martinovic J.
Gubler M.-C.
Boddaert N.
Munnich A.
Encha-Razavi F.
Valente E.M.
Saad A.
Saunier S.
Vekemans M.
Attie-Bitach T.

title: CC2D2A mutations in Meckel and Joubert syndromes indicate a genotype-phenotype correlation.

referencePositions: VARIANTS JBTS9 SER-721; MET-1114 AND VAL-1556

authors:
Gorden N.T.
Arts H.H.
Parisi M.A.
Coene K.L.M.
Letteboer S.J.F.
van Beersum S.E.C.
Mans D.A.
Hikida A.
Eckert M.
Knutzen D.
Alswaid A.F.
Oezyurek H.
Dibooglu S.
Otto E.A.
Liu Y.
Davis E.E.
Hutter C.M.
Bammler T.K.
Farin F.M.
Dorschner M.
Topcu M.
Zackai E.H.
Rosenthal P.
Owens K.N.
Katsanis N.
Vincent J.B.
Hildebrandt F.
Rubel E.W.
Raible D.W.
Knoers N.V.A.M.
Chance P.F.
Roepman R.
Moens C.B.
Glass I.A.
Doherty D.

title: CC2D2A is mutated in Joubert syndrome and interacts with the ciliopathy-associated basal body protein CEP290.

referencePositions: VARIANTS JBTS9 HIS-1096; SER-1122; CYS-1528 AND PRO-1551

authors:
Tallila J.
Salonen R.
Kohlschmidt N.
Peltonen L.
Kestilae M.

title: Mutation spectrum of Meckel syndrome genes: one group of syndromes or several distinct groups?

authors:
Doherty D.
Parisi M.A.
Finn L.S.
Gunay-Aygun M.
Al-Mateen M.
Bates D.
Clericuzio C.
Demir H.
Dorschner M.
van Essen A.J.
Gahl W.A.
Gentile M.
Gorden N.T.
Hikida A.
Knutzen D.
Ozyurek H.
Phelps I.
Rosenthal P.
Verloes A.
Weigand H.
Chance P.F.
Dobyns W.B.
Glass I.A.

title: Mutations in 3 genes (MKS3, CC2D2A and RPGRIP1L) cause COACH syndrome (Joubert syndrome with congenital hepatic fibrosis).

authors:
Srour M.
Schwartzentruber J.
Hamdan F.F.
Ospina L.H.
Patry L.
Labuda D.
Massicotte C.
Dobrzeniecka S.
Capo-Chichi J.M.
Papillon-Cavanagh S.
Samuels M.E.
Boycott K.M.
Shevell M.I.
Laframboise R.
Desilets V.
Maranda B.
Rouleau G.A.
Majewski J.
Michaud J.L.

title: Mutations in C5ORF42 cause Joubert syndrome in the French Canadian population.

authors:
Bachmann-Gagescu R.
Ishak G.E.
Dempsey J.C.
Adkins J.
O'Day D.
Phelps I.G.
Gunay-Aygun M.
Kline A.D.
Szczaluba K.
Martorell L.
Alswaid A.
Alrasheed S.
Pai S.
Izatt L.
Ronan A.
Parisi M.A.
Mefford H.
Glass I.
Doherty D.

title: Genotype-phenotype correlation in CC2D2A-related Joubert syndrome reveals an association with ventriculomegaly and seizures.

authors:
Srour M.
Hamdan F.F.
Schwartzentruber J.A.
Patry L.
Ospina L.H.
Shevell M.I.
Desilets V.
Dobrzeniecka S.
Mathonnet G.
Lemyre E.
Massicotte C.
Labuda D.
Amrom D.
Andermann E.
Sebire G.
Maranda B.
Rouleau G.A.
Majewski J.
Michaud J.L.

title: Mutations in TMEM231 cause Joubert syndrome in French Canadians.

referencePositions: VARIANTS JBTS9 LYS-1126; SER-1520; VAL-1556 AND HIS-1568

authors:
Lee J.E.
Silhavy J.L.
Zaki M.S.
Schroth J.
Bielas S.L.
Marsh S.E.
Olvera J.
Brancati F.
Iannicelli M.
Ikegami K.
Schlossman A.M.
Merriman B.
Attie-Bitach T.
Logan C.V.
Glass I.A.
Cluckey A.
Louie C.M.
Lee J.H.
Raynes H.R.
Rapin I.
Castroviejo I.P.
Setou M.
Barbot C.
Boltshauser E.
Nelson S.F.
Hildebrandt F.
Johnson C.A.
Doherty D.A.
Valente E.M.
Gleeson J.G.

title: CEP41 is mutated in Joubert syndrome and is required for tubulin glutamylation at the cilium.

authors:
Jones D.
Fiozzo F.
Waters B.
McKnight D.
Brown S.

title: First-trimester diagnosis of Meckel-Gruber syndrome by fetal ultrasound with molecular identification of CC2D2A mutations by next-generation sequencing.

authors:
Srour M.
Hamdan F.F.
McKnight D.
Davis E.
Mandel H.
Schwartzentruber J.
Martin B.
Patry L.
Nassif C.
Dionne-Laporte A.
Ospina L.H.
Lemyre E.
Massicotte C.
Laframboise R.
Maranda B.
Labuda D.
Decarie J.C.
Rypens F.
Goldsher D.
Fallet-Bianco C.
Soucy J.F.
Laberge A.M.
Maftei C.
Boycott K.
Brais B.
Boucher R.M.
Rouleau G.A.
Katsanis N.
Majewski J.
Elpeleg O.
Kukolich M.K.
Shalev S.
Michaud J.L.

title: Joubert Syndrome in French Canadians and Identification of Mutations in CEP104.

authors:
Mejecase C.
Hummel A.
Mohand-Said S.
Andrieu C.
El Shamieh S.
Antonio A.
Condroyer C.
Boyard F.
Foussard M.
Blanchard S.
Letexier M.
Saraiva J.P.
Sahel J.A.
Zeitz C.
Audo I.

title: Whole exome sequencing resolves complex phenotype and identifies CC2D2A mutations underlying non-syndromic rod-cone dystrophy.

referencePositions:
INVOLVEMENT IN RP93
VARIANT RP93 PRO-925

authors:
Radhakrishnan P.
Nayak S.S.
Shukla A.
Lindstrand A.
Girisha K.M.

title: Meckel syndrome: Clinical and mutation profile in six fetuses.

value: 3 GO annotations based on evolutionary models

value: Anchoring of the basal body to the plasma membrane

value: Expressed in right uterine tube and 172 other cell types or tissues

value: P:protein localization to ciliary transition zone

value: COILED-COIL AND C2 DOMAIN-CONTAINING PROTEIN 2A


entryType: UniProtKB reviewed (Swiss-Prot)

scientificName: Schizosaccharomyces pombe (strain 972 / ATCC 24843)

commonName: Fission yeast

lineage: Eukaryota Fungi Dikarya Ascomycota Taphrinomycotina Schizosaccharomycetes Schizosaccharomycetales Schizosaccharomycetaceae Schizosaccharomyces

proteinExistence: 1: Evidence at protein level

value: rRNA biogenesis protein rrp36

value: Ribosomal RNA-processing protein 36

value: Component of the 90S pre-ribosome involved in the maturation of rRNAs. Required for early cleavages of the pre-RNAs in the 40S ribosomal subunit maturation pathway (By similarity)

commentType: FUNCTION

value: Associates with 90S and pre-40S pre-ribosomal particles

commentType: SUBCELLULAR LOCATION

source: PubMed

value: Nucleus, nucleolus

value: Belongs to the RRP36 family

commentType: SIMILARITY

type: Chain

modifier: EXACT

description: rRNA biogenesis protein rrp36

type: Region

description: Disordered

source: SAM

description: Disordered

type: Coiled coil

description: Polar residues

description: Acidic residues

description: Basic and acidic residues

description: Basic residues

Coiled coil

category: Domain

Nucleus

category: Cellular component

Reference proteome

category: Technical term

Ribonucleoprotein

category: Molecular function

Ribosome biogenesis

category: Biological process

citationType: journal article

authors:
Wood V.
Gwilliam R.
Rajandream M.A.
Lyne M.H.
Lyne R.
Stewart A.
Sgouros J.G.
Peat N.
Hayles J.
Baker S.G.
Basham D.
Bowman S.
Brooks K.
Brown D.
Brown S.
Chillingworth T.
Churcher C.M.
Collins M.
Connor R.
Cronin A.
Davis P.
Feltwell T.
Fraser A.
Gentles S.
Goble A.
Hamlin N.
Harris D.E.
Hidalgo J.
Hodgson G.
Holroyd S.
Hornsby T.
Howarth S.
Huckle E.J.
Hunt S.
Jagels K.
James K.D.
Jones L.
Jones M.
Leather S.
McDonald S.
McLean J.
Mooney P.
Moule S.
Mungall K.L.
Murphy L.D.
Niblett D.
Odell C.
Oliver K.
O'Neil S.
Pearson D.
Quail M.A.
Rabbinowitsch E.
Rutherford K.M.
Rutter S.
Saunders D.
Seeger K.
Sharp S.
Skelton J.
Simmonds M.N.
Squares R.
Squares S.
Stevens K.
Taylor K.
Taylor R.G.
Tivey A.
Walsh S.V.
Warren T.
Whitehead S.
Woodward J.R.
Volckaert G.
Aert R.
Robben J.
Grymonprez B.
Weltjens I.
Vanstreels E.
Rieger M.
Schaefer M.
Mueller-Auer S.
Gabel C.
Fuchs M.
Duesterhoeft A.
Fritzc C.
Holzer E.
Moestl D.
Hilbert H.
Borzym K.
Langer I.
Beck A.
Lehrach H.
Reinhardt R.
Pohl T.M.
Eger P.
Zimmermann W.
Wedler H.
Wambutt R.
Purnelle B.
Goffeau A.
Cadieu E.
Dreano S.
Gloux S.
Lelaure V.
Mottier S.
Galibert F.
Aves S.J.
Xiang Z.
Hunt C.
Moore K.
Hurst S.M.
Lucas M.
Rochet M.
Gaillardin C.
Tallada V.A.
Garzon A.
Thode G.
Daga R.R.
Cruzado L.
Jimenez J.
Sanchez M.
del Rey F.
Benito J.
Dominguez A.
Revuelta J.L.
Moreno S.
Armstrong J.
Forsburg S.L.
Cerutti L.
Lowe T.
McCombie W.R.
Paulsen I.
Potashkin J.
Shpakovski G.V.
Ussery D.
Barrell B.G.
Nurse P.

database: PubMed

database: DOI

title: The genome sequence of Schizosaccharomyces pombe.

journal: Nature

type: STRAIN

authors:
Matsuyama A.
Arai R.
Yashiroda Y.
Shirai A.
Kamata A.
Sekido S.
Kobayashi Y.
Hashimoto A.
Hamamoto M.
Hiraoka Y.
Horinouchi S.
Yoshida M.

title: ORFeome cloning and global analysis of protein localization in the fission yeast Schizosaccharomyces pombe.

journal: Nat. Biotechnol.

referencePositions: SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS]

authors:
Bitton D.A.
Wood V.
Scutt P.J.
Grallert A.
Yates T.
Smith D.L.
Hagan I.M.
Miller C.J.

title: Augmented annotation of the Schizosaccharomyces pombe genome reveals additional genes required for growth and viability.

journal: Genetics

referencePositions:
REVISION OF GENE MODEL
IDENTIFICATION BY MASS SPECTROMETRY

authors:
Hu W.
Suo F.
Du L.L.

title: Bulk segregant analysis reveals the genetic basis of a natural trait variation in fission yeast.

journal: Genome Biol. Evol.

database: EMBL

key: ProteinId

key: Status

key: MoleculeType

database: AlphaFoldDB

key: Description

database: BioGRID

key: Interactions

database: FunCoup

key: Number of interactors

database: STRING

database: iPTMnet

database: PaxDb

database: PomBase

key: GeneName

database: VEuPathDB

database: eggNOG

key: ToxonomicScope

value: Eukaryota

database: HOGENOM

database: InParanoid

database: OMA

key: Fingerprint

database: Reactome

key: PathwayName

value: Major pathway of rRNA processing in the nucleolus and cytosol

database: PRO

database: Proteomes

value: P:maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)

value: RIBOSOMAL RNA PROCESSING PROTEIN 36 HOMOLOG


proteinExistence: 3: Inferred from homology

value: DNA-dependent metalloprotease WSS1 homolog

source: UniProtKB

value: DNA damage response protein WSS1 homolog

source: PomBase

value: Metalloendopeptidase that acts selectively on DNA-binding proteins. DNA is needed to bring the protease and substrates together to enable proteolysis. Involved in the repair of toxic DNA-protein cross-links (DPCs) such as covalently trapped topoisomerase 1 (top1) adducts on DNA lesions or DPCs induced by reactive compounds such as formaldehyde. Involved in DNA damage response and processing of stalled or collapsed replication forks by removing the covalently trapped top1 from chromatin. DPC proteolysis enables the repair of the lesions via downstream DNA repair pathways. May be recruited to DPCs via the SUMOylation of substrate proteins at damaged DNA sites (By similarity)

commentType: COFACTOR

database: ChEBI

value: Binds to DNA. Interacts with pmt3/smt3

value: Nucleus

value: The SUMO interaction motif (SIM) is important for binding to pmt3/smt3 (SUMO)

commentType: DOMAIN

value: Belongs to the peptidase M3 family. WSS1-like metalloprotease (WLM) subfamily

type: Domain

description: WLM

source: PROSITE-ProRule

description: Disordered

type: Motif

description: SUMO interaction motif (SIM)

description: Basic residues

type: Active site

type: Binding site

note: catalytic

Metal-binding

category: Ligand

database: PubMed

database: DOI

database: RefSeq

key: NucleotideSequenceId

database: SMR

database: MEROPS

database: GeneID

database: KEGG

value: P:protein-DNA covalent cross-linking repair


value: Copper amine oxidase 1

value: Copper amine oxidase involved in the metabolism of xenobiotic and biogenic amines. Capable of catalyzing the oxidative deamination of primary amines such as ethylamine as alternate sources of nitrogen to support growth

commentType: CATALYTIC ACTIVITY

name: a primary methyl amine + O2 + H2O = an aldehyde + H2O2 + NH4(+)

database: Rhea

value: Binds 1 copper ion per subunit (By similarity). Can also use zinc ion as cofactor (By similarity).

