# Pair analysis: sh3glb2a / sh3glb2b (run 2026-09-28) ## 0. Ensembl Compara homologies of the two zebrafish genes sh3glb2a: within-species paralogue ENSDARG00000035470 (within_species_paralog), duplication node Osteoglossocephalai sh3glb2a: ortholog_one2many lepisosteus_oculatus ENSLOCG00000006193 (node Neopterygii) sh3glb2a: ortholog_one2many homo_sapiens ENSG00000148341 (node Euteleostomi) sh3glb2a: ortholog_one2one oryzias_latipes ENSORLG00000016839 (node Clupeocephala) sh3glb2b: within-species paralogue ENSDARG00000008983 (within_species_paralog), duplication node Osteoglossocephalai sh3glb2b: ortholog_one2many lepisosteus_oculatus ENSLOCG00000006193 (node Neopterygii) sh3glb2b: ortholog_one2many homo_sapiens ENSG00000148341 (node Euteleostomi) sh3glb2b: ortholog_one2one oryzias_latipes ENSORLG00000014325 (node Osteoglossocephalai) gar orthologue gene(s): ['ENSLOCG00000006193'] ## 1. Sequence lengths and pairwise identities (global, BLOSUM62, -10/-0.5) length sh3glb2a: 381 aa length sh3glb2b: 421 aa length sh3glb2b_NP_Q802U5: 373 aa length SH3GLB2: 395 aa length SH3GLB1: 365 aa length gar_ENSLOCG00000006193: 393 aa length medaka_ENSORLG00000016839_orth_of_sh3glb2a: 363 aa length medaka_ENSORLG00000014325_orth_of_sh3glb2b: 490 aa identity sh3glb2a vs sh3glb2b: 73.6% over 421 columns identity sh3glb2a vs sh3glb2b_NP_Q802U5: 70.4% over 402 columns identity sh3glb2a vs SH3GLB2: 72.9% over 399 columns identity sh3glb2a vs SH3GLB1: 58.2% over 402 columns identity sh3glb2a vs gar_ENSLOCG00000006193: 74.9% over 399 columns identity sh3glb2a vs medaka_ENSORLG00000016839_orth_of_sh3glb2a: 70.7% over 382 columns identity sh3glb2a vs medaka_ENSORLG00000014325_orth_of_sh3glb2b: 58.2% over 500 columns identity sh3glb2b vs sh3glb2b_NP_Q802U5: 88.4% over 421 columns identity sh3glb2b vs SH3GLB2: 69.2% over 428 columns identity sh3glb2b vs SH3GLB1: 55.3% over 436 columns identity sh3glb2b vs gar_ENSLOCG00000006193: 73.7% over 426 columns identity sh3glb2b vs medaka_ENSORLG00000016839_orth_of_sh3glb2a: 65.3% over 421 columns identity sh3glb2b vs medaka_ENSORLG00000014325_orth_of_sh3glb2b: 61.5% over 522 columns identity sh3glb2b_NP_Q802U5 vs SH3GLB2: 66.7% over 409 columns identity sh3glb2b_NP_Q802U5 vs SH3GLB1: 62.1% over 388 columns identity sh3glb2b_NP_Q802U5 vs gar_ENSLOCG00000006193: 70.0% over 407 columns identity sh3glb2b_NP_Q802U5 vs medaka_ENSORLG00000016839_orth_of_sh3glb2a: 65.2% over 394 columns identity sh3glb2b_NP_Q802U5 vs medaka_ENSORLG00000014325_orth_of_sh3glb2b: 57.0% over 507 columns identity SH3GLB2 vs SH3GLB1: 59.4% over 399 columns identity SH3GLB2 vs gar_ENSLOCG00000006193: 71.7% over 407 columns identity SH3GLB2 vs