RetrogeneDB ID: | retro_ocun_1680 | ||
Retrocopy location | Organism: | Rabbit (Oryctolagus cuniculus) | |
| Coordinates: | GL018762:607107..607764(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSOCUG00000022587 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | ARL6IP6 | ||
| Ensembl ID: | ENSOCUG00000013257 | ||
| Aliases: | None | ||
| Description: | ADP-ribosylation-like factor 6 interacting protein 6 [Source:HGNC Symbol;Acc:24048] |
Retrocopy-Parental alignment summary:
>retro_ocun_1680
AGTGGGAAGCGTTCGGCACTGCACCACAGTCGCCTTTGCACCCCGGTGCCCTTTGCGGCTCCACATACCCTGCCTTCTCT
CAGGGGGACAGTTGGGGTGAAGGCAAAGTCGACGACCAGGAGGGATGCAACCAAGTGGTCCGTGACTTGAGAGAGTTCTC
AGCTGGACCATCTTTGGAGTGCAAGAGAGGTTCTCTGTTCCCACCAGATGGAGATGGGTCACCGGTGCTGCCAGAGAAGC
TCAATGCATCTTCCTGGCTGCTGCGGGAAGCCAAACCCCATCTCAGCAGTGGCCGGTTCAGGTCCTTTCTATTCTATGTT
CACTGCTATTCGCCATCCTCCTCGCCTTTCTGCTCGCCATCGTCTACCTGGCTGTTAAAGAGTTGCATGCTGAGAATTTG
AAAAATGAAGATGGTGTAGACGCTGGGCTGTTAGGGTTCTGGATGCTGCTTATAATATCCCTAACTGCTGGATTCTCCTG
TTGCAGCTTTTCTTGGACAGTGACTTATTTGATTCTTTTGAACCAGGAATGTTTCCTCCTACTCCTCTTTCACCTGCCAG
GTTCAAGAAACGGACTGGACACTCCTTCCACATGGGCGACAGCATGGCAATTTTGAATGGCATTGTGGCTGCTCTTACTG
TAGCATGGTGCCTCATG
ORF - retro_ocun_1680 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 84.82 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 3 |
Retrocopy - Parental Gene Alignment:
| Parental | SGRRSAPRRRRLGTPVPFAAPQ-YSAFSQGDSWGVGEVDDEEGCTQVARDLRAEFSAGPSSESRRGSLFP |
| SG.RSA....RL.TPVPFAAP..Y.AFSQGDSWG.G.VDD.EGC.QV.RDLR.EFSAGPS.E..RGSLFP | |
| Retrocopy | SGKRSALHHSRLCTPVPFAAPH<YPAFSQGDSWGEGKVDDQEGCNQVVRDLR-EFSAGPSLECKRGSLFP |
| Parental | PDGDGSPVLPEKRNG-IFPAAAGSRTSARQWPVQVLSILCALLFAILLAFLLAIVYLVVKELHAENLKNE |
| PDGDGSPVLPEK.N..IF.AAAGS.T...QWPVQVLSILC.LLFAILLAFLLAIVYL.VKELHAENLKNE | |
| Retrocopy | PDGDGSPVLPEKLNA<IFLAAAGSQTPSQQWPVQVLSILCSLLFAILLAFLLAIVYLAVKELHAENLKNE |
| Parental | DGIDTGLLGFWTLLIISLTAGFSCCSFSWTVTY-FDSFEPGMFPPTPLSPARFKKLTGHSFHMGYSMAIL |
| DG.D.GLLGFW.LLIISLTAGFSCCSFSWTVTY.FDSFEPGMFPPTPLSPARFKK.TGHSFHMG.SMAIL | |
| Retrocopy | DGVDAGLLGFWMLLIISLTAGFSCCSFSWTVTY<FDSFEPGMFPPTPLSPARFKKRTGHSFHMGDSMAIL |
| Parental | NGIVAALTVAWCLM |
| NGIVAALTVAWCLM | |
| Retrocopy | NGIVAALTVAWCLM |
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 | 6 .68 RPM |
| SRP017611_kidney | 0 .00 RPM | 10 .64 RPM |
| SRP017611_liver | 0 .00 RPM | 3 .55 RPM |
Oryctolagus cuniculus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ocun_1680 retrocopy.
Oryctolagus cuniculus was not studied using FANTOM5 data.
retro_ocun_1680 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_ocun_1680 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 2 parental genes, and 4 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Mustela putorius furo | ENSMPUG00000000415 | 1 retrocopy | |
| Oryctolagus cuniculus | ENSOCUG00000013257 | 3 retrocopies |
retro_ocun_1649, retro_ocun_1680 , retro_ocun_1727,
|