RetrogeneDB ID: | retro_ocun_828 | ||
Retrocopy location | Organism: | Rabbit (Oryctolagus cuniculus) | |
| Coordinates: | 15:39634161..39634404(-) | ||
| Located in intron of: | ENSOCUG00000003892 | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | PDCD5 | ||
| Ensembl ID: | ENSOCUG00000013220 | ||
| Aliases: | None | ||
| Description: | programmed cell death 5 [Source:HGNC Symbol;Acc:8764] |
Retrocopy-Parental alignment summary:
>retro_ocun_828
GAGGCGCTGAGGAAGCAGAGGCTGGCGGAGCTGCAGGCGAAGCACGGGGATCCCGACGATGCAGCGCCATAGGAAGCAAA
GCACAGGGAAGCAGAAATGAGAAACGGTATCTTAGCCCAAGTTCTGGATCAGTCAGCCCAGGCCAGGTTAAGTAACTTGG
CACTTGTAAAGCCTGAAAAAACTAAAGCAGTAGAAAATTCCCTTATACAGATGGCAAGATATGGACAACTGAGTGGCAAG
GTA
ORF - retro_ocun_828 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 92.59 % |
| Parental protein coverage: | 72.32 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | EALRKQRLAELQAKHGDPGDAAQQEAKHREAEMRNSILAQVLDQSARARLSNLALVKPEKTKAVENYLIQ |
| EALRKQRLAELQAKHGDP.DAA..EAKHREAEMRN.ILAQVLDQSA.ARLSNLALVKPEKTKAVEN.LIQ | |
| Retrocopy | EALRKQRLAELQAKHGDPDDAAP*EAKHREAEMRNGILAQVLDQSAQARLSNLALVKPEKTKAVENSLIQ |
| Parental | MARYGQLSGKV |
| MARYGQLSGKV | |
| Retrocopy | MARYGQLSGKV |
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 .50 RPM | 15 .23 RPM |
| SRP017611_kidney | 0 .51 RPM | 10 .95 RPM |
| SRP017611_liver | 0 .23 RPM | 5 .93 RPM |
Oryctolagus cuniculus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ocun_828 retrocopy.
Oryctolagus cuniculus was not studied using FANTOM5 data.
retro_ocun_828 was not experimentally validated.