RetrogeneDB ID: | retro_ocun_830 | ||
Retrocopy location | Organism: | Rabbit (Oryctolagus cuniculus) | |
| Coordinates: | 15:43393354..43395449(-) | ||
| Located in intron of: | ENSOCUG00000008514 | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | RPS6KA6 | ||
| Ensembl ID: | ENSOCUG00000006428 | ||
| Aliases: | None | ||
| Description: | ribosomal protein S6 kinase, 90kDa, polypeptide 6 [Source:HGNC Symbol;Acc:10435] |
Retrocopy-Parental alignment summary:
>retro_ocun_830
CAGGATGAAGATGTTAAAGAAATCCCTATTACTCATCACGTTAAAGAAGGATATGAGAAAGCAGATCCTGCACAGTTTGA
GCTGCTCAAGGTGCTTGGTCAGGGATCATTTGGAAAGGTTTTTCTTGTTAGAAAGAAGACTGGTCCTGATGCTGGTCAGC
TCTATGCAATGAAGGTGTTAAAAAAGGCTTCTTTAAAAGTTCGAGACAGAGTTCGGACAAAGATGGAAAGAGATATACTT
GTGGAAGTAAATCATCCATTTATTGTCAAATTGCACTATGCCTTTCAGACTGAAGGGAAGCTGTATTTAATACTGGATTT
TCTCAGGGGAGGAGATGTCTTCACAAGATTATCCAAAGAAGTTCTGTTTACAGAGGAAGATGTGAAATTCTACCTTGCTG
AATTGGCCCTTGCTTTGGATCATCTGCATCGATTAGGGATTGTATATAGAGACCTGAAGCCAGAAAACATTTTGCTTGAT
GAAATAGGACATATCAAGTTAACAGATTTTGGACTCAGCAAAGAGTCAGTAGATCAAGAAAAGAAGGCTTACTCATTTTG
TGGTACAGTAGAGTATATGGCTCCTGAAGTAGTAAATAGGAGAGGCCATTCCCAGAGTGCTGATTGGTGGTCATATGGTG
TACTTATGTTTGAAATGCTTACTGGTACTCTGCCATTTCAAGGTAAAGACAGAAACGAGACCATGAATATGATATTAAAA
GCAAAACTTGGAATGCCTCAGTTTCTTAGTGCTGAAGCACAGAGTCTTCTAAGGATGCTATTCAAAAGGAATCCAGCAAA
TAGATTGGGTTCAGAAGGAGTTGAAGAAATAAAAAGACACCTTTTTTTTTGCAAATATTGACTGGAATAAATTATATAAA
AGAGAAGTTCAACCTCCTTTCAAACCTGCTTCTGGAAAACCAGATGATACTTTTTGTTTTGATCCTGAATTTACTGCAAA
AACACCTAAAGATTCTCCTGGTTTACCAGCCAGTACAAATGCTCATCAACTCTTCAAAGGATTCAGCTTTGTTGCAACGT
CTATTGCAGAAGAATATAAAATAACTCCTATCACAAGTGCAAATGTATTACCAATTGTTCAGATAAATGGAAATGCTGCA
CAATTTGGTGAAGTGTATGAATTGAAAGAGGATATCGGTGTTGGCTCCTATTCCGTTTGCAAGCGATGTGTACATAAAAC
TACCAACATGGAATTTGCAGTGAAGATCATTGACAAAAGTAAATGAGACCCATCAGAAGAAATTGAGATTCTGATGCGCT
ATGGACAGCATCCAAACATTATTACTTTAAAGGATGTCTTTGATGATGGTAGATACATATACCTTGTTACAGATTTGATG
AAAGGAGGAGAACTCCTGGATCGTATTCTCAAACAAAAAAGTTTCTCAGAACAGGAAGCTAGTGATGTACTGTATGTAAT
AACTAAGACAGTTGACTGTCTTCATTGTCAAGGAGTTGTTCATCGTGATCTTAAACCTAGTAATATTTTATACATGGATG
AATCAGCCAATGCAGATTCAATTAGGATCTGTGATTTTGGGTTTGCAAAACAGCTTCGAGGAGAAAATGGACTTCTCTTA
ACTCCATGCTACACTGCAAACTTTGTAGCACCTGAGGTTCTTATGCAACAGGGATATGATGCTGCTTGTGATATTTGGAG
TTTAGGAGTCCTTTTTTACACGATGTTGGCTGGCTACACTCCATTTGCTAATGGCCCCAATGATACTCCTGAAGAGATAC
TACTGCGTATAGGCAATGGAAAGTTCTCCTTGAGTGGTGGAAACTGGGATGGTATTTCAGATGGAGCAAAGGATTTGCTT
TCCCATATGCTTCATGTGGACCCTCATCAACGGTACACTACTGAGCAAATATTAAAGCACTCATGGATAACTCACAGTGA
TCAGTTGCGGAATGATCAGCCAAAGAGAAGTGATGCATCACATGCTGTTAAGGGAGCAGTGGTTGCCACATTTTCTGCCC
TGACTCACAAGACCTTTCAACCAGTTCTTGAGCCTGTTGCTGCTTCAAGCTTAGCTCAGAGACGGAGCATGAAAAAGCGA
ACATCAACTGGCCTG
ORF - retro_ocun_830 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 92.89 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | QDEDVKEIPITHHVKEGYEKADPAQFELLKVLGQGSFGKVFLVRKKTGPDAGQLYAMKVLKKASLKVRDR |
| QDEDVKEIPITHHVKEGYEKADPAQFELLKVLGQGSFGKVFLVRKKTGPDAGQLYAMKVLKKASLKVRDR | |
| Retrocopy | QDEDVKEIPITHHVKEGYEKADPAQFELLKVLGQGSFGKVFLVRKKTGPDAGQLYAMKVLKKASLKVRDR |
