RetrogeneDB ID: | retro_dnov_2235 | ||
Retrocopy location | Organism: | Armadillo (Dasypus novemcinctus) | |
| Coordinates: | scaffold_57557:4634..6068(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSDNOG00000014481 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | ALDH1A2 | ||
| Ensembl ID: | ENSDNOG00000010541 | ||
| Aliases: | None | ||
| Description: | aldehyde dehydrogenase 1 family, member A2 [Source:HGNC Symbol;Acc:15472] |
Retrocopy-Parental alignment summary:
>retro_dnov_2235
CTCTTCATCAACAATGAGTGGCAAGATGCAGTCAGCAAGAAGACCTTCCCGACAGTCACCCCCACCACGGGGGAGGTCAT
CGGGCACGTTGCTGAAGGGGACCGGGCTGATGTGGACCTGGCGGTGAAAGCAGCCCGTGCGGCCTTCCGCCTGGGGTCTC
CATGGTGCCGGATGGACGCCTCCGAGCGGGGTCGGCTGTTGAACCGCCTGGCCGACCTAGTGGAGCGGGATCGGGTCTAC
TTGGCCTCATTGGAGACCTTGGATAACGGGAAGCCCTTCCAAGAGTCTTATGTCTTAGACCTGGATGAGGTCATCAAGGT
GTATCGGTACTTTGCTGGCTGGGCTGACAAATGGCATGGCAAGACCATCCCCATGGACGGTGAGCACTTCTGCTTCACTC
GGCACGAGCCCGTCGGTGTCTGTGGCCAGATCATCCCGTGGAACTTCCCCTTGGCCATGCAAGGCTGGAAGCTCGCCCCA
GCACTTGCCACGGGCAACACTGTGGTCATGAAAGTGGCAGAGCAGACGCCCCTGTCTGCCCTGTACCTGGCCTCCCTCAT
CAAGGAGGCGGGCTTTCCCCCGGGAGTGGTGAACATCATCACGGGCTACGGCCCAACGGCAGGAGCGGCCATCGCCCAGC
ACGTGGACATTGACAAAGTCGCCTTCACCGGCTCCACCGAGGTGGGCCACCTTATCCAGAAGGCGGCCGGCGACTCCAAC
CTCAAGAGGGTCACCCCGGAGCTGGGCGGGAAGAGCCCTAGCATCGTGTTGGCCGATGCCGACATGGACCATGCCGTGGA
GCAGTGCCACGAGGCCCTCTTCTTCAACGTGGGCCAGTGCTGCTGCGCCGGTTCCCGCACCTTTGTTGAGGAATCCATTT
ATGATGAGTTTCTCGAGAGAACTGTGGAGAAAGCCAAGCAGAGGAAAGTTGGGAACCCCTTTGAGCTGGACACCCAGCAG
GGACCCCAGGTGAACAAGGAGCAGTTTGAGCGAATCCTGGGCTCATCGTCTCACTAGAAAGAGGGAGCAAAGCTTCTCTG
TGGCGGAGAGCGTTTTGAGGAGCGCGATTCCTTTATCAAGCCCACGGTCTTTGAGGCCGTGCAGGATGACATGAGGATTG
CCAAGGAGGAGATCTTCGGGCCTGTGCAGCCGCTGTTCAAGTTCAGGAAGGTTGAGGAAGTGACTGAGAGGGCCAACAAT
ACCAGGTATGGCTTGGCTGCCGCCGTGCTCACGCGGGACCTGGACAAGGCCATGTACCTCACTCAGGCCCTCCAAGCCGG
GACGGTGTGGGTGAACACCTACAACATCGTCACCTGCCACACGCCATTCGGAGGCTTCAAGGAATCTGGCAGTGGAAGGG
AGCTGGGGGAGGATGGACTTCGGGCCTACACAGAGGTGAAGACGGTCACTATCAAGGTTCCCCAGAAGAATTCG
ORF - retro_dnov_2235 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 66.18 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | IFINNEWQNSESGKAFPVYNPATGEPVCEVQEADKADIDKAVQAARLAFSLGSVWRRMDASERGRLLDKL |
| .FINNEWQ...S.K.FP...P.TGE....V.E.D.AD.D.AV.AAR.AF.LGS.W.RMDASERGRLL..L | |
