RetrogeneDB ID: | retro_dnov_1562 | ||
Retrocopy location | Organism: | Armadillo (Dasypus novemcinctus) | |
| Coordinates: | scaffold_23506:42977..43441(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSDNOG00000005174 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | SYS1-DBNDD2 | ||
| Ensembl ID: | ENSDNOG00000011943 | ||
| Aliases: | None | ||
| Description: | SYS1-DBNDD2 readthrough (NMD candidate) [Source:HGNC Symbol;Acc:33535] |
Retrocopy-Parental alignment summary:
>retro_dnov_1562
ATGGCAGGCCAGTTCCGCAGCTACGTATGGGATCCGTTGCTGATCATGTCGCAGATCATCCTCATGCAGACCGTCTATTT
TGGCTCACTGGGCCTGTGGCTGGTGCTGGTGGATGGGCTGGTGCGCAGCGGCCCTTCGCTGGACCAGATGTTCAACGCTG
AGATCCTGGGCTTCTCCACCCCTCCAGGCCGGCTCTCCATGATGTCCTTCATCCTCAATGCCCTCACCTGTGCCCTGGGC
TTGCTGTACTTCATCCAGCGAGGGAAGCAGTGTCTGGATTTCACTGTCAATGTCCATTTCTTTCACCTGGCCTGCTGGTT
CTACAGCTCCCGTTTCCCTCGGTGCTGACCTGGTGGCTTGTCCAAGCTGTGTGCATTGCACTCATGGCTGTCATCAGGGA
GTACCTGTGCATGCAGATGGAGCTCAAGGAGATCCCCCTCAACTCAGCCCCTAAATCCAATGTC
ORF - retro_dnov_1562 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 91.08 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | MAGQFRSYVWDPLLIMSQIVLMQTVYYGSLGLWLALVDGLVRSSPSLDQMFDAEILGFSTPPGRLSMMSF |
| MAGQFRSYVWDPLLIMSQI.LMQTVY.GSLGLWL.LVDGLVRS.PSLDQMF.AEILGFSTPPGRLSMMSF | |
| Retrocopy | MAGQFRSYVWDPLLIMSQIILMQTVYFGSLGLWLVLVDGLVRSGPSLDQMFNAEILGFSTPPGRLSMMSF |
| Parental | ILNALTCALGLLYFIRRGKQCLDFTVTVHFFHLLGCWFYSSR-FPSALTWWLVQAVCIALMAVIGEYLCM |
| ILNALTCALGLLYFI.RGKQCLDFTV.VHFFH.L.CWFYSSR.FPS.LTWWLVQAVCIALMAVI.EYLCM | |
| Retrocopy | ILNALTCALGLLYFIQRGKQCLDFTVNVHFFH-LACWFYSSR<FPSVLTWWLVQAVCIALMAVIREYLCM |
| Parental | RTELKEIPLNSAPKSNV |
| ..ELKEIPLNSAPKSNV | |
| Retrocopy | QMELKEIPLNSAPKSNV |
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 | 21 .59 RPM |
| SRP012922_cerebellum | 0 .14 RPM | 24 .47 RPM |
| SRP012922_heart | 0 .00 RPM | 12 .99 RPM |
| SRP012922_kidney | 0 .00 RPM | 17 .80 RPM |
| SRP012922_liver | 0 .00 RPM | 60 .37 RPM |
| SRP012922_lung | 0 .00 RPM | 26 .12 RPM |
| SRP012922_quadricep_muscle | 0 .00 RPM | 13 .85 RPM |
| SRP012922_spleen | 0 .00 RPM | 28 .84 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_1562 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 3 parental genes, and 6 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Dasypus novemcinctus | ENSDNOG00000011943 | 2 retrocopies |
retro_dnov_1417, retro_dnov_1562 ,
|
| Echinops telfairi | ENSETEG00000014613 | 2 retrocopies | |
| Loxodonta africana | ENSLAFG00000008154 | 2 retrocopies |