RetrogeneDB ID:

retro_ptro_1582

Retrocopy
location
Organism:Chimpanzee (Pan troglodytes)
Coordinates:2A:26232333..26232601(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:NDUFB4
Ensembl ID:ENSPTRG00000015270
Aliases:None
Description:Pan troglodytes NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 4, 15kDa (NDUFB4), nuclear gene encoding mitochondrial protein, mRNA. [Source:RefSeq mRNA;Acc:NM_001071792]


Retrocopy-Parental alignment summary:






>retro_ptro_1582
TCCCGGCTGAAATGAGAGTACCTGCTTTCAGTACAACGAACCCAACTGCCGAGGGGTCATCGAAGATCCTGCCTTGATTC
GTTGGACCTATCCAAGATCAGCAAATGTCTATCCAAATTTCAGACCCACTCCTAAAAACTCACTCTTGGGAACTCTGTGT
GGATTTAGGCCCCTCTTCTTCTGGTATTATGTTTTCAAAACTGACAGAGATAGGAAAGAAAAACTTATCCGGGAAGGAAA
ATTGGATGGAACATTTAACCTTTCATAT

ORF - retro_ptro_1582 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 73.33 %
Parental protein coverage: 68.99 %
Number of stop codons detected: 1
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalAQLKREYLL-QYNDPNRRGLIENPALLRWAYARTINVYPNFRPTPKNSLMGALCGFGPLIFIYYIIKTER
..LK.EYLL.QYN.PN.RG.IE.PAL.RW.Y.R..NVYPNFRPTPKNSL.G.LCGF.PL.F.YY..KT.R
RetrocopySRLK*EYLL>QYNEPNCRGVIEDPALIRWTYPRSANVYPNFRPTPKNSLLGTLCGFRPLFFWYYVFKTDR
ParentalDRKEKLIQEGKLDRTFHLSY
DRKEKLI.EGKLD.TF.LSY
RetrocopyDRKEKLIREGKLDGTFNLSY

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
SRP007412_brain_prefrontal_cortex 0 .00 RPM 42 .36 RPM
SRP007412_cerebellum 0 .00 RPM 28 .93 RPM
SRP007412_heart 0 .00 RPM 78 .14 RPM
SRP007412_kidney 0 .00 RPM 50 .11 RPM
SRP007412_liver 0 .00 RPM 27 .33 RPM
SRP007412_testis 0 .00 RPM 28 .88 RPM
Pan troglodytes was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ptro_1582 retrocopy.
Pan troglodytes was not studied using FANTOM5 data.
retro_ptro_1582 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ptro_1582 has 1 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_2238

Parental genes homology:
Parental genes homology involve 26 parental genes, and 76 retrocopies.

Species Parental gene accession Retrocopies number
Anolis carolinensis ENSACAG000000114621 retrocopy
Ailuropoda melanoleuca ENSAMEG000000047612 retrocopies
Bos taurus ENSBTAG000000158922 retrocopies
Choloepus hoffmanni ENSCHOG000000000062 retrocopies
Callithrix jacchus ENSCJAG000000086954 retrocopies
Danio rerio ENSDARG000000193321 retrocopy
Dasypus novemcinctus ENSDNOG000000241234 retrocopies
Homo sapiens ENSG000000655186 retrocopies
Gorilla gorilla ENSGGOG000000139232 retrocopies
Loxodonta africana ENSLAFG000000214591 retrocopy
Microcebus murinus ENSMICG000000052264 retrocopies
Myotis lucifugus ENSMLUG000000279513 retrocopies
Macaca mulatta ENSMMUG000000015924 retrocopies
Monodelphis domestica ENSMODG000000182291 retrocopy
Mustela putorius furoENSMPUG000000082721 retrocopy
Mus musculus ENSMUSG000000228204 retrocopies
Nomascus leucogenys ENSNLEG000000077064 retrocopies
Otolemur garnettii ENSOGAG000000059565 retrocopies
Pongo abelii ENSPPYG000000135033 retrocopies
Pan troglodytes ENSPTRG00000015270 6 retrocopies
Rattus norvegicus ENSRNOG000000027213 retrocopies
Sorex araneus ENSSARG000000124821 retrocopy
Ictidomys tridecemlineatus ENSSTOG000000200923 retrocopies
Tarsius syrichta ENSTSYG000000064567 retrocopies
Tursiops truncatus ENSTTRG000000166581 retrocopy
Vicugna pacos ENSVPAG000000037741 retrocopy



Copyright © RetrogeneDB 2014-2017