value: Contains 1 topaquinone per subunit.

value: Binds 1 Mn(2+) ion per subunit.

value: Homodimer

value: Cytoplasm

value: Topaquinone (TPQ) is generated by copper-dependent autoxidation of a specific tyrosyl residue

commentType: PTM

value: Belongs to the copper/topaquinone oxidase family

description: Copper amine oxidase 1

description: Proton acceptor

description: Schiff-base intermediate with substrate; via topaquinone

type: Modified residue

type: Disulfide bond

description: Decreases copper amine oxidase activity.

description: Impairs copper amine oxidase activity.

description: Impairs copper amine oxidase activity.

description: Impairs copper amine oxidase activity.

title: Mechanisms of copper loading on the Schizosaccharomyces pombe copper amine oxidase 1 expressed in Saccharomyces cerevisiae.

authors:
Peter C.
Laliberte J.
Beaudoin J.
Labbe S.

title: Copper distributed by Atx1 is available to copper amine oxidase 1 in Schizosaccharomyces pombe.

referencePositions: MUTAGENESIS OF HIS-456; HIS-458; HIS-460 AND HIS-627


value: AP-1 complex subunit sigma-1

value: Valproic acid-sensitive protein 2

value: Component of the AP-1 complex which links clathrin to receptors in coated vesicles. Clathrin-associated protein complexes are believed to interact with the cytoplasmic tails of membrane proteins, leading to their selection and concentration

value: Adaptor protein complex 1 (AP-1) is a heterotetramer composed of two large adaptins (gamma-type subunit apl4 and beta-type subunit apl2), a medium adaptin (mu-type subunit apm1) and a small adaptin (sigma-type subunit aps1). AP-1 interacts with clathrin (By similarity)

value: Cytoplasmic vesicle, clathrin-coated vesicle membrane

value: Endosome

value: Golgi apparatus

value: Leads to hypersensitivity to valproic acid

commentType: DISRUPTION PHENOTYPE

value: Belongs to the adaptor complexes small subunit family

description: AP-1 complex subunit sigma-1

authors:
Ma Y.
Takeuchi M.
Sugiura R.
Sio S.O.
Kuno T.

title: Deletion mutants of AP-1 adaptin subunits display distinct phenotypes in fission yeast.

journal: Genes Cells

referencePositions:
DISRUPTION PHENOTYPE
IDENTIFICATION IN THE AP-1 COMPLEX
SUBCELLULAR LOCATION
FUNCTION

database: EMBL

database: AlphaFoldDB

database: BioGRID

database: ComplexPortal

key: EntryName

value: Adaptor complex AP-1

database: FunCoup

database: STRING

database: PaxDb

database: PomBase

database: VEuPathDB

value: Eukaryota

database: PhylomeDB

value: Lysosome Vesicle Biogenesis

key: Component

value: Chromosome I

database: GO

key: GoTerm

value: C:AP-1 adaptor complex

key: GoEvidenceType

value: P:endosome to plasma membrane protein transport

value: P:retrograde transport, endosome to Golgi

value: P:vesicle targeting, trans-Golgi to endosome


entryType: UniProtKB unreviewed (TrEMBL)

scientificName: Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1)

source: EMBL

source: Proteomes

lineage: Bacteria Thermotogati Deinococcota Deinococci Deinococcales Deinococcaceae Deinococcus

source: ARBA

value: Small ribosomal subunit protein bS1

value: 30S ribosomal protein S1

value: Belongs to the bacterial ribosomal protein bS1 family

description: S1 motif

source: PROSITE

description: S1 motif

description: S1 motif

description: S1 motif

description: S1 motif

description: Disordered

description: Disordered

description: Polar residues

description: Low complexity

description: Gly residues

authors:
White O.
Eisen J.A.
Heidelberg J.F.
Hickey E.K.
Peterson J.D.
Dodson R.J.
Haft D.H.
Gwinn M.L.
Nelson W.C.
Richardson D.L.
Moffat K.S.
Qin H.
Jiang L.
Pamphile W.
Crosby M.
Shen M.
Vamathevan J.J.
Lam P.
McDonald L.
Utterback T.
Zalewski C.
Makarova K.S.
Aravind L.
Daly M.J.
Minton K.W.
Fleischmann R.D.
Ketchum K.A.
Nelson K.E.
Salzberg S.
Smith H.O.
Venter J.C.
Fraser C.M.

database: PubMed

database: DOI

title: Genome sequence of the radioresistant bacterium Deinococcus radiodurans R1.

journal: Science

database: PIR

database: EnsemblBacteria

key: GeneId

database: PATRIC

key: GeneDesignation

database: eggNOG

value: Bacteria

database: HOGENOM

database: InParanoid

database: OrthoDB

value: RNA-binding transcriptional accessory protein


scientificName: Arabidopsis thaliana

commonName: Mouse-ear cress

lineage: Eukaryota Viridiplantae Streptophyta Embryophyta Tracheophyta Spermatophyta Magnoliopsida eudicotyledons Gunneridae Pentapetalae rosids malvids Brassicales Brassicaceae Camelineae Arabidopsis

value: WD repeat-containing protein 76

source: TAIR

value: DROUGHT SENSITIVE 1

source: Araport

value: Specifically binds 5-hydroxymethylcytosine (5hmC), suggesting that it acts as a specific reader of 5hmC

value: Belongs to the WD repeat DDB2/WDR76 family

type: Repeat

description: WD

description: Disordered

description: Polar residues

Proteomics identification

source: PeptideAtlas

source: ProteomicsDB

authors:
Theologis A.
Ecker J.R.
Palm C.J.
Federspiel N.A.
Kaul S.
White O.
Alonso J.
Altafi H.
Araujo R.
Bowman C.L.
Brooks S.Y.
Buehler E.
Chan A.
Chao Q.
Chen H.
Cheuk R.F.
Chin C.W.
Chung M.K.
Conn L.
Conway A.B.
Conway A.R.
Creasy T.H.
Dewar K.
Dunn P.
Etgu P.
Feldblyum T.V.
Feng J.
Fong B.
Fujii C.Y.
Gill J.E.
Goldsmith A.D.
Haas B.
Hansen N.F.
Hughes B.
Huizar L.
Hunter J.L.
Jenkins J.
Johnson-Hopson C.
Khan S.
Khaykin E.
Kim C.J.
Koo H.L.
Kremenetskaia I.
Kurtz D.B.
Kwan A.
Lam B.
Langin-Hooper S.
Lee A.
Lee J.M.
Lenz C.A.
Li J.H.
Li Y.
Lin X.
Liu S.X.
Liu Z.A.
Luros J.S.
Maiti R.
Marziali A.
Militscher J.
Miranda M.
Nguyen M.
Nierman W.C.
Osborne B.I.
Pai G.
Peterson J.
Pham P.K.
Rizzo M.
Rooney T.
Rowley D.
Sakano H.
Salzberg S.L.
Schwartz J.R.
Shinn P.
Southwick A.M.
Sun H.
Tallon L.J.
Tambunga G.
Toriumi M.J.
Town C.D.
Utterback T.
Van Aken S.
Vaysberg M.
Vysotskaia V.S.
Walker M.
Wu D.
Yu G.
Fraser C.M.
Venter J.C.
Davis R.W.

title: Sequence and analysis of chromosome 1 of the plant Arabidopsis thaliana.

value: cv. Columbia

authors:
Cheng C.Y.
Krishnakumar V.
Chan A.P.
Thibaud-Nissen F.
Schobel S.
Town C.D.

title: Araport11: a complete reannotation of the Arabidopsis thaliana reference genome.

journal: Plant J.

database: EMBL

key: ProteinId

database: RefSeq

database: AlphaFoldDB

database: SMR

database: ProteomicsDB

database: GeneID

database: KEGG

database: Araport

database: TAIR

database: OMA

database: Proteomes

value: Chromosome 1

value: YVTN repeat-like/Quinoprotein amine dehydrogenase


scientificName: Homo sapiens

commonName: Human

lineage: Eukaryota Metazoa Chordata Craniata Vertebrata Euteleostomi Mammalia Eutheria Euarchontoglires Primates Haplorrhini Catarrhini Hominidae Homo

value: Catalytically inactive regulatory factor of DNA methyltransferases that can either promote or inhibit DNA methylation depending on the context (By similarity). Essential for the function of DNMT3A and DNMT3B: activates DNMT3A and DNMT3B by binding to their catalytic domain (PubMed:17687327). Acts by accelerating the binding of DNA and S-adenosyl-L-methionine (AdoMet) to the methyltransferases and dissociates from the complex after DNA binding to the methyltransferases (PubMed:17687327). Recognizes unmethylated histone H3 lysine 4 (H3K4me0) and induces de novo DNA methylation by recruitment or activation of DNMT3 (PubMed:17687327). Plays a key role in embryonic stem cells and germ cells (By similarity). In germ cells, required for the methylation of imprinted loci together with DNMT3A (By similarity). In male germ cells, specifically required to methylate retrotransposons, preventing their mobilization (By similarity). Plays a key role in embryonic stem cells (ESCs) by acting both as an positive and negative regulator of DNA methylation (By similarity). While it promotes DNA methylation of housekeeping genes together with DNMT3A and DNMT3B, it also acts as an inhibitor of DNA methylation at the promoter of bivalent genes (By similarity). Interacts with the EZH2 component of the PRC2/EED-EZH2 complex, preventing interaction of DNMT3A and DNMT3B with the PRC2/EED-EZH2 complex, leading to maintain low methylation levels at the promoters of bivalent genes (By similarity). Promotes differentiation of ESCs into primordial germ cells by inhibiting DNA methylation at the promoter of RHOX5, thereby activating its expression (By similarity)

value: Homodimer (PubMed:17687327, PubMed:17713477). Heterotetramer composed of 1 DNMT3A homodimer and 2 DNMT3L subunits (DNMT3L-DNMT3A-DNMT3A-DNMT3L) (PubMed:17713477). Interacts with histone H3 (via N-terminus); interaction is strongly inhibited by methylation at lysine 4 (H3K4me) (PubMed:17687327). Interacts with EZH2; the interaction is direct (By similarity). Interacts with SPOCD1 (By similarity)

commentType: INTERACTION

value: Nucleus

isoformSequenceStatus: Displayed

isoformSequenceStatus: Described

value: Other splice isoforms seem to exist.

value: Expressed at low levels in several tissues including testis, ovary, and thymus

commentType: TISSUE SPECIFICITY

value: Interaction with histone H3 is strongly inhibited by methylation at lysine 4 (H3K4me)

commentType: MISCELLANEOUS

description: DNA (cytosine-5)-methyltransferase 3-like

description: ADD

type: Zinc finger

description: GATA-type; atypical

description: PHD-type; atypical

type: Alternative sequence

description: in isoform 2

originalSequence: S

type: Natural variant

description: in dbSNP:rs7354779

database: dbSNP

originalSequence: R

type: Mutagenesis

description: Loss of binding to DNMT3A.

originalSequence: F

type: Sequence conflict

description: in Ref. 1; AAF05812

originalSequence: P

description: in Ref. 1; AAF05812

originalSequence: L

type: Helix

source: PDB

type: Turn

type: Beta strand

authors:
Aapola U.
Shibuya K.
Scott H.S.
Ollila J.
Vihinen M.
Heino M.
Shintani A.
Kawasaki K.
Minoshima S.
Krohn K.
Antonarakis S.E.
Shimizu N.
Kudoh J.
Peterson P.

title: Isolation and initial characterization of a novel zinc finger gene, DNMT3L, on 21q22.3, related to the cytosine-5-methyltransferase 3 gene family.

referencePositions:
NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 2)
ALTERNATIVE SPLICING
TISSUE SPECIFICITY

authors:
Hattori M.
Fujiyama A.
Taylor T.D.
Watanabe H.
Yada T.
Park H.-S.
Toyoda A.
Ishii K.
Totoki Y.
Choi D.-K.
Groner Y.
Soeda E.
Ohki M.
Takagi T.
Sakaki Y.
Taudien S.
Blechschmidt K.
Polley A.
Menzel U.
Delabar J.
Kumpf K.
Lehmann R.
Patterson D.
Reichwald K.
Rump A.
Schillhabel M.
Schudy A.
Zimmermann W.
Rosenthal A.
Kudoh J.
Shibuya K.
Kawasaki K.
Asakawa S.
Shintani A.
Sasaki T.
Nagamine K.
Mitsuyama S.
Antonarakis S.E.
Minoshima S.
Shimizu N.
Nordsiek G.
Hornischer K.
Brandt P.
Scharfe M.
Schoen O.
Desario A.
Reichelt J.
Kauer G.
Bloecker H.
Ramser J.
Beck A.
Klages S.
Hennig S.
Riesselmann L.
Dagand E.
Wehrmeyer S.
Borzym K.
Gardiner K.
Nizetic D.
Francis F.
Lehrach H.
Reinhardt R.
Yaspo M.-L.