| Parental | VRTKMERDILVEVNHPFIVKLHYAFQTEGKLYLILDFLRGGDVFTRLSKEVLFTEEDVKFYLAELALALD |
| VRTKMERDILVEVNHPFIVKLHYAFQTEGKLYLILDFLRGGDVFTRLSKEVLFTEEDVKFYLAELALALD | |
| Retrocopy | VRTKMERDILVEVNHPFIVKLHYAFQTEGKLYLILDFLRGGDVFTRLSKEVLFTEEDVKFYLAELALALD |
| Parental | HLHRLGIVYRDLKPENILLDEIGHIKLTDFGLSKESVDQEKKAYSFCGTVEYMAPEVVNRRGHSQSADWW |
| HLHRLGIVYRDLKPENILLDEIGHIKLTDFGLSKESVDQEKKAYSFCGTVEYMAPEVVNRRGHSQSADWW | |
| Retrocopy | HLHRLGIVYRDLKPENILLDEIGHIKLTDFGLSKESVDQEKKAYSFCGTVEYMAPEVVNRRGHSQSADWW |
| Parental | SYGVLMVSSIVAIRPFQIQDLAFSVTQEVFVIFGRKQWSLREIEAGLEYLRFMRVPVLAGGSGKKGVEEI |
| SYGVLM........PFQ..D.............G..Q....E....L..L.F.R.P..A...G..GVEEI | |
| Retrocopy | SYGVLMFEMLTGTLPFQGKDRNETMNMILKAKLGMPQFLSAEAQSLLRML-FKRNP--ANRLGSEGVEEI |
| Parental | KRHLFF-ANIDWNKLYKREVQPPFKPASGKPDDTFCFDPEFTAKTPKDSPGLPASANAHQLFKGFSFVAT |
| KRHLFF.ANIDWNKLYKREVQPPFKPASGKPDDTFCFDPEFTAKTPKDSPGLPAS.NAHQLFKGFSFVAT | |
| Retrocopy | KRHLFF>ANIDWNKLYKREVQPPFKPASGKPDDTFCFDPEFTAKTPKDSPGLPASTNAHQLFKGFSFVAT |
| Parental | SIAEEYKITPITSANVLPIVQQINGNAAQFGEVYELKEDIGVGSYSVCKRCVHKTTNMEFAVKIIDKSKR |
| SIAEEYKITPITSANVLPIVQ.INGNAAQFGEVYELKEDIGVGSYSVCKRCVHKTTNMEFAVKIIDKSK. | |
| Retrocopy | SIAEEYKITPITSANVLPIVQ-INGNAAQFGEVYELKEDIGVGSYSVCKRCVHKTTNMEFAVKIIDKSK* |
| Parental | DPSEEIEILMRYGQHPNIITLKDVFDDGRYIYLVTDLMKGGELLDRILKQKSFSEQEASDVLYVITKTVD |
| DPSEEIEILMRYGQHPNIITLKDVFDDGRYIYLVTDLMKGGELLDRILKQKSFSEQEASDVLYVITKTVD | |
| Retrocopy | DPSEEIEILMRYGQHPNIITLKDVFDDGRYIYLVTDLMKGGELLDRILKQKSFSEQEASDVLYVITKTVD |
| Parental | YLHCQGVVHRDLKPSNILYMDESANADSIRICDFGFAKQLRGENGLLLTPCYTANFVAPEVLMQQGYDAA |
| .LHCQGVVHRDLKPSNILYMDESANADSIRICDFGFAKQLRGENGLLLTPCYTANFVAPEVLMQQGYDAA | |
| Retrocopy | CLHCQGVVHRDLKPSNILYMDESANADSIRICDFGFAKQLRGENGLLLTPCYTANFVAPEVLMQQGYDAA |
| Parental | CDIWSLGVLFYTMLAGYTPFANGPNDTPEEILLRIGNGKFSLSGGNWDGISDGAKDLLSHMLHVDPHQRY |
| CDIWSLGVLFYTMLAGYTPFANGPNDTPEEILLRIGNGKFSLSGGNWDGISDGAKDLLSHMLHVDPHQRY | |
| Retrocopy | CDIWSLGVLFYTMLAGYTPFANGPNDTPEEILLRIGNGKFSLSGGNWDGISDGAKDLLSHMLHVDPHQRY |
| Parental | TTEQILKHSWITHSDQLRNDQPKRSDASHAVKGAVVATFSALTHKTFQPVLEPVAASSLAQRRSMKKRTS |
| TTEQILKHSWITHSDQLRNDQPKRSDASHAVKGAVVATFSALTHKTFQPVLEPVAASSLAQRRSMKKRTS | |
| Retrocopy | TTEQILKHSWITHSDQLRNDQPKRSDASHAVKGAVVATFSALTHKTFQPVLEPVAASSLAQRRSMKKRTS |
| Parental | TGL |
| TGL | |
| Retrocopy | TGL |
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 |
|---|---|---|
| SRP017611_brain | 2 .98 RPM | 3 .42 RPM |
| SRP017611_kidney | 4 .87 RPM | 3 .34 RPM |
| SRP017611_liver | 0 .15 RPM | 0 .00 RPM |
Oryctolagus cuniculus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ocun_830 retrocopy.
Oryctolagus cuniculus was not studied using FANTOM5 data.
retro_ocun_830 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_ocun_830 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 2 parental genes, and 2 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Oryctolagus cuniculus | ENSOCUG00000006428 | 1 retrocopy |
retro_ocun_830 ,
|
| Oryctolagus cuniculus | ENSOCUG00000014367 | 1 retrocopy |