RetrogeneDB ID: | retro_dnov_685 | ||
Retrocopy location | Organism: | Armadillo (Dasypus novemcinctus) | |
| Coordinates: | GeneScaffold_784:26804..27205(+) | ||
| Located in intron of: | ENSDNOG00000019938 | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | ARPC3 | ||
| Ensembl ID: | ENSDNOG00000004987 | ||
| Aliases: | None | ||
| Description: | actin related protein 2/3 complex, subunit 3, 21kDa [Source:HGNC Symbol;Acc:706] |
Retrocopy-Parental alignment summary:
>retro_dnov_685
TATCACTCTTCTCTCATAGACCCCGACACCAGGCTAACTGGAAACATGGCATGGTTACCTATCAGAAGTAAGTTCAAAGG
ACCTACCCCTAGAAAGGCAAGATATACAGACGCTGTAAATGAGGCTATCTATTATTTCAAGGCCATTGTCTTCTTCAAAA
CTATGAAATTAAGAATGAAGCTAACAGAACCTTGATAGAGAAAACAGTCTACAAATCTGAGGGTCTAAAGAAACTCCAAA
AGTGTAATTCCAAAGACTAAGGAGAGAAAGAAATGTACACAATGGGCATCACTAGTTTTCCCATTCCCAGAGAGCCCAGT
TTTCCACTTGATGCAATCTATGCTAAATCTGCCAACCAACAGAAAGCTGAAGAGATGAGAACCTACTCAAAGCATTTAAG
G
ORF - retro_dnov_685 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 73.33 % |
| Parental protein coverage: | 85.9 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | YHSSLMDPDTRLIGNMALLPIRSQFKGPAPRETKDTDIVDEAIYYFKANVFFK-NYEIKSEADRTLIYIT |
| YHSSL.DPDTRL.GNMA.LPIRS.FKGP.PR....TD.V.EAIYYFKA.VFFK.NYEIK.EA.RTLI..T | |
| Retrocopy | YHSSLIDPDTRLTGNMAWLPIRSKFKGPTPRKARYTDAVNEAIYYFKAIVFFK<NYEIKNEANRTLIEKT |
| Parental | LYISECLKKLQKCNSKSQGEKEMYTLGITNFPIPGEPGFPLNAIYAKPANKQEDEVMRAYLQQLR |
| .Y.SE.LKKLQKCNSK..GEKEMYT.GIT.FPIP.EP.FPL.AIYAK.AN.Q..E.MR.Y...LR | |
| Retrocopy | VYKSEGLKKLQKCNSKD*GEKEMYTMGITSFPIPREPSFPLDAIYAKSANQQKAEEMRTYSKHLR |
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 | 67 .48 RPM |
| SRP012922_cerebellum | 0 .00 RPM | 26 .39 RPM |
| SRP012922_heart | 0 .00 RPM | 6 .73 RPM |
| SRP012922_kidney | 0 .00 RPM | 31 .21 RPM |
| SRP012922_liver | 0 .00 RPM | 24 .30 RPM |
| SRP012922_lung | 0 .00 RPM | 32 .99 RPM |
| SRP012922_quadricep_muscle | 0 .00 RPM | 4 .50 RPM |
| SRP012922_spleen | 0 .00 RPM | 46 .13 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_685 was not experimentally validated.