| Retrocopy | LFINNEWQDAVSKKTFPTVTPTTGEVIGHVAEGDRADVDLAVKAARAAFRLGSPWCRMDASERGRLLNRL |
| Parental | ADLVERDRAVLATRESLNGGKPFLQAFYVDLQGVIKTLRYYAGWADKIHGMTIPVDGDYFTFTRHEPIGV |
| ADLVERDR..LA..E.L..GKPF......DL..VIK..RY.AGWADK.HG.TIP.DG..F.FTRHEP.GV | |
| Retrocopy | ADLVERDRVYLASLETLDNGKPFQESYVLDLDEVIKVYRYFAGWADKWHGKTIPMDGEHFCFTRHEPVGV |
| Parental | CGQIIPWNFPLLMFAWKIAPALCCGNTVVIKPAEQTPLSALYMGALIKEAGFPPGVINILPGYGPTAGAA |
| CGQIIPWNFPL.M..WK.APAL..GNTVV.K.AEQTPLSALY...LIKEAGFPPGV.NI..GYGPTAGAA | |
| Retrocopy | CGQIIPWNFPLAMQGWKLAPALATGNTVVMKVAEQTPLSALYLASLIKEAGFPPGVVNIITGYGPTAGAA |
| Parental | IASHAGIDKIAFTGSTEVGKLIQEAAGRSNLKRVTLELGGKSPNIIFADADLDYAVEQAHQGVFFNQGQC |
| IA.H..IDK.AFTGSTEVG.LIQ.AAG.SNLKRVT.ELGGKSP.I..ADAD.D.AVEQ.H...FFN.GQC | |
| Retrocopy | IAQHVDIDKVAFTGSTEVGHLIQKAAGDSNLKRVTPELGGKSPSIVLADADMDHAVEQCHEALFFNVGQC |
| Parental | CTAGSRIFVEESIYEEFVRRSVERAKRRIVGSPFDPTTEQGPQIDKKQYNKILELIQSGVAEGAKLECGG |
| C.AGSR.FVEESIY.EF..R.VE.AK.R.VG.PF...T.QGPQ..K.Q...IL....S...EGAKL.CGG | |
| Retrocopy | CCAGSRTFVEESIYDEFLERTVEKAKQRKVGNPFELDTQQGPQVNKEQFERILG-SSSH*KEGAKLLCGG |
| Parental | KGLGRKGFFIEPTVFSNVTDDMRIAKEEIFGPVQEILRFKTMDEVIERANNSDFGLVAAVFTNDINKALT |
| ........FI.PTVF..V.DDMRIAKEEIFGPVQ....F....EV.ERANN...GL.AAV.T.D..KA.. | |
| Retrocopy | ERFEERDSFIKPTVFEAVQDDMRIAKEEIFGPVQPLFKFRKVEEVTERANNTRYGLAAAVLTRDLDKAMY |
| Parental | VSSAMQAGTVWINCYNALNAQSPFGGFKMSGNGREMGEFGLREYSEVKTVTVKIPQKNS |
| ...A.QAGTVW.N.YN......PFGGFK.SG.GRE.GE.GLR.Y.EVKTVT.K.PQKNS | |
| Retrocopy | LTQALQAGTVWVNTYNIVTCHTPFGGFKESGSGRELGEDGLRAYTEVKTVTIKVPQKNS |
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 | 4 .08 RPM | 2 .72 RPM |
| SRP012922_cerebellum | 4 .67 RPM | 0 .27 RPM |
| SRP012922_heart | 0 .46 RPM | 2 .78 RPM |
| SRP012922_kidney | 2 .74 RPM | 8 .76 RPM |
| SRP012922_liver | 17 .96 RPM | 13 .62 RPM |
| SRP012922_lung | 0 .15 RPM | 6 .72 RPM |
| SRP012922_quadricep_muscle | 0 .35 RPM | 3 .63 RPM |
| SRP012922_spleen | 0 .92 RPM | 6 .41 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_2235 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 3 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Dasypus novemcinctus | ENSDNOG00000010541 | 1 retrocopy |
retro_dnov_2235 ,
|
| Monodelphis domestica | ENSMODG00000008641 | 1 retrocopy | |
| Sarcophilus harrisii | ENSSHAG00000012217 | 1 retrocopy |