RetrogeneDB ID: | retro_dnov_2675 | ||
Retrocopy location | Organism: | Armadillo (Dasypus novemcinctus) | |
| Coordinates: | scaffold_97333:4189..4763(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | DERL3 | ||
| Ensembl ID: | ENSDNOG00000011041 | ||
| Aliases: | None | ||
| Description: | derlin 3 [Source:HGNC Symbol;Acc:14236] |
Retrocopy-Parental alignment summary:
>retro_dnov_2675
GAGTACCTGCAGATTGCACCAGTCAGCCATGCCTATACCACCACCTACATCCTCACTACCACCACTGTGCAGTTAGAATT
GATCACACCTTTTCAGTTACACTTCAATCCTGAATCAATCTTTAAACACTTTCAAATATGGAGATTAATCACTAATTTCT
TATTCTTTAGGCCAGTTGGATTCAATTTTTAATTCTAATATGATTTTTCTATATTATTACTGTCAAATGCCAGAAGAAGG
CTCTTTCCAAGGTCAAACAGCAGACTTTGTGTTTTTGTTCCTTTTTGGTGGATTCCTAATGACCCTTTATGATTTGTTTG
TGAGTTTAGTTTTCTTGGGTCAGACCTTTACAATAATGCTTGCACATGTGGATCTAAAGGCACCCATAAATCCACATGAA
CTTCTTCGGCCTTCTCAACTCACAAGCCCTCTTCTGCCCTGGGTACTCATGAGCTTTTCCTTATTATTGGGGAACTCAAT
GTGGACCTCTTGGGTATTGAAGTTGGGTACAAATATTTTTTGTTGGAAGATGTATTTCCCAAGTCAATCTGGTAGAATAA
GAATTCTGAAAACA
ORF - retro_dnov_2675 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 57.29 % |
| Parental protein coverage: | 97.97 % |
| Number of stop codons detected: | 4 |
| Number of frameshifts detected: | 6 |
Retrocopy - Parental Gene Alignment:
| Parental | EFLQVPAVTRVYTAACVLTTAAVQLELLSPFQLYFNPHLVFRKFQIWRLITNFLFFGPLGFSFFF-NMLF |
| E.LQ...V...YT....LTT..VQLEL..PFQL.FNP...F..FQIWRLITNFLFF.P.GF.F.F.NM.F | |
| Retrocopy | EYLQIAPVSHAYTTTYILTTTTVQLELITPFQLHFNPESIFKHFQIWRLITNFLFFRPVGFNF*F>NMIF |
| Parental | VFRYCRMLEEGSFRGRTADFVFMFLFGGFLMILLGFLGSLF-FLGQAL-MAMLVYVWSRRSPQIRVNFFG |
| ...YC.M.EEGSF.G.TADFVF.FLFGGFLM.L.....SL..FLG..L........W..R.P.I..NFFG | |
| Retrocopy | LYYYCQMPEEGSFQGQTADFVFLFLFGGFLMTLYDLFVSLV<FLGSDL<LQ*CLHMWI*RHP*IHMNFFG |
| Parental | LLTFQA-PFLPWALMGFSM-LLGNSILVDLLGIAVGHIYYFLEDV-FPNQPGGKRLLLT |
| LL..QA.P.LPW.LM.FS....G....VDLLGI.VG..Y..LEDV.FP.Q.G..R.L.T | |
| Retrocopy | LLNSQA<PLLPWVLMSFSL<IIGE-LNVDLLGIEVGYKYFLLEDV>FPSQSGRIRILKT |
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 .19 RPM | 9 .14 RPM |
| SRP012922_cerebellum | 0 .00 RPM | 0 .27 RPM |
| SRP012922_heart | 0 .00 RPM | 0 .00 RPM |
| SRP012922_kidney | 0 .00 RPM | 0 .55 RPM |
| SRP012922_liver | 0 .00 RPM | 0 .62 RPM |
| SRP012922_lung | 0 .00 RPM | 5 .65 RPM |
| SRP012922_quadricep_muscle | 0 .00 RPM | 0 .17 RPM |
| SRP012922_spleen | 0 .00 RPM | 57 .00 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_2675 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 2 parental genes, and 3 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Dasypus novemcinctus | ENSDNOG00000011041 | 2 retrocopies |
retro_dnov_2070, retro_dnov_2675 ,
|
| Sus scrofa | ENSSSCG00000010069 | 1 retrocopy |