RetrogeneDB ID: | retro_dnov_2496 | ||
Retrocopy location | Organism: | Armadillo (Dasypus novemcinctus) | |
| Coordinates: | scaffold_80345:6081..6609(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | STOM | ||
| Ensembl ID: | ENSDNOG00000015723 | ||
| Aliases: | None | ||
| Description: | stomatin [Source:HGNC Symbol;Acc:3383] |
Retrocopy-Parental alignment summary:
>retro_dnov_2496
ATGGCTGAGAAGTGGCAGGCAGTGGACACCCAAGCCCAGCGGCTCCCCGACTCCTTCAAAGATAGCCCCAATATAGGCCT
TGGGCCTTGTGGATGGATTTTGGTGGCTGCTGTCTCATTCTTATTCATGGTTATAACTTTCCCCATATCGATATGGATGT
GTATAAAGATCATCAAAGAGTATGAAAGAGCGATCATCTTTAGACTAGGACACATTTTACAAGGAGGAGCCAAAGGACCT
GGTTTGTTTTTTATTCTGCCATGCACTGACAACTTCATCAAAGTGTACATGAGAACTATTTCATTTGATATTCCTCCTCA
GGAGATCCTCACCAAGGACTCAGTGACAATTAGTGTGGATGGAATTGTCTATTACCATGTGCAGAATGCAACCCTGGCTG
TGGCAAATATCACCAATGCTGACTCAGCAACTCTTCTTTTGGCTTAGACTATGCTGAGGAATGTTCTGGGCACCAAGAAC
CTTTCTCAGATCCTCTCTGACAGAGAAGAAATTGCACATAACATGCAG
ORF - retro_dnov_2496 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 92.05 % |
| Parental protein coverage: | 60.55 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | MAEKRQGADTQARRLPDSFKDSPNTGLGPCGWILVA-VSFLFTVITFPISIWMCIKIIKEYERAIIFRLG |
| MAEK.Q..DTQA.RLPDSFKDSPN.GLGPCGWILVA.VSFLF.VITFPISIWMCIKIIKEYERAIIFRLG | |
| Retrocopy | MAEKWQAVDTQAQRLPDSFKDSPNIGLGPCGWILVAAVSFLFMVITFPISIWMCIKIIKEYERAIIFRLG |
| Parental | RILQGGAKGPGLFFILPCTDNFIKVDMRTISFDIPPQEILTKDSVTISVDGVVYYRVQNATLAVANITNA |
| .ILQGGAKGPGLFFILPCTDNFIKV.MRTISFDIPPQEILTKDSVTISVDG.VYY.VQNATLAVANITNA | |
| Retrocopy | HILQGGAKGPGLFFILPCTDNFIKVYMRTISFDIPPQEILTKDSVTISVDGIVYYHVQNATLAVANITNA |
| Parental | DSATRLLAQTTLRNVLGTKNLSQILSDREEIAHNMQ |
| DSAT.LLA.T.LRNVLGTKNLSQILSDREEIAHNMQ | |
| Retrocopy | DSATLLLA*TMLRNVLGTKNLSQILSDREEIAHNMQ |
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 | 15 .17 RPM | 82 .07 RPM |
| SRP012922_cerebellum | 0 .27 RPM | 1 .92 RPM |
| SRP012922_heart | 2 .09 RPM | 9 .75 RPM |
| SRP012922_kidney | 3 .56 RPM | 15 .61 RPM |
| SRP012922_liver | 10 .22 RPM | 57 .59 RPM |
| SRP012922_lung | 7 .18 RPM | 55 .29 RPM |
| SRP012922_quadricep_muscle | 1 .21 RPM | 5 .71 RPM |
| SRP012922_spleen | 10 .30 RPM | 61 .81 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_2496 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 4 parental genes, and 5 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Dasypus novemcinctus | ENSDNOG00000015723 | 1 retrocopy |
retro_dnov_2496 ,
|
| Nomascus leucogenys | ENSNLEG00000017145 | 1 retrocopy | |
| Otolemur garnettii | ENSOGAG00000002879 | 2 retrocopies | |
| Oreochromis niloticus | ENSONIG00000013021 | 1 retrocopy |