title: The DNA sequence of human chromosome 21.

authors:
Mural R.J.
Istrail S.
Sutton G.G.
Florea L.
Halpern A.L.
Mobarry C.M.
Lippert R.
Walenz B.
Shatkay H.
Dew I.
Miller J.R.
Flanigan M.J.
Edwards N.J.
Bolanos R.
Fasulo D.
Halldorsson B.V.
Hannenhalli S.
Turner R.
Yooseph S.
Lu F.
Nusskern D.R.
Shue B.C.
Zheng X.H.
Zhong F.
Delcher A.L.
Huson D.H.
Kravitz S.A.
Mouchard L.
Reinert K.
Remington K.A.
Clark A.G.
Waterman M.S.
Eichler E.E.
Adams M.D.
Hunkapiller M.W.
Myers E.W.
Venter J.C.

title: The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC).

referencePositions: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1)

authors:
Ooi S.K.
Qiu C.
Bernstein E.
Li K.
Jia D.
Yang Z.
Erdjument-Bromage H.
Tempst P.
Lin S.-P.
Allis C.D.
Cheng X.
Bestor T.H.

title: DNMT3L connects unmethylated lysine 4 of histone H3 to de novo methylation of DNA.

referencePositions:
X-RAY CRYSTALLOGRAPHY (3.3 ANGSTROMS)
FUNCTION
HOMODIMERIZATION

authors:
Jia D.
Jurkowska R.Z.
Zhang X.
Jeltsch A.
Cheng X.

title: Structure of Dnmt3a bound to Dnmt3L suggests a model for de novo DNA methylation.

referencePositions: X-RAY CRYSTALLOGRAPHY (2.89 ANGSTROMS) OF 160-387

value: DNA (cytosine-5)-methyltransferase 3B complex

value: DNA (cytosine-5)-methyltransferase 3A complex

value: 4 GO annotations based on evolutionary models

value: Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs)

value: Expressed in male germ line stem cell (sensu Vertebrata) in testis and 58 other cell types or tissues

value: P:DNA methylation-dependent constitutive heterochromatin formation

value: P:negative regulation of DNA methylation-dependent heterochromatin formation

value: P:negative regulation of DNA-templated transcription

value: P:negative regulation of gene expression, epigenetic

value: P:transposable element silencing by heterochromatin formation

value: P:transposable element silencing by piRNA-mediated DNA methylation

value: Zinc/RING finger domain, C3HC4 (zinc finger)

value: DNA CYTOSINE-5- -METHYLTRANSFERASE 3-RELATED


value: Probable methyltransferase

value: Cytoplasm

value: Nucleus

value: Belongs to the methyltransferase superfamily

type: Chain

description: Uncharacterized methyltransferase C25B8.09

database: PubMed

database: DOI

referencePositions: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]

key: Status

database: PIR

database: BioGRID

database: FunCoup

database: STRING

database: iPTMnet

database: PaxDb

database: PomBase

database: VEuPathDB

value: Eukaryota

database: PhylomeDB

database: PRO

value: Chromosome I

database: GO

value: F:methyltransferase activity

value: P:cellular detoxification

value: P:cellular response to amino acid starvation

database: CDD

key: MatchStatus

database: FunFam

value: Vaccinia Virus protein VP39

value: METHYLTRANSFERASE TYPE 11 DOMAIN-CONTAINING PROTEIN


value: Ubiquitin carboxyl-terminal hydrolase 2

value: Ubiquitin-protein hydrolase is involved both in the processing of ubiquitin precursors and of ubiquitinated proteins. This enzyme is a thiol protease that recognizes and hydrolyzes a peptide bond at the C-terminal glycine of ubiquitin

name: Thiol-dependent hydrolysis of ester, thioester, amide, peptide and isopeptide bonds formed by the C-terminal Gly of ubiquitin (a 76-residue protein attached to proteins as an intracellular targeting signal).

value: Component of the 26S proteasome. Interacts with rpn10

value: Belongs to the peptidase C12 family

description: Ubiquitin carboxyl-terminal hydrolase 2

description: UCH catalytic

description: ULD

description: Nucleophile

description: Proton donor

type: Site

description: Transition state stabilizer

description: Important for enzyme activity

type: STRAIN

authors:
Stone M.
Hartmann-Petersen R.
Seeger M.
Bech-Otschir D.
Wallace M.
Gordon C.

title: Uch2/Uch37 is the major deubiquitinating enzyme associated with the 26S proteasome in fission yeast.

journal: J. Mol. Biol.

referencePositions:
FUNCTION
INTERACTION WITH RPN10
SUBCELLULAR LOCATION

authors:
Li T.
Naqvi N.I.
Yang H.
Teo T.S.

title: Identification of a 26S proteasome-associated UCH in fission yeast.

journal: Biochem. Biophys. Res. Commun.

database: EMBL

key: MoleculeType

database: RefSeq

database: AlphaFoldDB

key: Description

database: SMR

database: ComplexPortal

value: 26S proteasome complex

database: IntAct

database: MEROPS

database: GeneID

database: KEGG

value: P:cytoplasm protein quality control by the ubiquitin-proteasome system

value: Peptidase C12, ubiquitin carboxyl-terminal hydrolase

value: UBIQUITIN CARBOXYL-TERMINAL HYDROLASE ISOZYME L5


value: LSM complex subunit lsm6

value: Component of LSm protein complexes, which are involved in RNA processing and may function in a chaperone-like manner (PubMed:22615807, PubMed:32518066). Component of the cytoplasmic LSM1-LSM7 complex which is involved in mRNA degradation by activating the decapping step (PubMed:32518066). The LSM1-LSM7 complex loads onto the 3'-end of single stranded RNA (PubMed:32518066). Component of the nuclear LSM2-LSM8 complex, which is involved in spliceosome assembly (PubMed:32518066). The LSM2-LSM8 complex plays a role in the biogenesis of the spliceosomal U4/U6-U5 tri-snRNP complex by accelerating prp24-mediated annealing of U4/U6 di-snRNA (By similarity). The LSM2-LSM8 complex binds U6 snRNA terminating with a cyclic 2',3' phosphate group; RNA with an unmodified 3' hydroxyl or non-cyclic 3' phosphate is bound less tightly (PubMed:32518066)

value: Component of the heptameric LSM1-LSM7 complex that forms a seven-membered ring structure with a donut shape (Probable) (PubMed:32518066). The LSm subunits are arranged in the order lsm1, lsm2, lsm3, lsm6, lsm5, lsm7 and lsm4 (PubMed:22001694, PubMed:22615807, PubMed:32518066). Component of the heptameric LSM2-LSM8 complex that forms a seven-membered ring structure with a donut shape (Probable) (PubMed:32518066). The LSm subunits are arranged in the order lsm8, lsm2, lsm3, lsm6, lsm5, lsm7 and lsm4 (PubMed:22001694, PubMed:22615807, PubMed:32518066)

value: LSM1 and LSM8 act competitively with respect to the localization of LSM1-LSM7 to the cytoplasm and LSM2-LSM8 to the nucleus. LSm proteins shift to the cytoplasm under conditions of stress

value: Cytoplasm

value: Nucleus, nucleolus

value: Belongs to the snRNP Sm proteins family. SmF/LSm6 subfamily

description: LSM complex subunit lsm6

type: Domain

description: Sm

database: PubMed

database: DOI

title: The genome sequence of Schizosaccharomyces pombe.

authors:
Mund M.
Neu A.
Ullmann J.
Neu U.
Sprangers R.

title: Structure of the LSm657 complex: an assembly intermediate of the LSm1-7 and LSm2-8 rings.

referencePositions: IDENTIFICATION IN THE LSM1-LSM7 AND LSM2-LSM8 COMPLEXES

authors:
Wu D.
Jiang S.
Bowler M.W.
Song H.

title: Crystal structures of Lsm3, Lsm4 and Lsm5/6/7 from Schizosaccharomyces pombe.

journal: PLoS ONE

authors:
Montemayor E.J.
Virta J.M.
Hayes S.M.
Nomura Y.
Brow D.A.
Butcher S.E.

title: Molecular basis for the distinct cellular functions of the Lsm1-7 and Lsm2-8 complexes.

journal: RNA

referencePositions: X-RAY CRYSTALLOGRAPHY (1.81 ANGSTROMS) IN COMPLEX WITH RNA

database: PIR

database: PDB

value: U6 small nuclear ribonucleoprotein complex

value: P:telomerase holoenzyme complex assembly

value: Probable U6 snRNA-associated Sm-like protein LSm6

value: SMALL NUCLEAR RIBONUCLEOPROTEIN F SNRNP-F

value: U6 SNRNA-ASSOCIATED SM-LIKE PROTEIN LSM6


scientificName: Drosophila melanogaster

commonName: Fruit fly

lineage: Eukaryota Metazoa Ecdysozoa Arthropoda Altocrustacea Allotriocarida Hexapoda Insecta Pterygota Neoptera Eumetabola Endopterygota Aparaglossata Panorpida Diptera Brachycera Muscomorpha Ephydroidea Drosophilidae Drosophila Sophophora

value: I-kappaB kinase epsilon, isoform B

value: I-kappaB kinase epsilon, isoform C

source: FlyBase

value: IKKepsilon

value: dIKK

value: dIKKepsilon

value: DmIKKepsilon

value: IKK

value: ikkepsilon

geneName: spn-F

description: Protein kinase

database: ChEBI

authors:
Adams M.D.
Celniker S.E.
Holt R.A.
Evans C.A.
Gocayne J.D.
Amanatides P.G.
Scherer S.E.
Li P.W.
Hoskins R.A.
Galle R.F.
George R.A.
Lewis S.E.
Richards S.
Ashburner M.
Henderson S.N.
Sutton G.G.
Wortman J.R.
Yandell M.D.
Zhang Q.
Chen L.X.
Brandon R.C.
Rogers Y.H.
Blazej R.G.
Champe M.
Pfeiffer B.D.
Wan K.H.
Doyle C.
Baxter E.G.
Helt G.
Nelson C.R.
Gabor G.L.
Abril J.F.
Agbayani A.
An H.J.
Andrews-Pfannkoch C.
Baldwin D.
Ballew R.M.
Basu A.
Baxendale J.
Bayraktaroglu L.
Beasley E.M.
Beeson K.Y.
Benos P.V.
Berman B.P.
Bhandari D.
Bolshakov S.
Borkova D.
Botchan M.R.
Bouck J.
Brokstein P.
Brottier P.
Burtis K.C.
Busam D.A.
Butler H.
Cadieu E.
Center A.
Chandra I.
Cherry J.M.
Cawley S.
Dahlke C.
Davenport L.B.
Davies P.
de Pablos B.
Delcher A.
Deng Z.
Mays A.D.
Dew I.
Dietz S.M.
Dodson K.
Doup L.E.
Downes M.
Dugan-Rocha S.
Dunkov B.C.
Dunn P.
Durbin K.J.
Evangelista C.C.
Ferraz C.
Ferriera S.
Fleischmann W.
Fosler C.
Gabrielian A.E.
Garg N.S.
Gelbart W.M.
Glasser K.
Glodek A.
Gong F.
Gorrell J.H.
Gu Z.
Guan P.
Harris M.
Harris N.L.
Harvey D.
Heiman T.J.
Hernandez J.R.
Houck J.
Hostin D.
Houston K.A.
Howland T.J.
Wei M.H.
Ibegwam C.
Jalali M.
Kalush F.
Karpen G.H.
Ke Z.
Kennison J.A.
Ketchum K.A.
Kimmel B.E.
Kodira C.D.
Kraft C.
Kravitz S.
Kulp D.
Lai Z.
Lasko P.
Lei Y.
Levitsky A.A.
Li J.
Li Z.
Liang Y.
Lin X.
Liu X.
Mattei B.
McIntosh T.C.
McLeod M.P.
McPherson D.
Merkulov G.
Milshina N.V.
Mobarry C.
Morris J.
Moshrefi A.
Mount S.M.
Moy M.
Murphy B.
Murphy L.
Muzny D.M.
Nelson D.L.
Nelson D.R.
Nelson K.A.
Nixon K.
Nusskern D.R.
Pacleb J.M.
Palazzolo M.
Pittman G.S.
Pan S.
Pollard J.
Puri V.
Reese M.G.
Reinert K.
Remington K.
Saunders R.D.
Scheeler F.
Shen H.
Shue B.C.
Siden-Kiamos I.
Simpson M.
Skupski M.P.
Smith T.
Spier E.
Spradling A.C.
Stapleton M.
Strong R.
Sun E.
Svirskas R.
Tector C.
Turner R.
Venter E.
Wang A.H.
Wang X.
Wang Z.Y.
Wassarman D.A.
Weinstock G.M.
Weissenbach J.
Williams S.M.
WoodageT
Worley K.C.
Wu D.
Yang S.
Yao Q.A.
Ye J.
Yeh R.F.
Zaveri J.S.
Zhan M.
Zhang G.
Zhao Q.
Zheng L.
Zheng X.H.
Zhong F.N.
Zhong W.
Zhou X.
Zhu S.
Zhu X.
Smith H.O.
Gibbs R.A.
Myers E.W.
Rubin G.M.
Venter J.C.

title: The genome sequence of Drosophila melanogaster.

