RetrogeneDB ID: | retro_ocun_1030 | ||
Retrocopy location | Organism: | Rabbit (Oryctolagus cuniculus) | |
| Coordinates: | 2:25348698..25349505(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | MAPK1IP1L | ||
| Ensembl ID: | ENSOCUG00000004003 | ||
| Aliases: | None | ||
| Description: | mitogen-activated protein kinase 1 interacting protein 1-like [Source:HGNC Symbol;Acc:19840] |
Retrocopy-Parental alignment summary:
>retro_ocun_1030
GTCGGGCTGACCCCGGTTCCTCAGCGCTCAGGTCCCTCGGCTCCATCGTTGTTTCCAGACCCTGCTGGGGGCTCAGATCT
TGCCAAGGGAAATGTCTGATGAGTTTTCGTTGGCAGATGCACTACCTGAACACTCCCCTGCCAAGACCTCTGTGAGCAAT
ACAAAGCCTGCCCAAGCGCAAGGCTGGCCAGGTTCCAACCCTTGGAATAACCCAAGTGCTCCACCTTCAGTGCCATCTGG
ACTCCCGCCAAGTGCAGCCCCCTCTACGTGCCTTTGGACCAGCGCCAATGGAATGTACCCTCGTGCTCCACTGACCGCTC
AGGACCTCCCGCCCCCTTTCCTCCTCTGGACCATCGTGCCCCCCACCTGGTGGTCCTTACCCAGCCCCAACTGTGCCAGG
CCCTGGGCCCACAGAGCCATATCCTACACCAAATATGCCCTTTCCAGAGCTACCCAGACCATATGGTGCACCCACAGATC
CAGCCATAGCTGGTCCCTTAGGTCCATGGGGATCCATGTCTTCTGGACCTTGGGCACCTGGGATGGGAGGGCAGTATCCT
ACCCCTAATATGCCAAATTCATCTTCAGGCCATATCCCGCTCCTCCTCCCCAAAAGCACCAGGGGTGGCACCCCCTGTTC
CCTGGGGCACTGTTCCACCAGGAGCCTGGGGACCGCCGGCACCATATCCTGCCCCTGCAGGGTCGTATCCTGCACCAGGA
CTCTATCCTTCCCCCAGCAATCCTTTCCAAGTGCCTTCAGGACCTGCTGGTGCTCCACCGATGCCGGGTGGCCCCCATTC
ATACCAT
ORF - retro_ocun_1030 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 81.07 % |
| Parental protein coverage: | 73.71 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 7 |
Retrocopy - Parental Gene Alignment:
| Parental | VRLRSAPRSSLLSGPSPPLGPAGGSHPA-RKMSDEFSLADALPEHSPAKTSVSNTKPAQAQGWPGSNPWN |
| V.L...P..S..S.PS....PAGGS..A.R.MSDEFSLADALPEHSPAKTSVSNTKPAQAQGWPGSNPWN | |
| Retrocopy | VGLTPVPQRSGPSAPSLFPDPAGGSDLA>REMSDEFSLADALPEHSPAKTSVSNTKPAQAQGWPGSNPWN |
| Parental | NPSAPPSVPSGLPPSAAPST-VP-FGPAP-TGMYPSVPPTGPPPGPP-APFPPSGPSCPPPGGPYPAPAV |
| NPSAPPSVPSGLPPSAAPST.VP.FGPAP..GMYP..P.T.....PP.....PS.P..PP.GGPYPAP.V | |
| Retrocopy | NPSAPPSVPSGLPPSAAPST<VP<FGPAP<NGMYPRAPLTAQDLPPP>SSSGPSCP--PP-GGPYPAPTV |
| Parental | PGPGPTGPYPTPNMPFPELPRPYGAPTDPATAGPLGPWGSMSSGPWAPGMGGQYPTPNMPYPSPG-PYPA |
| PGPGPT.PYPTPNMPFPELPRPYGAPTDPA.AGPLGPWGSMSSGPWAPGMGGQYPTPNMP..S.G.PYPA | |
| Retrocopy | PGPGPTEPYPTPNMPFPELPRPYGAPTDPAIAGPLGPWGSMSSGPWAPGMGGQYPTPNMPNSSSG<PYPA |
| Parental | PPPQA-PGAAPPVP-WGTVPPGAWGPPAPYPAPAGSYPAPGLYPSPSNPFQVPSGPAGAPPMPGGPHSYH |
| PPPQ...G..P..P.WGTVPPGAWGPPAPYPAPAGSYPAPGLYPSPSNPFQVPSGPAGAPPMPGGPHSYH | |
| Retrocopy | PPPQKHQGWHPLFP<WGTVPPGAWGPPAPYPAPAGSYPAPGLYPSPSNPFQVPSGPAGAPPMPGGPHSYH |
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 | 0 .06 RPM | 13 .74 RPM |
| SRP017611_kidney | 0 .81 RPM | 12 .77 RPM |
| SRP017611_liver | 0 .15 RPM | 7 .01 RPM |
Oryctolagus cuniculus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ocun_1030 retrocopy.
Oryctolagus cuniculus was not studied using FANTOM5 data.
retro_ocun_1030 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_ocun_1030 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 3 parental genes, and 4 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Nomascus leucogenys | ENSNLEG00000012787 | 1 retrocopy | |
| Oryctolagus cuniculus | ENSOCUG00000004003 | 1 retrocopy |
retro_ocun_1030 ,
|
| Pongo abelii | ENSPPYG00000005836 | 2 retrocopies |