RetrogeneDB ID: | retro_btau_368 | ||
Retrocopy location | Organism: | Cow (Bos taurus) | |
| Coordinates: | 10:26332082..26333873(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSBTAG00000003769 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | UTP6 | ||
| Ensembl ID: | ENSBTAG00000015612 | ||
| Aliases: | None | ||
| Description: | U3 small nucleolar RNA-associated protein 6 homolog [Source:RefSeq peptide;Acc:NP_001092610] |
Retrocopy-Parental alignment summary:
>retro_btau_368
ATGGCGGAAGTAATTCAGGAACGTGTAGAGGATCGACTTCCCGAATTACAACAGCTGGAGCGCACTGGACTCTTCAGTCA
TGCGGAGATTAAGGCAATCATTAGGAAGGCTTTAGAACTAGAATACAGAATACAGCGAAGAAGTCTTTTAAAGGATGACT
TTATCAGATATGTTCAGTATGAAATTAATCTTTTGGATCTGATCGAGAAAAGGAGAGCTCGCGTTGGATATACATTTAAG
AAGGATGAGATTGAGGATCCTATAATACATCGGATACAGAGTGTCTTCCGACGTGCATCAATTAAGTGGAAAGATGATGT
TCGACTTTGGCTGTCTTTTATAGCCTTTTGTAGGAAGTGGGCTTCCAACGTTCACCTTGGCAAGATATTTTCTTGCTTGT
TGGCCTTTCATTCAAACAAGCCAGGTTTGTGGATTTTGGCGGCCAAATGGGAACTGGAAGACCGCTTTTCTTCAGAAAGT
GCAAGACAGTTATTTCTTCGGGCTCTGCGCTTTCACCCACGTTGCCCGAAACTTTATGAAGAATACTTTAGGATGGAGCT
GATGCATGCTGAAAAATTGAGGAAGGAAAAGCAAGAGTTTGAAAAAGCCAACATGGATGTGGGGAATCTCGAGCATGCTG
AAGAAATCCTTACGGGCGAGTTGGCATGGATCATCTATAAGAATTCTACAAGTGTAATTAAAAGTGCAAAATTTCGTGTG
TCACTGCTTTCAGTGGCACGGCTGTTCAACTTTGCCAAAGATCTGCAAAGAGAAATTTACAATGACCTTAAGGCTCTGCA
CGCAGATGACCCCATCACTTGGGACTATGTGGCCCGGCAAGAATTAGTGATTGAATCACAGCCAGTAGAAGAGCTGCCTA
CAACCAAACAAGCCAAAGCAAAGGAGGTGGGCTGCCGGGAGGAGAGGAGCTGTGCTGTGTACGAGGAAGCGGTAAAAACT
GTGCCCACAGAGGCTATGTGGAAATGTTACATGAACTTCTGCATGGAGAGGTTTACTAAGAAGACAAGCAGTCGCCTCCT
CAGAAAGAAGAGTCTGGAAAGAACCATGGTTGCATTCTGGAAGGCACATGAGCTCAAACTTTTACCAGAACTCCAGTACA
GGCAGTTGAGCAAGTTGTTGCTGCATCACCAGTTGTTAAAGGAATCCCTGGAGGTGGCAGACGCTGGGGTGAAATTGTTC
AAAAAATCAGTGGAGATGTGGCAGGTGAAGCTGGAGGCCCTGATTACGTCAGAGAGCCACGAGATGTCCAAGGGTTTTGA
GCAAGCCTTTGAGTACCTGAAACCTCAGATTTGCCTTCCATTGTGGCTTACTTGGGCCCAGTGGAGTGAAGATGCTGGAA
AGCAAGAAGAAACTGAAGCAATCTATAAGAGAGATATCTTTGGTCTCCCAGGAGCTGACTCAGTCCCTGTGAAGGAAATG
TATCTGAATTGGGCTTATCGAAGTGGTGGTTACAAAAAGGCCAGAGATGTGTTTAAAAGTTTACAGGAAAACCGTCCATT
TTCAGTTGATTTTTTCAGGAAGATGATCCAGTTTGAGAAGGAGCAAGAATCCTGTAAGATGGAGAACTTAAGAGAGTATT
ATGAAAGGGCTTTGAGAGAATTTGGAACTAATGATTCTGATCTCTGGATGGATCACATCAAAGAAGAATTGAACCACCCG
CTTGGTAGACCTGAGAACTGGGGACAGATCTATTGGCGAGCCATGAAAATGTTGCAGGGAGAGTCAATAGAGCAGTTTAT
GGCTAAACATGCTTTGTATCAAGCCGGCCGT
ORF - retro_btau_368 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 97.15 % |
| Parental protein coverage: | 99.83 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | MAEVIQERVEDRLPELQQLERTGLFSHAEIKAIIRKALELEYRIQRRSLLKDDFIRYVQYEIHLLDLIEK |
| MAEVIQERVEDRLPELQQLERTGLFSHAEIKAIIRKALELEYRIQRRSLLKDDFIRYVQYEI.LLDLIEK | |
| Retrocopy | MAEVIQERVEDRLPELQQLERTGLFSHAEIKAIIRKALELEYRIQRRSLLKDDFIRYVQYEINLLDLIEK |