value: Berkeley

authors:
Celniker S.E.
Wheeler D.A.
Kronmiller B.
Carlson J.W.
Halpern A.
Patel S.
Adams M.
Champe M.
Dugan S.P.
Frise E.
Hodgson A.
George R.A.
Hoskins R.A.
Laverty T.
Muzny D.M.
Nelson C.R.
Pacleb J.M.
Park S.
Pfeiffer B.D.
Richards S.
Sodergren E.J.
Svirskas R.
Tabor P.E.
Wan K.
Stapleton M.
Sutton G.G.
Venter C.
Weinstock G.
Scherer S.E.
Myers E.W.
Gibbs R.A.
Rubin G.M.

title: Finishing a whole-genome shotgun: release 3 of the Drosophila melanogaster euchromatic genome sequence.

journal: Genome Biol.

authors:
Misra S.
Crosby M.A.
Mungall C.J.
Matthews B.B.
Campbell K.S.
Hradecky P.
Huang Y.
Kaminker J.S.
Millburn G.H.
Prochnik S.E.
Smith C.D.
Tupy J.L.
Whitfied E.J.
Bayraktaroglu L.
Berman B.P.
Bettencourt B.R.
Celniker S.E.
de Grey A.D.
Drysdale R.A.
Harris N.L.
Richter J.
Russo S.
Schroeder A.J.
Shu S.Q.
Stapleton M.
Yamada C.
Ashburner M.
Gelbart W.M.
Rubin G.M.
Lewis S.E.

title: Annotation of the Drosophila melanogaster euchromatic genome: a systematic review.

authors:
Kaminker J.S.
Bergman C.M.
Kronmiller B.
Carlson J.
Svirskas R.
Patel S.
Frise E.
Wheeler D.A.
Lewis S.E.
Rubin G.M.
Ashburner M.
Celniker S.E.

title: The transposable elements of the Drosophila melanogaster euchromatin: a genomics perspective.

authors:
Hoskins R.A.
Smith C.D.
Carlson J.W.
Carvalho A.B.
Halpern A.
Kaminker J.S.
Kennedy C.
Mungall C.J.
Sullivan B.A.
Sutton G.G.
Yasuhara J.C.
Wakimoto B.T.
Myers E.W.
Celniker S.E.
Rubin G.M.
Karpen G.H.

title: Heterochromatic sequences in a Drosophila whole-genome shotgun assembly.

authors:
Quesneville H.
Bergman C.M.
Andrieu O.
Autard D.
Nouaud D.
Ashburner M.
Anxolabehere D.

title: Combined evidence annotation of transposable elements in genome sequences.

authors:
Celniker S.
Carlson J.
Wan K.
Frise E.
Hoskins R.
Park S.
Svirskas R.
Rubin G.

authors:
Smith C.D.
Shu S.
Mungall C.J.
Karpen G.H.

title: The Release 5.1 annotation of Drosophila melanogaster heterochromatin.

authors:
Hoskins R.A.
Carlson J.W.
Kennedy C.
Acevedo D.
Evans-Holm M.
Frise E.
Wan K.H.
Park S.
Mendez-Lago M.
Rossi F.
Villasante A.
Dimitri P.
Karpen G.H.
Celniker S.E.

title: Sequence finishing and mapping of Drosophila melanogaster heterochromatin.

authors:
Matthews B.B.
Dos Santos G.
Crosby M.A.
Emmert D.B.
St Pierre S.E.
Gramates L.S.
Zhou P.
Schroeder A.J.
Falls K.
Strelets V.
Russo S.M.
Gelbart W.M.

title: Gene Model Annotations for Drosophila melanogaster: Impact of High-Throughput Data.

authors:
Crosby M.A.
Gramates L.S.
Dos Santos G.
Matthews B.B.
St Pierre S.E.
Zhou P.
Schroeder A.J.
Falls K.
Emmert D.B.
Russo S.M.
Gelbart W.M.

title: Gene Model Annotations for Drosophila melanogaster: The Rule-Benders.

authors:
Hoskins R.A.
Carlson J.W.
Wan K.H.
Park S.
Mendez I.
Galle S.E.
Booth B.W.
Pfeiffer B.D.
George R.A.
Svirskas R.
Krzywinski M.
Schein J.
Accardo M.C.
Damia E.
Messina G.
Mendez-Lago M.
de Pablos B.
Demakova O.V.
Andreyeva E.N.
Boldyreva L.V.
Marra M.
Carvalho A.B.
Dimitri P.
Villasante A.
Zhimulev I.F.
Rubin G.M.
Karpen G.H.
Celniker S.E.

title: The Release 6 reference sequence of the Drosophila melanogaster genome.

authors:
Celniker S.
Carlson J.
Wan K.
Pfeiffer B.
Frise E.
George R.
Hoskins R.
Stapleton M.
Pacleb J.
Park S.
Svirskas R.
Smith E.
Yu C.
Rubin G.

title: Drosophila melanogaster release 4 sequence.

value: Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells

value: Expressed in second segment of antenna (Drosophila) and 70 other cell types or tissues

value: F:protein serine/threonine kinase activity

value: P:maintenance of epithelial integrity, open tracheal system

value: P:oocyte anterior/posterior axis specification

value: P:positive regulation of apoptotic process

value: P:positive regulation of signal transduction

value: P:positive regulation of type I interferon production

value: P:regulation of cytoskeleton organization

value: inhibitor of nuclear factor kappa-B kinase subunit epsilon

value: serine/threonine-protein kinase TBK1 isoform X1

value: Phosphatidylinositol 3-kinase Catalytic Subunit, Chain A, domain 1


proteinExistence: 4: Predicted

value: Datilografo, isoform B

value: dati

value: Nucleus

type: Region

description: Disordered

description: Disordered

description: Disordered

description: Disordered

description: Disordered

description: Disordered

description: Disordered

type: Compositional bias

description: Polar residues

description: Polar residues

description: Polar residues

description: Polar residues

description: Low complexity

description: Polar residues

description: Low complexity

description: Low complexity

description: Low complexity

description: Basic residues

description: Basic residues

value: Expressed in alpha'/beta' Kenyon cell (Drosophila) in insect head and 98 other cell types or tissues

value: P:positive regulation of female receptivity

value: GASTRULA ZINC FINGER PROTEIN XLCGF49.1-LIKE-RELATED


value: Neprilysin-like 19

value: Cell membrane

value: Single-pass type II membrane protein

value: Belongs to the peptidase M13 family

value: Lacks conserved residue(s) required for the propagation of feature annotation

commentType: CAUTION

type: Signal

description: Peptidase M13 N-terminal

source: Pfam

description: Peptidase M13 C-terminal

value: Berkeley

value: Expressed in embryonic/larval hemocyte (Drosophila) and 16 other cell types or tissues

value: ZINC METALLOPROTEASE FAMILY M13 NEPRILYSIN-RELATED

value: Metalloproteases ('zincins'), catalytic domain


value: Enoyl-CoA hydratase/isomerase-like domain-containing protein

value: Belongs to the enoyl-CoA hydratase/isomerase family

description: Enoyl-CoA hydratase/isomerase-like

journal: PLoS Comput. Biol.

citationType: submission

submissionDatabase: EMBL/GenBank/DDBJ databases

journal: G3 (Bethesda)

value: Expressed in dorsal cluster neuron (Drosophila) in brain and 49 other cell types or tissues

value: 2-enoyl-CoA Hydratase, Chain A, domain 1


value: Neuroendocrine convertase 2

value: NEC 2

value: DMH #5

value: Prohormone convertase 2

value: Protein amontillado

flag: Precursor

value: amon

value: Serine endopeptidase which is involved in the processing of hormone and other protein precursors at sites comprised of pairs of basic amino acid residues (PubMed:10749852, PubMed:20523747, PubMed:21138435). Required during embryonic and larval development, probably by proteolytically processing peptide hormones involved in hatching, larval growth and larval molting (PubMed:12586710). Required for the processing and activation of Akh which maintains normal hemolymph sugar levels (PubMed:20523747). Has been shown in one study to be required for processing of sli into slit N-product and slit C-product in the embryo which is necessary for lateral transverse muscle elongation but has been shown in another study not to be required for sli cleavage (PubMed:27628033, PubMed:32994163). Required for larval hatching (PubMed:10436051). Also required for normal larval wandering behavior which occurs prior to pupariation (PubMed:21138435). Required during pupal development for head eversion, leg and wing disk extension, and abdominal differentiation (PubMed:19559693). Required during eye development for R8 photoreceptor cell specification by regulating processing of ligands required for the BMP and activin signaling pathways (PubMed:28853393)

name: Release of protein hormones and neuropeptides from their precursors, generally by hydrolysis of -Lys-Arg-|- bonds.

value: Secreted

value: Expressed in the central nervous system (CNS) and midgut endocrine cells of third instar larva (at protein level) (PubMed:19559693). In the CNS, expressed in the CA-LP1 and CA-LP2 neurons which innervate the corpus allatum, and in the CC-MS2 neurons which innervate the corpora cardiaca of the ring gland (PubMed:19559693, PubMed:21138435). Also expressed in the CC-MS1, SP3, Tv and Va neurons (PubMed:21138435). Expressed in Akh-producing cells of the corpora cardiaca (PubMed:20523747). In the embryo, restricted to the final stages of embryogenesis where expression is found in anterior sensory structures and in only 168 cells in the brain and ventral nerve cord (PubMed:10436051). After larvae hatch, the sensory structures and most cells in the CNS turn off or substantially reduce expression (PubMed:10436051). In third instar larva, expressed at higher levels in the anterior section than in the posterior section (PubMed:10749852). Little expression is detected in the adult head (PubMed:10749852). In the developing eye, expressed at higher levels in pale-type R7 photoreceptor cells than in yellow-type R7 cells although expression is not seen in all pale-type R7 cells (PubMed:28853393). Also expressed in outer photoreceptor cells (PubMed:28853393)

value: Detected during embryogenesis, larval development, and pupal development (at protein level) (PubMed:10749852, PubMed:19559693). Also expressed in the adult (PubMed:10749852). In the embryo, first observed at 12-16 hours and peaks at the end of embryogenesis (PubMed:10436051). Levels drop in the first larval stage and reach a very low level by the second larval stage which continues throughout the remainder of larval and most of pupal life (PubMed:10436051). Expression increases in late pupae and peaks once again in adults (PubMed:10436051)

commentType: DEVELOPMENTAL STAGE

value: RNAi-mediated knockdown in Akh-producing cells of the corpora cardiaca results in a significant decrease in combined glucose and trehalose levels (PubMed:20523747). RNAi-mediated knockdown results in defective muscle patterning (PubMed:27628033). RNAi-mediated knockdown results in a reduction in the pale ommatidia subtype (PubMed:28853393)

value: Belongs to the peptidase S8 family. Furin subfamily

value: Has been shown in one study to be required for processing of sli into slit N-product and slit C-product (PubMed:27628033). However, has been shown in another study not to be required for sli cleavage with the protease required for sli cleavage being identified as tok (PubMed:27628033)

type: Propeptide

description: Neuroendocrine convertase 2

description: Peptidase S8

description: P/Homo B

type: Active site

description: Charge relay system

description: Charge relay system

description: Charge relay system

type: Glycosylation

description: N-linked (GlcNAc...) asparagine

description: N-linked (GlcNAc...) asparagine

description: N-linked (GlcNAc...) asparagine

type: Disulfide bond

description: In amonC241Y: Partial embryonic lethality and defective larval growth with no pupariation or survival to adulthood. Defective Akh processing. Does not affect sli processing.

description: In amonC254Y: Partial embryonic lethality and defective larval growth with no pupariation or survival to adulthood.

description: In amonG367V: Partial embryonic lethality and defective larval growth with no pupariation or survival to adulthood.

description: In amonG473R: Partial embryonic lethality and defective larval growth with no pupariation or survival to adulthood.

description: In amonS557L1 and amonS557L2: Partial embryonic lethality and defective larval growth with no pupariation or survival to adulthood.

description: in Ref. 1; AAD49105

title: A role for amontillado, the Drosophila homolog of the neuropeptide precursor processing protease PC2, in triggering hatching behavior.

