# Pair analysis: tp53bp2a / tp53bp2b (run 2026-09-28) ## 1. Sequence lengths and pairwise identities length tp53bp2a: 1060 aa length tp53bp2b: 1063 aa length TP53BP2: 1128 aa length gar_TP53BP2: 1087 aa length medaka_ortholog_of_tp53bp2a: 1152 aa length medaka_ortholog_of_tp53bp2b: 1111 aa identity tp53bp2a vs tp53bp2b: 60.9% over 1100 columns identity tp53bp2a vs TP53BP2: 60.5% over 1144 columns identity tp53bp2a vs gar_TP53BP2: 62.7% over 1113 columns identity tp53bp2a vs medaka_ortholog_of_tp53bp2a: 61.9% over 1177 columns identity tp53bp2a vs medaka_ortholog_of_tp53bp2b: 53.5% over 1151 columns identity tp53bp2b vs TP53BP2: 60.1% over 1163 columns identity tp53bp2b vs gar_TP53BP2: 58.9% over 1144 columns identity tp53bp2b vs medaka_ortholog_of_tp53bp2a: 57.3% over 1194 columns identity tp53bp2b vs medaka_ortholog_of_tp53bp2b: 61.6% over 1127 columns identity TP53BP2 vs gar_TP53BP2: 61.2% over 1176 columns identity TP53BP2 vs medaka_ortholog_of_tp53bp2a: 59.4% over 1220 columns identity TP53BP2 vs medaka_ortholog_of_tp53bp2b: 54.9% over 1173 columns identity gar_TP53BP2 vs medaka_ortholog_of_tp53bp2a: 62.1% over 1192 columns identity gar_TP53BP2 vs medaka_ortholog_of_tp53bp2b: 54.3% over 1178 columns identity medaka_ortholog_of_tp53bp2a vs medaka_ortholog_of_tp53bp2b: 55.5% over 1204 columns ## 1b. Zebrafish copies vs each human isoform identity tp53bp2a vs Q13625 (1128 aa): 60.5% over 1144 columns identity tp53bp2b vs Q13625 (1128 aa): 60.1% over 1163 columns identity tp53bp2a vs Q13625-3 (1134 aa): 60.2% over 1150 columns identity tp53bp2b vs Q13625-3 (1134 aa): 59.8% over 1169 columns identity tp53bp2a vs Q13625-2 (1005 aa): 54.1% over 1137 columns identity tp53bp2b vs Q13625-2 (1005 aa): 53.8% over 1158 columns ## 2. Regions of the human protein (UniProt features) and of the zebrafish 'a' copy ### human TP53BP2 (Q13625) features Repeat: ANK 1 [926-957] tp53bp2a: aligned 32/32, identical 29/32 (90.6%) Repeat: ANK 1 [926-957] tp53bp2b: aligned 32/32, identical 31/32 (96.9%) Repeat: ANK 1 [926-957] gar_TP53BP2: aligned 32/32, identical 30/32 (93.8%) Repeat: ANK 2 [958-990] tp53bp2a: aligned 33/33, identical 32/33 (97.0%) Repeat: ANK 2 [958-990] tp53bp2b: aligned 33/33, identical 32/33 (97.0%) Repeat: ANK 2 [958-990] gar_TP53BP2: aligned 33/33, identical 33/33 (100.0%) Repeat: ANK 3 [991-1024] tp53bp2a: aligned 34/34, identical 34/34 (100.0%) Repeat: ANK 3 [991-1024] tp53bp2b: aligned 34/34, identical 33/34 (97.1%) Repeat: ANK 3 [991-1024] gar_TP53BP2: aligned 34/34, identical 34/34 (100.0%) Repeat: ANK 4 [1025-1067] tp53bp2a: aligned 43/43, identical 40/43 (93.0%) Repeat: ANK 4 [1025-1067] tp53bp2b: aligned 43/43, identical 39/43 (90.7%) Repeat: ANK 4 [1025-1067] gar_TP53BP2: aligned 43/43, identical 39/43 (90.7%) Domain: SH3 [1057-1119] tp53bp2a: aligned 63/63, identical 41/63 (65.1%) Domain: SH3 [1057-1119] tp53bp2b: aligned 63/63, identical 43/63 (68.3%) Domain: SH3 [1057-1119] gar_TP53BP2: aligned 63/63, identical 51/63 (81.0%) Motif: SH3-binding [866-875] tp53bp2a: aligned 10/10, identical 9/10 (90.0%) Motif: SH3-binding [866-875] tp53bp2b: aligned 10/10, identical 10/10 (100.0%) Motif: SH3-binding [866-875] gar_TP53BP2: aligned 10/10, identical 10/10 (100.0%) Mutagenesis: Loss of interaction with