RetrogeneDB ID:

retro_dnov_90

Retrocopy
location
Organism:Armadillo (Dasypus novemcinctus)
Coordinates:GeneScaffold_142:138973..139543(+)
Located in intron of:ENSDNOG00000018282
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:VDAC1
Ensembl ID:ENSDNOG00000002680
Aliases:None
Description:voltage-dependent anion channel 1 [Source:HGNC Symbol;Acc:12669]


Retrocopy-Parental alignment summary:






>retro_dnov_90
GGACTGAAGCTGACTTTTGATTCATCCTTCTCATCTAACACTGGCAGGGCGGGGAATGCTAAAATCCAGACAGGATACAA
GCGGGAGCACATCAACCTGGGCTGCAACACAGATTTTGCCAGGCTTTCAATCCAGGGTGTTCCAGTCCTGGGTTGTGAGG
GCTGGCTGACTGACTACCAGATGAATTTTGAGACCGCAAGGTCCCAAGTGACACAGAACAGTTTTGCTGTTGATTACAAG
ACTGATTAATTCTAGCTTCACACTAATGTGAATGATGGGACAGAGTTTGGTGACTTCATTTAACAGAAGGTGAACAAGAA
GTTGGAGATTGCTGTCAATCTCACCTGGACAGGAGGAGACAGTAACACCCATTTTTTTTGGAATAGCAGCCAAGTATCAG
ATTGACCCTGCCCATTCTTCTCAGCTAAAGTGAACAAATCCAGCTTGATAGGTTTAGGATACACTCAGACCCTAAAGCCT
GGTATCAAACTGACACTGTCATCTCTGCTGGATGGCAAGAATGTCAATGGTAATGACTGCAAGTTTGGTCTAGGACTGGA
ACTTCAAGCA

ORF - retro_dnov_90 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 72.4 %
Parental protein coverage: 67.14 %
Number of stop codons detected: 4
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalGLKLTFDSSFSPNTGKK-NAKIKTGYKREHINLGCDVDFDIAGPSIRGALVLGYEGWLAGYQMNFETAKS
GLKLTFDSSFS.NTG...NAKI.TGYKREHINLGC..DF..A..SI.G..VLG.EGWL..YQMNFETA.S
RetrocopyGLKLTFDSSFSSNTGRAGNAKIQTGYKREHINLGCNTDF--ARLSIQGVPVLGCEGWLTDYQMNFETARS
ParentalRVTQSNFAVGYKTDEFQLHTNVNDGTEFGGSIYQKVNKKLETAVNLAWTAGNSNTRFGIAAKYQID-PDA
.VTQ..FAV.YKTD.F.LHTNVNDGTEFG..I.QKVNKKLE.AVNL.WT.G.SNT..........D.P..
RetrocopyQVTQNSFAVDYKTD*F*LHTNVNDGTEFGDFI*QKVNKKLEIAVNLTWTGGDSNTXXXXNSSQVSD*PCP
ParentalCFSAKVNNSSLIGLGYTQTLKPGIKLTLSALLDGKNVNAGGHKLGLGLEFQA
.FSAKVN.SSLIGLGYTQTLKPGIKLTLS.LLDGKNVN....K.GLGLE.QA
RetrocopyFFSAKVNKSSLIGLGYTQTLKPGIKLTLSSLLDGKNVNGNDCKFGLGLELQA

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 .78 RPM 297 .92 RPM
SRP012922_cerebellum 2 .61 RPM 100 .49 RPM
SRP012922_heart 0 .46 RPM 155 .46 RPM
SRP012922_kidney 3 .29 RPM 108 .70 RPM
SRP012922_liver 1 .24 RPM 31 .12 RPM
SRP012922_lung 2 .29 RPM 46 .73 RPM
SRP012922_quadricep_muscle 0 .17 RPM 402 .08 RPM
SRP012922_spleen 2 .29 RPM 42 .92 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_90 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 26 parental genes, and 104 retrocopies.

Species Parental gene accession Retrocopies number
Canis familiaris ENSCAFG000000009851 retrocopy
Choloepus hoffmanni ENSCHOG000000056316 retrocopies
Callithrix jacchus ENSCJAG000000135568 retrocopies
Cavia porcellus ENSCPOG000000238402 retrocopies
Dasypus novemcinctus ENSDNOG00000002680 5 retrocopies
Dasypus novemcinctus ENSDNOG000000138851 retrocopy
Dipodomys ordii ENSDORG000000007141 retrocopy
Equus caballus ENSECAG000000123652 retrocopies
Felis catus ENSFCAG000000084211 retrocopy
Homo sapiens ENSG0000021358513 retrocopies
Gorilla gorilla ENSGGOG000000108803 retrocopies
Loxodonta africana ENSLAFG000000288181 retrocopy
Macaca mulatta ENSMMUG000000162356 retrocopies
Monodelphis domestica ENSMODG000000141571 retrocopy
Mustela putorius furoENSMPUG000000102201 retrocopy
Mus musculus ENSMUSG000000204023 retrocopies
Nomascus leucogenys ENSNLEG0000000802311 retrocopies
Otolemur garnettii ENSOGAG000000307422 retrocopies
Ochotona princeps ENSOPRG000000066052 retrocopies
Pongo abelii ENSPPYG000000157816 retrocopies
Pan troglodytes ENSPTRG0000001723512 retrocopies
Rattus norvegicus ENSRNOG000000063758 retrocopies
Sus scrofa ENSSSCG000000142962 retrocopies
Ictidomys tridecemlineatus ENSSTOG000000077643 retrocopies
Tursiops truncatus ENSTTRG000000168562 retrocopies
Vicugna pacos ENSVPAG000000104481 retrocopy



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