RetrogeneDB ID: | retro_lcha_77 | ||
Retrocopy location | Organism: | Coelacanth (Latimeria chalumnae) | |
| Coordinates: | JH127241.1:79056..79446(+) | ||
| 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: | ENSLACG00000003157 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_lcha_77
AATGTAACTCAGTTGCCAGGATCTCTGACTGCTAAAGAAGGTGAAGAAACAACATTAAGCTGCAGTAACAGTTCTCCCCT
AACAAGCGGTGATAGCCTCCAGTGGTATTATCAGTCCTTCAATGGAGCACCAAGCTATCTTATACAGAGCTACAGAACCT
ACTCAGGATCAGAGGAAAAGAAAGCTGAAGGAGTTGAAGATCGTTTTTCTGTTTTCCTGGATGCTTCAAACAAAGTCAGT
ACTTTAACCATCAGAGAAGTGCAGATGGCTGACTCTGGGCTTTATCACTGTGCTTTGAAACCCACAGTGATACTAAAGCT
CAGAATGGCTTTACAAAAACTCCCTTGTCATGTTTCCATCTTCCTGTTTGCAATATTCTTTGAAAGCAAT
ORF - retro_lcha_77 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 74.63 % |
| Parental protein coverage: | 57.51 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | NITQLPGSLTAKEGEETTLNCSNSSPLATGDSLQWYYQPFNGAPSYFIQSYKTLSGSEEKKAEGVEDRFS |
| N.TQLPGSLTAKEGEETTL.CSNSSPL..GDSLQWYYQ.FNGAPSY.IQSY.T.SGSEEKKAEGVEDRFS | |
| Retrocopy | NVTQLPGSLTAKEGEETTLSCSNSSPLTSGDSLQWYYQSFNGAPSYLIQSYRTYSGSEEKKAEGVEDRFS |
| Parental | VSLDASNKVSTLTIREVQMADSGLYHCALKPTQFLLSSLDLVVNLKKLKKYLTILVIGLTLEDS |
| V.LDASNKVSTLTIREVQMADSGLYHCALKPT..L.....L...L.KL.....I.......E.. | |
| Retrocopy | VFLDASNKVSTLTIREVQMADSGLYHCALKPTVIL----KLRMALQKLPCHVSIFLFAIFFESN |
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 .00 RPM |
| DRP000627_kidney | 0 .00 RPM | 0 .00 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 .00 RPM |
| DRP000627_tail_muscle | 0 .00 RPM | 0 .00 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_77 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 1 parental gene, and 2 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Latimeria chalumnae | ENSLACG00000003157 | 2 retrocopies |
retro_lcha_76, retro_lcha_77 ,
|