APC2. [1098-1098] tp53bp2a: aligned 1/1, identical 1/1 (100.0%) residues: W1098->W Mutagenesis: Loss of interaction with APC2. [1098-1098] tp53bp2b: aligned 1/1, identical 1/1 (100.0%) residues: W1098->W Mutagenesis: Loss of interaction with APC2. [1098-1098] gar_TP53BP2: aligned 1/1, identical 1/1 (100.0%) residues: W1098->W ### zebrafish tp53bp2a features (cached UniProt record) mapped to tp53bp2b DOMAIN Ras-associating [23-86] tp53bp2a vs tp53bp2b: aligned 63/64, identical 41/64 (64.1%) REPEAT ANK [890-922] tp53bp2a vs tp53bp2b: aligned 33/33, identical 33/33 (100.0%) REPEAT ANK [923-955] tp53bp2a vs tp53bp2b: aligned 33/33, identical 32/33 (97.0%) DOMAIN SH3 [989-1051] tp53bp2a vs tp53bp2b: aligned 63/63, identical 44/63 (69.8%) COILED [122-235] tp53bp2a vs tp53bp2b: aligned 114/114, identical 83/114 (72.8%) N-terminus of tp53bp2a: MMPMFLTVYLSN (Gly at position 2: False) N-terminus of tp53bp2b: MMPMFLTVYLSN (Gly at position 2: False) N-terminus of TP53BP2: MMPMFLTVYLSN (Gly at position 2: False) N-terminus of gar_TP53BP2: QMFLTVYLSNND (Gly at position 2: False) ## 3. Tajima-style relative-rate test (outgroup = gar) gar positions aligned in both copies: 973 changes unique to tp53bp2a (m1): 115; unique to tp53bp2b (m2): 124; chi2 (1 df) = 0.34 (not significant at 0.05) ## 4. Whole-embryo time course, E-ERAD-475 (TPM, median of replicates) | stage | tp53bp2a | tp53bp2b | |---|---|---| | zygote | 26 | 15 | | cleavage 2-cell | 37 | 12 | | blastula 128-cell | 76 | 22 | | blastula 1k-cell | 78 | 25 | | blastula dome | 77 | 16 | | gastrula 50%-epiboly | 91 | 4 | | gastrula shield | 88 | 2 | | gastrula 75%-epiboly | 61 | 4 | | segmentation 1-4 somites | 75 | 6 | | segmentation 14-19 somites | 56 | 5 | | segmentation 20-25 somites | 59 | 5 | | pharyngula prim-5 | 51 | 6 | | pharyngula prim-15 | 39 | 7 | | pharyngula prim-25 | 45 | 9 | | hatching long-pec | 29 | 11 | | larval protruding mouth | 29 | 15 | | larval day 4 | 34 | 13 | | larval day 5 | 43 | 15 | ## 5. Bgee expressed calls per anatomical entity (expression score 0-100; only 'expressed' calls are returned) ### tp53bp2a: 27 calls - presomitic mesoderm: 93.3 (gold; Affymetrix) - zone of skin: 92.9 (gold; RNA-Seq) - somite: 92.2 (gold; Affymetrix) - caudal fin: 91.6 (gold; Affymetrix) - spleen: 91.2 (gold; RNA-Seq) - tail bud paraxial mesoderm: 91.2 (gold; Affymetrix) - cleaving embryo: 91.0 (gold; Affymetrix) - pharyngeal gill: 90.1 (gold; RNA-Seq) - liver: 89.0 (gold; Affymetrix,RNA-Seq) - gastrula: 87.1 (gold; Affymetrix,RNA-Seq) - blastula: 86.3 (gold; Affymetrix,RNA-Seq) - heart: 85.3 (gold; Affymetrix,RNA-Seq) - cardiac ventricle: 84.2 (gold; Affymetrix) - early embryo: 84.0 (gold; RNA-Seq) - larva: 83.4 (gold; Affymetrix,RNA-Seq) - testis: 83.3 (gold; RNA-Seq) - swim bladder: 79.0 (gold; RNA-Seq) - muscle tissue: 78.3 (gold; RNA-Seq) - mature ovarian follicle: 77.5 (gold; RNA-Seq) - intestine: 76.5 (gold; RNA-Seq) - mesonephros: 73.2 (gold; EST,RNA-Seq) - brain: 72.5 (gold; Affymetrix,RNA-Seq) - head kidney: 71.0 (gold; RNA-Seq) - camera-type eye: 69.8 (gold; Affymetrix,EST,RNA-Seq) - bone element: 66.7 (gold; RNA-Seq) - retina: 65.6 (gold; Affymetrix,RNA-Seq) - granulocyte: 51.5 (gold; RNA-Seq) ### tp53bp2b: 20 calls - retina: 87.9 (gold; RNA-Seq) - mature