RetrogeneDB ID:

retro_ptro_331

Retrocopy
location
Organism:Chimpanzee (Pan troglodytes)
Coordinates:1:112085656..112087167(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSPTRG00000040450
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:PDIA3
Ensembl ID:ENSPTRG00000007002
Aliases:None
Description:Pan troglodytes protein disulfide isomerase family A, member 3 (PDIA3), mRNA. [Source:RefSeq mRNA;Acc:NM_001246452]


Retrocopy-Parental alignment summary:






>retro_ptro_331
ATGTGCCTCCGCCGCCTAGCGCTGTTCCCGGGCGTGGCGCTGCTTCTCGCCGCGGCCCGCCTCGCGGCTGCCTCCGACGT
GCTAGGACTCAGGGACGACAACTTGGAGAGTCGCATCTCCGACACGGGCTCTGCGGGCCTCATGCTCGTCGAGTTCTTCG
CCCCCTGGTGTGGACACTGCAAGAGACTTGCTCCTGAGTATGAAGCTGCAGCTACCAGATTAAAAGGAATAGTCCCATTA
GCAAAGGCTGATTGCACTGCCAACACTAACACCTGTAATAAATATGGAGTCAGTGGATATCCAACCCTGAAGATATTTAG
AGATGGTGAAGAAGCAGGTGCTTATGATGGACCTAGGACTGCTGATGGAATTGTCAGCCACCTGAAGAAGCAGGCAGGAC
CAGCTTCAGTGCCTCTCAGGACTGAGGAAGAATTTAAGAAATTCATTAGTGATAAAGATGCCTCTATAGTAGGTTTTTTA
GATGATTCATTCAGTGAAGCTCACTCCGAGTTCCTAAAAGCAGCCAGCAACTTGAGGGATAACTACCGATTTGCACATAC
GAATGTTGAGTCTCTGGTGAACGAGTATGATGATAATGGAGATGGTATCATCTTATTTCGTCCTTCACATCTCACTAACA
AGTTGGAGGACAAGACTGTGGCATATACAGAGCAAAAAATGACCAGTGGCAAAATTAAAAAGTTTATCCAGGAAAACATT
TTTGGTATCTGCCCTCACATGACAGAAGACAATAAAGATTTGATACAGGGCAAGGACTTAGTTATTGCTTACTATGATGT
GGACTATGAAAAGAATGCTAAAGGTTCCAACTACTGGAGAAACAGGGTAATGATGGTGGCAAAGAAATTCCTGGATGCTG
GGCACAAACTCAACTTTGCTGTAGCTAGCCGCAAAACCTTTAGCCATGAACTTTCTGATTTTGGCTTGGAGAGCACTGCT
GGAGAGATTCCTGTTGTTGCTATCAGAACTGCTAAAGGAGAGAAGTTTGTCATGCAGGAGGATTTCTCGCATGATGGGAA
TGCTCTGGAGAGGTTCCTGCAGGATTACTTTGATGGCAATCTGAAGAGATACCTGAAGTCTGAACCTATCCCAGAGAGCA
ATGATGGGCCTGTGAAGGTAGTGGTAGCAGAGAATTTTGATGAAATAGTGAATAATGAAAATAAAGATGTGCTGATTGAA
TTTTATGCCCCTTGGTGTGGTCACTGTAAGAACCTGGAGCCCAAGTATAAAGAACTTGGCGAGAAGCTCAGCAAAGACCT
GAATATTGTCATAGCCAAGATGGATGCCACAGCCAATGATGTGCCTTCTCCATATGAAGTCAGAGTTTTCCTACCATATA
CTTCTCTCCAGCCAACAAGAAGCTAAATCCAAAGAAATATGAAGGTGGCCATGAATTAAGTGATTTTATTAGCTATCTAC
AAAGAGAAGCTACAAACCCCCCTGTAATTCAAGAAGAAAAACCCAAGAAGAAGAAGGCACAGGAGGATCTC

