RetrogeneDB ID: | retro_pabe_697 | ||
Retrocopy location | Organism: | Orangutan (Pongo abelii) | |
| Coordinates: | 11:56954920..56956770(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | BAP1 | ||
| Ensembl ID: | ENSPPYG00000013809 | ||
| Aliases: | None | ||
| Description: | BRCA1 associated protein-1 (ubiquitin carboxy-terminal hydrolase) [Source:HGNC Symbol;Acc:950] |
Retrocopy-Parental alignment summary:
>retro_pabe_697
ATGAATAAGGGCTGGCTGGAGCTGGAGAGCGACCCAGGCCTCTTCACCCTGCTCGTGGAAGATTTCGGTGTCAAAGGGGT
GCAAGTGGAGGAGATCTATGACCTTCAGAGCAAATGTCAGGGCCCTGTATATGGATTTATCCTGTTCAAATGGATCGAAG
AGCGCCAGTCCAGGCGAAAGATCTCTATCTTGGTGGATGATACGTCCATGATTGATGATGATATTGTGAATAACATGTTC
TTTGCCCACCAGCTGATACCCAACTCTTGTGCCACTCATGCCTTGCTGAGCGTGCTCCTGAACCGCAGCACCATGGACCT
GGGACCCACCCTGAGTCTCATGAAGGACTTCACCAAGGGCTTCAGCCCTGAGAGCAAAGGATATGCGATTGGCAATGCCC
CGGAGTTGGCCAAGGCACATAATAGCCATGCCAGGCCCGAGCCACGCCACCTCCGTGAGAAGCAGAATGGCCTTAGTGCA
GTGCGGACCATGGAGGCGTTCCACTTTATCAGCTATGTGCCTATCACAGGCCGGCTCTTTGAGCTGGATGGGCTGAAGGT
CTACCCCATTGACCATGGGCCCTGGGGGGAGGACGAGGAGTGGACAGACAAGTCCCGGCGGGTCATCATGGAGCGTATCG
GCCTCGCCACTGCAGGAGAGCCCTACCACGACATCCGCTTCAACCTGATGGCAGTGGTGCCCGACCGCAGGATCAAGTAT
GAGGCCAGGATGCACGTGCTGAAGGTGAACCGTCAGACAGTACTAGAGGCTCTGCAGCAGCTGATAAGAGTAACACAGCC
AGAGCTGATTTAGACCCACAAGTCTCAAGAGTCACAGCTGCCTGAGGAGTCCAAGTCAGCCAGCAACAAGTCCCCGCTGG
TGCTGGAAGCAAACAGGGCCCCTGCAGCCTCTGAGGGCACCCACACAGATGGTGCAGAGGAGGCAGCTGGTTCATGCGCA
CAAGCCCCATCCCACAGCCCTCCCAACAAACCCAAGCTGGTAGTGAAGCCTCCAGGCAGCAGCCTCAATGGGGTTCCCCC
CAACCCCACTCCCATTGTCCAGCGGCTGCCAGCCTTTCTAGACAATCACAATTATGCCAAGTCCCCCATGCAGGAGGAAG
AAGACCTGGCGGCAGGTGTGGGCTACGGCCGAGTTCCAGTCCGCCCCCCCCAGCAGTACTCAGATGACGAGGATGACTAT
GAGGATGATGAGGAGGATGGCGTGCAGAACACCAACTCTGCCCTTAGGTATAAGGGGAAGAGAACAGGGAAGCCAGGGGC
ATTGAGCGGTTCTGCTGATGGGCAACTCTCAGTGCTGCAGCCCAACACCATCAACGTCTTGGCTGAGAAGCTCAAAGAGT
CCCAGAAGGACCTCTCAGTTCCTCTGTCCATCAAGACTAGCAGCGGGGCTGGGAGTGCAGCTGTCCAGCTGTGGCAGTGC
CCACACACTCGCAGCCCTCACCCACCCCCAGCAATGAGAGTACGGACACGGCCTCTGAGATCGGCAGTGCTTTCAACTCG
CCACTGCGCTCGCCCATCCGCTCGGCCAACCGGACGCGGCCCTCCAGCCCTGTCACCTCCTACATCTCCAAGGTGCTTTT
TGGAGAGGATGACAGCCTGCTGCGTGTTGACTGCATACACTACAACCGTGCTGTCCGTGATCTGGGTCCTGTCATCAGCA
CAGGCCTGCTGCACCTGGCTGAGGATGGGGTGCTGAGTCCCCTGGCGCTGACAGAGGGTAGGAAGGTTTCCTCGCCCTCC
GTCAGACCAATCCAAGGCAGCCAGGGGTCCAGCAGCCCAGTGGAGAAGGAGGTCATGGAAGCCACGGACAGCAGAGAGAA
GACGGGGATG
ORF - retro_pabe_697 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 93.38 % |
| Parental protein coverage: | 84.36 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | MNKGWLELESDPGLFTLLVEDFGVKGVQVEEIYDLQSKCQGPVYGFIFLFKWIEERRSRRKVSTLVDDTS |
| MNKGWLELESDPGLFTLLVEDFGVKGVQVEEIYDLQSKCQGPVYGFI.LFKWIEER.SRRK.S.LVDDTS | |
| Retrocopy | MNKGWLELESDPGLFTLLVEDFGVKGVQVEEIYDLQSKCQGPVYGFI-LFKWIEERQSRRKISILVDDTS |
| Parental | VIDDDIVNNMFFAHQLIPNSCATHALLSVLLNCSNVDLGPTLSRMKDFTKGFSPESKGYAIGNAPELAKA |
| .IDDDIVNNMFFAHQLIPNSCATHALLSVLLN.S..DLGPTLS.MKDFTKGFSPESKGYAIGNAPELAKA | |
