RetrogeneDB ID: | retro_ocun_1489 | ||
Retrocopy location | Organism: | Rabbit (Oryctolagus cuniculus) | |
| Coordinates: | 9:92279201..92279603(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | C1orf52 | ||
| Ensembl ID: | ENSOCUG00000002803 | ||
| Aliases: | None | ||
| Description: | chromosome 1 open reading frame 52 [Source:HGNC Symbol;Acc:24871] |
Retrocopy-Parental alignment summary:
>retro_ocun_1489
AGGAGGATAACAGCGAGCCGGAGACAGGCGCAGGGCCCTGGATGCAGCGAAGTCGGCGGGCGGCTGCCCTGACCCGACAA
GCTGTTCTGGAGCGTGACCTGCCCGGCCTTTCTCTACAATCCGCTCAACAAGCAGATGGACTGGGAGAGGCACGTCGTGG
AGGCGCCGGAGGAGCCTCCAAAGGAGTTCAAAATCTGGAAGTCAAACTATGTGTCCCCGCCGGAAACCCACACAGCGAAG
AAACCACCGCCTACAGAGCTGGACATTGCTATAAAATGGTCTAACATATACGAGGACAATGGCGATGATGCCCCCAGAAT
GCTAAAGAAGCCAGGCTTCTACTGGAAGGGGAAGAGACATTAGAGTCAGATGATGGAAAAAGACGAGCATACTTCTAGAA
AG
ORF - retro_ocun_1489 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 77.37 % |
| Parental protein coverage: | 73.63 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 2 |
Retrocopy - Parental Gene Alignment:
| Parental | RRASDAAKSAGGCG-NKAEKRLPGPDELFRSVTRPAFLYNPLNKQIDWERHVVKAPEEPPKEFKIWKSNY |
| RR.......A.G.G......RLP.PD.LF.SVT.PAFLYNPLNKQ.DWERHVV.APEEPPKEFKIWKSNY | |
| Retrocopy | RRITASRRQAQGPGCSEVGGRLP*PDKLFWSVTCPAFLYNPLNKQMDWERHVVEAPEEPPKEFKIWKSNY |
| Parental | VPPPETYTAEKKPPPPELDMAIKWSNIYEDNGDDA-PQNAKKARLLPEGEETLESDD-EKDEHTSKK |
| V.PPET.TA.KKPPP.ELD.AIKWSNIYEDNGDDA.PQNAK.ARLL.EGEETLESDD.EKDEHTS.K | |
| Retrocopy | VSPPETHTA-KKPPPTELDIAIKWSNIYEDNGDDA<PQNAKEARLLLEGEETLESDD>EKDEHTSRK |
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 .00 RPM | 19 .37 RPM |
| SRP017611_kidney | 0 .00 RPM | 7 .80 RPM |
| SRP017611_liver | 0 .00 RPM | 3 .24 RPM |
Oryctolagus cuniculus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ocun_1489 retrocopy.
Oryctolagus cuniculus was not studied using FANTOM5 data.
retro_ocun_1489 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_ocun_1489 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 | |
|---|---|---|---|
| Choloepus hoffmanni | ENSCHOG00000012863 | 1 retrocopy | |
| Oryctolagus cuniculus | ENSOCUG00000002803 | 2 retrocopies |
retro_ocun_1489 , retro_ocun_1892,
|