RetrogeneDB ID: | retro_ocun_876 | ||
Retrocopy location | Organism: | Rabbit (Oryctolagus cuniculus) | |
| Coordinates: | 16:52623632..52624450(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | TMEM19 | ||
| Ensembl ID: | ENSOCUG00000012539 | ||
| Aliases: | None | ||
| Description: | transmembrane protein 19 [Source:HGNC Symbol;Acc:25605] |
Retrocopy-Parental alignment summary:
>retro_ocun_876
GCTTTCTGGATTATGTGAATGATAGCAAGCACCTGTTATGGTAATTTACGGCCAATTTCTCCTTGGCGTTGGCTGTTTTC
TGTTCCTGTTGTGATTGTCTCTAATGGCATTAAAAAGAAAAGTCTGGATCACAGTGGGGCTCTCGGAGGGTGAGTGGTTG
GATTTATGTTAACCATTGCAAATTTCAGTTTCTTTACCTCTTTGCTTATGTTTTTCATTTCTTCTTCAAAACTTACTAAA
TGGAAAGGAGAAACAAAGAAGTGTCTAGATTCAGAATGAAAGGAAGGTGGGCAAAAGAATTGGGTTCAGGTATTCTGTAA
TGGTGCCGTGCCTACAGAGCTGACCCTGCCATTCATGACAGAAAATGGCCCCAGGGAAATCCCAATTGATTTCTCCAAGC
AGTACACTGCTTCCTGGATGTGTTTGTCTCTTTTGGCTGCGCTGGCCTGCTCTGCTGGAGACATGTGGGCTTCGGAAGTT
GGCCAGGTTCTGAGTAAAAGCCCACCAAGACTGATAACAACCTGGAAGAAAGTTCCCATTGGGACAAATGGAGAAGTTAC
CATGGTGGACCTTGCTCCAGTCTCTTTGGTAGTACCTTTGTGGGCATCACATACTTCTTTACACAGTTGGTTTTTTGTGA
ATGATTTAGACATATCTGCTCCCCAGTGACCAATTATTGCATTTGGGGGTACAGCTATGTTACTAGATCAATTGTGGACT
CGTATTTAGGAGCAACAATGCAATTTTCAGGGTTGGATGAAAGCACTGGCATGGTAATCAATAGCCCAACAAATGAGGCA
AAGCACATATCAGGGAAA
ORF - retro_ocun_876 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 86.33 % |
| Parental protein coverage: | 71.24 % |
| Number of stop codons detected: | 4 |
| Number of frameshifts detected: | 3 |
Retrocopy - Parental Gene Alignment:
| Parental | AFWIMSMTASTYYGNLRPISPWRWLFSVVVPVLIVSNGIKKKSLDHSGALGGLVVGFILTIANYSFFTSL |
| AFWIM.M.AST.YGNLRPISPWRWLFSV..PV.IVSNGIKKKSLDHSGALGG.VVGF.LTIAN.SFFTSL | |
| Retrocopy | AFWIM*MIASTCYGNLRPISPWRWLFSV--PVVIVSNGIKKKSLDHSGALGG*VVGFMLTIANFSFFTSL |
| Parental | LMFFLSSSKLTKWKGETKKRLDSEYKEGGQRNWVQVFCNGAVPTELALLFMIENGPGEIPIDFSKQYTAS |
| LMFF.SSSKLTKWKGETKK.LDSE.KEGGQ.NWVQVFCNGAVPTEL.L.FM.ENGP.EIPIDFSKQYTAS | |
| Retrocopy | LMFFISSSKLTKWKGETKKCLDSE*KEGGQKNWVQVFCNGAVPTELTLPFMTENGPREIPIDFSKQYTAS |
| Parental | WMCLSLLAALACSAGDTWASEVGPVLSKSPPRLITTWKKVPVGTNGGVTMVGLA-SSLLGGTFVGLAYFL |
| WMCLSLLAALACSAGD.WASEVG.VLSKSPPRLITTWKKVP.GTNG.VTMV.LA.SSL.G.TFVG..YF. | |
| Retrocopy | WMCLSLLAALACSAGDMWASEVGQVLSKSPPRLITTWKKVPIGTNGEVTMVDLA<SSLFGSTFVGITYFF |
| Parental | TQLI-FVNDLDLSAPQWPIIAFGGIAGLLG-SIVDSYLGATMQFSGLDETTGMVVNSPTNEAKHISGK |
| TQL..FVNDLD.SAPQ.PIIAFGG.A.LL..SIVDSYLGATMQFSGLDE.TGMV.NSPTNEAKHISGK | |
| Retrocopy | TQLV>FVNDLDISAPQ*PIIAFGGTAMLLD<SIVDSYLGATMQFSGLDESTGMVINSPTNEAKHISGK |
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 | 56 .46 RPM |
| SRP017611_kidney | 0 .00 RPM | 55 .04 RPM |
| SRP017611_liver | 0 .00 RPM | 59 .50 RPM |
Oryctolagus cuniculus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ocun_876 retrocopy.
Oryctolagus cuniculus was not studied using FANTOM5 data.
retro_ocun_876 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_ocun_876 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 | ENSOCUG00000012539 | 1 retrocopy |
retro_ocun_876 ,
|
| Sarcophilus harrisii | ENSSHAG00000001776 | 1 retrocopy |