RetrogeneDB ID: | retro_dnov_1912 | ||
Retrocopy location | Organism: | Armadillo (Dasypus novemcinctus) | |
| Coordinates: | scaffold_36269:6203..6509(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | UBE2D3 | ||
| Ensembl ID: | ENSDNOG00000009320 | ||
| Aliases: | None | ||
| Description: | ubiquitin-conjugating enzyme E2D 3 [Source:HGNC Symbol;Acc:12476] |
Retrocopy-Parental alignment summary:
>retro_dnov_1912
GCCCGGGACCCCAGCCCACGTCCTGCAGGGCCGGGTGGGGGGAAATGCTCCACTGCAAGTCACCAGCAGGGGACCTAGTG
ACAGCCCATCTCCAGGCGGTGAATTCTTTTGGACAGTTCATTTTCCTCCAGACCAGCCCTTCAGCCAGCTAAGGTGGCCT
TTACCAGGAGAGTTTATCATCCAAGTATTAACAGCGATGGCAGCGTTTGGCGCCATAAAAGATGACAGTGCTCTCCTGCT
TGAGCTATTTCGAAAGTTCTTTGATGCATTTCTTCACAGCTATGTGAGCTGAACCCAGATGATCCC
ORF - retro_dnov_1912 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 57.41 % |
| Parental protein coverage: | 75.54 % |
| Number of stop codons detected: | 3 |
| Number of frameshifts detected: | 3 |
Retrocopy - Parental Gene Alignment:
| Parental | ARDPPAQCSAGPVGD-DMFHW-QATIMGPNDSPYQGGVFFLTIHFPTDYPF-KPPKVAFTTRIYHPNINS |
| ARDP.....AGP.G...M.H..Q.T..GP.DSP..GG.FF.T.HFP.D.PF..P.KVAFT.R.YHP.INS | |
| Retrocopy | ARDPSPR-PAGPGGG<EMLHC<QVTSRGPSDSPSPGGEFFWTVHFPPDQPF<QPAKVAFTRRVYHPSINS |
| Parental | NGSICLDILRSQWSPALTISKVLLSICSLLCDPNPDDP |
| .GS......R.Q.SPA..ISKVL..I.S.LC..NPDDP | |
| Retrocopy | DGSVWRH-KR*QCSPA*AISKVL*CISSQLCELNPDDP |
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 | 44 .92 RPM |
| SRP012922_cerebellum | 0 .00 RPM | 32 .86 RPM |
| SRP012922_heart | 0 .00 RPM | 30 .16 RPM |
| SRP012922_kidney | 0 .00 RPM | 28 .75 RPM |
| SRP012922_liver | 0 .00 RPM | 33 .28 RPM |
| SRP012922_lung | 0 .00 RPM | 42 .15 RPM |
| SRP012922_quadricep_muscle | 0 .00 RPM | 52 .27 RPM |
| SRP012922_spleen | 0 .00 RPM | 60 .89 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_1912 was not experimentally validated.