# Pair analysis: gria1a / gria1b (run 2026-09-28) ## 0. Ensembl Compara homologies gria1a: ENSDARG00000021352 chr14:34125855-34276574 danio_rerio within_species_paralog ENSDARG00000032714 node=Osteoglossocephalai lepisosteus_oculatus ortholog_one2many ENSLOCG00000009807 node=Neopterygii homo_sapiens ortholog_one2many ENSG00000155511 node=Euteleostomi oryzias_latipes ortholog_one2one ENSORLG00000007719 node=Clupeocephala gria1b: ENSDARG00000032714 chr21:26152332-26250744 danio_rerio within_species_paralog ENSDARG00000021352 node=Osteoglossocephalai lepisosteus_oculatus ortholog_one2many ENSLOCG00000009807 node=Neopterygii homo_sapiens ortholog_one2many ENSG00000155511 node=Euteleostomi oryzias_latipes ortholog_one2one ENSORLG00000022427 node=Clupeocephala gar orthologs (union): ['ENSLOCG00000009807'] ## 1. Sequence lengths and pairwise identities length gria1a: 914 aa length gria1b: 917 aa length GRIA1: 906 aa length GRIA2: 883 aa length gar_ENSLOCG00000009807: 906 aa length medaka_ENSORLG00000007719(orth of gria1a): 921 aa length medaka_ENSORLG00000022427(orth of gria1b): 969 aa identity gria1a vs gria1b: 82.5% over 920 columns identity gria1a vs GRIA1: 74.4% over 927 columns identity gria1a vs GRIA2: 65.0% over 933 columns identity gria1a vs gar_ENSLOCG00000009807: 88.3% over 914 columns identity gria1a vs medaka_ENSORLG00000007719(orth of gria1a): 89.9% over 921 columns identity gria1a vs medaka_ENSORLG00000022427(orth of gria1b): 72.2% over 970 columns identity gria1b vs GRIA1: 71.0% over 933 columns identity gria1b vs GRIA2: 63.1% over 928 columns identity gria1b vs gar_ENSLOCG00000009807: 81.7% over 920 columns identity gria1b vs medaka_ENSORLG00000007719(orth of gria1a): 80.1% over 926 columns identity gria1b vs medaka_ENSORLG00000022427(orth of gria1b): 76.4% over 969 columns identity GRIA1 vs GRIA2: 67.7% over 914 columns identity GRIA1 vs gar_ENSLOCG00000009807: 76.8% over 919 columns identity GRIA1 vs medaka_ENSORLG00000007719(orth of gria1a): 73.1% over 938 columns identity GRIA1 vs medaka_ENSORLG00000022427(orth of gria1b): 65.1% over 978 columns identity GRIA2 vs gar_ENSLOCG00000009807: 65.7% over 923 columns identity GRIA2 vs medaka_ENSORLG00000007719(orth of gria1a): 63.8% over 943 columns identity GRIA2 vs medaka_ENSORLG00000022427(orth of gria1b): 57.6% over 976 columns identity gar_ENSLOCG00000009807 vs medaka_ENSORLG00000007719(orth of gria1a): 87.4% over 921 columns identity gar_ENSLOCG00000009807 vs medaka_ENSORLG00000022427(orth of gria1b): 71.6% over 969 columns identity medaka_ENSORLG00000007719(orth of gria1a) vs medaka_ENSORLG00000022427(orth of gria1b): 71.1% over 972 columns ## 2. Regions and point features of the human ortholog Topological domain: Extracellular [19-536]: gria1a 367/518 identical (70.8%; aligned 516); gria1b 356/518 identical (68.7%; aligned 516); gar_ENSLOCG00000009807 376/518 identical (72.6%; aligned 516); medaka_ENSORLG00000007719(orth of gria1a) 364/518 identical (70.3%; aligned 512); medaka_ENSORLG00000022427(orth of gria1b) 334/518 identical (64.5%; aligned 516) Transmembrane: Helical [537-557]: gria1a 21/21 identical (100.0%; aligned 21); gria1b 21/21 identical (100.0%; aligned 21); gar_ENSLOCG00000009807 21/21 identical (100.0%; aligned 