RetrogeneDB ID:

retro_dnov_1243

Retrocopy
location
Organism:Armadillo (Dasypus novemcinctus)
Coordinates:scaffold_168368:407..870(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:RAP1B
Ensembl ID:ENSDNOG00000019724
Aliases:None
Description:RAP1B, member of RAS oncogene family [Source:HGNC Symbol;Acc:9857]


Retrocopy-Parental alignment summary:






>retro_dnov_1243
ATGTGTGAATATATGCTTGTCCTTCTAGGCACAGCAGGCATTGGAACTCTGCTCGGATCATGCAGTTTGTTCAAGGAATT
TTGCTGAAAATATGATCTTATGATAAAAGTTTCTTATAGAAACAAATTGAATTAGATACACAACAGTGTATCCTTGAAAT
CTTGGATGCTGCAGGAATGGAACATTTTACAGCAATGATGGATTTGTACATGAAAAATGGACAAAGTTATAGCTTATTCC
ATGACATTAGAGTACAGTGTGCATTTAATAATTTACCAGATCTGAGAGAACAGATTCCTTAAATAAAAGACACTGATGAT
GTTCCAATGAAAATAGTTGGCAATAAATGTAACTTGGAGGATGAAAGAGTCATAGGAAAGTAGAAAGGATGAAATCTAGC
AAGAAATGGGACAACTATACATTCTTAGAATTTCCTCTAAAATAAAAAATAAATGCTAATGAG

ORF - retro_dnov_1243 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 62.73 %
Parental protein coverage: 100. %
Number of stop codons detected: 4
Number of frameshifts detected 5


Retrocopy - Parental Gene Alignment:

ParentalMREYKLVVLGSGGVG-KSALTVQFVQGI-FVE-KYDPTIEDSYR-KQVEVDAQQCMLEILDTAGTEQFTA
M.EY.LV.LG..G.G..SA...QFVQGI.F.E.KYD..I..SYR.KQ.E.D.QQC.LEILD.AG.E.FTA
RetrocopyMCEYMLVLLGTAGIG<NSARIMQFVQGI<FAE<KYDLMIKVSYR<KQIELDTQQCILEILDAAGMEHFTA
ParentalMRDLYMKNGKGFALVYSITAQSTFNDLQDLREQIL-RKDTDDVPMILVGNKCDLEDERVVGKEQGQNLAR
M.DLYMKNG....L...I..Q..FN.L.DLREQI...KDTDDVPM..VGNKC.LEDERV.GK..G.NLAR
RetrocopyMMDLYMKNGQSYSLFHDIRVQCAFNNLPDLREQIP*IKDTDDVPMKIVGNKCNLEDERVIGK*KG*NLAR
Parental-QWNNCAFLESSAKSKINVNE
..W.N..FLE...K.KIN.NE
Retrocopy<KWDNYTFLEFPLK*KINANE

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 6 .81 RPM
SRP012922_cerebellum 0 .00 RPM 1 .92 RPM
SRP012922_heart 0 .00 RPM 1 .16 RPM
SRP012922_kidney 0 .00 RPM 4 .38 RPM
SRP012922_liver 0 .00 RPM 4 .33 RPM
SRP012922_lung 0 .00 RPM 8 .25 RPM
SRP012922_quadricep_muscle 0 .00 RPM 1 .38 RPM
SRP012922_spleen 0 .00 RPM 15 .68 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_1243 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 19 parental genes, and 57 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000086371 retrocopy
Cavia porcellus ENSCPOG000000082724 retrocopies
Dasypus novemcinctus ENSDNOG000000078095 retrocopies
Dasypus novemcinctus ENSDNOG000000152933 retrocopies
Dasypus novemcinctus ENSDNOG000000174131 retrocopy
Dasypus novemcinctus ENSDNOG00000019724 18 retrocopies
Erinaceus europaeus ENSEEUG000000100521 retrocopy
Echinops telfairi ENSETEG000000002421 retrocopy
Gorilla gorilla ENSGGOG000000256491 retrocopy
Loxodonta africana ENSLAFG000000164601 retrocopy
Microcebus murinus ENSMICG000000131481 retrocopy
Macaca mulatta ENSMMUG000000114422 retrocopies
Oryctolagus cuniculus ENSOCUG000000295525 retrocopies
Otolemur garnettii ENSOGAG000000057462 retrocopies
Pongo abelii ENSPPYG000000047511 retrocopy
Pan troglodytes ENSPTRG000000051973 retrocopies
Rattus norvegicus ENSRNOG000000070484 retrocopies
Sus scrofa ENSSSCG000000211481 retrocopy
Sus scrofa ENSSSCG000000300142 retrocopies



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