referencePositions:
NUCLEOTIDE SEQUENCE [MRNA]
FUNCTION
TISSUE SPECIFICITY
DEVELOPMENTAL STAGE

authors:
Adams M.D.
Celniker S.E.
Holt R.A.
Evans C.A.
Gocayne J.D.
Amanatides P.G.
Scherer S.E.
Li P.W.
Hoskins R.A.
Galle R.F.
George R.A.
Lewis S.E.
Richards S.
Ashburner M.
Henderson S.N.
Sutton G.G.
Wortman J.R.
Yandell M.D.
Zhang Q.
Chen L.X.
Brandon R.C.
Rogers Y.-H.C.
Blazej R.G.
Champe M.
Pfeiffer B.D.
Wan K.H.
Doyle C.
Baxter E.G.
Helt G.
Nelson C.R.
Miklos G.L.G.
Abril J.F.
Agbayani A.
An H.-J.
Andrews-Pfannkoch C.
Baldwin D.
Ballew R.M.
Basu A.
Baxendale J.
Bayraktaroglu L.
Beasley E.M.
Beeson K.Y.
Benos P.V.
Berman B.P.
Bhandari D.
Bolshakov S.
Borkova D.
Botchan M.R.
Bouck J.
Brokstein P.
Brottier P.
Burtis K.C.
Busam D.A.
Butler H.
Cadieu E.
Center A.
Chandra I.
Cherry J.M.
Cawley S.
Dahlke C.
Davenport L.B.
Davies P.
de Pablos B.
Delcher A.
Deng Z.
Mays A.D.
Dew I.
Dietz S.M.
Dodson K.
Doup L.E.
Downes M.
Dugan-Rocha S.
Dunkov B.C.
Dunn P.
Durbin K.J.
Evangelista C.C.
Ferraz C.
Ferriera S.
Fleischmann W.
Fosler C.
Gabrielian A.E.
Garg N.S.
Gelbart W.M.
Glasser K.
Glodek A.
Gong F.
Gorrell J.H.
Gu Z.
Guan P.
Harris M.
Harris N.L.
Harvey D.A.
Heiman T.J.
Hernandez J.R.
Houck J.
Hostin D.
Houston K.A.
Howland T.J.
Wei M.-H.
Ibegwam C.
Jalali M.
Kalush F.
Karpen G.H.
Ke Z.
Kennison J.A.
Ketchum K.A.
Kimmel B.E.
Kodira C.D.
Kraft C.L.
Kravitz S.
Kulp D.
Lai Z.
Lasko P.
Lei Y.
Levitsky A.A.
Li J.H.
Li Z.
Liang Y.
Lin X.
Liu X.
Mattei B.
McIntosh T.C.
McLeod M.P.
McPherson D.
Merkulov G.
Milshina N.V.
Mobarry C.
Morris J.
Moshrefi A.
Mount S.M.
Moy M.
Murphy B.
Murphy L.
Muzny D.M.
Nelson D.L.
Nelson D.R.
Nelson K.A.
Nixon K.
Nusskern D.R.
Pacleb J.M.
Palazzolo M.
Pittman G.S.
Pan S.
Pollard J.
Puri V.
Reese M.G.
Reinert K.
Remington K.
Saunders R.D.C.
Scheeler F.
Shen H.
Shue B.C.
Siden-Kiamos I.
Simpson M.
Skupski M.P.
Smith T.J.
Spier E.
Spradling A.C.
Stapleton M.
Strong R.
Sun E.
Svirskas R.
Tector C.
Turner R.
Venter E.
Wang A.H.
Wang X.
Wang Z.-Y.
Wassarman D.A.
Weinstock G.M.
Weissenbach J.
Williams S.M.
Woodage T.
Worley K.C.
Wu D.
Yang S.
Yao Q.A.
Ye J.
Yeh R.-F.
Zaveri J.S.
Zhan M.
Zhang G.
Zhao Q.
Zheng L.
Zheng X.H.
Zhong F.N.
Zhong W.
Zhou X.
Zhu S.C.
Zhu X.
Smith H.O.
Gibbs R.A.
Myers E.W.
Rubin G.M.
Venter J.C.

authors:
Misra S.
Crosby M.A.
Mungall C.J.
Matthews B.B.
Campbell K.S.
Hradecky P.
Huang Y.
Kaminker J.S.
Millburn G.H.
Prochnik S.E.
Smith C.D.
Tupy J.L.
Whitfield E.J.
Bayraktaroglu L.
Berman B.P.
Bettencourt B.R.
Celniker S.E.
de Grey A.D.N.J.
Drysdale R.A.
Harris N.L.
Richter J.
Russo S.
Schroeder A.J.
Shu S.Q.
Stapleton M.
Yamada C.
Ashburner M.
Gelbart W.M.
Rubin G.M.
Lewis S.E.

authors:
Stapleton M.
Carlson J.W.
Brokstein P.
Yu C.
Champe M.
George R.A.
Guarin H.
Kronmiller B.
Pacleb J.M.
Park S.
Wan K.H.
Rubin G.M.
Celniker S.E.

title: A Drosophila full-length cDNA resource.

authors:
Hwang J.R.
Siekhaus D.E.
Fuller R.S.
Taghert P.H.
Lindberg I.

title: Interaction of Drosophila melanogaster prohormone convertase 2 and 7B2. Insect cell-specific processing and secretion.

referencePositions:
FUNCTION
CATALYTIC ACTIVITY
SUBCELLULAR LOCATION
TISSUE SPECIFICITY
DEVELOPMENTAL STAGE

authors:
Rayburn L.Y.
Gooding H.C.
Choksi S.P.
Maloney D.
Kidd A.R. III
Siekhaus D.E.
Bender M.

title: amontillado, the Drosophila homolog of the prohormone processing protease PC2, is required during embryogenesis and early larval development.

referencePositions: MUTAGENESIS OF CYS-241; CYS-254; GLY-367; GLY-473 AND SER-557

authors:
Rayburn L.Y.
Rhea J.
Jocoy S.R.
Bender M.

title: The proprotein convertase amontillado (amon) is required during Drosophila pupal development.

title: The proprotein convertase encoded by amontillado (amon) is required in Drosophila corpora cardiaca endocrine cells producing the glucose regulatory hormone AKH.

referencePositions:
FUNCTION
TISSUE SPECIFICITY
DISRUPTION PHENOTYPE
MUTAGENESIS OF CYS-241

authors:
Wegener C.
Herbert H.
Kahnt J.
Bender M.
Rhea J.M.

title: Deficiency of prohormone convertase dPC2 (AMONTILLADO) results in impaired production of bioactive neuropeptide hormones in Drosophila.

title: Amontillado is required for Drosophila Slit processing and for tendon-mediated muscle patterning.

authors:
Wells B.S.
Pistillo D.
Barnhart E.
Desplan C.

title: Parallel Activin and BMP signaling coordinates R7/R8 photoreceptor subtype pairing in the stochastic Drosophila retina.

authors:
Kellermeyer R.
Heydman L.M.
Gillis T.
Mastick G.S.
Song M.
Kidd T.

title: Proteolytic cleavage of Slit by the Tolkin protease converts an axon repulsion cue to an axon growth cue in vivo.

value: Expressed in adult anterior midgut class I enteroendocrine cell in adult midgut (Drosophila) and 174 other cell types or tissues


value: Uncharacterized protein

H2O2 + AH2 = A + 2 H2O

database: Rhea

value: Binds 1 Ca(2+) ion per heterodimer.

value: Binds 1 heme b (iron(II)-protoporphyrin IX) group covalently per heterodimer.

value: Belongs to the peroxidase family

value: Lacks conserved residue(s) required for the propagation of feature annotation

description: Disordered

description: Disordered

description: Disordered

description: Disordered

description: Disordered

description: Disordered

description: Disordered

description: Basic and acidic residues

description: Low complexity

description: Acidic residues

description: Basic and acidic residues

description: Basic and acidic residues

description: Basic and acidic residues

description: Polar residues

description: Low complexity

description: Polar residues

description: Proton acceptor

description: covalent

description: covalent

description: axial binding residue

description: Transition state stabilizer

authors:
Adams M.D.
Celniker S.E.
Holt R.A.
Evans C.A.
Gocayne J.D.
Amanatides P.G.
Scherer S.E.
Li P.W.
Hoskins R.A.
Galle R.F.
George R.A.
Lewis S.E.
Richards S.
Ashburner M.
Henderson S.N.
Sutton G.G.
Wortman J.R.
Yandell M.D.
Zhang Q.
Chen L.X.
Brandon R.C.
Rogers Y.H.
Blazej R.G.
Champe M.
Pfeiffer B.D.
Wan K.H.
Doyle C.
Baxter E.G.
Helt G.
Nelson C.R.
Gabor G.L.
Abril J.F.
Agbayani A.
An H.J.
Andrews-Pfannkoch C.
Baldwin D.
Ballew R.M.
Basu A.
Baxendale J.
Bayraktaroglu L.
Beasley E.M.
Beeson K.Y.
Benos P.V.
Berman B.P.
Bhandari D.
Bolshakov S.
Borkova D.
Botchan M.R.
Bouck J.
Brokstein P.
Brottier P.
Burtis K.C.
Busam D.A.
Butler H.
Cadieu E.
Center A.
Chandra I.
Cherry J.M.
Cawley S.
Dahlke C.
Davenport L.B.
Davies P.
de Pablos B.
Delcher A.
Deng Z.
Mays A.D.
Dew I.
Dietz S.M.
Dodson K.
Doup L.E.
Downes M.
Dugan-Rocha S.
Dunkov B.C.
Dunn P.
Durbin K.J.
Evangelista C.C.
Ferraz C.
Ferriera S.
Fleischmann W.
Fosler C.
Gabrielian A.E.
Garg N.S.
Gelbart W.M.
Glasser K.
Glodek A.
Gong F.
Gorrell J.H.
Gu Z.
Guan P.
Harris M.
Harris N.L.
Harvey D.
Heiman T.J.
Hernandez J.R.
Houck J.
Hostin D.
Houston K.A.
Howland T.J.
Wei M.H.
Ibegwam C.
Jalali M.
Kalush F.
Karpen G.H.
Ke Z.
Kennison J.A.
Ketchum K.A.
Kimmel B.E.
Kodira C.D.
Kraft C.
Kravitz S.
Kulp D.
Lai Z.
Lasko P.
Lei Y.
Levitsky A.A.
Li J.
Li Z.
Liang Y.
Lin X.
Liu X.
Mattei B.
McIntosh T.C.
McLeod M.P.
McPherson D.
Merkulov G.
Milshina N.V.
Mobarry C.
Morris J.
Moshrefi A.
Mount S.M.
Moy M.
Murphy B.
Murphy L.
Muzny D.M.
Nelson D.L.
Nelson D.R.
Nelson K.A.
Nixon K.
Nusskern D.R.
Pacleb J.M.
Palazzolo M.
Pittman G.S.
Pan S.
Pollard J.
Puri V.
Reese M.G.
Reinert K.
Remington K.
Saunders R.D.
Scheeler F.
Shen H.
Shue B.C.
Siden-Kiamos I.
Simpson M.
Skupski M.P.
Smith T.
Spier E.
Spradling A.C.
Stapleton M.
Strong R.
Sun E.
Svirskas R.
Tector C.
Turner R.
Venter E.
Wang A.H.
Wang X.
Wang Z.Y.
Wassarman D.A.
Weinstock G.M.
Weissenbach J.
Williams S.M.
WoodageT
Worley K.C.
Wu D.
Yang S.
Yao Q.A.
Ye J.
Yeh R.F.
Zaveri J.S.
Zhan M.
Zhang G.
Zhao Q.
Zheng L.
Zheng X.H.
Zhong F.N.
Zhong W.
Zhou X.
Zhu S.
Zhu X.
Smith H.O.
Gibbs R.A.
Myers E.W.
Rubin G.M.
Venter J.C.

title: The genome sequence of Drosophila melanogaster.

authors:
Celniker S.E.
Wheeler D.A.
Kronmiller B.
Carlson J.W.
Halpern A.
Patel S.
Adams M.
Champe M.
Dugan S.P.
Frise E.
Hodgson A.
George R.A.
Hoskins R.A.
Laverty T.
Muzny D.M.
Nelson C.R.
Pacleb J.M.
Park S.
Pfeiffer B.D.
Richards S.
Sodergren E.J.
Svirskas R.
Tabor P.E.
Wan K.
Stapleton M.
Sutton G.G.
Venter C.
Weinstock G.
Scherer S.E.
Myers E.W.
Gibbs R.A.
Rubin G.M.

title: Finishing a whole-genome shotgun: release 3 of the Drosophila melanogaster euchromatic genome sequence.

authors:
Misra S.
Crosby M.A.
Mungall C.J.
Matthews B.B.
Campbell K.S.
Hradecky P.
Huang Y.
Kaminker J.S.
Millburn G.H.
Prochnik S.E.
Smith C.D.
Tupy J.L.
Whitfied E.J.
Bayraktaroglu L.
Berman B.P.
Bettencourt B.R.
Celniker S.E.
de Grey A.D.
Drysdale R.A.
Harris N.L.
Richter J.
Russo S.
Schroeder A.J.
Shu S.Q.
Stapleton M.
Yamada C.
Ashburner M.
Gelbart W.M.
Rubin G.M.
Lewis S.E.

title: Annotation of the Drosophila melanogaster euchromatic genome: a systematic review.

authors:
Kaminker J.S.
Bergman C.M.
Kronmiller B.
Carlson J.
Svirskas R.
Patel S.
Frise E.
Wheeler D.A.
Lewis S.E.
Rubin G.M.
Ashburner M.
Celniker S.E.

title: The transposable elements of the Drosophila melanogaster euchromatin: a genomics perspective.

authors:
Hoskins R.A.
Smith C.D.
Carlson J.W.
Carvalho A.B.
Halpern A.
Kaminker J.S.
Kennedy C.
Mungall C.J.
Sullivan B.A.
Sutton G.G.
Yasuhara J.C.
Wakimoto B.T.
Myers E.W.
Celniker S.E.
Rubin G.M.
Karpen G.H.

title: Heterochromatic sequences in a Drosophila whole-genome shotgun assembly.

authors:
Quesneville H.
Bergman C.M.
Andrieu O.
Autard D.
Nouaud D.
Ashburner M.
Anxolabehere D.

value: Expressed in esophagus (Drosophila) and 18 other cell types or tissues

value: P:cellular process involved in reproduction in multicellular organism

value: Haem peroxidase domain superfamily, animal type


value: Cystinosin

value: dCTNS

value: Ctns

value: Cystine/H(+) symporter that mediates export of cystine, the oxidized dimer of cysteine, from lysosomes (PubMed:35175796). Involved in cysteine homeostasis during periods of fasting, which indirectly regulates mTORC1-mediated signaling by supporting de novo CoA synthesis, the TCA cycle and amino acid metabolism during periods of food shortage (PubMed:35175796). Important for maintaining autophagy, and for development and survival during periods of fasting (PubMed:35175796)

name: L-cystine(out) + H(+)(out) = L-cystine(in) + H(+)(in)

directionType: left-to-right

value: Lysosome membrane

value: Multi-pass membrane protein

value: No effect on adult lifespan but larvae show a developmental delay (PubMed:35175796). The larval developmental delay is more severe when raised on a low-protein diet and adults die more quickly of starvation (PubMed:35175796). Accumulation of cystine in larvae (PubMed:35175796). Under fed conditions no difference in larval cysteine levels, however cysteine levels are reduced in fasting larvae (PubMed:35175796). Conditional RNAi-mediated knockdown in the fat body causes a developmental delay when on a low-protein diet (PubMed:35175796)

value: Belongs to the cystinosin family

description: Cystinosin

type: Topological domain

description: Lumenal

type: Transmembrane

description: Helical

description: Cytoplasmic

description: Helical

description: Lumenal

description: Helical

description: Cytoplasmic

description: Helical

description: Lumenal

description: Helical

description: Cytoplasmic

description: Helical

description: Lumenal

description: Helical

description: Cytoplasmic

description: PQ-loop 1

description: PQ-loop 2

description: Disordered

description: Polar residues

description: N-linked (GlcNAc...) asparagine

description: N-linked (GlcNAc...) asparagine

title: A Drosophila full-length cDNA resource.