21); medaka_ENSORLG00000007719(orth of gria1a) 21/21 identical (100.0%; aligned 21); medaka_ENSORLG00000022427(orth of gria1b) 21/21 identical (100.0%; aligned 21) Topological domain: Cytoplasmic [558-584]: gria1a 15/27 identical (55.6%; aligned 27); gria1b 16/27 identical (59.3%; aligned 27); gar_ENSLOCG00000009807 18/27 identical (66.7%; aligned 27); medaka_ENSORLG00000007719(orth of gria1a) 16/27 identical (59.3%; aligned 27); medaka_ENSORLG00000022427(orth of gria1b) 15/27 identical (55.6%; aligned 27) Intramembrane: Helical; Pore-forming [585-600]: gria1a 16/16 identical (100.0%; aligned 16); gria1b 16/16 identical (100.0%; aligned 16); gar_ENSLOCG00000009807 16/16 identical (100.0%; aligned 16); medaka_ENSORLG00000007719(orth of gria1a) 16/16 identical (100.0%; aligned 16); medaka_ENSORLG00000022427(orth of gria1b) 16/16 identical (100.0%; aligned 16) Intramembrane [601-603]: gria1a 3/3 identical (100.0%; aligned 3); gria1b 3/3 identical (100.0%; aligned 3); gar_ENSLOCG00000009807 3/3 identical (100.0%; aligned 3); medaka_ENSORLG00000007719(orth of gria1a) 3/3 identical (100.0%; aligned 3); medaka_ENSORLG00000022427(orth of gria1b) 3/3 identical (100.0%; aligned 3) Topological domain: Cytoplasmic [604-609]: gria1a 6/6 identical (100.0%; aligned 6); gria1b 6/6 identical (100.0%; aligned 6); gar_ENSLOCG00000009807 6/6 identical (100.0%; aligned 6); medaka_ENSORLG00000007719(orth of gria1a) 6/6 identical (100.0%; aligned 6); medaka_ENSORLG00000022427(orth of gria1b) 6/6 identical (100.0%; aligned 6) Transmembrane: Helical [610-630]: gria1a 21/21 identical (100.0%; aligned 21); gria1b 21/21 identical (100.0%; aligned 21); gar_ENSLOCG00000009807 21/21 identical (100.0%; aligned 21); medaka_ENSORLG00000007719(orth of gria1a) 21/21 identical (100.0%; aligned 21); medaka_ENSORLG00000022427(orth of gria1b) 21/21 identical (100.0%; aligned 21) Topological domain: Extracellular [631-805]: gria1a 167/175 identical (95.4%; aligned 175); gria1b 158/175 identical (90.3%; aligned 175); gar_ENSLOCG00000009807 166/175 identical (94.9%; aligned 175); medaka_ENSORLG00000007719(orth of gria1a) 167/175 identical (95.4%; aligned 175); medaka_ENSORLG00000022427(orth of gria1b) 154/175 identical (88.0%; aligned 175) Transmembrane: Helical; Name=M4 [806-826]: gria1a 20/21 identical (95.2%; aligned 21); gria1b 20/21 identical (95.2%; aligned 21); gar_ENSLOCG00000009807 20/21 identical (95.2%; aligned 21); medaka_ENSORLG00000007719(orth of gria1a) 20/21 identical (95.2%; aligned 21); medaka_ENSORLG00000022427(orth of gria1b) 19/21 identical (90.5%; aligned 21) Topological domain: Cytoplasmic [827-906]: gria1a 46/80 identical (57.5%; aligned 69); gria1b 39/80 identical (48.8%; aligned 66); gar_ENSLOCG00000009807 50/80 identical (62.5%; aligned 69); medaka_ENSORLG00000007719(orth of gria1a) 46/80 identical (57.5%; aligned 69); medaka_ENSORLG00000022427(orth of gria1b) 40/80 identical (50.0%; aligned 73) Region: Disordered [861-880]: gria1a 10/20 identical (50.0%; aligned 16); gria1b 8/20 identical (40.0%; aligned 13); gar_ENSLOCG00000009807 10/20 identical (50.0%; aligned 16); medaka_ENSORLG00000007719(orth of gria1a) 9/20 identical (45.0%; aligned 16); medaka_ENSORLG00000022427(orth of gria1b) 12/20 identical (60.0%; aligned 20) Motif 903-906 (PDZ-binding) human=ATGL: gria1a=ASGM (DIFFERENT); gria1b=TTGM (DIFFERENT); gar_ENSLOCG00000009807=ATGM (DIFFERENT); medaka_ENSORLG00000007719(orth of gria1a)=ASGM (DIFFERENT); medaka_ENSORLG00000022427(orth of gria1b)=STGM (DIFFERENT) Binding site 492-492 (L-glutamate) human=P: gria1a=P; gria1b=P; gar_ENSLOCG00000009807=P; medaka_ENSORLG00000007719(orth of gria1a)=P; medaka_ENSORLG00000022427(orth of gria1b)=P Binding site 494-494 (L-glutamate) human=T: gria1a=T; gria1b=T; gar_ENSLOCG00000009807=T; medaka_ENSORLG00000007719(orth of gria1a)=T; medaka_ENSORLG00000022427(orth of gria1b)=T Binding site 499-499 (L-glutamate) human=R: gria1a=R; gria1b=R; gar_ENSLOCG00000009807=R; medaka_ENSORLG00000007719(orth of gria1a)=R; medaka_ENSORLG00000022427(orth of gria1b)=R Binding site 668-668 (L-glutamate) human=S: gria1a=S; gria1b=S; gar_ENSLOCG00000009807=S; medaka_ENSORLG00000007719(orth of gria1a)=S; medaka_ENSORLG00000022427(orth of gria1b)=S Binding site 669-669 (L-glutamate) human=T: gria1a=T; gria1b=T; gar_ENSLOCG00000009807=T; medaka_ENSORLG00000007719(orth of gria1a)=T; medaka_ENSORLG00000022427(orth of gria1b)=T Binding site 719-719 (L-glutamate) human=E: gria1a=E; gria1b=E; gar_ENSLOCG00000009807=E; medaka_ENSORLG00000007719(orth of gria1a)=E; medaka_ENSORLG00000022427(orth of gria1b)=E Modified residue 645-645 (Phosphoserine) human=S: gria1a=S; gria1b=S; gar_ENSLOCG00000009807=S; medaka_ENSORLG00000007719(orth of gria1a)=S; medaka_ENSORLG00000022427(orth of gria1b)=S Modified residue 710-710 (Phosphoserine) human=S: gria1a=S; gria1b=S; gar_ENSLOCG00000009807=S; medaka_ENSORLG00000007719(orth of gria1a)=S; medaka_ENSORLG00000022427(orth of gria1b)=S Modified residue 849-849 (Phosphoserine) human=S: gria1a=S; gria1b=I (DIFFERENT); gar_ENSLOCG00000009807=S; medaka_ENSORLG00000007719(orth of gria1a)=S; medaka_ENSORLG00000022427(orth of gria1b)=L (DIFFERENT) Modified residue 863-863 (Phosphoserine) human=S: gria1a=S; gria1b=- (DIFFERENT); gar_ENSLOCG00000009807=S; medaka_ENSORLG00000007719(orth of gria1a)=S; medaka_ENSORLG00000022427(orth of gria1b)=S Lipidation 603-603 (S-palmitoyl cysteine) human=C: gria1a=C; gria1b=C; gar_ENSLOCG00000009807=C; medaka_ENSORLG00000007719(orth of gria1a)=C; medaka_ENSORLG00000022427(orth of gria1b)=C Lipidation 829-829 (S-palmitoyl cysteine) human=C: gria1a=C; gria1b=C; gar_ENSLOCG00000009807=C; medaka_ENSORLG00000007719(orth of gria1a)=C; medaka_ENSORLG00000022427(orth of gria1b)=C aligned segment pore loop and M2-M3 (Q/R site region) [585-612] human=FGIFNSLWFSLGAFMQQGCDISPRSLSG: gria1a=FGIFNSLWFSLGAFMQQGCDISPRSLSG; gria1b=FGIFNSLWFSLGAFMQQGCDISPRSLSG; gar_ENSLOCG00000009807=FGIFNSLWFSLGAFMQQGCDISPRSLSG; medaka_ENSORLG00000007719(orth of gria1a)=FGIFNSLWFSLGAFMQQGCDISPRSLSG; medaka_ENSORLG00000022427(orth of gria1b)=FGIFNSLWFSLGAFMQQGCDISPRSLSG aligned segment C-terminal tail [827-906] human=EFCYKSRSESKRMKGFCLIPQQSINEAIRTSTLPRNSGAGASSGGSGENGRVVSHDFPKSMQSIPCMSHSSGMPLGATGL: gria1a=EFCYKSRTESRRMK-------QSINDAMHCSTLTRMSG----NGSGGENGRIVTHDFPKAVQTLPCMSHAASMGLGASGM; gria1b=EFCYKSRIESRRMK-------QIIDAAMLSSTLTR-------MGSGGENGRVMAHDFPKGAQTLPCMGQAAAMGLSTTGM; gar_ENSLOCG00000009807=EFCYKSRTESRRMK-------QSINDAMRTSTLTRMSG----NGSGGENGRIVTHDFPKSMQTLPCMSHAAGLGLSATGM; medaka_ENSORLG00000007719(orth