RetrogeneDB ID: | retro_dnov_2578 | ||
Retrocopy location | Organism: | Armadillo (Dasypus novemcinctus) | |
| Coordinates: | scaffold_8711:71064..71825(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | PSMA3 | ||
| Ensembl ID: | ENSDNOG00000004077 | ||
| Aliases: | None | ||
| Description: | proteasome (prosome, macropain) subunit, alpha type, 3 [Source:HGNC Symbol;Acc:9532] |
Retrocopy-Parental alignment summary:
>retro_dnov_2578
AGCTCTCTCGGCACTGGGTATGACCTGTCAGCCTCTACATTCCCTCCTGATGGGAGAGTTTTTCAAGTTGAATATGCTAT
GAAGGCTGTGGAAAATAGTAGTACAGCTATTGGAATCAGATGTAAAGATGGTGTTGTCTTTGGAGTAGAAAAATTAGTCC
TTTCTAAACTTTATGAAGAAGATTCCAACAAATGGTGTTTTAATGTTGATCGGCATGCAGGAATGGTGGTAGCAGGTGTG
TTGGCAGATGCTCGTTCTTTAGCAGACATAGCAAGAGAAGAGGCTTCCAACTTTAGATCTAACTTTGGCTGTAACATTCC
ACTCAAACATCTTGCAGACAGAGTGATCATGTATGTTCATGCCTGTACACTGTACAGTGCTGTTAACCTTTTGGATGCAG
TTTCACGTTAGGGTCTTACATTGTGAATGATGGTGCACAGCTCCACAGGATTGAGCCATCAGGTGTTTCATATGGTTACT
GGGGCTGTGCCCTTGGTAAAGCCAGGCAAGCTGCAAAGACAGAAATCGAAAAGCTTCAGATGAAAGAAATGACCTGCCGT
GACGTTGTTAAAGAAGTTGCAAAAATAATTTACATAGTACATGATGAAGTTAAAGATAAAGCATTTGAACTAGAGCTCAG
CTGGGTTGGTGAATTAAGTAAAGGAAGACATGAAATTGTTCCAAAAGATATAAGGGAAGAAGCAGAGAAATATGCTAAGG
AATCTTTGAAGGAAGAAGATGAATCTGATGATGATAATATG
ORF - retro_dnov_2578 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 91.76 % |
| Parental protein coverage: | 99.61 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | SSIGTGYDLSASTFSPDGRVFQVEYAMKAVENSSTAIGIRCKDGVVFGVEKLVLSKLYEEGSNKRLFNVD |
| SS.GTGYDLSASTF.PDGRVFQVEYAMKAVENSSTAIGIRCKDGVVFGVEKLVLSKLYEE.SNK..FNVD | |
| Retrocopy | SSLGTGYDLSASTFPPDGRVFQVEYAMKAVENSSTAIGIRCKDGVVFGVEKLVLSKLYEEDSNKWCFNVD |
| Parental | RHVGMAVAGLLADARSLADIAREEASNFRSNFGYNIPLKHLADRVAMYVHAYTLYSAVR-PFGCSFMLGS |
| RH.GM.VAG.LADARSLADIAREEASNFRSNFG.NIPLKHLADRV.MYVHA.TLYSAV..PFGCSF.LGS | |
| Retrocopy | RHAGMVVAGVLADARSLADIAREEASNFRSNFGCNIPLKHLADRVIMYVHACTLYSAVN<PFGCSFTLGS |
| Parental | YSVNDGAQLYMIDPSGVSYGYWGCAIGKARQAAKTEIEKLQMKEMTCRDVVKEVAKIIYIVHDEVKDKAF |
| Y.VNDGAQL..I.PSGVSYGYWGCA.GKARQAAKTEIEKLQMKEMTCRDVVKEVAKIIYIVHDEVKDKAF | |
| Retrocopy | YIVNDGAQLHRIEPSGVSYGYWGCALGKARQAAKTEIEKLQMKEMTCRDVVKEVAKIIYIVHDEVKDKAF |
| Parental | ELELSWVGELTKGRHEIVPKDIREEAEKYAKESLKEEDESDDNNM |
| ELELSWVGEL.KGRHEIVPKDIREEAEKYAKESLKEEDESDD.NM | |
| Retrocopy | ELELSWVGELSKGRHEIVPKDIREEAEKYAKESLKEEDESDDDNM |
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 | 46 .09 RPM |
| SRP012922_cerebellum | 0 .00 RPM | 24 .19 RPM |
| SRP012922_heart | 0 .00 RPM | 32 .72 RPM |
| SRP012922_kidney | 0 .00 RPM | 42 .71 RPM |
| SRP012922_liver | 0 .00 RPM | 30 .81 RPM |
| SRP012922_lung | 0 .00 RPM | 32 .53 RPM |
| SRP012922_quadricep_muscle | 0 .00 RPM | 33 .41 RPM |
| SRP012922_spleen | 0 .00 RPM | 43 .95 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_2578 was not experimentally validated.