RetrogeneDB ID: | retro_dnov_2360 | ||
Retrocopy location | Organism: | Armadillo (Dasypus novemcinctus) | |
| Coordinates: | scaffold_67391:622..1215(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | ABCB10 | ||
| Ensembl ID: | ENSDNOG00000023785 | ||
| Aliases: | None | ||
| Description: | ATP-binding cassette, sub-family B (MDR/TAP), member 10 [Source:HGNC Symbol;Acc:41] |
Retrocopy-Parental alignment summary:
>retro_dnov_2360
AGTCTTTCTTTGCCATCGGGCTCTGTCACAGCACTGGTTGGCTGAAGAGGTGCTGGCAAATCAAAGTAGTTTTAGTCCTT
TTGAAGTTGTATGACCTCATTTCTGGAAATGTCAGTCTGGATGATTGTGACATTCATCAGCTACATCCAGTCTGATTGAG
AGCCAAGATTGGGACAGTGAGTTAGGAACCAATTTTATTTTCTTGCTCAGTTGCTGAGAACATAGCTTATAGCACAGACA
ACCCTGCCCTAGTGACTGCAGAACAGGCAGAGAACATGGTTGATGTAGCAAATGCATCTGCTTTCATTAAATATTTCCCC
TAAAGATTCAACACTGTGATTGGAGAAAAGGGTGTTCTCCTTTCAGGTGGACATAAACAGTGGATTGTACCTGCCTATAC
TCTGCTTAAGAATCCCCAAATTCTTCTCCTGGATGAAGCATTTAGTACAGTGGATGCTGAAAATGAATTTCTTGTACAAG
AAGCTCTAGATTGCCTAATGGAAGGAAGATCAGTGTTAGTTATTGCCCATTGTCTGTCCACAATTAATGCTAATATGGTT
GCTGTTCTTAAGCAAGGAAAAGTTAGTGAATAT
ORF - retro_dnov_2360 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 71.0 % |
| Parental protein coverage: | 51.55 % |
| Number of stop codons detected: | 4 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | SLRIPAGSVTALVGPSGSGKST-VVSLLLRLYDPVSGTVSLDGCDIRQLNPVWLRSKIGTVSQEPILFSC |
| SL..P.GSVTALVG..G.GKS..VV..LL.LYD..SG.VSLD.CDI.QL.PV.LR.KIGTVS.EPILFSC | |
| Retrocopy | SLSLPSGSVTALVG*RGAGKSK<VVLVLLKLYDLISGNVSLDDCDIHQLHPV*LRAKIGTVS*EPILFSC |
| Parental | SIAENIAYGADDPALVTAEQVEKVADVANAAAFIRNFPQGFSTVVGEKGVLLSGGQKQRIAIARALLKNP |
| S.AENIAY..D.PALVTAEQ.E...DVANA.AFI..FP..F.TV.GEKGVLLSGG.KQ.I..A..LLKNP | |
| Retrocopy | SVAENIAYSTDNPALVTAEQAENMVDVANASAFIKYFP*RFNTVIGEKGVLLSGGHKQWIVPAYTLLKNP |
| Parental | KILLLDEATSALDAENEHLVQEALDRLMEGRTVLVIAHRLSTVKRAHRVAVLSQGRIAEY |
| .ILLLDEA.S..DAENE.LVQEALD.LMEGR.VLVIAH.LST...A..VAVL.QG...EY | |
| Retrocopy | QILLLDEAFSTVDAENEFLVQEALDCLMEGRSVLVIAHCLSTI-NANMVAVLKQGKVSEY |
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 | 16 .92 RPM |
| SRP012922_cerebellum | 0 .00 RPM | 31 .34 RPM |
| SRP012922_heart | 0 .00 RPM | 14 .62 RPM |
| SRP012922_kidney | 0 .00 RPM | 22 .18 RPM |
| SRP012922_liver | 0 .00 RPM | 22 .60 RPM |
| SRP012922_lung | 0 .00 RPM | 42 .15 RPM |
| SRP012922_quadricep_muscle | 0 .00 RPM | 46 .73 RPM |
| SRP012922_spleen | 0 .00 RPM | 244 .26 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_2360 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 5 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Callithrix jacchus | ENSCJAG00000011011 | 1 retrocopy | |
| Dasypus novemcinctus | ENSDNOG00000023785 | 1 retrocopy |
retro_dnov_2360 ,
|
| Homo sapiens | ENSG00000135776 | 3 retrocopies |