RetrogeneDB ID: | retro_lcha_126 | ||
Retrocopy location | Organism: | Coelacanth (Latimeria chalumnae) | |
| Coordinates: | JH131319.1:60515..61248(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | None | ||
| Ensembl ID: | ENSLACG00000000522 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_lcha_126
AGGGCTCCACAACTGACCGTCAGTGATACGATGGCCGAAGATATAAAGAACATACATGCTCTTTTAGTGCAGCTTTCTTC
CAGTGTGTCGGAGGTTAAGCTGGCGATTCAAAATCTGCAGAATTCGCAGAATCGGCTGGGGCCAGGATAGCAGAGGTGGA
ACAGCGCGTCTCCAAGATCGAGGACGATGGGGTAGGAGAGAGTCAGCGACTACAGCAACTGGAACAGCGGCTTGCCGCTG
CCGCCGAGAAGATCGACGACTTGGAAAACAGGTTGAGGAGGAACAATGTTAGAATCATTGGATTTCCCGAGGGGGCTGAA
GAAGGGAATCCTGTGAATTTTTTTACAGAGGGTCCTCCCCGGGCTGCTGGATTTGGAGGAGGGGATGGCCCTAGAAATGG
AGAGGGCGCACCGGGCGCTGGGTCCACACCCTGAGCCGGGGCAGCGTCCGAGGGCGATTATAGTCAAGCTCCTGCGGTAT
CCCAACAGAGATCTCCTCTTTTGGGCTGCCAGGCTGAAGGGGACAGTGTTGTGGCAAGATCATTGGATTTCTATTTATCC
CGACTGGTCCAAGGAGTTGCAGTTTGAAGAAGCAGTGGTTCTGGGGCATCAGGAAGATTCTTCAGGAAAGGAAGATTAAG
TACGGGATGTTTTACCCCGCTACTTTGAAGATTACGGTTAACGGAGAGACTTTGGCCTTTACTAACCCAGAGGACGCCAG
GAAATTCCTCTCC
ORF - retro_lcha_126 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 72.87 % |
| Parental protein coverage: | 85.56 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 3 |
Retrocopy - Parental Gene Alignment:
| Parental | RQMHFPISSNMIYHSNNLSRNRVQLTANVSEVKLAIPNLQNLQDQLG-ARIAEVEQHVSKIEGDGVGESQ |
| R......S..M.....N.....VQL...VSEVKLAI.NLQN.Q..LG.ARIAEVEQ.VSKIE.DGVGESQ | |
| Retrocopy | RAPQLTVSDTMAEDIKNIHALLVQLSSSVSEVKLAIQNLQNSQNRLG<ARIAEVEQRVSKIEDDGVGESQ |
| Parental | RLWHLEQRLAAAAKWIDNLENRSRKNNVRIIGFPEGVEEGNPMN-FLQKVLPGLLDL-EGKILEMERAHW |
| RL..LEQRLAAAA..ID.LENR.R.NNVRIIGFPEG.EEGNP.N.FLQ.VLPGLLDL.EG..LEMERAH. | |
| Retrocopy | RLQQLEQRLAAAAEKIDDLENRLRRNNVRIIGFPEGAEEGNPVN>FLQRVLPGLLDLEEGMALEMERAHR |
| Parental | ALGPHPAPGQSTRALIVKLLRYPTRDLLLQAAKLKGQVMWREHRISIFPDWSRELQ-LKRQWFWDIRKIL |
| ALGPHP.PGQ..RA.IVKLLRYP.RDLL..AA.LKG.V.W..H.ISI.PDWS.ELQ.LK.QWFW.IRKIL | |
| Retrocopy | ALGPHPEPGQRPRAIIVKLLRYPNRDLLFWAARLKGTVLWQDHWISIYPDWSKELQ>LKKQWFWGIRKIL |
| Parental | REKKIKYGLFYPAILKITVNGEALAFTNPEDARKFLA |
| .E.KIKYG.FYPA.LKITVNGE.LAFTNPEDARKFL. | |
| Retrocopy | QERKIKYGMFYPATLKITVNGETLAFTNPEDARKFLS |
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 |
|---|---|---|
| DRP000627_gill | 0 .00 RPM | 0 .11 RPM |
| DRP000627_kidney | 0 .00 RPM | 0 .03 RPM |
| DRP000627_pectoral_fin | 0 .00 RPM | 0 .00 RPM |
| DRP000627_pelvic_fin | 0 .00 RPM | 0 .00 RPM |
| DRP000627_pharynx | 0 .00 RPM | 0 .03 RPM |
| DRP000627_tail_muscle | 0 .02 RPM | 0 .04 RPM |
Latimeria chalumnae was not studied using ChIP-Seq data.
Latimeria chalumnae was not studied using EST data.
Latimeria chalumnae was not studied using FANTOM5 data.
retro_lcha_126 was not experimentally validated.
Retrocopy orthology:
Latimeria chalumnae does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.Parental genes homology:
Parental genes homology involve 2 parental genes, and 2 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Latimeria chalumnae | ENSLACG00000000522 | 1 retrocopy |
retro_lcha_126 ,
|
| Latimeria chalumnae | ENSLACG00000002156 | 1 retrocopy |