RetrogeneDB ID: | retro_lcha_14 | ||
Retrocopy location | Organism: | Coelacanth (Latimeria chalumnae) | |
| Coordinates: | AFYH01279356.1:2500..3289(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSLACG00000000472 | |
| Aliases: | None | ||
| Status: | KNOWN_PROTEIN_CODING | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | PLSCR3 | ||
| Ensembl ID: | ENSLACG00000011730 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_lcha_14
TTTTTTGGGCAGGATTCAAACGGCTCCATGGCTCTGCAAGGCTCTGAAGACAACATTCTTGGTCCACCAGCCTCTGCTTT
CCAGAACCAACCTCAAAATCAAATAACAATTTGGATGCCAGCTCCCCCCATTCCTAGAGACTGTCCACCAGGATTAGAAT
ACCTCACTCAGATAGACCAGATTCTTATTCACCAGCAGGTGTCATTAGTTGAAGCCCTCACTGGCTTTGAAGCAAACAGC
AAATTTGAAATTAAAAACAGCCTGGGGCAGAGAGTCTATTTTGCAGCAGAGGAGAATGACTGCTGTAATCGTAACTTCTG
TGGCGCATTCCGTTCTTTTACTATCAGAGTTCTCGATAATACTGGCCGAGATGTGATGGTGGTATCCAGACCCTTGAGAT
GCAGCACCTGCTGCTTCCCATGCTGCCTCCAGGAGCTGGAGGTTCAGGCTCCTCCAGGGATACCAGTCGGTTACGTTGTC
CAGGAGTGGCATCCTTGCCTGCCTAAGTTCACCATTCAAAACGAAAACAAAGAGGCCGTGCTAAAAATCGTTGGCCCATG
CATTAAATGCAGCTGCTTTAATGATGTTAGCTTTGAGGTGAAATCCGTTGATGAAACAGCAACAGTCGGCAAGATCAGCA
AGCAGTGGACCGGGCTGCTGAAGGAGGCTCTAAGTGCTAGCGACAACTTTGGGATCCAGTTTCCTATGGACCTTGATGTA
AAAATGAAGGCTGTAATGGTTGGTGCTTGCTTCTTAATAGACTTCATGTTTTTTGAACATGGTTCTTAA
ORF - retro_lcha_14 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 59.17 % |
| Parental protein coverage: | 79.53 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | MGPSPGIGSPDPHGTLT---PYVPIATGVPHGLEYLTQVDQILIHQTVELVEAFIGFETNNKYEIKNSLG |
| .GP........P....T...P..PI....P.GLEYLTQ.DQILIHQ.V.LVEA..GFE.N.K.EIKNSLG | |
| Retrocopy | LGPPASAFQNQPQNQITIWMPAPPIPRDCPPGLEYLTQIDQILIHQQVSLVEALTGFEANSKFEIKNSLG |
| Parental | QKIYYAKEENDCCTRNCCGPLRHFNMKITDNTDREVIHLVRPFKCASCWCPCCLQEMEVQSPPGTTIGFI |
| Q..Y.A.EENDCC.RN.CG..R.F.....DNT.R.V....RP..C..C..PCCLQE.EVQ.PPG...G.. | |
| Retrocopy | QRVYFAAEENDCCNRNFCGAFRSFTIRVLDNTGRDVMVVSRPLRCSTCCFPCCLQELEVQAPPGIPVGYV |
| Parental | IQNWHPFIPKFSIQNVERETVLKVTGSCCMCNCCGDVVFDVKTRDESRSVGRISKQWSGLLKEVFTDTDN |
| .Q.WHP..PKF.IQN...E.VLK..G.C..C.C..DV.F.VK..DE...VG.ISKQW.GLLKE.....DN | |
| Retrocopy | VQEWHPCLPKFTIQNENKEAVLKIVGPCIKCSCFNDVSFEVKSVDETATVGKISKQWTGLLKEALSASDN |
| Parental | FGIQFPMDLDVKMKATLMGACFLIDFMFFE |
| FGIQFPMDLDVKMKA...GACFLIDFMFFE | |
| Retrocopy | FGIQFPMDLDVKMKAVMVGACFLIDFMFFE |
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 .08 RPM | 1 .07 RPM |
| DRP000627_kidney | 0 .00 RPM | 0 .95 RPM |
| DRP000627_pectoral_fin | 0 .08 RPM | 1 .26 RPM |
| DRP000627_pelvic_fin | 0 .79 RPM | 5 .39 RPM |
| DRP000627_pharynx | 0 .01 RPM | 0 .31 RPM |
| DRP000627_tail_muscle | 0 .00 RPM | 0 .75 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_14 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 | ENSLACG00000011730 | 1 retrocopy |
retro_lcha_14 ,
|
| Mus musculus | ENSMUSG00000019461 | 1 retrocopy |