RetrogeneDB ID: | retro_ocun_1892 | ||
Retrocopy location | Organism: | Rabbit (Oryctolagus cuniculus) | |
| Coordinates: | X:63714744..63715280(+) | ||
| Located in intron of: | ENSOCUG00000016267 | ||
Retrocopy information | Ensembl ID: | ENSOCUG00000024343 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
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_1892
GCAGCGGAGAAGGACCACCTGAGCTATTTCACAGTTTATAGGAGCAGTAGTTCGGCTCCTCTGGCGAGAAGGACAACAGC
AAGCTGGATGAGACGGATCACAGGGCTCCGAATGCAGCGAAGTCAGGGGGCGGCTGCAAGAATAAGGTGGAGAAGCAGCT
GCCAGGACCTGACGCACTGTTCCGGAGTGTGACTCGTTGGGCCTTTCTCTACAATCCACTCAACAAGCAGACAGACTGGG
AAAGGCAAGTTGTCAAGGCGCCCGAGGAGCCTCCAAAGGAGTTCAAAATATGGAAGTCAAACTATGTGCGCCTTCCAGAG
ACCTACACAACGGAGAAGAAACCTCTGCCTCCAGAGCTGGACATGGTAATACGATGGTCTAACATATATGAGGACAAAGG
CGATGATGCCCCGCAGAATGCTAAGAAAGCTAGGCTTCTACCGGAAGGGGAGGAGACGTTGGAGTCAGATGATGAAAAAG
ATGAGCATACTTCTCAAAAGTGCAAAGTAGAACCAGGAGAACCAGCAAAGAAGAAA
ORF - retro_ocun_1892 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 82.22 % |
| Parental protein coverage: | 98.35 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | AEEKDPLSYFAAYGSSSS-GSSGEEDNSEPEETGRRASDAAKSAGGCGNKAEKRLPGPDELFRSVTRPAF |
| A.EKD.LSYF..Y.SSSS.GSSGE.DNS...ET..RA..AAKS.GGC.NK.EK.LPGPD.LFRSVTR.AF | |
| Retrocopy | AAEKDHLSYFTVYRSSSS<GSSGEKDNSKLDETDHRAPNAAKSGGGCKNKVEKQLPGPDALFRSVTRWAF |
| Parental | LYNPLNKQIDWERHVVKAPEEPPKEFKIWKSNYVPPPETYTAEKKPPPPELDMAIKWSNIYEDNGDDAPQ |
| LYNPLNKQ.DWER.VVKAPEEPPKEFKIWKSNYV..PETYT.EKKP.PPELDM.I.WSNIYED.GDDAPQ | |
| Retrocopy | LYNPLNKQTDWERQVVKAPEEPPKEFKIWKSNYVRLPETYTTEKKPLPPELDMVIRWSNIYEDKGDDAPQ |
| Parental | NAKKARLLPEGEETLESDDEKDEHTSKKRKVEPGEPTKKK |
| NAKKARLLPEGEETLESDDEKDEHTS.K.KVEPGEP.KKK | |
| Retrocopy | NAKKARLLPEGEETLESDDEKDEHTSQKCKVEPGEPAKKK |
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 | 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_1892 retrocopy.
Oryctolagus cuniculus was not studied using FANTOM5 data.
retro_ocun_1892 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_ocun_1892 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 ,
|