authors:
Koles K.
Lim J.-M.
Aoki K.
Porterfield M.
Tiemeyer M.
Wells L.
Panin V.

title: Identification of N-glycosylated proteins from the central nervous system of Drosophila melanogaster.

referencePositions: GLYCOSYLATION [LARGE SCALE ANALYSIS] AT ASN-86

authors:
Jouandin P.
Marelja Z.
Shih Y.H.
Parkhitko A.A.
Dambowsky M.
Asara J.M.
Nemazanyy I.
Dibble C.C.
Simons M.
Perrimon N.

title: Lysosomal cystine mobilization shapes the response of TORC1 and tissue growth to fasting.

value: the lysosomal cystine transporter (lct) family

value: Miscellaneous transport and binding events

value: Expressed in adult Malpighian tubule (Drosophila) and 42 other cell types or tissues

value: F:amino acid transmembrane transporter activity

value: F:L-cystine transmembrane transporter activity

value: P:L-cystine transmembrane transport from lysosomal lumen to cytosol


proteinExistence: 2: Evidence at transcript level

value: rRNA methyltransferase 2, mitochondrial

value: rRNA (uridine-2'-O)-methyltransferase

value: S-adenosyl-L-methionine-dependent 2'-O-ribose methyltransferase that catalyzes the formation of 2'-O-methyluridine at position 1579 (Um1579) in the mitochondrial large subunit ribosomal RNA (mtLSU rRNA), a universally conserved modification in the peptidyl transferase domain of the mtLSU rRNA. This activity may require prior 2'-O-methylguanosine modification at position 1580 (Gm1580) by MRM3. Essential for late-stage assembly of mtLSU required for efficient translation of mitochondrial DNA encoded proteins; methyltransferase activity is not required for this function. Essential for mitochondrial respiratory function

name: a uridine in rRNA + S-adenosyl-L-methionine = a 2'-O-methyluridine in rRNA + S-adenosyl-L-homocysteine + H(+)

value: Mitochondrion

value: RNAi-mediated knock down is larval to late pupal lethal with developmental delay (PubMed:35177605). Escaper adults show wing deformation and flattened abdomen, and most are unable to emerge from pupae or get stuck in the food medium due to weakness (PubMed:35177605). Conditional muscle specific RNAi-mediated knockdown results in impaired locomotor ability (PubMed:35177605)

value: Belongs to the class I-like SAM-binding methyltransferase superfamily. RNA methyltransferase RlmE family

type: Transit peptide

description: Mitochondrion

description: rRNA methyltransferase 2, mitochondrial

description: Proton acceptor

type: Binding site

authors:
Adams M.D.
Celniker S.E.
Holt R.A.
Evans C.A.
Gocayne J.D.
Amanatides P.G.
Scherer S.E.
Li P.W.
Hoskins R.A.
Galle R.F.
George R.A.
Lewis S.E.
Richards S.
Ashburner M.
Henderson S.N.
Sutton G.G.
Wortman J.R.
Yandell M.D.
Zhang Q.
Chen L.X.
Brandon R.C.
Rogers Y.-H.C.
Blazej R.G.
Champe M.
Pfeiffer B.D.
Wan K.H.
Doyle C.
Baxter E.G.
Helt G.
Nelson C.R.
Miklos G.L.G.
Abril J.F.
Agbayani A.
An H.-J.
Andrews-Pfannkoch C.
Baldwin D.
Ballew R.M.
Basu A.
Baxendale J.
Bayraktaroglu L.
Beasley E.M.
Beeson K.Y.
Benos P.V.
Berman B.P.
Bhandari D.
Bolshakov S.
Borkova D.
Botchan M.R.
Bouck J.
Brokstein P.
Brottier P.
Burtis K.C.
Busam D.A.
Butler H.
Cadieu E.
Center A.
Chandra I.
Cherry J.M.
Cawley S.
Dahlke C.
Davenport L.B.
Davies P.
de Pablos B.
Delcher A.
Deng Z.
Mays A.D.
Dew I.
Dietz S.M.
Dodson K.
Doup L.E.
Downes M.
Dugan-Rocha S.
Dunkov B.C.
Dunn P.
Durbin K.J.
Evangelista C.C.
Ferraz C.
Ferriera S.
Fleischmann W.
Fosler C.
Gabrielian A.E.
Garg N.S.
Gelbart W.M.
Glasser K.
Glodek A.
Gong F.
Gorrell J.H.
Gu Z.
Guan P.
Harris M.
Harris N.L.
Harvey D.A.
Heiman T.J.
Hernandez J.R.
Houck J.
Hostin D.
Houston K.A.
Howland T.J.
Wei M.-H.
Ibegwam C.
Jalali M.
Kalush F.
Karpen G.H.
Ke Z.
Kennison J.A.
Ketchum K.A.
Kimmel B.E.
Kodira C.D.
Kraft C.L.
Kravitz S.
Kulp D.
Lai Z.
Lasko P.
Lei Y.
Levitsky A.A.
Li J.H.
Li Z.
Liang Y.
Lin X.
Liu X.
Mattei B.
McIntosh T.C.
McLeod M.P.
McPherson D.
Merkulov G.
Milshina N.V.
Mobarry C.
Morris J.
Moshrefi A.
Mount S.M.
Moy M.
Murphy B.
Murphy L.
Muzny D.M.
Nelson D.L.
Nelson D.R.
Nelson K.A.
Nixon K.
Nusskern D.R.
Pacleb J.M.
Palazzolo M.
Pittman G.S.
Pan S.
Pollard J.
Puri V.
Reese M.G.
Reinert K.
Remington K.
Saunders R.D.C.
Scheeler F.
Shen H.
Shue B.C.
Siden-Kiamos I.
Simpson M.
Skupski M.P.
Smith T.J.
Spier E.
Spradling A.C.
Stapleton M.
Strong R.
Sun E.
Svirskas R.
Tector C.
Turner R.
Venter E.
Wang A.H.
Wang X.
Wang Z.-Y.
Wassarman D.A.
Weinstock G.M.
Weissenbach J.
Williams S.M.
Woodage T.
Worley K.C.
Wu D.
Yang S.
Yao Q.A.
Ye J.
Yeh R.-F.
Zaveri J.S.
Zhan M.
Zhang G.
Zhao Q.
Zheng L.
Zheng X.H.
Zhong F.N.
Zhong W.
Zhou X.
Zhu S.C.
Zhu X.
Smith H.O.
Gibbs R.A.
Myers E.W.
Rubin G.M.
Venter J.C.

value: Berkeley

title: A Drosophila full-length cDNA resource.

value: Embryo

type: TISSUE

authors:
Rorbach J.
Boesch P.
Gammage P.A.
Nicholls T.J.
Pearce S.F.
Patel D.
Hauser A.
Perocchi F.
Minczuk M.

title: MRM2 and MRM3 are involved in biogenesis of the large subunit of the mitochondrial ribosome.

journal: Mol. Biol. Cell

referencePositions: POSITION OF MODIFIED METHYLURIDINE IN MTLSU RRNA

authors:
Rebelo-Guiomar P.
Pellegrino S.
Dent K.C.
Sas-Chen A.
Miller-Fleming L.
Garone C.
Van Haute L.
Rogan J.F.
Dinan A.
Firth A.E.
Andrews B.
Whitworth A.J.
Schwartz S.
Warren A.J.
Minczuk M.

title: A late-stage assembly checkpoint of the human mitochondrial ribosome large subunit.

journal: Nat. Commun.

value: Expressed in adult anterior midgut class II enteroendocrine cell in adult midgut (Drosophila) and 58 other cell types or tissues

value: P:mitochondrial large ribosomal subunit assembly


value: cdm

value: Cdm

value: Interacts with UBC9, RAN, RBM8A, eIF-1A and PAX6

value: Nucleus

value: Belongs to the importin beta family

description: Importin N-terminal

title: Combined evidence annotation of transposable elements in genome sequences.

authors:
Celniker S.
Carlson J.
Wan K.
Frise E.
Hoskins R.
Park S.
Svirskas R.
Rubin G.

authors:
Smith C.D.
Shu S.
Mungall C.J.
Karpen G.H.

title: The Release 5.1 annotation of Drosophila melanogaster heterochromatin.

authors:
Hoskins R.A.
Carlson J.W.
Kennedy C.
Acevedo D.
Evans-Holm M.
Frise E.
Wan K.H.
Park S.
Mendez-Lago M.
Rossi F.
Villasante A.
Dimitri P.
Karpen G.H.
Celniker S.E.

title: Sequence finishing and mapping of Drosophila melanogaster heterochromatin.

authors:
Bono F.
Cook A.G.
Grunwald M.
Ebert J.
Conti E.

title: Nuclear import mechanism of the EJC component Mago-Y14 revealed by structural studies of importin 13.

title: Structural basis for the nuclear export activity of Importin13.

authors:
Matthews B.B.
Dos Santos G.
Crosby M.A.
Emmert D.B.
St Pierre S.E.
Gramates L.S.
Zhou P.
Schroeder A.J.
Falls K.
Strelets V.
Russo S.M.
Gelbart W.M.

title: Gene Model Annotations for Drosophila melanogaster: Impact of High-Throughput Data.

authors:
Crosby M.A.
Gramates L.S.
Dos Santos G.
Matthews B.B.
St Pierre S.E.
Zhou P.
Schroeder A.J.
Falls K.
Emmert D.B.
Russo S.M.
Gelbart W.M.

title: Gene Model Annotations for Drosophila melanogaster: The Rule-Benders.

authors:
Hoskins R.A.
Carlson J.W.
Wan K.H.
Park S.
Mendez I.
Galle S.E.
Booth B.W.
Pfeiffer B.D.
George R.A.
Svirskas R.
Krzywinski M.
Schein J.
Accardo M.C.
Damia E.
Messina G.
Mendez-Lago M.
de Pablos B.
Demakova O.V.
Andreyeva E.N.
Boldyreva L.V.
Marra M.
Carvalho A.B.
Dimitri P.
Villasante A.
Zhimulev I.F.
Rubin G.M.
Karpen G.H.
Celniker S.E.

title: The Release 6 reference sequence of the Drosophila melanogaster genome.

authors:
Celniker S.
Carlson J.
Wan K.
Pfeiffer B.
Frise E.
George R.
Hoskins R.
Stapleton M.
Pacleb J.
Park S.
Svirskas R.
Smith E.
Yu C.
Rubin G.

title: Drosophila melanogaster release 4 sequence.

value: Expressed in oviduct (Drosophila) and 80 other cell types or tissues

value: C:NLS-dependent protein nuclear import complex

value: P:modulation of chemical synaptic transmission

value: P:positive regulation of protein-containing complex disassembly


value: ABC-type heme transporter ABCB6

name: coproporphyrin I(in) + ATP + H2O = coproporphyrin I(out) + ADP + phosphate + H(+)

name: coproporphyrin III(in) + ATP + H2O = coproporphyrin III(out) + ADP + phosphate + H(+)

name: coproporphyrinogen III(in) + ATP + H2O = coproporphyrinogen III(out) + ADP + phosphate + H(+)

name: heme b(in) + ATP + H2O = heme b(out) + ADP + phosphate + H(+)

name: pheophorbide a(in) + ATP + H2O = pheophorbide a(out) + ADP + phosphate + H(+)

name: protoporphyrin IX(in) + ATP + H2O = protoporphyrin IX(out) + ADP + phosphate + H(+)

name: uroporphyrin I(in) + ATP + H2O = uroporphyrin I(out) + ADP + phosphate + H(+)

name: uroporphyrin III(in) + ATP + H2O = uroporphyrin III(out) + ADP + phosphate + H(+)

value: Belongs to the ABC transporter superfamily. ABCB family. Heavy Metal importer (TC 3.A.1.210) subfamily

