RetrogeneDB ID: | retro_lcha_19 | ||
Retrocopy location | Organism: | Coelacanth (Latimeria chalumnae) | |
| Coordinates: | JH127234.1:101501..102635(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSLACG00000003922 | |
| Aliases: | None | ||
| Status: | KNOWN_PROTEIN_CODING | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | ACTC1 | ||
| Ensembl ID: | ENSLACG00000011801 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_lcha_19
ATGTGTGACAATGAAGAAACTACTGCACTGGTCTGCGACAATGGCTCTGGCCTGGTGAAAGCTGGCTTTGCTGGGGATGA
TGCTCCAAGGGCAGTATTTCCATCCATTGTAGGACGCCCACGTCACCAGGGCGTGATGGTAGGCATGGGCCAGAAAGACG
CCTACGTAGGTGATGAGGCACAGAGCAAGAGAGGTATCCTGACACTGAAGTACCCCATCGAACATGGCATTATCACAAAC
TGGGATGACATGGAGAAGATCTGGCACCACACCTTCTACAATGAGCTTCGTGTGGCCCCTGAAGAGCACCCCACTCTGCT
CACAGAGGCACCACTCAATCCCAAGGCCAATCGTGAAAAGATGACCCAAATCATGTTTGAAACCTTCAATGTTCCTGCAA
TGTTTGTTGCTATCCAGGCTGTGCTGTCCCTCTATGCTTCTGGTCGTACCACTGGTATCGTGCTGGACTCTGGAGATGGT
GTCACACACAACGTGCCAATTTATGAAGGTTACGCTCTGCCTCATGCTATCATGCGGTTGGATTTGGCTGGCCGTGACCT
CACTGACTACCTTATGAAGATTCTCACAGAGCGTGGCTACTCCTTTGTCACCACTGCAGAAAGAGAGATTGTCCGTGACA
TTAAAGAGAAACTATGCTATGTTGCACTTGACTTTGAAAATGAGATGGCTACAGCAGCTTCGTCTTCCTCTCTAGAGAAA
AGCTACGAACTTCCTGATGGACAGGTCATCACTATTGGCAATGAGCGTTTCCGCTGCCCTGAAACACTCTTCCAGCCATC
CTTCATTGGAATGGAATCTGCTGGCATCCATGAAACAGCTTACAATAGCATTATGAAGTGCGATATTGACATCAGGAAAG
ACCTTTACGCGAACAACGTCCTGTCTGGTGGCTCCACCATGTACCCCGGTATTGCTGACCGTATGCAAAAGGAAATCACT
GCACTGGCTCCCAGCACCATGAAAATCAAAATCATTGCCCCACCAGAACGCAAGTACTCAGTCTGGATCGGTGGCTCCAT
CCTTGCCTCTCTGTCCACCTTTCAGCAAATGTGGATCACCAAACAAGAATATGATGAGGCTGGCCCATCCATTGTCCATC
GCAAATGTTTCTAA
ORF - retro_lcha_19 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 98.41 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | MCDDEETTALVCDNGSGLVKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEAQSKRGILTLK |
| MCD.EETTALVCDNGSGLVKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKD.YVGDEAQSKRGILTLK | |
| Retrocopy | MCDNEETTALVCDNGSGLVKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKDAYVGDEAQSKRGILTLK |
| Parental | YPIEHGIITNWDDMEKIWHHTFYNELRVAPEEHPTLLTEAPLNPKANREKMTQIMFETFNVPAMYVAIQA |
| YPIEHGIITNWDDMEKIWHHTFYNELRVAPEEHPTLLTEAPLNPKANREKMTQIMFETFNVPAM.VAIQA | |
| Retrocopy | YPIEHGIITNWDDMEKIWHHTFYNELRVAPEEHPTLLTEAPLNPKANREKMTQIMFETFNVPAMFVAIQA |
| Parental | VLSLYASGRTTGIVLDSGDGVTHNVPIYEGYALPHAIMRLDLAGRDLTDYLMKILTERGYSFVTTAEREI |
| VLSLYASGRTTGIVLDSGDGVTHNVPIYEGYALPHAIMRLDLAGRDLTDYLMKILTERGYSFVTTAEREI | |
| Retrocopy | VLSLYASGRTTGIVLDSGDGVTHNVPIYEGYALPHAIMRLDLAGRDLTDYLMKILTERGYSFVTTAEREI |
| Parental | VRDIKEKLCYVALDFENEMATAASSSSLEKSYELPDGQVITIGNERFRCPETLFQPSFIGMESAGIHETT |
| VRDIKEKLCYVALDFENEMATAASSSSLEKSYELPDGQVITIGNERFRCPETLFQPSFIGMESAGIHET. | |
| Retrocopy | VRDIKEKLCYVALDFENEMATAASSSSLEKSYELPDGQVITIGNERFRCPETLFQPSFIGMESAGIHETA |
| Parental | YNSIMKCDIDIRKDLYANNVLSGGTTMYPGIADRMQKEITALAPSTMKIKIIAPPERKYSVWIGGSILAS |
| YNSIMKCDIDIRKDLYANNVLSGG.TMYPGIADRMQKEITALAPSTMKIKIIAPPERKYSVWIGGSILAS | |
| Retrocopy | YNSIMKCDIDIRKDLYANNVLSGGSTMYPGIADRMQKEITALAPSTMKIKIIAPPERKYSVWIGGSILAS |
| Parental | LSTFQQMWISKQEYDEAGPSIVHRKCF |
| LSTFQQMWI.KQEYDEAGPSIVHRKCF | |
| Retrocopy | LSTFQQMWITKQEYDEAGPSIVHRKCF |
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 | 10 .23 RPM | 0 .29 RPM |
| DRP000627_kidney | 31 .31 RPM | 21 .00 RPM |
| DRP000627_pectoral_fin | 4 .21 RPM | 5 .20 RPM |
| DRP000627_pelvic_fin | 3 .06 RPM | 2 .64 RPM |
| DRP000627_pharynx | 55 .82 RPM | 0 .02 RPM |
| DRP000627_tail_muscle | 87 .36 RPM | 0 .13 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_19 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 3 parental genes, and 3 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Latimeria chalumnae | ENSLACG00000011801 | 1 retrocopy |
retro_lcha_19 ,
|
| Oryctolagus cuniculus | ENSOCUG00000004074 | 1 retrocopy | |
| Pongo abelii | ENSPPYG00000006318 | 1 retrocopy |