RetrogeneDB ID: | retro_btau_1333 | ||
Retrocopy location | Organism: | Cow (Bos taurus) | |
| Coordinates: | 4:101019787..101021510(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSBTAG00000031458 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | BT.52586 | ||
| Ensembl ID: | ENSBTAG00000009854 | ||
| Aliases: | None | ||
| Description: | U3 small nucleolar ribonucleoprotein protein MPP10 [Source:RefSeq peptide;Acc:NP_001039782] |
Retrocopy-Parental alignment summary:
>retro_btau_1333
ATGGCCCGGCCAGCCTGGCGTTGGCGGACCCTGGAGCGGTGCCTGAGGGAGGTCGGTAAAGCCACTGACAGCCCAGAGTG
CTTCCTCACCATTCAAGATGAACTGGCATCAAAGTATACTTCTTTAACAAAAGTACTTTATGACTTTAATAAAGTACTAG
AGAATGACAGGAAACATGGGAGTCCTTTAGAAAAATTGATGATAAATAATTTCGATGATGAGCAGATTTGGCAACAGTTG
GAACTGCAAAATGAACCAATTTTACAGCACTTCCAGAGTGCAGTTAGTGAAACCATTGAAGATGAAGACATCAGTCTTCT
CCCAGAGAGTGAAGAGCAGGAGTGTGAAGAGGATATGATGGAGCTGGAGGCTGCTGGCCAGGAGGACCTGGAACAAGATT
TAGAGGAGGAGGAGGTGGAGGAAGCAGAGGAGGTGGAAGTGTCAGACCTGAGTGGTGATGATCCTGAAGCAGATGAGAGA
GCCAAAAACTCAAGCAAATTGGATCTGAGGAAAAGCCCAGATTTCAGCGATGAGGACTCTGATCTTGATTTTGATATCAG
CAAACTGGAACGTCAGAGCAAGGTGTAAAGCAGAGTGCCTAGGAAACCAACAAGTAGATGATAAATTCTTCAAGCTCTCT
GAGATGGAGACCTTTTTAGAAAACATGGAAAAAGAAGAGGAACAAAGAGATGACCAAGAGGAAGATGATATTGATTTTTT
TGAAGATGTGGATTCCAATGAAGATGAAGGAGGACTGTTTGGAGGCCAGGATCTTAAGTCAGGTAAAAGTTCCAGAAACC
TGAAATACAAAGATTTCTTTGATCCAGTTGAAAGTGATGAAGACGTAGCAAGTGTCCACGATGATGGGAATGAACTGGCT
TCAAATGAAGAGGAAGAGATTGCTGAAGGAGAAGAAAGCATTTCTGAGACGGATGAAGATGATGACCTTGAAGAAAGTGG
AGACAGTAAACAACGTAAAGAAACCTTGAAAAGAGTGACCTTTGCTCTGCCCAATGATGAGGACACTGAAGATACAAATG
TCTTAAATGTACAGAAAGACTCTGATGAAGTAAAATCCTCTTTTGAAAAAAGACAAGAAAAGATGAATGAAAAAATTGCA
TCTTTGGAAAAAGAGTTGTTGGAGAAGAAACCTTGGCAGCTTCAAGGAGAAGTGACAGCGCAGAAGCGGCCCGAGAACAG
CCTCCTGGAAGAGACCCTGCACTTCGACCACGCCGTGCGCATGGCACCTGTGATCACAGAGGAAACCACTCTCCAACTAG
AGGATATCATTAAGCAGAGGATAAAAGATCAGGCTTGGGATGATGTCGTACGCAAAGAAAAGCCTAAAGAGGATGCATTT
GAGTATAAAAAGCGTTTAACACTGGACCACGAAAAGAGTAAATTGAGCCTTGCTGAAATTTACGAACAGGAGTACATCAA
ACTCAACCAGCAAAAAACAGCAGAGGAAGAAAATCCAGAGCATGTAGAAATCCAGAAGATGATGGACTCCCTCTTCTTAA
AGTTGGATGTGCTCTCAAACTTCCACTTCATCCCCAAGCCACCTGTTCCAGAAATTAAAGTGGTATCAAATCTGCCCGCT
GTCACCATGGAGGAGGTTGCCCCTGTGAGTGTCAGTGACGCAGCCCTCCTGGCCCCAGAGGAGGTCAAGGAGAAAAATAA
AGCTGGAGATATAAAAACAGCTGCTGAGAAAACAGCTACAGAC
ORF - retro_btau_1333 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 93.78 % |
| Parental protein coverage: | 84.26 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | MARPAWRRRTLERCLREVGKATDSPECFLTIQDELASKFTSLTKVLYDFNKVLENDRKHGSPLKKLMINN |
| MARPAWR.RTLERCLREVGKATDSPECFLTIQDELASK.TSLTKVLYDFNKVLENDRKHGSPL.KLMINN | |
| Retrocopy | MARPAWRWRTLERCLREVGKATDSPECFLTIQDELASKYTSLTKVLYDFNKVLENDRKHGSPLEKLMINN |
