RetrogeneDB ID:

retro_ptro_706

Retrocopy
location
Organism:Chimpanzee (Pan troglodytes)
Coordinates:12:84749437..84749769(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:COX5A
Ensembl ID:ENSPTRG00000007289
Aliases:None
Description:Pan troglodytes mitochondrial cytochrome c oxidase subunit Va (COX5A), nuclear gene encoding mitochondrial protein, mRNA. [Source:RefSeq mRNA;Acc:NM_001118913]


Retrocopy-Parental alignment summary:






>retro_ptro_706
TCAGTTCACTGCAATTCCCATGGGTTTCATGAAATAAATGAGAAGTTTGATGCTCGCTCGGTGACATACTGCAACAAGCC
AGATATAGAGGTCTGGGAATTGCGTAAAGAAATGAACACATTTATTATCTACTATCTGGTTCCAGGGCCCAAAATTATTG
ATGCTGCTTGTAGATGGTTAAATGATTTTGCTAGTGCAGTTCTCATCCTAGAGATTGTTGAAGACAAAGAAGGACCTGAT
AAAGAAAATCTACCCCATGTCATCTAAAACTTAGACAAATTTTAAATGTATTAGGCATATCCACTCTAGAGGAACATGGC
CTTGAGAAAGTG

ORF - retro_ptro_706 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 64.35 %
Parental protein coverage: 76. %
Number of stop codons detected: 0
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalSVRCYSHGSQETDEEFDARWVTYFNKPDIDAWELRKGINTLVTYDMVPEPKIIDAALRACRRLNDFASTV
SV.C.SHG..E..E.FDAR.VTY.NKPDI..WELRK..NT...Y..VP.PKIIDAA...CR.LNDFAS.V
RetrocopySVHCNSHGFHEINEKFDARSVTYCNKPDIEVWELRKEMNTFIIYYLVPGPKIIDAA---CRWLNDFASAV
ParentalRILEAVKDKAGPHKEIYPYVI-QELRPTLNELGISTPEELGLDKV
.ILE.V.DK.GP.KE..P.VI...LR..LN.LGIST.EE.GL.KV
RetrocopyLILEIVEDKEGPDKENLPHVI<LKLRQILNVLGISTLEEHGLEKV

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 82 .19 RPM
SRP007412_cerebellum 0 .00 RPM 32 .51 RPM
SRP007412_heart 0 .00 RPM 174 .38 RPM
SRP007412_kidney 0 .00 RPM 84 .94 RPM
SRP007412_liver 0 .00 RPM 41 .87 RPM
SRP007412_testis 0 .00 RPM 71 .66 RPM
Pan troglodytes was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ptro_706 retrocopy.
Pan troglodytes was not studied using FANTOM5 data.
retro_ptro_706 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ptro_706 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_1036
Gorilla gorilla retro_ggor_817
Callithrix jacchus retro_cjac_3229

Parental genes homology:
Parental genes homology involve 21 parental genes, and 47 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000086432 retrocopies
Bos taurus ENSBTAG000000172671 retrocopy
Canis familiaris ENSCAFG000000179771 retrocopy
Choloepus hoffmanni ENSCHOG000000061084 retrocopies
Callithrix jacchus ENSCJAG000000156136 retrocopies
Cavia porcellus ENSCPOG000000248323 retrocopies
Felis catus ENSFCAG000000105873 retrocopies
Homo sapiens ENSG000001787413 retrocopies
Loxodonta africana ENSLAFG000000062661 retrocopy
Macropus eugenii ENSMEUG000000139422 retrocopies
Myotis lucifugus ENSMLUG000000137021 retrocopy
Macaca mulatta ENSMMUG000000116772 retrocopies
Monodelphis domestica ENSMODG000000281681 retrocopy
Mustela putorius furoENSMPUG000000173141 retrocopy
Mus musculus ENSMUSG000000000882 retrocopies
Otolemur garnettii ENSOGAG000000056115 retrocopies
Pan troglodytes ENSPTRG00000007289 3 retrocopies
retro_ptro_706 , retro_ptro_914, retro_ptro_969,
Pteropus vampyrus ENSPVAG000000129571 retrocopy
Rattus norvegicus ENSRNOG000000188161 retrocopy
Sarcophilus harrisii ENSSHAG000000159412 retrocopies
Tursiops truncatus ENSTTRG000000080042 retrocopies



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