ovarian follicle: 83.7 (gold; RNA-Seq) - heart: 79.0 (gold; RNA-Seq) - brain: 79.0 (gold; RNA-Seq) - early embryo: 78.9 (gold; RNA-Seq) - blastula: 73.5 (gold; RNA-Seq) - testis: 67.7 (gold; RNA-Seq) - tail: 66.3 (gold; RNA-Seq) - mesonephros: 64.0 (gold; RNA-Seq) - larva: 63.0 (gold; RNA-Seq) - pharyngeal gill: 62.3 (gold; RNA-Seq) - muscle tissue: 61.5 (gold; RNA-Seq) - head kidney: 59.9 (gold; RNA-Seq) - swim bladder: 59.8 (gold; RNA-Seq) - spleen: 57.4 (gold; RNA-Seq) - gastrula: 56.5 (gold; RNA-Seq) - bone element: 56.0 (gold; RNA-Seq) - zone of skin: 54.6 (gold; RNA-Seq) - granulocyte: 45.8 (gold; RNA-Seq) - intestine: 39.2 (silver; RNA-Seq) ### gar_TP53BP2 (spotted gar): 14 calls - ovary: 70.6 (gold; RNA-Seq) - zone of skin: 68.9 (gold; RNA-Seq) - liver: 65.2 (gold; RNA-Seq) - camera-type eye: 65.0 (gold; RNA-Seq) - mesonephros: 56.5 (gold; RNA-Seq) - testis: 55.8 (gold; RNA-Seq) - heart: 54.4 (gold; RNA-Seq) - embryo: 53.5 (gold; RNA-Seq) - intestine: 52.8 (gold; RNA-Seq) - muscle tissue: 52.3 (gold; RNA-Seq) - brain: 51.9 (gold; RNA-Seq) - pharyngeal gill: 51.3 (gold; RNA-Seq) - bone element: 45.9 (gold; RNA-Seq) - larva: 43.5 (gold; RNA-Seq) RNA-Seq-supported entities: tp53bp2a only: ['camera-type eye', 'liver'] RNA-Seq-supported entities: tp53bp2b only: ['tail'] RNA-Seq-supported entities: both: ['blastula', 'bone element', 'brain', 'early embryo', 'gastrula', 'granulocyte', 'head kidney', 'heart', 'intestine', 'larva', 'mature ovarian follicle', 'mesonephros', 'muscle tissue', 'pharyngeal gill', 'retina', 'spleen', 'swim bladder', 'testis', 'zone of skin'] entities called for both: 19; tp53bp2a score higher in 16, median difference (tp53bp2a - tp53bp2b) = 12.9 ## 6. ZFIN curated wild-type expression (wildtype-expression_fish.txt) ### tp53bp2a (ZDB-GENE-040516-8): 17 rows - brain | Adult to Adult | assay Reverse transcription PCR | ZDB-PUB-140220-26 - gill | Adult to Adult | assay Reverse transcription PCR | ZDB-PUB-140220-26 - heart | Adult to Adult | assay Reverse transcription PCR | ZDB-PUB-140220-26 - intestine | Adult to Adult | assay Reverse transcription PCR | ZDB-PUB-140220-26 - kidney | Adult to Adult | assay Reverse transcription PCR | ZDB-PUB-140220-26 - liver | Adult to Adult | assay Reverse transcription PCR | ZDB-PUB-140220-26 - muscle | Adult to Adult | assay Reverse transcription PCR | ZDB-PUB-140220-26 - ovary | Adult to Adult | assay Reverse transcription PCR | ZDB-PUB-140220-26 - spleen | Adult to Adult | assay Reverse transcription PCR | ZDB-PUB-140220-26 - testis | Adult to Adult | assay Reverse transcription PCR | ZDB-PUB-140220-26 - whole organism | Blastula:Sphere to Blastula:Sphere | assay mRNA in situ hybridization | ZDB-PUB-140220-26 - whole organism | Gastrula:Shield to Gastrula:Shield | assay mRNA in situ hybridization | ZDB-PUB-140220-26 - whole organism | Hatching:Long-pec to Hatching:Long-pec | assay mRNA in situ hybridization | ZDB-PUB-140220-26 - whole organism | Larval:Protruding-mouth to Larval:Protruding-mouth | assay mRNA in situ hybridization | ZDB-PUB-140220-26 - whole organism | Pharyngula:Prim-5 to Pharyngula:Prim-5 | assay mRNA in situ hybridization | ZDB-PUB-140220-26 - whole organism | Segmentation:5-9 somites to Segmentation:5-9 somites | assay