| Parental | FDDEQIWQQLELQNEPILQHFQSAVSETIEDEDISLLPESEEQECEEDVMELEAAGQEDLEQDLEEEEVE |
| FDDEQIWQQLELQNEPILQHFQSAVSETIEDEDISLLPESEEQECEED.MELEAAGQEDLEQDLEEEEVE | |
| Retrocopy | FDDEQIWQQLELQNEPILQHFQSAVSETIEDEDISLLPESEEQECEEDMMELEAAGQEDLEQDLEEEEVE |
| Parental | EAEEVEVSDLSADDPEADERAKNSSKLDLRKSPDFSDEDSDLDFDISKLERQSKVQSRVPRKPTEKSI-V |
| EAEEVEVSDLS.DDPEADERAKNSSKLDLRKSPDF....SD.D.D..........QS.V......K...V | |
| Retrocopy | EAEEVEVSDLSGDDPEADERAKNSSKLDLRKSPDF----SDEDSDLDFDISKLERQSKV*SRVPRKPT>V |
| Parental | DDKFFKLSEMETFLENMEKEEEQRDDQEEDDIDFFEDVDSDEDEGGLFGGQDLKSGKSSRNLKYKDFFDP |
| DDKFFKLSEMETFLENMEKEEEQRDDQEEDDIDFFEDVDS.EDEGGLFGGQDLKSGKSSRNLKYKDFFDP | |
| Retrocopy | DDKFFKLSEMETFLENMEKEEEQRDDQEEDDIDFFEDVDSNEDEGGLFGGQDLKSGKSSRNLKYKDFFDP |
| Parental | VESDEDVASVQDDGNELASNEEEEIAEGEESISETDEDDDLEESGDSKQHKETLKRVTFALPNDEDTEDT |
| VESDEDVASV.DDGNELASNEEEEIAEGEESISETDEDDDLEESGDSKQ.KETLKRVTFALPNDEDTEDT | |
| Retrocopy | VESDEDVASVHDDGNELASNEEEEIAEGEESISETDEDDDLEESGDSKQRKETLKRVTFALPNDEDTEDT |
| Parental | NILNVQKDSDEVKSSFEKRQEKMNEKIASLEKELLEKKPWQLQGEVTAQKRPENSLLEETLHFDHAVRMA |
| N.LNVQKDSDEVKSSFEKRQEKMNEKIASLEKELLEKKPWQLQGEVTAQKRPENSLLEETLHFDHAVRMA | |
| Retrocopy | NVLNVQKDSDEVKSSFEKRQEKMNEKIASLEKELLEKKPWQLQGEVTAQKRPENSLLEETLHFDHAVRMA |
| Parental | PVITEETTLQLEDIIKQRIKDQAWDDVVRKEKPKEDAFEYKKRLTLDHEKSKLSLAEIYEQEYIKLNQQK |
| PVITEETTLQLEDIIKQRIKDQAWDDVVRKEKPKEDAFEYKKRLTLDHEKSKLSLAEIYEQEYIKLNQQK | |
| Retrocopy | PVITEETTLQLEDIIKQRIKDQAWDDVVRKEKPKEDAFEYKKRLTLDHEKSKLSLAEIYEQEYIKLNQQK |
| Parental | TAEEENPEHVEIQKMMDSLFLKLDALSNFHFIPKPPVPEIKVVSNLPAVTMEEVAPVSVSDAALLAPEEV |
| TAEEENPEHVEIQKMMDSLFLKLD.LSNFHFIPKPPVPEIKVVSNLPAVTMEEVAPVSVSDAALLAPEEV | |
| Retrocopy | TAEEENPEHVEIQKMMDSLFLKLDVLSNFHFIPKPPVPEIKVVSNLPAVTMEEVAPVSVSDAALLAPEEV |
| Parental | KEKNKAGDIKTAAEKTATD |
| KEKNKAGDIKTAAEKTATD | |
| Retrocopy | KEKNKAGDIKTAAEKTATD |
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 |
|---|---|---|
| ERP005899_liver | 0 .36 RPM | 17 .95 RPM |
| ERP005899_muscle | 0 .05 RPM | 11 .51 RPM |
| SRP017611_brain | 0 .00 RPM | 9 .96 RPM |
| SRP017611_kidney | 0 .06 RPM | 16 .66 RPM |
| SRP017611_liver | 0 .00 RPM | 13 .21 RPM |
| SRP030211_testis | 0 .18 RPM | 36 .18 RPM |
Bos taurus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_btau_1333 retrocopy.
Bos taurus was not studied using FANTOM5 data.
retro_btau_1333 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_btau_1333 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 3 parental genes, and 3 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Bos taurus | ENSBTAG00000009854 | 1 retrocopy |
retro_btau_1333 ,
|
| Echinops telfairi | ENSETEG00000016641 | 1 retrocopy | |
| Otolemur garnettii | ENSOGAG00000003177 | 1 retrocopy |