description: Helical

description: Helical

description: Helical

description: Helical

description: Helical

description: Helical

description: Helical

description: Helical

description: Helical

description: Helical

description: ABC transmembrane type-1

description: ABC transporter

description: Disordered

description: Gly residues

description: Basic residues

authors:
Adams M.D.
Celniker S.E.
Holt R.A.
Evans C.A.
Gocayne J.D.
Amanatides P.G.
Scherer S.E.
Li P.W.
Hoskins R.A.
Galle R.F.
George R.A.
Lewis S.E.
Richards S.
Ashburner M.
Henderson S.N.
Sutton G.G.
Wortman J.R.
Yandell M.D.
Zhang Q.
Chen L.X.
Brandon R.C.
Rogers Y.H.
Blazej R.G.
Champe M.
Pfeiffer B.D.
Wan K.H.
Doyle C.
Baxter E.G.
Helt G.
Nelson C.R.
Gabor G.L.
Abril J.F.
Agbayani A.
An H.J.
Andrews-Pfannkoch C.
Baldwin D.
Ballew R.M.
Basu A.
Baxendale J.
Bayraktaroglu L.
Beasley E.M.
Beeson K.Y.
Benos P.V.
Berman B.P.
Bhandari D.
Bolshakov S.
Borkova D.
Botchan M.R.
Bouck J.
Brokstein P.
Brottier P.
Burtis K.C.
Busam D.A.
Butler H.
Cadieu E.
Center A.
Chandra I.
Cherry J.M.
Cawley S.
Dahlke C.
Davenport L.B.
Davies P.
de Pablos B.
Delcher A.
Deng Z.
Mays A.D.
Dew I.
Dietz S.M.
Dodson K.
Doup L.E.
Downes M.
Dugan-Rocha S.
Dunkov B.C.
Dunn P.
Durbin K.J.
Evangelista C.C.
Ferraz C.
Ferriera S.
Fleischmann W.
Fosler C.
Gabrielian A.E.
Garg N.S.
Gelbart W.M.
Glasser K.
Glodek A.
Gong F.
Gorrell J.H.
Gu Z.
Guan P.
Harris M.
Harris N.L.
Harvey D.
Heiman T.J.
Hernandez J.R.
Houck J.
Hostin D.
Houston K.A.
Howland T.J.
Wei M.H.
Ibegwam C.
Jalali M.
Kalush F.
Karpen G.H.
Ke Z.
Kennison J.A.
Ketchum K.A.
Kimmel B.E.
Kodira C.D.
Kraft C.
Kravitz S.
Kulp D.
Lai Z.
Lasko P.
Lei Y.
Levitsky A.A.
Li J.
Li Z.
Liang Y.
Lin X.
Liu X.
Mattei B.
McIntosh T.C.
McLeod M.P.
McPherson D.
Merkulov G.
Milshina N.V.
Mobarry C.
Morris J.
Moshrefi A.
Mount S.M.
Moy M.
Murphy B.
Murphy L.
Muzny D.M.
Nelson D.L.
Nelson D.R.
Nelson K.A.
Nixon K.
Nusskern D.R.
Pacleb J.M.
Palazzolo M.
Pittman G.S.
Pan S.
Pollard J.
Puri V.
Reese M.G.
Reinert K.
Remington K.
Saunders R.D.
Scheeler F.
Shen H.
Shue B.C.
Siden-Kiamos I.
Simpson M.
Skupski M.P.
Smith T.
Spier E.
Spradling A.C.
Stapleton M.
Strong R.
Sun E.
Svirskas R.
Tector C.
Turner R.
Venter E.
Wang A.H.
Wang X.
Wang Z.Y.
Wassarman D.A.
Weinstock G.M.
Weissenbach J.
Williams S.M.
WoodageT
Worley K.C.
Wu D.
Yang S.
Yao Q.A.
Ye J.
Yeh R.F.
Zaveri J.S.
Zhan M.
Zhang G.
Zhao Q.
Zheng L.
Zheng X.H.
Zhong F.N.
Zhong W.
Zhou X.
Zhu S.
Zhu X.
Smith H.O.
Gibbs R.A.
Myers E.W.
Rubin G.M.
Venter J.C.

title: The genome sequence of Drosophila melanogaster.

authors:
Celniker S.E.
Wheeler D.A.
Kronmiller B.
Carlson J.W.
Halpern A.
Patel S.
Adams M.
Champe M.
Dugan S.P.
Frise E.
Hodgson A.
George R.A.
Hoskins R.A.
Laverty T.
Muzny D.M.
Nelson C.R.
Pacleb J.M.
Park S.
Pfeiffer B.D.
Richards S.
Sodergren E.J.
Svirskas R.
Tabor P.E.
Wan K.
Stapleton M.
Sutton G.G.
Venter C.
Weinstock G.
Scherer S.E.
Myers E.W.
Gibbs R.A.
Rubin G.M.

title: Finishing a whole-genome shotgun: release 3 of the Drosophila melanogaster euchromatic genome sequence.

authors:
Misra S.
Crosby M.A.
Mungall C.J.
Matthews B.B.
Campbell K.S.
Hradecky P.
Huang Y.
Kaminker J.S.
Millburn G.H.
Prochnik S.E.
Smith C.D.
Tupy J.L.
Whitfied E.J.
Bayraktaroglu L.
Berman B.P.
Bettencourt B.R.
Celniker S.E.
de Grey A.D.
Drysdale R.A.
Harris N.L.
Richter J.
Russo S.
Schroeder A.J.
Shu S.Q.
Stapleton M.
Yamada C.
Ashburner M.
Gelbart W.M.
Rubin G.M.
Lewis S.E.

value: Expressed in adult Malpighian tubule (Drosophila) and 147 other cell types or tissues

value: P:cellular detoxification of cadmium ion

value: ATP-binding cassette sub-family B member 6, mitochondrial

value: ATP-binding cassette sub-family B member 7, mitochondrial

value: ABC transporter type 1, transmembrane domain

value: P-loop containing nucleotide triphosphate hydrolases

value: ATP-BINDING CASSETTE SUB-FAMILY B MEMBER 6

value: P-loop containing nucleoside triphosphate hydrolases


value: VWFC domain-containing protein

description: Helical

description: VWFC

description: Disordered

description: Disordered

description: Disordered

description: Disordered

description: Disordered

description: Disordered

description: Disordered

description: Disordered

description: Disordered

description: Low complexity

description: Polar residues

description: Low complexity

description: Low complexity

description: Polar residues

description: Polar residues

description: Low complexity

description: Low complexity

description: Low complexity

description: Polar residues

description: Polar residues

description: Basic and acidic residues

description: Polar residues

title: Annotation of the Drosophila melanogaster euchromatic genome: a systematic review.

authors:
Kaminker J.S.
Bergman C.M.
Kronmiller B.
Carlson J.
Svirskas R.
Patel S.
Frise E.
Wheeler D.A.
Lewis S.E.
Rubin G.M.
Ashburner M.
Celniker S.E.

title: The transposable elements of the Drosophila melanogaster euchromatin: a genomics perspective.

authors:
Hoskins R.A.
Smith C.D.
Carlson J.W.
Carvalho A.B.
Halpern A.
Kaminker J.S.
Kennedy C.
Mungall C.J.
Sullivan B.A.
Sutton G.G.
Yasuhara J.C.
Wakimoto B.T.
Myers E.W.
Celniker S.E.
Rubin G.M.
Karpen G.H.

authors:
Quesneville H.
Bergman C.M.
Andrieu O.
Autard D.
Nouaud D.
Ashburner M.
Anxolabehere D.

value: Expressed in gamma Kenyon cell (Drosophila) in insect head and 124 other cell types or tissues


value: Chymotrypsin

name: Preferential cleavage: Tyr-|-Xaa, Trp-|-Xaa, Phe-|-Xaa, Leu-|-Xaa.

value: Belongs to the peptidase S1 family. CLIP subfamily

value: Lacks conserved residue(s) required for the propagation of feature annotation

description: Chymotrypsin

description: Peptidase S1

description: Charge relay system

description: Charge relay system

description: Charge relay system

Disulfide bond

category: PTM

Hydrolase

source: RuleBase

value: Berkeley

title: Heterochromatic sequences in a Drosophila whole-genome shotgun assembly.


value: NADP-dependent oxidoreductase domain-containing protein

description: NADP-dependent oxidoreductase

value: Expressed in adult anterior midgut class II enteroendocrine cell in adult midgut (Drosophila) and 54 other cell types or tissues


source: SMART

value: CHK kinase-like domain-containing protein

description: CHK kinase-like

description: CHK kinase-like

description: Disordered

description: Basic and acidic residues

value: Expressed in midgut large flat cell (Drosophila) in digestive tract and 52 other cell types or tissues


value: dIPK

value: Endoplasmic reticulum

source: SAM

type: Repeat

description: TPR

description: TPR

description: TPR

description: TPR

description: TPR

description: J

description: Disordered

value: Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs)

value: Expressed in embryonic/larval hemocyte (Drosophila) and 156 other cell types or tissues

value: P:protein folding in endoplasmic reticulum


source: Google

value: Ethanolaminephosphotransferase 1

value: Membrane

value: Belongs to the CDP-alcohol phosphatidyltransferase class-I family

description: Helical

description: Helical

description: Helical

description: Helical

description: Helical

description: Helical

description: Helical

value: Expressed in adult differentiating enterocyte in digestive tract and 108 other cell types or tissues


value: Headbutt, isoform D

value: hbt

description: Helical

description: Helical

description: Helical

description: Helical

description: Helical

description: Helical

description: Disordered

description: Disordered

description: Disordered

description: Gly residues

description: Low complexity

description: Gly residues

value: Expressed in outer photoreceptor cell (Drosophila) in insect head and 142 other cell types or tissues


value: Pseudouridylate synthase RPUSD2

value: RNA pseudouridylate synthase domain-containing protein 2

value: Pseudouridine synthase that catalyzes pseudouridylation of mRNAs. In addition, it catalyzes the formation of pseudouridine mainly at positions 31 and 32 in the anticodon loop of cytosolic and mitochondrial tRNAs, and at position 34 of certain cytosolic tRNAs such as tRNA(Ile)

name: a uridine in mRNA = a pseudouridine in mRNA

name: a uridine in tRNA = a pseudouridine in tRNA

name: uridine(31) in tRNA = pseudouridine(31) in tRNA

name: uridine(32) in tRNA = pseudouridine(32) in tRNA

value: Belongs to the pseudouridine synthase RluA family

description: Pseudouridine synthase RsuA/RluA-like

description: Disordered

description: Disordered

description: Low complexity

description: Polar residues

source: PIRSR

value: Berkeley

value: Expressed in transmedullary neuron Tm1 (Drosophila) in insect head and 81 other cell types or tissues

value: P:enzyme-directed rRNA pseudouridine synthesis

value: RNA pseudouridine synthase domain-containing 2

value: MITOCHONDRIAL RNA PSEUDOURIDINE SYNTHASE


value: Cytidine deaminase

value: Cytidine aminohydrolase

value: This enzyme scavenges exogenous and endogenous cytidine and 2'-deoxycytidine for UMP synthesis

name: 2'-deoxycytidine + H2O + H(+) = 2'-deoxyuridine + NH4(+)

name: cytidine + H2O + H(+) = uridine + NH4(+)

value: Belongs to the cytidine and deoxycytidylate deaminase family

description: CMP/dCMP-type deaminase

description: Proton donor

value: Expressed in seminal fluid secreting gland and 86 other cell types or tissues


value: Uncharacterized protein

description: Helical

description: Helical

description: Disordered

description: Disordered

description: Low complexity

value: Expressed in adult posterior midgut class II enteroendocrine cell in adult midgut (Drosophila) and 19 other cell types or tissues


value: Expressed in early-mid elongation-stage spermatid (Drosophila) in testis and 22 other cell types or tissues

value: Haloacid dehalogenase-like hydrolase family protein


value: WD repeat-containing protein 82

value: Nucleus

value: Belongs to the WD repeat SWD2 family

description: WD

source: PROSITE-ProRule

value: Expressed in spermatocyte in testis and 14 other cell types or tissues

value: YVTN repeat-like/Quinoprotein amine dehydrogenase


source: EMBL

value: Moleskin

value: msk

value: Imp 7

value: Msk

value: Cytoplasm

value: Belongs to the importin beta family

description: Importin N-terminal

description: Disordered

description: Disordered

description: Acidic residues

description: Acidic residues

value: Berkeley

value: Transcriptional regulation by small RNAs

value: Expressed in cleaving embryo and 210 other cell types or tissues

value: F:nuclear import signal receptor activity

value: P:compound eye cone cell differentiation

value: P:imaginal disc-derived wing morphogenesis

value: P:imaginal disc-derived wing vein morphogenesis

value: P:imaginal disc-derived wing vein specification

value: P:negative regulation of neuron apoptotic process


source: Proteomes

value: Kazal-like domain-containing protein

value: Lacks conserved residue(s) required for the propagation of feature annotation

description: Helical

description: Kazal-like

description: Kazal-like

description: Kazal-like

description: Kazal-like

description: Kazal-like

description: Kazal-like

description: Kazal-like

description: Disordered

description: Polar residues

description: Reactive bond

description: Reactive bond

description: Reactive bond

description: Reactive bond

description: Reactive bond

description: Reactive bond

description: Reactive bond

value: Expressed in peripheral glial cell (Drosophila) in insect leg and 115 other cell types or tissues

value: Serine protease inhibitor dipetalogastin


source: UniProtKB

value: Belongs to the class-III pyridoxal-phosphate-dependent aminotransferase family