medaka_ENSORLG00000016839_orth_of_sh3glb2a: 67.3% over 395 columns identity SH3GLB2 vs medaka_ENSORLG00000014325_orth_of_sh3glb2b: 55.2% over 504 columns identity SH3GLB1 vs gar_ENSLOCG00000006193: 57.3% over 405 columns identity SH3GLB1 vs medaka_ENSORLG00000016839_orth_of_sh3glb2a: 54.9% over 390 columns identity SH3GLB1 vs medaka_ENSORLG00000014325_orth_of_sh3glb2b: 45.3% over 501 columns identity gar_ENSLOCG00000006193 vs medaka_ENSORLG00000016839_orth_of_sh3glb2a: 65.9% over 399 columns identity gar_ENSLOCG00000006193 vs medaka_ENSORLG00000014325_orth_of_sh3glb2b: 56.0% over 507 columns identity medaka_ENSORLG00000016839_orth_of_sh3glb2a vs medaka_ENSORLG00000014325_orth_of_sh3glb2b: 53.3% over 490 columns ## 2. Regions of the human reference (UniProt features) and C-terminal tails Domain: BAR [24-287] sh3glb2a: aligned 264/264, identical 203/264 (76.9%) Domain: BAR [24-287] sh3glb2b: aligned 264/264, identical 208/264 (78.8%) Domain: BAR [24-287] sh3glb2b_NP_Q802U5: aligned 235/264, identical 185/264 (70.1%) Domain: BAR [24-287] gar_ENSLOCG00000006193: aligned 264/264, identical 212/264 (80.3%) Domain: SH3 [335-395] sh3glb2a: aligned 61/61, identical 54/61 (88.5%) Domain: SH3 [335-395] sh3glb2b: aligned 61/61, identical 53/61 (86.9%) Domain: SH3 [335-395] sh3glb2b_NP_Q802U5: aligned 61/61, identical 53/61 (86.9%) Domain: SH3 [335-395] gar_ENSLOCG00000006193: aligned 61/61, identical 53/61 (86.9%) Region: Membrane-binding amphipathic helix [1-27] sh3glb2a: aligned 27/27, identical 23/27 (85.2%) Region: Membrane-binding amphipathic helix [1-27] sh3glb2b: aligned 27/27, identical 23/27 (85.2%) Region: Membrane-binding amphipathic helix [1-27] sh3glb2b_NP_Q802U5: aligned 27/27, identical 23/27 (85.2%) Region: Membrane-binding amphipathic helix [1-27] gar_ENSLOCG00000006193: aligned 21/27, identical 9/27 (33.3%) Coiled coil [116-132] sh3glb2a: aligned 17/17, identical 9/17 (52.9%) Coiled coil [116-132] sh3glb2b: aligned 17/17, identical 9/17 (52.9%) Coiled coil [116-132] sh3glb2b_NP_Q802U5: aligned 17/17, identical 9/17 (52.9%) Coiled coil [116-132] gar_ENSLOCG00000006193: aligned 17/17, identical 10/17 (58.8%) Coiled coil [206-240] sh3glb2a: aligned 35/35, identical 30/35 (85.7%) Coiled coil [206-240] sh3glb2b: aligned 35/35, identical 32/35 (91.4%) Coiled coil [206-240] sh3glb2b_NP_Q802U5: aligned 24/35, identical 23/35 (65.7%) Coiled coil [206-240] gar_ENSLOCG00000006193: aligned 35/35, identical 32/35 (91.4%) C-terminal 12 aa of SH3GLB2: GKVPVTYLELLS C-terminal 12 aa of SH3GLB1: GKVPITYLELLN C-terminal 12 aa of sh3glb2a: GKVPVTYLELLS C-terminal 12 aa of sh3glb2b: GKVPVTYLELLS C-terminal 12 aa of sh3glb2b_NP_Q802U5: GKVPVTYLELLS C-terminal 12 aa of gar_ENSLOCG00000006193: GKVPVTYLELLS C-terminal 12 aa of medaka_ENSORLG00000016839_orth_of_sh3glb2a: GRVPVTYLELLS C-terminal 12 aa of medaka_ENSORLG00000014325_orth_of_sh3glb2b: GKVPVTYLELLS Alignment sh3glb2a (top) vs sh3glb2b (bottom): MDFNVRKLASDAGIFFSRAVQFTEEKLGQAEKTELDTHFENLLARADCTKNWTEKIYRQTEVLLQPNP-- |||||.