RetrogeneDB ID: | retro_lcha_27 | ||
Retrocopy location | Organism: | Coelacanth (Latimeria chalumnae) | |
| Coordinates: | JH126600.1:1315168..1315713(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | ATP5B | ||
| Ensembl ID: | ENSLACG00000009340 | ||
| Aliases: | None | ||
| Description: | ATP synthase subunit beta [Source:UniProtKB/TrEMBL;Acc:H3ALT2] |
Retrocopy-Parental alignment summary:
>retro_lcha_27
GTTGCCCTGACTGGTCTAACTGTTGCAAAGTGCTTCCATGAGCAAGGAGGACAGGATGTGTTGCTTTTTATTGTCAACAT
TATCAGATTCACCCAGGTTGGGTCAGAGGTATCTTTCCTTCTGGGTTGTATTCCCTCCATTGTGAGATAGCAGCCAGCAC
TGGCTACTGGTATGGGCACCATGCAGGAAATAATTACAACTACCAAAAAGGGATCCATCACATTAGTACAGGTCATTTTT
GTGTCTGCTGATGACTTGACTGATCCTACTTTTGCTTACTTAGATGCCACAGCTGTTTTGTCCCATGCTAATATAGAAGT
GGGTACACCCAGTTGTGGACCCTTTGGACTCTACTTCCCATATCATAGACCCCCAACATTGTGTGACAAAAGAATTAAGA
TGTGGTCTGTGGTGTGTGGAGGATCTTGCAAGATTAGAAATCACTCCCAGATATTATTGCAGTCTTGGGTGTGAATGAGT
TATCTGAAGGAGACAAGATGACTGTAGCTCATGTTTGTAAAATTCAGCATTTCCTGTCCTGTCCT
ORF - retro_lcha_27 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 68.62 % |
| Parental protein coverage: | 59.62 % |
| Number of stop codons detected: | 4 |
| Number of frameshifts detected: | 2 |
Retrocopy - Parental Gene Alignment:
| Parental | VALTGLTVAEYFRDQEGQDVLLFIDNIFRFTQAGSEVSALLGRIPSAVGYQPTLATDMGTMQERITTTKK |
| VALTGLTVA..F..Q.GQDVLLFI.NI.RFTQ.GSEVS.LLG.IPS.V..QP.LAT.MGTMQE.ITTTKK | |
| Retrocopy | VALTGLTVAKCFHEQGGQDVLLFIVNIIRFTQVGSEVSFLLGCIPSIVR*QPALATGMGTMQEIITTTKK |
| Parental | GSITSVQAIYVPADDLTDPAPATTFAHLDATTVLSRAIAELGIYPAVDP-LDSTSRILD-PNIVGQEHYD |
| GSIT.VQ.I.V.ADDLTDP....TFA.LDAT.VLS.A..E.G..P...P.LDSTS.I.D.PNIV.Q...D | |
| Retrocopy | GSITLVQVIFVSADDLTDP----TFAYLDATAVLSHANIEVGT-PSCGP>LDSTSHIID>PNIV*QKN*D |
| Parental | VARGVQKILQDYKSLQDIIAILGMDELSEEDKLTVARARKIQRFLSQP |
| V..GV..ILQD.KSL.DIIA.LG..ELSE.DK.TVA...KIQ.FLS.P | |
| Retrocopy | VVCGVWRILQD*KSLPDIIAVLGVNELSEGDKMTVAHVCKIQHFLSCP |
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 | 82 .22 RPM |
| DRP000627_kidney | 0 .00 RPM | 101 .52 RPM |
| DRP000627_pectoral_fin | 0 .00 RPM | 116 .33 RPM |
| DRP000627_pelvic_fin | 0 .00 RPM | 166 .60 RPM |
| DRP000627_pharynx | 0 .00 RPM | 104 .41 RPM |
| DRP000627_tail_muscle | 0 .00 RPM | 86 .33 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_27 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 4 parental genes, and 4 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Echinops telfairi | ENSETEG00000010208 | 1 retrocopy | |
| Latimeria chalumnae | ENSLACG00000009340 | 1 retrocopy |
retro_lcha_27 ,
|
| Macaca mulatta | ENSMMUG00000001027 | 1 retrocopy | |
| Xenopus tropicalis | ENSXETG00000024665 | 1 retrocopy |