value: Does not seem to possess aminotransferase activity

type: Chain

description: Alanine--glyoxylate aminotransferase 2-like

type: Modified residue

description: N6-(pyridoxal phosphate)lysine

authors:
Adams M.D.
Celniker S.E.
Holt R.A.
Evans C.A.
Gocayne J.D.
Amanatides P.G.
Scherer S.E.
Li P.W.
Hoskins R.A.
Galle R.F.
George R.A.
Lewis S.E.
Richards S.
Ashburner M.
Henderson S.N.
Sutton G.G.
Wortman J.R.
Yandell M.D.
Zhang Q.
Chen L.X.
Brandon R.C.
Rogers Y.-H.C.
Blazej R.G.
Champe M.
Pfeiffer B.D.
Wan K.H.
Doyle C.
Baxter E.G.
Helt G.
Nelson C.R.
Miklos G.L.G.
Abril J.F.
Agbayani A.
An H.-J.
Andrews-Pfannkoch C.
Baldwin D.
Ballew R.M.
Basu A.
Baxendale J.
Bayraktaroglu L.
Beasley E.M.
Beeson K.Y.
Benos P.V.
Berman B.P.
Bhandari D.
Bolshakov S.
Borkova D.
Botchan M.R.
Bouck J.
Brokstein P.
Brottier P.
Burtis K.C.
Busam D.A.
Butler H.
Cadieu E.
Center A.
Chandra I.
Cherry J.M.
Cawley S.
Dahlke C.
Davenport L.B.
Davies P.
de Pablos B.
Delcher A.
Deng Z.
Mays A.D.
Dew I.
Dietz S.M.
Dodson K.
Doup L.E.
Downes M.
Dugan-Rocha S.
Dunkov B.C.
Dunn P.
Durbin K.J.
Evangelista C.C.
Ferraz C.
Ferriera S.
Fleischmann W.
Fosler C.
Gabrielian A.E.
Garg N.S.
Gelbart W.M.
Glasser K.
Glodek A.
Gong F.
Gorrell J.H.
Gu Z.
Guan P.
Harris M.
Harris N.L.
Harvey D.A.
Heiman T.J.
Hernandez J.R.
Houck J.
Hostin D.
Houston K.A.
Howland T.J.
Wei M.-H.
Ibegwam C.
Jalali M.
Kalush F.
Karpen G.H.
Ke Z.
Kennison J.A.
Ketchum K.A.
Kimmel B.E.
Kodira C.D.
Kraft C.L.
Kravitz S.
Kulp D.
Lai Z.
Lasko P.
Lei Y.
Levitsky A.A.
Li J.H.
Li Z.
Liang Y.
Lin X.
Liu X.
Mattei B.
McIntosh T.C.
McLeod M.P.
McPherson D.
Merkulov G.
Milshina N.V.
Mobarry C.
Morris J.
Moshrefi A.
Mount S.M.
Moy M.
Murphy B.
Murphy L.
Muzny D.M.
Nelson D.L.
Nelson D.R.
Nelson K.A.
Nixon K.
Nusskern D.R.
Pacleb J.M.
Palazzolo M.
Pittman G.S.
Pan S.
Pollard J.
Puri V.
Reese M.G.
Reinert K.
Remington K.
Saunders R.D.C.
Scheeler F.
Shen H.
Shue B.C.
Siden-Kiamos I.
Simpson M.
Skupski M.P.
Smith T.J.
Spier E.
Spradling A.C.
Stapleton M.
Strong R.
Sun E.
Svirskas R.
Tector C.
Turner R.
Venter E.
Wang A.H.
Wang X.
Wang Z.-Y.
Wassarman D.A.
Weinstock G.M.
Weissenbach J.
Williams S.M.
Woodage T.
Worley K.C.
Wu D.
Yang S.
Yao Q.A.
Ye J.
Yeh R.-F.
Zaveri J.S.
Zhan M.
Zhang G.
Zhao Q.
Zheng L.
Zheng X.H.
Zhong F.N.
Zhong W.
Zhou X.
Zhu S.C.
Zhu X.
Smith H.O.
Gibbs R.A.
Myers E.W.
Rubin G.M.
Venter J.C.

authors:
Misra S.
Crosby M.A.
Mungall C.J.
Matthews B.B.
Campbell K.S.
Hradecky P.
Huang Y.
Kaminker J.S.
Millburn G.H.
Prochnik S.E.
Smith C.D.
Tupy J.L.
Whitfield E.J.
Bayraktaroglu L.
Berman B.P.
Bettencourt B.R.
Celniker S.E.
de Grey A.D.N.J.
Drysdale R.A.
Harris N.L.
Richter J.
Russo S.
Schroeder A.J.
Shu S.Q.
Stapleton M.
Yamada C.
Ashburner M.
Gelbart W.M.
Rubin G.M.
Lewis S.E.

authors:
Stapleton M.
Carlson J.W.
Brokstein P.
Yu C.
Champe M.
George R.A.
Guarin H.
Kronmiller B.
Pacleb J.M.
Park S.
Wan K.H.
Rubin G.M.
Celniker S.E.

title: A Drosophila full-length cDNA resource.

value: Embryo

value: mRNA

database: BioGRID

key: Interactions

database: FunCoup

key: Number of interactors

database: STRING

database: PaxDb

database: PeptideAtlas

database: DNASU

database: EnsemblMetazoa

database: UCSC

key: OrganismName

value: d. melanogaster

database: AGR

database: FlyBase

database: VEuPathDB

database: eggNOG

value: Eukaryota

database: HOGENOM

database: InParanoid

database: OMA

database: OrthoDB

database: PhylomeDB

database: Reactome

value: Expressed in adult Malpighian tubule principal cell of lower segment in Malpighian tubule and 182 other cell types or tissues

value: ethanolamine-phosphate phospho-lyase isoform X1

value: Type I PLP-dependent aspartate aminotransferase-like (Major domain)


value: Tyrosine--tRNA ligase

value: Tyrosyl-tRNA synthetase

value: TyrRS

value: Aats-tyr

value: dTyrRS

value: dYARS

value: EMAP

value: YARS

value: YRS

name: tRNA(Tyr) + L-tyrosine + ATP = L-tyrosyl-tRNA(Tyr) + AMP + diphosphate + H(+)

database: Rhea

database: ChEBI

source: ARBA

value: Cytoplasm

value: Nucleus

value: Belongs to the class-I aminoacyl-tRNA synthetase family

description: TRNA-binding

source: PROSITE

database: PubMed

database: DOI

value: Berkeley

type: STRAIN

value: Expressed in oviduct (Drosophila) and 149 other cell types or tissues

value: tyrosine--tRNA ligase, cytoplasmic isoform X2

value: TRNA-AMINOACYLATION COFACTOR ARC1 FAMILY MEMBER


value: Dicarboxylate carrier 4, isoform A

value: Dicarboxylate carrier 4, isoform C

value: Membrane

value: Multi-pass membrane protein

value: Belongs to the mitochondrial carrier (TC 2.A.29) family

description: Helical

description: Helical

description: Solcar

description: Solcar

description: Solcar

authors:
Celniker S.
Carlson J.
Wan K.
Frise E.
Hoskins R.
Park S.
Svirskas R.
Rubin G.

value: Expressed in early-mid elongation-stage spermatid (Drosophila) in testis and 17 other cell types or tissues

value: F:sulfate transmembrane transporter activity

value: F:thiosulfate transmembrane transporter activity


value: Organic solute transporter alpha-like protein

value: Solute carrier family 51 subunit alpha homolog

value: Probable transporter

value: Cell membrane

value: Belongs to the OST-alpha family

description: Extracellular

description: Helical

description: Cytoplasmic

description: Helical

description: Extracellular

description: Helical

description: Cytoplasmic

description: Helical

description: Extracellular

description: Helical

description: Cytoplasmic

description: Helical

description: Extracellular

description: Helical

description: Cytoplasmic

description: N-linked (GlcNAc...) asparagine

description: N-linked (GlcNAc...) asparagine

description: N-linked (GlcNAc...) asparagine

description: N-linked (GlcNAc...) asparagine

description: N-linked (GlcNAc...) asparagine

type: Sequence conflict

description: in Ref. 3; AAL39357

originalSequence: I

title: A Drosophila full-length cDNA resource.

value: Expressed in thoracico-abdominal ganglion (Drosophila) and 70 other cell types or tissues


value: RNA helicase

type: Domain

description: Helicase ATP-binding

description: Helicase C-terminal

type: Region

description: Disordered

description: Basic residues

description: Basic and acidic residues

value: Berkeley

authors:
Smith C.D.
Shu S.
Mungall C.J.
Karpen G.H.

value: Expressed in cleaving embryo and 29 other cell types or tissues

value: P-loop containing nucleotide triphosphate hydrolases

value: P-loop containing nucleoside triphosphate hydrolases


value: Quaking related 58E-1, isoform A

description: K Homology

description: Disordered

description: Disordered

description: Disordered

type: Compositional bias

description: Basic and acidic residues

description: Basic and acidic residues

description: Low complexity

description: Basic and acidic residues

authors:
Hoskins R.A.
Carlson J.W.
Kennedy C.
Acevedo D.
Evans-Holm M.
Frise E.
Wan K.H.
Park S.
Mendez-Lago M.
Rossi F.
Villasante A.
Dimitri P.
Karpen G.H.
Celniker S.E.

value: PTK6 Regulates Proteins Involved in RNA Processing

value: Expressed in distal medullary amacrine neuron Dm9 in insect head and 266 other cell types or tissues

value: P:regulation of alternative mRNA splicing, via spliceosome

value: Eukaryotic type KH-domain (KH-domain type I)


value: F-box protein 42

description: F-box

description: Disordered

description: Disordered

description: Gly residues

description: Low complexity

description: Low complexity

description: Pro residues

value: Expressed in medullary tangential neuron Mt1 (Drosophila) in brain and 64 other cell types or tissues

value: F:ubiquitin-like ligase-substrate adaptor activity

value: P:positive regulation of synaptonemal complex assembly

value: P:SCF-dependent proteasomal ubiquitin-dependent protein catabolic process


value: NtR, isoform A

value: NtR

value: DNtR

value: NTR

type: Signal

description: Helical

description: Helical

description: Helical

description: Helical

description: Farnesoic acid O-methyl transferase

value: Expressed in embryonic/larval hemocyte (Drosophila) and 58 other cell types or tissues

value: F:extracellular ligand-gated monoatomic ion channel activity

value: P:monoatomic ion transmembrane transport

value: Neurotransmitter-gated ion-channel ligand-binding domain

value: Multidrug efflux transporter AcrB transmembrane domain

value: Nicotinic receptor ligand binding domain-like


value: 3',5'-cyclic-AMP phosphodiesterase, isoforms N/G

value: Learning/memory process protein

value: Protein dunce

value: cAMP-specific phosphodiesterase, isoforms N/G

value: dnc

value: Hydrolyzes the second messenger cAMP, which is a key regulator of many important physiological processes (By similarity). Vital for female fertility. Required for learning/memory (By similarity)

value: Binds 2 divalent metal cations per subunit. Site 1 may preferentially bind zinc ions, while site 2 has a preference for magnesium and/or manganese ions.

value: Purine metabolism; 3',5'-cyclic AMP degradation; AMP from 3',5'-cyclic AMP: step 1/1

commentType: PATHWAY

value: Monomer

events:
Alternative splicing
Alternative initiation

source: PubMed

value: N

value: G

value: F

isoformSequenceStatus: External

value: I

value: B

value: S

value: II

value: J

value: III

value: E

value: P

value: IV

value: A

value: V

value: C

value: VI

value: D

value: VII

value: L

value: R

value: Q

value: U

value: T

value: Belongs to the cyclic nucleotide phosphodiesterase family. PDE4 subfamily

commentType: SEQUENCE CAUTION

sequenceCautionType: Erroneous gene model prediction

description: PDEase

description: Disordered

description: Disordered

description: Disordered

description: Disordered

description: Disordered

description: Basic and acidic residues

description: Polar residues

description: Gly residues

description: Low complexity

description: Low complexity

description: Acidic residues

description: Low complexity

description: Low complexity

description: Polar residues

description: Polar residues

description: Polar residues

description: Acidic residues

description: Low complexity

description: Gly residues

description: Polar residues

description: Proton donor

description: Binds AMP, but not cAMP

description: in isoform G

referencePositions:
GENOME REANNOTATION
ALTERNATIVE SPLICING

authors:
Benos P.V.
Gatt M.K.
Ashburner M.
Murphy L.
Harris D.
Barrell B.G.
Ferraz C.
Vidal S.
Brun C.
Demailles J.
Cadieu E.
Dreano S.
Gloux S.
Lelaure V.
Mottier S.
Galibert F.
Borkova D.
Minana B.
Kafatos F.C.
Louis C.
Siden-Kiamos I.
Bolshakov S.
Papagiannakis G.
Spanos L.
Cox S.
Madueno E.
de Pablos B.
Modolell J.
Peter A.
Schoettler P.
Werner M.
Mourkioti F.
Beinert N.
Dowe G.
Schaefer U.
Jaeckle H.
Bucheton A.
Callister D.M.
Campbell L.A.
Darlamitsou A.
Henderson N.S.
McMillan P.J.
Salles C.
Tait E.A.
Valenti P.
Saunders R.D.C.
Glover D.M.

title: From sequence to chromosome: the tip of the X chromosome of D. melanogaster.

referencePositions: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA] OF 170-479

value: Expressed in muscle cell in antenna and 285 other cell types or tissues

value: 3'5'-cyclic nucleotide phosphodiesterase, catalytic domain


value: Jumeau

value: jumu

value: Dmjumu

value: Dom

value: Dwhn

value: jumeaux

value: Jumu

value: jumu/Dom

value: Whn

value: Nucleus

description: Fork-head

type: DNA binding

description: Fork-head

description: Disordered

description: Disordered

description: Disordered

description: Polar residues

description: Polar residues

description: Low complexity

description: Acidic residues

value: Berkeley

authors:
Matthews B.B.
Dos Santos G.
Crosby M.A.
Emmert D.B.
St Pierre S.E.
Gramates L.S.
Zhou P.
Schroeder A.J.
Falls K.
Strelets V.
Russo S.M.
Gelbart W.M.

value: Expressed in wing disc and 65 other cell types or tissues

value: F:cis-regulatory region sequence-specific DNA binding

value: F:DNA-binding transcription factor activity

value: F:transcription cis-regulatory region binding

value: P:imaginal disc-derived wing morphogenesis

value: P:positive regulation of receptor signaling pathway via JAK-STAT

value: P:regulation of DNA-templated transcription

value: Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain