RetrogeneDB ID: | retro_ocun_1422 | ||
Retrocopy location | Organism: | Rabbit (Oryctolagus cuniculus) | |
| Coordinates: | 8:80809954..80810787(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | LPCAT4 | ||
| Ensembl ID: | ENSOCUG00000006180 | ||
| Aliases: | None | ||
| Description: | lysophosphatidylcholine acyltransferase 4 [Source:HGNC Symbol;Acc:30059] |
Retrocopy-Parental alignment summary:
>retro_ocun_1422
GGCCCTGGCGTACTCAAAGTCCTCTGGCTCACAGCCTCTCAGCCCTGCAGCATCGTGGATGTGGAGTTCCTCCCTGTGTA
TCACCCCAGCCCGGAGGAGAGCAGGGACCCCACCCTCTATGCTAACAATGTCCAGAGGGTCATGACAAAGGCCCTGGGCA
TTCCTGCCACCGAGTGTGAGTTTGTAGGGAGCTTGCCTGTGATTGTGGTGGGCCTGCTGAAGGTGGTGTTGGAGCCGCAG
CTCTGGAACTGGGAAAGGTGCTTCAGAGCTGGCTGTCCCCAGCTGTGTGGACGCTGGGGCAGAGCCAGGCCCGGAGTCGA
ATGATCAGCCAGGAAGAGTTTGCCAGGCAGCTGCGGCTCTCTGGTCCTCAGACAGTGGCTGGTGGCTTTAGCTACTTCCA
GCAGGATGCCCAGGGTTTGGTGGATTTCCGCGATGTGGCACTCTCACTAGCAGCTCTAGATGGGGGCAGGAGCCTGGAGG
AGCTGACCCGCCTGACCTTTGAGCACTTCACTGAGGAGCAGGCAGAGGGGTCTGGCCACGTACTGTACAAAGACGGATTT
AGCACCATCCTGCACCTGCTGCTGGGTTCACCCCACCTTGCTGCCATGACTTAGCATGCTGAGCTGTGCCAGGCAGGACC
CAGCCAAGGCCTCTCCCTCTGTCAATTCTAAAACTTCTCCCTCCATGACCCACTCTATGGGAAGCTGTTCAGCACCTACC
TGCGCCCCCCACACACCCCTCCAGGCACCTCCCAGATGCAACATGCCTCGTCCCCAGGCAGCCCCACTGCTCGGGCCAAT
GGCACTGTATAGGTGCCCAAGCAGAAGGGTGAC
ORF - retro_ocun_1422 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 88.3 % |
| Parental protein coverage: | 53.14 % |
| Number of stop codons detected: | 3 |
| Number of frameshifts detected: | 3 |
Retrocopy - Parental Gene Alignment:
| Parental | GPGVLKVLWLTASQPCSVVDVEFLPVYHPSPEESRDPTLYANNVQRVMAQALGIPATECEFVGSLPVIVV |
| GPGVLKVLWLTASQPCS.VDVEFLPVYHPSPEESRDPTLYANNVQRVM..ALGIPATECEFVGSLPVIVV | |
| Retrocopy | GPGVLKVLWLTASQPCSIVDVEFLPVYHPSPEESRDPTLYANNVQRVMTKALGIPATECEFVGSLPVIVV |
| Parental | GRLKVALEPQLW-ELGKVLRKAGLSPGR-VDAGAEPG-RSRMISQEEFARQLQLSDPQTVAGAFSYFQQD |
| G.LKV.LEPQLW.ELGKVL....LSP...VDAGAEPG.RSRMISQEEFARQL.LS.PQTVAG.FSYFQQD | |
| Retrocopy | GLLKVVLEPQLW<ELGKVL-QSWLSPAV<VDAGAEPG>RSRMISQEEFARQLRLSGPQTVAGGFSYFQQD |
| Parental | AQGLVDFRDVALALAALDGGRSLEELTRLAFELFAEEQAEGPGRLLYKDGFSTILHLLLGSPHPAATTLH |
| AQGLVDFRDVAL.LAALDGGRSLEELTRL.FE.F.EEQAEG.G..LYKDGFSTILHLLLGSPH.AA.T.H | |
| Retrocopy | AQGLVDFRDVALSLAALDGGRSLEELTRLTFEHFTEEQAEGSGHVLYKDGFSTILHLLLGSPHLAAMT*H |
| Parental | AELCQAGPSQGLSLCQFQNFSLHDPLYGKLFSTYLRPPHTPRGTSQMQRASSPGSPTALANGTVQAPKQK |
| AELCQAGPSQGLSLCQF.NFSLHDPLYGKLFSTYLRPPHTP.GTSQMQ.ASSPGSPTA.ANGTV..PKQK | |
| Retrocopy | AELCQAGPSQGLSLCQF*NFSLHDPLYGKLFSTYLRPPHTPPGTSQMQHASSPGSPTARANGTV*VPKQK |
| Parental | GD |
| GD | |
| Retrocopy | GD |
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 .11 RPM | 156 .46 RPM |
| SRP017611_kidney | 0 .00 RPM | 13 .58 RPM |
| SRP017611_liver | 0 .00 RPM | 4 .32 RPM |
Oryctolagus cuniculus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ocun_1422 retrocopy.
Oryctolagus cuniculus was not studied using FANTOM5 data.
retro_ocun_1422 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_ocun_1422 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 2 parental genes, and 2 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Cavia porcellus | ENSCPOG00000023492 | 1 retrocopy | |
| Oryctolagus cuniculus | ENSOCUG00000006180 | 1 retrocopy |
retro_ocun_1422 ,
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