mRNA in situ hybridization | ZDB-PUB-140220-26 - whole organism | Zygote:1-cell to Larval:Day 4 | assay Reverse transcription PCR | ZDB-PUB-140220-26 ### tp53bp2b (ZDB-GENE-050208-453): 18 rows - whole organism | Segmentation:26+ somites to Segmentation:26+ somites | assay Reverse transcription PCR | ZDB-PUB-140821-3 - brain | Adult to Adult | assay Reverse transcription PCR | ZDB-PUB-140220-26 - gill | Adult to Adult | assay Reverse transcription PCR | ZDB-PUB-140220-26 - heart | Adult to Adult | assay Reverse transcription PCR | ZDB-PUB-140220-26 - intestine | Adult to Adult | assay Reverse transcription PCR | ZDB-PUB-140220-26 - kidney | Adult to Adult | assay Reverse transcription PCR | ZDB-PUB-140220-26 - liver | Adult to Adult | assay Reverse transcription PCR | ZDB-PUB-140220-26 - muscle | Adult to Adult | assay Reverse transcription PCR | ZDB-PUB-140220-26 - ovary | Adult to Adult | assay Reverse transcription PCR | ZDB-PUB-140220-26 - spleen | Adult to Adult | assay Reverse transcription PCR | ZDB-PUB-140220-26 - testis | Adult to Adult | assay Reverse transcription PCR | ZDB-PUB-140220-26 - whole organism | Blastula:Sphere to Blastula:Sphere | assay mRNA in situ hybridization | ZDB-PUB-140220-26 - whole organism | Gastrula:Shield to Gastrula:Shield | assay mRNA in situ hybridization | ZDB-PUB-140220-26 - whole organism | Hatching:Long-pec to Hatching:Long-pec | assay mRNA in situ hybridization | ZDB-PUB-140220-26 - whole organism | Larval:Protruding-mouth to Larval:Protruding-mouth | assay mRNA in situ hybridization | ZDB-PUB-140220-26 - whole organism | Pharyngula:Prim-5 to Pharyngula:Prim-5 | assay mRNA in situ hybridization | ZDB-PUB-140220-26 - whole organism | Segmentation:5-9 somites to Segmentation:5-9 somites | assay mRNA in situ hybridization | ZDB-PUB-140220-26 - whole organism | Zygote:1-cell to Larval:Day 4 | assay Reverse transcription PCR | ZDB-PUB-140220-26 ## 7. Local synteny between the two copies (Ensembl REST) tp53bp2a: chr13:646700-664472 tp53bp2b: chr22:28803739-28849279 tp53bp2a +/- 1.5 Mb: 75 other protein-coding genes (0 homology queries failed); 9 have a teleost-level (Clupeocephala, Osteoglossocephalai, Teleostei) zebrafish paralogue; 0 such paralogue pairs have their partner within 1.5 Mb of tp53bp2b: Of the teleost-level paralogue pairs, 1 have their partner anywhere on chr22 (the chromosome of tp53bp2b, 1007 protein-coding genes): - efemp1 -> si:ch73-173h19.3 (chr22:35068046) tp53bp2b +/- 1.5 Mb: 40 other protein-coding genes (0 homology queries failed); 16 have a teleost-level (Clupeocephala, Osteoglossocephalai, Teleostei) zebrafish paralogue; 0 such paralogue pairs have their partner within 1.5 Mb of tp53bp2a: Of the teleost-level paralogue pairs, 12 have their partner anywhere on chr13 (the chromosome of tp53bp2a, 903 protein-coding genes): - pimr98 -> pimr47 (chr13:13660564) - pimr98 -> pimr48 (chr13:13668991) - pimr95 -> pimr47 (chr13:13660564) - pimr95 -> pimr48 (chr13:13668991) - pimr99 -> pimr47 (chr13:13660564) - pimr99 -> pimr48 (chr13:13668991) - pimr97 -> pimr47 (chr13:13660564) - pimr97 -> pimr48 (chr13:13668991) - pimr96 -> pimr47 (chr13:13660564) - pimr96 -> pimr48 (chr13:13668991) - pimr100 -> pimr47 (chr13:13660564) - pimr100 -> pimr48 (chr13:13668991)