RetrogeneDB ID: | retro_dnov_876 | ||
Retrocopy location | Organism: | Armadillo (Dasypus novemcinctus) | |
| Coordinates: | scaffold_117000:5463..5830(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSDNOG00000011863 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | LEPROTL1 | ||
| Ensembl ID: | ENSDNOG00000014538 | ||
| Aliases: | None | ||
| Description: | leptin receptor overlapping transcript-like 1 [Source:HGNC Symbol;Acc:6555] |
Retrocopy-Parental alignment summary:
>retro_dnov_876
ATTAGTTTGTCCTTTGGAGGAGCAACTGGCCTGATGTTTTGGTGCTTGGAGTGCCCTTCTGATATACAATCAATACTGGC
CCCTCATTGTTCTCTTTTTTTATGTCCTTTCATCTATTCCATGCTGCATAACAAGATTTTAGCGGATGATACAGATGCTG
TGAGTAATGCTTGTAAGGAACTTGCCGTTGTCTGACAACAGGCATTGTTGTCTCAGGTTTTAGACTCTCTCTTGTATTTC
CAGAGCACATCTGATTGGGTGGGGAGCTTGTGCACTTGTTCTCACAGGAAACACAGTCATCTTTGCAACTCTACTAGGCT
TTTCCCTGGTCTTTGGAAGCAATGATGACTTCAGCTGGCGGCAGTGG
ORF - retro_dnov_876 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 79.07 % |
| Parental protein coverage: | 99.2 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 5 |
Retrocopy - Parental Gene Alignment:
| Parental | ISLSFGGAIGLMF-LMLGC-ALPIYNQYWPLFVLFFYVLSPIPYCIARR-LVDDTDAMSNACKELAIF-L |
| ISLSFGGA.GLMF.L.LG..AL.IYNQYWPL.VLFFYVLS.IP.CI.R..L.DDTDA.SNACKELA...L | |
| Retrocopy | ISLSFGGATGLMF<LVLGV<ALLIYNQYWPLIVLFFYVLSSIPCCITRF<LADDTDAVSNACKELAVV<L |
| Parental | TTGIVVSAFGLPIVF-ARAHLIEWGACALVLTGNTVIFATILGFFLVFGSNDDFSWQQW |
| TTGIVVS.F.L..VF..RAHLI.WGACALVLTGNTVIFAT.LGF.LVFGSNDDFSW.QW | |
| Retrocopy | TTGIVVSGFRLSLVF<SRAHLIGWGACALVLTGNTVIFATLLGFSLVFGSNDDFSWRQW |
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 |
|---|---|---|
| SRP012922_ascending_colon | 0 .00 RPM | 25 .86 RPM |
| SRP012922_cerebellum | 0 .14 RPM | 13 .88 RPM |
| SRP012922_heart | 0 .00 RPM | 9 .51 RPM |
| SRP012922_kidney | 0 .00 RPM | 26 .56 RPM |
| SRP012922_liver | 0 .15 RPM | 19 .35 RPM |
| SRP012922_lung | 0 .15 RPM | 33 .14 RPM |
| SRP012922_quadricep_muscle | 0 .00 RPM | 6 .40 RPM |
| SRP012922_spleen | 0 .34 RPM | 57 .80 RPM |
Dasypus novemcinctus was not studied using ChIP-Seq data.
Dasypus novemcinctus was not studied using EST data.
Dasypus novemcinctus was not studied using FANTOM5 data.
retro_dnov_876 was not experimentally validated.
Retrocopy orthology:
Dasypus novemcinctus 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 5 parental genes, and 7 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Canis familiaris | ENSCAFG00000006530 | 1 retrocopy | |
| Choloepus hoffmanni | ENSCHOG00000012299 | 1 retrocopy | |
| Dasypus novemcinctus | ENSDNOG00000014538 | 3 retrocopies |
retro_dnov_1528, retro_dnov_2606, retro_dnov_876 ,
|
| Erinaceus europaeus | ENSEEUG00000001360 | 1 retrocopy | |
| Oryctolagus cuniculus | ENSOCUG00000013931 | 1 retrocopy |