| Parental | RRARVGYTFKKDEIEDPIIHRIQSVFRRASIKWKDDVRLWLSFIAFCRKWASNVHLSKIFSSLLAFHSNK |
| RRARVGYTFKKDEIEDPIIHRIQSVFRRASIKWKDDVRLWLSFIAFCRKWASNVHL.KIFS.LLAFHSNK | |
| Retrocopy | RRARVGYTFKKDEIEDPIIHRIQSVFRRASIKWKDDVRLWLSFIAFCRKWASNVHLGKIFSCLLAFHSNK |
| Parental | PGLWILAAKWELEDRFSSESARQLFLRALRFHPRCPKLYEEYFRMELMHAEKLRKEKQEFEKANMDVGNL |
| PGLWILAAKWELEDRFSSESARQLFLRALRFHPRCPKLYEEYFRMELMHAEKLRKEKQEFEKANMDVGNL | |
| Retrocopy | PGLWILAAKWELEDRFSSESARQLFLRALRFHPRCPKLYEEYFRMELMHAEKLRKEKQEFEKANMDVGNL |
| Parental | EHAEEILTGELARIIYKNSTSVIKSAKFHVSLLSIARLFDFAKDLQREIYNDLKALHADDPVTWDYVARQ |
| EHAEEILTGELA.IIYKNSTSVIKSAKF.VSLLS.ARLF.FAKDLQREIYNDLKALHADDP.TWDYVARQ | |
| Retrocopy | EHAEEILTGELAWIIYKNSTSVIKSAKFRVSLLSVARLFNFAKDLQREIYNDLKALHADDPITWDYVARQ |
| Parental | ELVIESQPVEELPATKQAKAKEVGRREERCCAVYEEAVKTVPTEAMWKCYMNFCMERFTKKTSSRLLRKK |
| ELVIESQPVEELP.TKQAKAKEVG.REER.CAVYEEAVKTVPTEAMWKCYMNFCMERFTKKTSSRLLRKK | |
| Retrocopy | ELVIESQPVEELPTTKQAKAKEVGCREERSCAVYEEAVKTVPTEAMWKCYMNFCMERFTKKTSSRLLRKK |
| Parental | RLERTMVAFWKAHELKLLPELQYRQLSKLLLHRQLLKESLEVADAGVKLFKKSVEMWQVKLEALITSESH |
| .LERTMVAFWKAHELKLLPELQYRQLSKLLLH.QLLKESLEVADAGVKLFKKSVEMWQVKLEALITSESH | |
| Retrocopy | SLERTMVAFWKAHELKLLPELQYRQLSKLLLHHQLLKESLEVADAGVKLFKKSVEMWQVKLEALITSESH |
| Parental | EMSKGFEQAFEYLKPQICLPLWLTWAQWSEDAGKQEETEAIYKRAIFGLPGADSVPVKEMYLNWAYRSGG |
| EMSKGFEQAFEYLKPQICLPLWLTWAQWSEDAGKQEETEAIYKR.IFGLPGADSVPVKEMYLNWAYRSGG | |
| Retrocopy | EMSKGFEQAFEYLKPQICLPLWLTWAQWSEDAGKQEETEAIYKRDIFGLPGADSVPVKEMYLNWAYRSGG |
| Parental | YKKARDVFKSLQENRPFSVDFFRKMIQFEKEQESCKMENLREYYERALREFGTNDSDLWMDYIKEELNHP |
| YKKARDVFKSLQENRPFSVDFFRKMIQFEKEQESCKMENLREYYERALREFGTNDSDLWMD.IKEELNHP | |
| Retrocopy | YKKARDVFKSLQENRPFSVDFFRKMIQFEKEQESCKMENLREYYERALREFGTNDSDLWMDHIKEELNHP |
| Parental | LGRPENCGQIYWRAMKMLQGESVEQFMAKHALYQAGR |
| LGRPEN.GQIYWRAMKMLQGES.EQFMAKHALYQAGR | |
| Retrocopy | LGRPENWGQIYWRAMKMLQGESIEQFMAKHALYQAGR |
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 .00 RPM | 43 .26 RPM |
| ERP005899_muscle | 0 .11 RPM | 47 .25 RPM |
| SRP017611_brain | 0 .18 RPM | 96 .84 RPM |
| SRP017611_kidney | 0 .12 RPM | 94 .78 RPM |
| SRP017611_liver | 0 .15 RPM | 37 .91 RPM |
| SRP030211_testis | 2 .03 RPM | 419 .12 RPM |
Bos taurus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_btau_368 retrocopy.
Bos taurus was not studied using FANTOM5 data.
retro_btau_368 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_btau_368 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 2 parental genes, and 3 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Bos taurus | ENSBTAG00000015612 | 1 retrocopy |
retro_btau_368 ,
|
| Nomascus leucogenys | ENSNLEG00000011009 | 2 retrocopies |