|||||||.||.||||.||||||||||||||.|.|||.|||||||||||||.||||||||||| MDFNVKKLASDAGVFFTRAVQYTEEKLGQAEKTELDAHLENLIARADCTKNWTEKIFRQTEVLLQPNPID --GARIEEFLYEKLDRKIPPRATNGEILSQFMLEAAKEFGPGTPYGSTLIKVGDCQRRLGGAEREFLQAS |||||||.|||||.|||.|.||.|.|.|.|..|||.||||.|||||||.||..|.||||.||||||.| QTGARIEEFFYEKLDKKIPSRITNAELLGQYMQDAAKDFGPGSPYGSTLITVGEYQKRLGGSEREFLQTS SISFLTPLRNFLEGDWRTISRERRLLENRRLDLDACKARLKKAKAAEAKAAAVPDFQETRPRNYVLSASA .|.|||||||||||||.|||||||||||||||||.|||||||||.|||||||.||||||||||||||||| AINFLTPLRNFLEGDWKTISRERRLLENRRLDLDVCKARLKKAKLAEAKAAAAPDFQETRPRNYVLSASA SA---------------LWSEELDKSEQELRVAQAEFDRQAEVTRLLLEGISSTHVNHLRCLREFAEAQA || |||||.||.|.||||||.|||||||||||||||||||||||||||.||.|||| SAWDREVDESCLADREKLWSEEVDKAEHELRVAQTEFDRQAEVTRLLLEGISSTHVNHLRCLHEFVEAQA MYYNQCHKYMQELQREL----GRRCPDSLEVNCEPSG-----------------SPSDLLNSPSPLDSDT .||.|||..||.||.|| |...|....||...|| |||...|.|..|.|.| AYYAQCHRHMQDLQKELSSANGDTFPNAFAVNASTSGVSAGPSPLSTGTQPGPSSPSRPPNPPNALESNT LQIEEVQPPASGTRKARVLYDYTAADSSELSLRADELITVYTMPGMDSDWLIGERGNQKGKVPVTYLELL |.||||.|||.|||||.|||||.|||.|||||.|||||||||.||||.|||||||||||||||||||||| LKIEEVKPPATGTRKAKVLYDYDAADTSELSLLADELITVYTVPGMDPDWLIGERGNQKGKVPVTYLELL S | S ## 3. Tajima-style relative-rate test (outgroup = gar orthologue) gar_ENSLOCG00000006193: positions aligned in both copies: 374 changes unique to sh3glb2a (m1): 36; unique to sh3glb2b (m2): 23; chi2 (1 df) = 2.86 (not significant at 0.05) ## 4. Whole-embryo time course, E-ERAD-475 (TPM, median of replicates) | stage | sh3glb2a | sh3glb2b | |---|---|---| | zygote | 2 | 71 | | cleavage 2-cell | 6 | 69 | | blastula 128-cell | 27 | 45 | | blastula 1k-cell | 28 | 46 | | blastula dome | 28 | 32 | | gastrula 50%-epiboly | 14 | 17 | | gastrula shield | 7 | 7 | | gastrula 75%-epiboly | 2 | 2 | | segmentation 1-4 somites | 3 | 15 | | segmentation 14-19 somites | 3 | 13 | | segmentation 20-25 somites | 3 | 13 | | pharyngula prim-5 | 3 | 11 | | pharyngula prim-15 | 2 | 11 | | pharyngula prim-25 | 4 | 14 | | hatching long-pec | 2 | 13 | | larval protruding mouth | 3 | 15 | | larval day 4 | 4 | 12 | | larval day 5 | 4 | 10 | ## 5. Bgee expressed calls per anatomical entity (score 0-100; only 'expressed' calls are returned) ### sh3glb2a: 20 calls - retina: 92.3 (gold; RNA-Seq) - blastula: 86.5 (gold; RNA-Seq) - brain: 82.0 (gold; RNA-Seq) - swim bladder: 79.8 (gold; RNA-Seq) - granulocyte: 76.8 (gold; RNA-Seq) - heart: 