of gria1a)=EFCYKSRTESRRMK-------QSINDALRCSTLTRVSG----NGSGGENGRILTHDFPKTVQTLPCMSHTASMGLGASGM; medaka_ENSORLG00000022427(orth of gria1b)=EFCYKSRIESRRMK-------ELIDAAMMSSSLGGVSGGGEAGGGTGENGRVVTHDFPSGVKRLPCMSKAAGLGLSSTGM C-terminal 10 residues gria1a: ASMGLGASGM C-terminal 10 residues gria1b: AAMGLSTTGM C-terminal 10 residues GRIA1: SGMPLGATGL C-terminal 10 residues gar_ENSLOCG00000009807: AGLGLSATGM ## 2b. Point features across all Ensembl translations of each zebrafish copy gria1a ENSDART00000021437 (914 aa, canonical): C-term LGASGM; differing point features: ['Motif 903 ATGL->ASGM'] gria1b ENSDART00000134761 (155 aa): C-term RIRPVL; differing point features: ['Motif 903 ATGL->---L', 'Binding site 492 P->-', 'Binding site 494 T->-', 'Binding site 499 R->-', 'Modified residue 849 S->-', 'Modified residue 863 S->-', 'Lipidation 603 C->-', 'Lipidation 829 C->-'] gria1b ENSDART00000123713 (917 aa): C-term LSTTGM; differing point features: ['Motif 903 ATGL->TTGM', 'Modified residue 849 S->I', 'Modified residue 863 S->-'] gria1b ENSDART00000044735 (917 aa, canonical): C-term LSTTGM; differing point features: ['Motif 903 ATGL->TTGM', 'Modified residue 849 S->I', 'Modified residue 863 S->-'] ## 3. Tajima-style relative-rate test (outgroup = gar) gar protein length 906; positions aligned in both copies: 903 changes unique to gria1a (m1): 34; unique to gria1b (m2): 86; chi2 (1 df) = 22.53 (P<0.05) ## 4. Whole-embryo time course, E-ERAD-475 (TPM, median of replicates) | stage | gria1a | gria1b | |---|---|---| | zygote | 0.2 | 0 | | cleavage 2-cell | 0.4 | 0 | | blastula 128-cell | 1 | 0 | | blastula 1k-cell | 0.4 | 0.3 | | blastula dome | 0.6 | 0 | | gastrula 50%-epiboly | 0.3 | 0 | | gastrula shield | 0 | 0.2 | | gastrula 75%-epiboly | 0 | 0.2 | | segmentation 1-4 somites | 1 | 0.5 | | segmentation 14-19 somites | 2 | 1 | | segmentation 20-25 somites | 2 | 1 | | pharyngula prim-5 | 2 | 1 | | pharyngula prim-15 | 2 | 1 | | pharyngula prim-25 | 4 | 0.6 | | hatching long-pec | 6 | 1 | | larval protruding mouth | 14 | 5 | | larval day 4 | 12 | 5 | | larval day 5 | 14 | 6 | ## 5. Bgee expressed calls per anatomical entity (expression score 0-100; only 'expressed' calls) ### gria1a: 6 calls - brain: 81.0 (gold; RNA-Seq) - retina: 66.3 (silver; RNA-Seq) - larva: 53.3 (gold; RNA-Seq) - embryo: 37.1 (gold; RNA-Seq) - bone element: 27.1 (silver; RNA-Seq) - testis: 22.4 (silver; RNA-Seq) ### gria1b: 8 calls - brain: 79.6 (gold; RNA-Seq) - retina: 75.4 (gold; EST,RNA-Seq) - mature ovarian follicle: 65.2 (gold; RNA-Seq) - spleen: 64.7 (gold; RNA-Seq) - testis: 49.6 (gold; RNA-Seq) - larva: 40.7 (gold; RNA-Seq) - pharyngeal gill: 31.4 (silver; RNA-Seq) - embryo: 31.3 (silver; RNA-Seq) ### gar ENSLOCG00000009807: 6 calls - brain: 87.7 (gold; RNA-Seq) - camera-type eye: 63.9 (gold; RNA-Seq) - larva: 62.0 (gold; RNA-Seq) - ovary: 34.8 (silver; RNA-Seq) - bone element: 33.2 (gold; RNA-Seq) - embryo: 24.8 (gold; RNA-Seq) entities called for gria1a only: ['bone element'] entities called for gria1b only: ['mature ovarian follicle', 'pharyngeal gill', 'spleen'] entities called for both (5); score gria1a - gria1b: - brain: 81.0 vs 79.6 (diff +1.4) - embryo: 37.1 vs 31.3 (diff +5.8) - larva: 53.3 vs 40.7 (diff +12.6) - retina: 66.3 vs 75.4 (diff -9.1) - testis: 22.4 vs 49.6 (diff -27.1) ## 6. ZFIN curated wild-type expression (wildtype-expression_fish.txt) ### gria1a: 35 records, 26 anatomy terms, publications: ['ZDB-PUB-060807-11', 'ZDB-PUB-080226-9', 'ZDB-PUB-120705-10'] - ZDB-PUB-060807-11: brain; whole organism - ZDB-PUB-080226-9: dorsal telencephalon; dorsal thalamus; dorso-rostral cluster; habenula; hypothalamus; medulla oblongata; motor neuron; olfactory bulb; optic tectum; preoptic area; retinal ganglion cell; retinal ganglion cell layer; retinal inner nuclear layer; rhombomere; sensory neuron; spinal cord; spinal cord interneuron; tegmentum; telencephalon; thalamus; ventral telencephalon; ventral thalamus; ventro-caudal cluster; ventro-rostral cluster - ZDB-PUB-120705-10: whole organism ### gria1b: 26 records, 20 anatomy terms, publications: ['ZDB-PUB-051025-1', 'ZDB-PUB-060807-11', 'ZDB-PUB-080226-9'] - ZDB-PUB-051025-1: whole organism - ZDB-PUB-060807-11: brain; whole organism - ZDB-PUB-080226-9: dorso-rostral cluster; habenula; hypothalamus; medulla oblongata; motor neuron; olfactory bulb; optic tectum; otic vesicle; preoptic area; retinal ganglion cell layer; retinal inner nuclear layer; sensory neuron; spinal cord interneuron; tegmentum; thalamus; ventral thalamus; ventro-caudal cluster; ventro-rostral cluster terms for gria1a only: ['dorsal telencephalon', 'dorsal thalamus', 'retinal ganglion cell', 'rhombomere', 'spinal cord', 'telencephalon', 'ventral telencephalon'] terms for gria1b only: ['otic vesicle'] terms for both: ['brain', 'dorso-rostral cluster', 'habenula', 'hypothalamus', 'medulla oblongata', 'motor neuron', 'olfactory bulb', 'optic tectum', 'preoptic area', 'retinal ganglion cell layer', 'retinal inner nuclear layer', 'sensory neuron', 'spinal cord interneuron', 'tegmentum', 'thalamus', 'ventral thalamus', 'ventro-caudal cluster', 'ventro-rostral cluster', 'whole organism'] ## 7. Local synteny between the two copies (Ensembl REST) gria1a chr14:34125855 +/- 1.5 Mb: 83 other protein-coding genes (0 homology queries failed); 15 have a teleost-level (Clupeocephala/Osteoglossocephalai/Teleostei) zebrafish paralogue; 0 such pairs have their partner within 1.5 Mb of gria1b: 6 have their partner anywhere on chr21 (chromosome of gria1b, 962 protein-coding genes): - lcp2b -> lcp2a (chr21:30306369) - foxi3b -> foxi3a (chr21:30351256) - afap1l1a -> afap1l1b (chr21:30418034) - adrb2a -> adrb2b (chr21:35078766) - il12ba -> il12bb (chr21:35289469) - rnf145a -> rnf145b (chr21:34001712) gria1b chr21:26152332 +/- 1.5 Mb: 102 other protein-coding genes (0 homology queries failed); 46 have a teleost-level (Clupeocephala/Osteoglossocephalai/Teleostei) zebrafish paralogue; 0 such pairs have their partner within 1.5 Mb of gria1a: 11 have their partner anywhere on chr14 (chromosome of gria1a, 823 protein-coding genes): - npas4b -> npas4a (chr14:30636955) - efemp2b -> efemp2a (chr14:30669662) - fibpb -> fibpa (chr14:30713736) - fosl1b -> fosl1a (chr14:30739476) - eif4ebp3 -> eif4ebp3l (chr14:6972868) - vegfbb -> vegfba (chr14:8504410) - stx5al -> stx5a (chr14:8594367) - nxf1b -> nxf1a (chr14:8893529) - bscl2 -> bscl2l (chr14:6159162) - si:dkey-175m17.6 -> si:dkey-160o24.3 (chr14:8442248) - ENSDARG00000044534 -> zgc:162144 (chr14:8619126)