| Retrocopy | MIDDDIVNNMFFAHQLIPNSCATHALLSVLLNRSTMDLGPTLSLMKDFTKGFSPESKGYAIGNAPELAKA |
| Parental | HNSHARPEPRHLPEKQNGLSAVRTMEAFHFVSYVPITGRLFELDGLKVYPIDHGPWGEDEEWTDKARRVI |
| HNSHARPEPRHL.EKQNGLSAVRTMEAFHF.SYVPITGRLFELDGLKVYPIDHGPWGEDEEWTDK.RRVI | |
| Retrocopy | HNSHARPEPRHLREKQNGLSAVRTMEAFHFISYVPITGRLFELDGLKVYPIDHGPWGEDEEWTDKSRRVI |
| Parental | MERIGLATAGEPYHDIRFNLMAVVPDRRIKYEARLHVLKVNRQTVLEALQQLIRVTQPELIQTHKSQESQ |
| MERIGLATAGEPYHDIRFNLMAVVPDRRIKYEAR.HVLKVNRQTVLEALQQLIRVTQPELI.THKSQESQ | |
| Retrocopy | MERIGLATAGEPYHDIRFNLMAVVPDRRIKYEARMHVLKVNRQTVLEALQQLIRVTQPELI*THKSQESQ |
| Parental | LPEESKSASNKSPLVLEANRAPAASEGTHTDGAEEAAGSCAQAPSHSPPNKPKLVVKPPGSSLNGVPPNP |
| LPEESKSASNKSPLVLEANRAPAASEGTHTDGAEEAAGSCAQAPSHSPPNKPKLVVKPPGSSLNGVPPNP | |
| Retrocopy | LPEESKSASNKSPLVLEANRAPAASEGTHTDGAEEAAGSCAQAPSHSPPNKPKLVVKPPGSSLNGVPPNP |
| Parental | TPIVQRLPAFLDNHNYAKSPMQEEEDLAAGVGRSRVPVRPPQQYSDDEDDYEDDEEDDVQNTNSALRYKG |
| TPIVQRLPAFLDNHNYAKSPMQEEEDLAAGVG..RVPV....QYSDDEDDYEDDEED.VQNTNSALRYKG | |
| Retrocopy | TPIVQRLPAFLDNHNYAKSPMQEEEDLAAGVGYGRVPVXXXXQYSDDEDDYEDDEEDGVQNTNSALRYKG |
| Parental | KGTGKPGALSGSADGQLSVLQPNTINVLAEKLKESQKDLSIPLSIKTSSGAGSPAVAV---PTHSQPSP- |
| K.TGKPGALSGSADGQLSVLQPNTINVLAEKLKESQKDLS.PLSIKTSSGAGS.AV.....P....P.P. | |
| Retrocopy | KRTGKPGALSGSADGQLSVLQPNTINVLAEKLKESQKDLSVPLSIKTSSGAGSAAVQLWQCPHTRSPHP< |
| Parental | TPSNESTDTASEIGSAFNSPLRSPIRSANPTRPSSPVTSHISKVLFGEDDSLLRVDCIRYNRAVRDLGPV |
| TPSNESTDTASEIGSAFNSPLRSPIRSAN.TRPSSPVTS.ISKVLFGEDDSLLRVDCI.YNRAVRDLGPV | |
| Retrocopy | TPSNESTDTASEIGSAFNSPLRSPIRSANRTRPSSPVTSYISKVLFGEDDSLLRVDCIHYNRAVRDLGPV |
| Parental | ISTGLLHLAEDGVLSPLALTEGGKGSSPSVRPIQGSQGSSSPVEKEVVEATDSREKTGM |
| ISTGLLHLAEDGVLSPLALTEG.K.SSPSVRPIQGSQGSSSPVEKEV.EATDSREKTGM | |
| Retrocopy | ISTGLLHLAEDGVLSPLALTEGRKVSSPSVRPIQGSQGSSSPVEKEVMEATDSREKTGM |
Legend:
| * | Stop codon |
| > | Forward frameshift by one nucleotide |
| < | Reverse frameshift by one nucleotide |
(Hint: click retrocopy or parental gene accession number on the plot's legend, to show / hide expression level values)
Expression validation based on RNA-Seq data:
| Library | Retrocopy expression | Parental gene expression |
|---|---|---|
| SRP007412_brain_prefrontal_cortex | 0 .44 RPM | 212 .76 RPM |
| SRP007412_cerebellum | 0 .12 RPM | 71 .02 RPM |
| SRP007412_heart | 0 .06 RPM | 25 .89 RPM |
| SRP007412_kidney | 0 .20 RPM | 73 .85 RPM |
| SRP007412_liver | 0 .06 RPM | 30 .08 RPM |
Pongo abelii was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_pabe_697 retrocopy.
Pongo abelii was not studied using FANTOM5 data.
retro_pabe_697 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_pabe_697 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 1 parental gene, and 1 retrocopy.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Pongo abelii | ENSPPYG00000013809 | 1 retrocopy |
retro_pabe_697 ,
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