RetrogeneDB ID: | retro_ocun_358 | ||
Retrocopy location | Organism: | Rabbit (Oryctolagus cuniculus) | |
| Coordinates: | 1:42741442..42742015(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | RDM1 | ||
| Ensembl ID: | ENSOCUG00000022704 | ||
| Aliases: | None | ||
| Description: | RAD52 motif 1 [Source:HGNC Symbol;Acc:19950] |
Retrocopy-Parental alignment summary:
>retro_ocun_358
GCGAGGGACGCGCGCAGAGCCCAGGCGGCCTGTGACCGGAAGCTGCTTTTCCAGGAGACTCCAGTGAAGGTTCGTCTTGG
CCCCAGACATAAGGCAGTTCAACATCAGGCCCTTGCCCTAAACGGCTCCTGATGCCAAGAGCTGGCAAACTACTGCTTGG
GTTTCAATGGATGGTCAAAAAGGATCATCAAGCTTCAGGAGCTCTCCGACCTTGAAGAGAGGGAAAATGAAGAGACGGAG
CGGCGACTTGCGGAGCGGAGCCTGAAGGTCTTCTGTGCCTCGGAGGTGGTGCTGCCATCCTATGAGTGCTCGAGTCGTGG
AGTCGGCGTGGCCGAGGAGCCGCTGGATACGCTGGAGGAGGAAGGACCATTGTTGTTCCTTATGAAGAAGAAGACAGCCC
AGAACCTTGCCATTCAGAAGGCTTTGTCAAATGCGTTCCAGAAACTGTCGATTGTGGTTTTAGAAAGTGGTAAAATAGCC
GTGGAGTACAGACCCGGTGAAGAGATCCTAGATACCGGAAGCGAAGAAGAACTACACAACTTGATTGAAGTATGTGGAGA
TGAAAGCTGGAGT
ORF - retro_ocun_358 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 95.81 % |
| Parental protein coverage: | 73.36 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | ARDARRAQAACDRKLLFQETPVKVRLGTRHKAVQHQALALNGSRCQELANYYLGFNGWSKRIIKLQELSA |
| ARDARRAQAACDRKLLFQETPVKVRLG.RHKAVQHQALALNGS.CQELANY.LGFNGWSKRIIKLQELS. | |
| Retrocopy | ARDARRAQAACDRKLLFQETPVKVRLGPRHKAVQHQALALNGS*CQELANYCLGFNGWSKRIIKLQELSD |
| Parental | LEERENEETARRLAERSLKVFCALEVVLPSYECSSRGVGVAEEPLDTLQEEGPLLFLMKKKTAQNLAIQK |
| LEERENEET.RRLAERSLKVFCA.EVVLPSYECSSRGVGVAEEPLDTL.EEGPLLFLMKKKTAQNLAIQK | |
| Retrocopy | LEERENEETERRLAERSLKVFCASEVVLPSYECSSRGVGVAEEPLDTLEEEGPLLFLMKKKTAQNLAIQK |
| Parental | ALSNAFQKLSIVVLESGKIAVEYRPGEEILDTGSEE-LHNLIEVCGDESWS |
| ALSNAFQKLSIVVLESGKIAVEYRPGEEILDTGSEE.LHNLIEVCGDESWS | |
| Retrocopy | ALSNAFQKLSIVVLESGKIAVEYRPGEEILDTGSEEELHNLIEVCGDESWS |
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 | 8 .50 RPM |
| SRP017611_kidney | 0 .00 RPM | 0 .61 RPM |
| SRP017611_liver | 0 .00 RPM | 0 .23 RPM |
Oryctolagus cuniculus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ocun_358 retrocopy.
Oryctolagus cuniculus was not studied using FANTOM5 data.
retro_ocun_358 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_ocun_358 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 3 parental genes, and 3 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Bos taurus | ENSBTAG00000000030 | 1 retrocopy | |
| Oryctolagus cuniculus | ENSOCUG00000022704 | 1 retrocopy |
retro_ocun_358 ,
|
| Tursiops truncatus | ENSTTRG00000006200 | 1 retrocopy |