RetrogeneDB ID: | retro_dnov_2495 | ||
Retrocopy location | Organism: | Armadillo (Dasypus novemcinctus) | |
| Coordinates: | scaffold_80315:9984..10303(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | ARPC5 | ||
| Ensembl ID: | ENSDNOG00000010375 | ||
| Aliases: | None | ||
| Description: | actin related protein 2/3 complex, subunit 5, 16kDa [Source:HGNC Symbol;Acc:708] |
Retrocopy-Parental alignment summary:
>retro_dnov_2495
GAGAACACCGTGTCGTCGGCCTCGTTCTGGAAGGTGGACATGGGTGAGTACAACAAGAACAAGTTCATGGACGAGGAAGA
TGGAGGCGACGGCCAGGCTGGGCCCAAGGAAGGCTGAGGTGGGCTCCTGTATGCGGCAAAAACACACGACAGCTGCTCCG
CAAGCCGCGCTGGAAAAGCCCCCAGTCAACACCAAGAGTCAGGCCATGCAGGCCCAAGCAGGCAGCAGTGTCCTGAAGGT
GCTCATCTCTCTTAAAGTCAATGATGTTGAAAAGGCAATTCAACCTCTGGACCAGAAGGGTGTGGATCTGCTAACACGT
ORF - retro_dnov_2495 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 67.27 % |
| Parental protein coverage: | 81.34 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | KNTVSSARFRKVDVDEYDENKFVDEEDGGDGQAGPDEG-EVDSCLRHSVTGNMTAALQAALKNPPINTKS |
| .NTVSSA.F.KVD..EY..NKF.DEEDGGDGQAGP.EG.EV.SC.R...T...TAA.QAAL..PP.NTKS | |
| Retrocopy | ENTVSSASFWKVDMGEYNKNKFMDEEDGGDGQAGPKEG>EVGSCMRQKHT---TAAPQAALEKPPVNTKS |
| Parental | QAVKDRAGSIVLKVLISFKANDIEKAVQSLDKNGVDLLMK |
| QA....AGS.VLKVLIS.K.ND.EKA.Q.LD..GVDLL.. | |
| Retrocopy | QAMQAQAGSSVLKVLISLKVNDVEKAIQPLDQKGVDLLTR |
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 .58 RPM | 102 .87 RPM |
| SRP012922_cerebellum | 0 .00 RPM | 25 .71 RPM |
| SRP012922_heart | 0 .00 RPM | 10 .91 RPM |
| SRP012922_kidney | 0 .55 RPM | 21 .36 RPM |
| SRP012922_liver | 0 .00 RPM | 40 .25 RPM |
| SRP012922_lung | 0 .15 RPM | 71 .63 RPM |
| SRP012922_quadricep_muscle | 0 .00 RPM | 6 .23 RPM |
| SRP012922_spleen | 0 .80 RPM | 121 .44 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_2495 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 6 parental genes, and 9 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Choloepus hoffmanni | ENSCHOG00000000560 | 2 retrocopies | |
| Dasypus novemcinctus | ENSDNOG00000010375 | 3 retrocopies |
retro_dnov_1277, retro_dnov_199, retro_dnov_2495 ,
|
| Echinops telfairi | ENSETEG00000014969 | 1 retrocopy | |
| Monodelphis domestica | ENSMODG00000007194 | 1 retrocopy | |
| Mus musculus | ENSMUSG00000008475 | 1 retrocopy | |
| Rattus norvegicus | ENSRNOG00000028062 | 1 retrocopy |