RetrogeneDB ID: | retro_dnov_1941 | ||
Retrocopy location | Organism: | Armadillo (Dasypus novemcinctus) | |
| Coordinates: | scaffold_3813:148202..148622(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | MRPL49 | ||
| Ensembl ID: | ENSDNOG00000004494 | ||
| Aliases: | None | ||
| Description: | mitochondrial ribosomal protein L49 [Source:HGNC Symbol;Acc:1176] |
Retrocopy-Parental alignment summary:
>retro_dnov_1941
AGCCAGCCCCAGGGGCCTCCTGATTACACCAGTTTTGTGGAGTCTGTGCATGAATACCAGTTTGTGGAGCGCCTTATACC
CCCAACCAGCATTCCAAAGCCCCCAAAGCATGAACAGTATTCCACCCCCAGTGGCTGGCAGCCCCCGCAGGACACCCCAC
CCAACCTGCCTTATTTCGTGCGGCGCTCTCGGATGCATAACATTCCTGTCTACAAGGATATCACACATGGCAACCGTCAG
ATGACAGTGATCCGGAAGGTGGAGGGCGACATCTGGGCCCTGCAGAAAGGATGTGGAGGATTTTCTGAGCCCACTGCTGG
GGAAGACACCTGTTACCCAGTCAACGAGGTAACATGTACCCTGCGGGTCAAGGGCTACGTTGATCAGCAGCTCAAAGCTT
GGCTCCTGGAGAAGGGCTTC
ORF - retro_dnov_1941 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 97.18 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 2 |
Retrocopy - Parental Gene Alignment:
| Parental | SQTQGPPDYTSFVESVHEYQFVERLIPPTSIPKPPKHEQYSTPSGWQPPQDTPPNLPYFVRRSRMHNIPV |
| SQ.QGPPDYTSFVESVHEYQFVERLIPPTSIPKPPKHEQYSTPSGWQPPQDTPPNLPYFVRRSRMHNIPV | |
| Retrocopy | SQPQGPPDYTSFVESVHEYQFVERLIPPTSIPKPPKHEQYSTPSGWQPPQDTPPNLPYFVRRSRMHNIPV |
| Parental | YKDITHGNRQMTVIRKVEGDIWALQK-DVEDFLSPLLGKTPVTQ-VNEVTGTLRVKGYVDQQLKAWLLEK |
| YKDITHGNRQMTVIRKVEGDIWALQK.DVEDFLSPLLGKTPVTQ.VNEVT.TLRVKGYVDQQLKAWLLEK | |
| Retrocopy | YKDITHGNRQMTVIRKVEGDIWALQK>DVEDFLSPLLGKTPVTQ<VNEVTCTLRVKGYVDQQLKAWLLEK |
| Parental | GF |
| GF | |
| Retrocopy | GF |
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 | 11 .28 RPM | 9 .14 RPM |
| SRP012922_cerebellum | 9 .35 RPM | 8 .11 RPM |
| SRP012922_heart | 3 .71 RPM | 7 .19 RPM |
| SRP012922_kidney | 7 .67 RPM | 12 .32 RPM |
| SRP012922_liver | 3 .41 RPM | 3 .10 RPM |
| SRP012922_lung | 11 .45 RPM | 13 .59 RPM |
| SRP012922_quadricep_muscle | 7 .27 RPM | 6 .06 RPM |
| SRP012922_spleen | 14 .77 RPM | 12 .48 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_1941 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 11 parental genes, and 17 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Choloepus hoffmanni | ENSCHOG00000012855 | 1 retrocopy | |
| Dasypus novemcinctus | ENSDNOG00000004494 | 6 retrocopies |
retro_dnov_1396, retro_dnov_1488, retro_dnov_1941 , retro_dnov_2272, retro_dnov_2473, retro_dnov_2686,
|
| Dipodomys ordii | ENSDORG00000003613 | 1 retrocopy | |
| Homo sapiens | ENSG00000149792 | 1 retrocopy | |
| Macropus eugenii | ENSMEUG00000009437 | 1 retrocopy | |
| Microcebus murinus | ENSMICG00000016604 | 1 retrocopy | |
| Macaca mulatta | ENSMMUG00000018778 | 1 retrocopy | |
| Nomascus leucogenys | ENSNLEG00000005505 | 1 retrocopy | |
| Oryctolagus cuniculus | ENSOCUG00000014882 | 1 retrocopy | |
| Pan troglodytes | ENSPTRG00000003867 | 1 retrocopy | |
| Tupaia belangeri | ENSTBEG00000007929 | 2 retrocopies |