RetrogeneDB ID: | retro_ocun_1819 | ||
Retrocopy location | Organism: | Rabbit (Oryctolagus cuniculus) | |
| Coordinates: | GL019030:23365..23923(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | RAE1 | ||
| Ensembl ID: | ENSOCUG00000001585 | ||
| Aliases: | None | ||
| Description: | RAE1 RNA export 1 homolog (S. pombe) [Source:HGNC Symbol;Acc:9828] |
Retrocopy-Parental alignment summary:
>retro_ocun_1819
TACAGTATGACTATGGTAGCAACTGTGGAGACAGGCTATCAGTAAGAGAATCAACCTTCTGAATTCAGAGGAATTAAAAT
CTCTACCTAAACATCAGCATGGATGTGTGGCTATTTTTATAAACAAACAGAACAAGCCAACTTGTTTTGCCCTGGGAAGT
ATTGCATGGAGAGTTGTTGTTCGTTATATCAATCTTGCAAACCCAGCCAAAGATAACTGCATCTCTAAATGTCATCTATC
CAATGGAATCAGCACTTCAGTGCCTCAAGTTCTCTGTGGAGTAAATGGAATTTCAATCCATCTTGGTTTTGGCACCTTGC
CAAAGGTGCAACTGTGGGACCTGTTTTGTCAATTCTAGAACAAAAATGCCAGAAGAAAACTAAAGCTTCAGGACAGCTCA
ATCACAGAGCAACTTGCTGACTCAATCACAATGGAAACAGCCCTGCCTATCCTTGCAGCTATGACTGGTCCAAGGGACAG
GCGTTTTTTAATCCCTCAAAGAAAGACTGCATTTTCCTGCATAAGGGAGCAGAAGAGCTACAGCTTAGAGGTCAGAGG
ORF - retro_ocun_1819 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 57.29 % |
| Parental protein coverage: | 51.36 % |
| Number of stop codons detected: | 3 |
| Number of frameshifts detected: | 2 |
Retrocopy - Parental Gene Alignment:
| Parental | YPMAVVATAERGLIVYQLENQPSEFRRIE-SPLKHQHRCVAIFKDKQNKPTGFALGSIEGRVAIHYINPP |
| Y.M..VAT.E.G...YQ.ENQPSEFR.I..S..KHQH.CVAIF..KQNKPT.FALGSI..RV...YIN.. | |
| Retrocopy | YSMTMVATVETG---YQ*ENQPSEFRGIK>SLPKHQHGCVAIFINKQNKPTCFALGSIAWRVVVRYINLA |
| Parental | NPAKDNFTFKCHRSNGTNTSAPQDIYAVNGIAFHPVHGTLATVGSDGRF-SFWDKDARTKL-KTSEQLDQ |
| NPAKDN...KCH.SNG..TS.PQ....VNGI..H...GTL..V.....F..F..K.AR.KL.K.S.QL.. | |
| Retrocopy | NPAKDNCISKCHLSNGISTSVPQVLCGVNGISIHLGFGTLPKVQLWDLFCQF*NKNARRKL<KASGQLNH |
| Parental | PIAACGFNHNGNIFAYASSYDWSKGHEFYNPQKKNYIFLRNAAEELKPRNKK |
| ..A.C..NHNGN..AY..SYDWSKG..F.NP.KK..IFL...AEEL..R... | |
| Retrocopy | R-ATC*LNHNGNSPAYPCSYDWSKGQAFFNPSKKDCIFLHKGAEELQLRGQR |
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 | 22 .79 RPM |
| SRP017611_kidney | 0 .00 RPM | 16 .83 RPM |
| SRP017611_liver | 0 .00 RPM | 8 .09 RPM |
Oryctolagus cuniculus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ocun_1819 retrocopy.
Oryctolagus cuniculus was not studied using FANTOM5 data.
retro_ocun_1819 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_ocun_1819 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 5 parental genes, and 7 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Oryctolagus cuniculus | ENSOCUG00000001585 | 2 retrocopies |
retro_ocun_1819 , retro_ocun_646,
|
| Otolemur garnettii | ENSOGAG00000014649 | 2 retrocopies | |
| Ochotona princeps | ENSOPRG00000000228 | 1 retrocopy | |
| Sarcophilus harrisii | ENSSHAG00000000550 | 1 retrocopy | |
| Sarcophilus harrisii | ENSSHAG00000002438 | 1 retrocopy |