RetrogeneDB ID: | retro_ocun_315 | ||
Retrocopy location | Organism: | Rabbit (Oryctolagus cuniculus) | |
| Coordinates: | 1:147686697..147687458(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSOCUG00000022999 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | LDB1 | ||
| Ensembl ID: | ENSOCUG00000025582 | ||
| Aliases: | None | ||
| Description: | LIM domain binding 1 [Source:HGNC Symbol;Acc:6532] |
Retrocopy-Parental alignment summary:
>retro_ocun_315
TTTGTGTCCCTCGACTGTGACCAGGGTAGCAGGGTGACCCAGCACGGCAAACCCATGTTCACTCAGGTGTGCGTGGAGGG
CCGGCTATACCTGGAGTTCATGTGCGACGACATGATGAGGATAAAGACGTGGCACTTCAGCATCCGGCAGCACCGAGAGC
TCATCCCCTGCAGCATCCTTGCCATGCACGCCCAGGACCCCCAGATGTTGGATCAGCTGTCCAAAAACATCACACGGTGT
GGGCTGTCCAACTCCACTCTCAACTACCTCCGACACTGTGTGATACTCGAGCCCATGCAGGAGCTCATGTCCTGCCACAA
GACTTACAGCCTCAGCCCCCAAGACTGCCTCAAGACCTGCCTTTTCCAGAAGTGGCAGCGCATGGTAGCACCCCCCGCGG
AACCCGCACGGCAGCAGCCCAGCAAGCGGCGGAAACGGAAGATGTCAGGGGCAGCATCATGAGTTCGGAGGGTGGCTACA
CCAACAACAGCAACAGCAAGAAGAAGAGCCCGGCCAGCACCTTCGCCCTCTCCAGCCAGGATGTGATGGTGGTGGGGGAG
CCCACCCTGATGGGCGGGGAGTTCGGGGACGAGGACGAGAGGCTCATCACCCGTCTGGAGAACACCCAGTTTGACGCGGC
CAACGGCATTGACGACAGCTTTAACAACTCCCCTGCACTGGGTGCCAACAGCCCCTGGAACAGCAAGCCTCCGTCCAGCC
AAGAAAGCAAATCGGAGAACCCCACGTCACAGGCCTCCCAG
ORF - retro_ocun_315 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 94.59 % |
| Parental protein coverage: | 62.77 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | FVSLDCDQGSMVTQHGKPMFTQVCVEGRLYLEFMFDDMMRIKTWHFSIRQHRELIPRSILAMHAQDPQML |
| FVSLDCDQGS.VTQHGKPMFTQVCVEGRLYLEFM.DDMMRIKTWHFSIRQHRELIP.SILAMHAQDPQML | |
| Retrocopy | FVSLDCDQGSRVTQHGKPMFTQVCVEGRLYLEFMCDDMMRIKTWHFSIRQHRELIPCSILAMHAQDPQML |
| Parental | DQLSKNITRCGLSNSTLNYLRLCVILEPMQELMSRHKTYSLSPRDCLKTCLFQKWQRMVAPPAEPARQQP |
| DQLSKNITRCGLSNSTLNYLR.CVILEPMQELMS.HKTYSLSP.DCLKTCLFQKWQRMVAPPAEPARQQP | |
| Retrocopy | DQLSKNITRCGLSNSTLNYLRHCVILEPMQELMSCHKTYSLSPQDCLKTCLFQKWQRMVAPPAEPARQQP |
| Parental | SKRRKRKMSG-GSTMSSGGGNTNNSNSKKKSPASTFALSSQVPDVMVVGEPTLMGGEFGDEDERLITRLE |
| SKRRKRKMSG.GS.MSS.GG.TNNSNSKKKSPASTFALSSQ..DVMVVGEPTLMGGEFGDEDERLITRLE | |
| Retrocopy | SKRRKRKMSG<GSIMSSEGGYTNNSNSKKKSPASTFALSSQ--DVMVVGEPTLMGGEFGDEDERLITRLE |
| Parental | NTQFDAANGIDDEDSFNNSPALGANSPWNSKPPSSQESKSENPTSQASQ |
| NTQFDAANGID..DSFNNSPALGANSPWNSKPPSSQESKSENPTSQASQ | |
| Retrocopy | NTQFDAANGID--DSFNNSPALGANSPWNSKPPSSQESKSENPTSQASQ |
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 .44 RPM | 42 .38 RPM |
| SRP017611_kidney | 1 .01 RPM | 25 .95 RPM |
| SRP017611_liver | 0 .08 RPM | 11 .10 RPM |
Oryctolagus cuniculus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ocun_315 retrocopy.
Oryctolagus cuniculus was not studied using FANTOM5 data.
retro_ocun_315 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_ocun_315 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 1 parental gene, and 1 retrocopy.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Oryctolagus cuniculus | ENSOCUG00000025582 | 1 retrocopy |
retro_ocun_315 ,
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