RetrogeneDB ID:

retro_ptro_2217

Retrocopy
location
Organism:Chimpanzee (Pan troglodytes)
Coordinates:5:180709842..180710379(+)
Located in intron of:ENSPTRG00000017616
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:PRDX2
Ensembl ID:ENSPTRG00000010541
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_ptro_2217
ATGGCTTCCAGTCAGTCGCAGCTCGGAAAGCCAGCCCCTGACTTCAAGGCCATCGCCCTGGTGGATGGCGCCTTCCAGGA
GGTGAAGCTGTGGGCTACAAAGGGAAGTACGTCATCCTCTTTTTCTACCCTCTGGACTTCACTTTTCTGTGGCCCATGGA
GAACGTCGCATTCAGCGACCATGCCGAGGATTTCCGCAAGCTGGGCTGCGAAGTGCTGGGTGTCTGGGTGGACTTAGTTC
ACCCACCTGGCTTGGATCAACAACCCCCAGAAGTAGGGAGGCTTAGGCTCCCGAGCATCCCCCACCCGTTGATGTGACGG
GAAGCTTGTCTGAGGATTACCGTGTGCTGAAAACCAATGAGGGCATTGCCTACCCTGCCTCTTTATCATCGATGGCAAGG
GAGACTTTTGCCAGATCACTGTTAATGATTTGCCTCTGGGGTGCTCCATGGATGAGGCTCTGCAGCTGGTCCAGGCATTC
CAGTACGCAGATGAGCACGGGGAAGTTTGTCCCACTGGCTGGAAGCCTGGTAGCGAC

ORF - retro_ptro_2217 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 67.2 %
Parental protein coverage: 91.41 %
Number of stop codons detected: 2
Number of frameshifts detected 5


Retrocopy - Parental Gene Alignment:

ParentalMASGNARIGKPAPDFKATAVVDGAFKEVKL-SDYKGKYVVLFFYPLDFTFVCPTEIIAFSNRAED-FRKL
MAS.....GKPAPDFKA.A.VDGAF.EVKL...YKGKYV.LFFYPLDFTF..P.E..AFS..AED.F...
RetrocopyMASSQSQLGKPAPDFKAIALVDGAFQEVKL<VGYKGKYVILFFYPLDFTFLWPMENVAFSDHAED<FPQA
ParentalGCEVLG-VSVDSQFTHLAWIN-TPRKEGGLGPLNIPLLADVTRRLSEDYGVLKTDEGIAYRG-LFIIDGK
G....G.VS....FTHLAWIN.TPR......P...P...DVT..LSEDY.VLKT.EGIAY...LFIIDGK
RetrocopyGLRSAG<VSGWT*FTHLAWIN>TPRSREA*APEHPPPV-DVTGSLSEDYRVLKTNEGIAYPA<LFIIDGK
ParentalGVLRQITVNDLPVGRSVDEALRLVQAFQYTDEHGEVCPAGWKPGSD
G...QITVNDLP.G.S.DEAL.LVQAFQY.DEHGEVCP.GWKPGSD
RetrocopyGDFCQITVNDLPLGCSMDEALQLVQAFQYADEHGEVCPTGWKPGSD

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 .29 RPM 248 .54 RPM
SRP007412_cerebellum 0 .29 RPM 154 .61 RPM
SRP007412_heart 0 .00 RPM 162 .69 RPM
SRP007412_kidney 0 .03 RPM 171 .84 RPM
SRP007412_liver 0 .03 RPM 66 .52 RPM
SRP007412_testis 0 .00 RPM 6 .11 RPM
Pan troglodytes was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ptro_2217 retrocopy.
Pan troglodytes was not studied using FANTOM5 data.
retro_ptro_2217 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ptro_2217 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_3278
Pongo abelii retro_pabe_2711
Callithrix jacchus retro_cjac_1795

Parental genes homology:
Parental genes homology involve 23 parental genes, and 45 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000123073 retrocopies
Canis familiaris ENSCAFG000000171633 retrocopies
Ciona intestinalis ENSCING000000030021 retrocopy
Callithrix jacchus ENSCJAG000000048824 retrocopies
Dipodomys ordii ENSDORG000000090051 retrocopy
Felis catus ENSFCAG000000004731 retrocopy
Homo sapiens ENSG000001678153 retrocopies
Gorilla gorilla ENSGGOG000000250893 retrocopies
Macaca mulatta ENSMMUG000000056892 retrocopies
Monodelphis domestica ENSMODG000000069781 retrocopy
Mustela putorius furoENSMPUG000000045912 retrocopies
Mus musculus ENSMUSG000000051612 retrocopies
Nomascus leucogenys ENSNLEG000000128002 retrocopies
Otolemur garnettii ENSOGAG000000249982 retrocopies
Pongo abelii ENSPPYG000000096073 retrocopies
Pan troglodytes ENSPTRG000000006751 retrocopy
Pan troglodytes ENSPTRG000000029921 retrocopy
Pan troglodytes ENSPTRG00000010541 3 retrocopies
retro_ptro_2217 , retro_ptro_2372, retro_ptro_812,
Rattus norvegicus ENSRNOG000000035202 retrocopies
Sorex araneus ENSSARG000000001461 retrocopy
Sarcophilus harrisii ENSSHAG000000155961 retrocopy
Sus scrofa ENSSSCG000000137362 retrocopies
Ictidomys tridecemlineatus ENSSTOG000000258621 retrocopy



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