75.8 (gold; RNA-Seq) - early embryo: 73.7 (gold; RNA-Seq) - gastrula: 72.5 (gold; RNA-Seq) - mature ovarian follicle: 71.9 (gold; RNA-Seq) - testis: 71.7 (gold; EST,RNA-Seq) - head kidney: 70.1 (gold; RNA-Seq) - bone element: 66.0 (gold; RNA-Seq) - spleen: 63.9 (gold; RNA-Seq) - pharyngeal gill: 63.0 (gold; RNA-Seq) - larva: 56.7 (gold; RNA-Seq) - muscle tissue: 54.5 (gold; RNA-Seq) - zone of skin: 53.8 (gold; RNA-Seq) - liver: 52.3 (silver; RNA-Seq) - tail: 50.6 (gold; RNA-Seq) - intestine: 50.2 (gold; RNA-Seq) ### sh3glb2b: 27 calls - mature ovarian follicle: 98.0 (gold; RNA-Seq) - early embryo: 96.8 (gold; RNA-Seq) - cleaving embryo: 95.4 (gold; Affymetrix) - brain: 93.0 (gold; Affymetrix,RNA-Seq) - blastula: 92.0 (gold; Affymetrix,RNA-Seq) - somite: 90.8 (gold; Affymetrix) - retina: 90.6 (gold; Affymetrix,RNA-Seq) - tail bud paraxial mesoderm: 87.3 (gold; Affymetrix) - presomitic mesoderm: 85.9 (gold; Affymetrix) - larva: 85.9 (gold; Affymetrix,RNA-Seq) - bone element: 82.0 (gold; RNA-Seq) - gastrula: 78.1 (gold; Affymetrix,RNA-Seq) - tail: 74.9 (gold; Affymetrix,RNA-Seq) - testis: 73.0 (gold; RNA-Seq) - mesonephros: 71.8 (gold; RNA-Seq) - head kidney: 69.1 (gold; RNA-Seq) - caudal fin: 67.9 (gold; Affymetrix) - swim bladder: 63.4 (gold; RNA-Seq) - granulocyte: 62.1 (gold; RNA-Seq) - heart: 59.7 (gold; Affymetrix,RNA-Seq) - pharyngeal gill: 56.4 (gold; RNA-Seq) - muscle tissue: 54.8 (gold; RNA-Seq) - integument: 54.6 (gold; Affymetrix,RNA-Seq) - zone of skin: 54.2 (gold; RNA-Seq) - spleen: 51.6 (gold; RNA-Seq) - liver: 44.6 (gold; Affymetrix,RNA-Seq) - intestine: 42.9 (silver; RNA-Seq) ### gar ENSLOCG00000006193: 14 calls - camera-type eye: 94.6 (gold; RNA-Seq) - brain: 91.9 (gold; RNA-Seq) - larva: 85.4 (gold; RNA-Seq) - zone of skin: 82.4 (gold; RNA-Seq) - embryo: 73.4 (gold; RNA-Seq) - liver: 71.3 (gold; RNA-Seq) - mesonephros: 69.8 (gold; RNA-Seq) - testis: 69.4 (gold; RNA-Seq) - ovary: 67.6 (gold; RNA-Seq) - bone element: 66.8 (gold; RNA-Seq) - heart: 64.6 (gold; RNA-Seq) - pharyngeal gill: 57.1 (gold; RNA-Seq) - muscle tissue: 56.1 (gold; RNA-Seq) - intestine: 44.8 (gold; RNA-Seq) entities called for sh3glb2a only: [] entities called for sh3glb2b only: ['caudal fin', 'cleaving embryo', 'integument', 'mesonephros', 'presomitic mesoderm', 'somite', 'tail bud paraxial mesoderm'] entities called for both: ['blastula', 'bone element', 'brain', 'early embryo', 'gastrula', 'granulocyte', 'head kidney', 'heart', 'intestine', 'larva', 'liver', 'mature ovarian follicle', 'muscle tissue', 'pharyngeal gill', 'retina', 'spleen', 'swim bladder', 'tail', 'testis', 'zone of skin'] ## 6. ZFIN curated wild-type expression (wildtype-expression_fish.txt) ### sh3glb2a: 1 records - whole organism | Zygote:1-cell - Hatching:Pec-fin | mRNA in situ hybridization | ZDB-PUB-040907-1 ### sh3glb2b: 9 records - central nervous system | Pharyngula:High-pec - Hatching:Long-pec | mRNA in situ hybridization | ZDB-PUB-040907-1 - central nervous system | Pharyngula:Prim-15 - Pharyngula:Prim-25 | mRNA in situ hybridization | ZDB-PUB-040907-1 - central nervous system | Segmentation:14-19 somites - Segmentation:14-19 somites | mRNA in situ hybridization | ZDB-PUB-040907-1 - central nervous system | Segmentation:20-25 somites - Pharyngula:Prim-5 | mRNA in situ hybridization | ZDB-PUB-040907-1 - eye | Pharyngula:High-pec - Hatching:Long-pec | mRNA in situ hybridization | ZDB-PUB-040907-1 - eye | Pharyngula:Prim-15 - Pharyngula:Prim-25 | mRNA in situ hybridization | ZDB-PUB-040907-1 - immature eye | Segmentation:20-25 somites - Pharyngula:Prim-5 | mRNA in situ hybridization | ZDB-PUB-040907-1 - lens | Pharyngula:Prim-15 - Pharyngula:Prim-25 | mRNA in situ hybridization | ZDB-PUB-040907-1 - solid lens vesicle | Segmentation:20-25 somites - Pharyngula:Prim-5 | mRNA in situ hybridization | ZDB-PUB-040907-1 ## 7. Local synteny between the two copies (Ensembl REST) sh3glb2a: chr8:2757821-2789783 sh3glb2b: chr5:31640881-31689911 sh3glb2a +/- 1.5 Mb: 54 other protein-coding genes (0 homology queries failed); 8 have a teleost-level (Clupeocephala/Osteoglossocephalai/Teleostei) zebrafish paralogue; 3 such pairs have their partner within 1.5 Mb of sh3glb2b: - zdhhc12a -> zdhhc12b (chr5:31819436) - slc25a25a -> slc25a25b (chr5:31779911) - eeig1a -> eeig1b (chr5:31723404) Of the teleost-level paralogue pairs, 5 have their partner anywhere on chr5 (the chromosome of sh3glb2b, 1323 protein-coding genes): - zdhhc12a -> zdhhc12b (chr5:31819436) - slc25a25a -> slc25a25b (chr5:31779911) - eeig1a -> eeig1b (chr5:31723404) - citb -> cita (chr5:2409554) - pxnb -> pxna (chr5:6670945) sh3glb2b +/- 1.5 Mb: 86 other protein-coding genes (0 homology queries failed); 27 have a teleost-level (Clupeocephala/Osteoglossocephalai/Teleostei) zebrafish paralogue; 3 such pairs have their partner within 1.5 Mb of sh3glb2a: - eeig1b -> eeig1a (chr8:2656231) - slc25a25b -> slc25a25a (chr8:2606068) - zdhhc12b -> zdhhc12a (chr8:2595424) Of the teleost-level paralogue pairs, 7 have their partner anywhere on chr8 (the chromosome of sh3glb2a, 1047 protein-coding genes): - si:dkey-220k22.1 -> si:ch211-158d24.2 (chr8:41533268) - eeig1b -> eeig1a (chr8:2656231) - slc25a25b -> slc25a25a (chr8:2606068) - zdhhc12b -> zdhhc12a (chr8:2595424) - arpc5lb -> arpc5la (chr8:41453691) - ccn1l1 -> ccn1l2 (chr8:52619365) - zgc:55461 -> tubb2b (chr8:52713232)