RetrogeneDB ID:

retro_ptro_358

Retrocopy
location
Organism:Chimpanzee (Pan troglodytes)
Coordinates:1:153340877..153341343(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:NDUFAF4
Ensembl ID:ENSPTRG00000018435
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_ptro_358
ATGGGGGCTGCAGTGACTCACAGGATCAGGAATTTCAACCTAGAGAACTGAGCAGAATGGGAAATCAACAAGATGAAGCC
CCCTCCCAATCCCAGACACCCCTCTACCAACAGCCTCCTGCAAGAGCAGATTAGTTTCTATCCAGATTAAGGGAGAGATT
GCTCATAAAGATGACAAGCTGCTGTCATTTCTAAAAGATGTGTATGTTGATTCCAAAGATCCTGTGTCTTCCGTGCAGGT
AAAAGCTGCTGAAAGATGTCAAGAGCTGAAAGAATTCAGATTGCCTTTTGGCCATCACTTTAATATGATAAATATTAAGA
TCATTCCCAAAGGCAAAATTTCCATTGTAGAAGCATTGACACTTCTCAATAATCATAAACTTTATCCAGAAACATGAACT
GCTGAGAAAATAGCCCAAGAATACCATTTAGAACAGAAAGATGCGAATTCAGAAGTCGAAATCTTC

ORF - retro_ptro_358 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 70.06 %
Parental protein coverage: 89.14 %
Number of stop codons detected: 2
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalMGALVIRGIRNFNLENRAEREISKMK-PSVAPRHPSTNSLLREQISLYPEVKGEIACKDEKLLSFLKDVY
MGA.V...IRNFNLEN.AE.EI.KMK.P...P..P................KGEIA.KD.KLLSFLKDVY
RetrocopyMGAAVTHRIRNFNLEN*AEWEINKMK>PLPIPDTPLPTASCKSRL-VSIQIKGEIAHKDDKLLSFLKDVY
ParentalVDSKDPVSSLQVKAAETCQEPKEFRLPKDHHFDMINIKSIPKGKISIVEALTLLNNHKLFPETWTAEKIM
VDSKDPVSS.QVKAAE.CQE.KEFRLP..HHF.MINIK.IPKGKISIVEALTLLNNHKL.PET.TAEKI.
RetrocopyVDSKDPVSSVQVKAAERCQELKEFRLPFGHHFNMINIKIIPKGKISIVEALTLLNNHKLYPET*TAEKIA
ParentalQEYQLEQKDVNSLLKYF
QEY.LEQKD.NS....F
RetrocopyQEYHLEQKDANSEVEIF

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 .13 RPM 17 .93 RPM
SRP007412_cerebellum 0 .36 RPM 12 .12 RPM
SRP007412_heart 0 .12 RPM 15 .59 RPM
SRP007412_kidney 0 .05 RPM 10 .36 RPM
SRP007412_liver 0 .03 RPM 7 .46 RPM
SRP007412_testis 0 .00 RPM 4 .43 RPM
Pan troglodytes was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ptro_358 retrocopy.
Pan troglodytes was not studied using FANTOM5 data.
retro_ptro_358 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ptro_358 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_477
Pongo abelii retro_pabe_257

Parental genes homology:
Parental genes homology involve 15 parental genes, and 39 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000031741 retrocopy
Choloepus hoffmanni ENSCHOG000000051452 retrocopies
Callithrix jacchus ENSCJAG000000012352 retrocopies
Cavia porcellus ENSCPOG000000076181 retrocopy
Homo sapiens ENSG000001235454 retrocopies
Gorilla gorilla ENSGGOG000000120704 retrocopies
Microcebus murinus ENSMICG000000157341 retrocopy
Macaca mulatta ENSMMUG000000188434 retrocopies
Mus musculus ENSMUSG000000282613 retrocopies
Nomascus leucogenys ENSNLEG000000135684 retrocopies
Oryctolagus cuniculus ENSOCUG000000021521 retrocopy
Pongo abelii ENSPPYG000000168574 retrocopies
Pan troglodytes ENSPTRG00000018435 4 retrocopies
Rattus norvegicus ENSRNOG000000075063 retrocopies
Tursiops truncatus ENSTTRG000000109111 retrocopy



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