ORF - retro_ptro_331 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 96.64 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalMRLRRLALFPGVALLLAAARLAAASDVLELTDDNFESRISDTGSAGLMLVEFFAPWCGHCKRLAPEYEAA
M.LRRLALFPGVALLLAAARLAAASDVL.L.DDN.ESRISDTGSAGLMLVEFFAPWCGHCKRLAPEYEAA
RetrocopyMCLRRLALFPGVALLLAAARLAAASDVLGLRDDNLESRISDTGSAGLMLVEFFAPWCGHCKRLAPEYEAA
ParentalATRLKGIVPLAKVDCTANTNTCNKYGVSGYPTLKIFRDGEEAGAYDGPRTADGIVSHLKKQAGPASVPLR
ATRLKGIVPLAK.DCTANTNTCNKYGVSGYPTLKIFRDGEEAGAYDGPRTADGIVSHLKKQAGPASVPLR
RetrocopyATRLKGIVPLAKADCTANTNTCNKYGVSGYPTLKIFRDGEEAGAYDGPRTADGIVSHLKKQAGPASVPLR
ParentalTEEEFKKFISDKDASIVGFFDDSFSEAHSEFLKAASNLRDNYRFAHTNVESLVNEYDDNGEGIILFRPSH
TEEEFKKFISDKDASIVGF.DDSFSEAHSEFLKAASNLRDNYRFAHTNVESLVNEYDDNG.GIILFRPSH
RetrocopyTEEEFKKFISDKDASIVGFLDDSFSEAHSEFLKAASNLRDNYRFAHTNVESLVNEYDDNGDGIILFRPSH
ParentalLTNKFEDKTVAYTEQKMTSGKIKKFIQENIFGICPHMTEDNKDLIQGKDLLIAYYDVDYEKNAKGSNYWR
LTNK.EDKTVAYTEQKMTSGKIKKFIQENIFGICPHMTEDNKDLIQGKDL.IAYYDVDYEKNAKGSNYWR
RetrocopyLTNKLEDKTVAYTEQKMTSGKIKKFIQENIFGICPHMTEDNKDLIQGKDLVIAYYDVDYEKNAKGSNYWR
ParentalNRVMMVAKKFLDAGHKLNFAVASRKTFSHELSDFGLESTAGEIPVVAIRTAKGEKFVMQEEFSRDGKALE
NRVMMVAKKFLDAGHKLNFAVASRKTFSHELSDFGLESTAGEIPVVAIRTAKGEKFVMQE.FS.DG.ALE
RetrocopyNRVMMVAKKFLDAGHKLNFAVASRKTFSHELSDFGLESTAGEIPVVAIRTAKGEKFVMQEDFSHDGNALE
ParentalRFLQDYFDGNLKRYLKSEPIPESNDGPVKVVVAENFDEIVNNENKDVLIEFYAPWCGHCKNLEPKYKELG
RFLQDYFDGNLKRYLKSEPIPESNDGPVKVVVAENFDEIVNNENKDVLIEFYAPWCGHCKNLEPKYKELG
RetrocopyRFLQDYFDGNLKRYLKSEPIPESNDGPVKVVVAENFDEIVNNENKDVLIEFYAPWCGHCKNLEPKYKELG
ParentalEKLSKDPNIVIAKMDATANDVPSPYEVR-GFPTIYFSPANKKLNPKKYEGGRELSDFISYLQREATNPPV
EKLSKD.NIVIAKMDATANDVPSPYEVR..FPTIYFSPANKKLNPKKYEGG.ELSDFISYLQREATNPPV
RetrocopyEKLSKDLNIVIAKMDATANDVPSPYEVR<SFPTIYFSPANKKLNPKKYEGGHELSDFISYLQREATNPPV
ParentalIQEEKPKKKKKAQEDL
IQEEKP.KKKKAQEDL
RetrocopyIQEEKP-KKKKAQEDL

Legend:
*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide






RNA-Seq - click to see more details

(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 1 .66 RPM 64 .24 RPM
SRP007412_cerebellum 1 .33 RPM 57 .21 RPM
SRP007412_heart 1 .11 RPM 77 .85 RPM
SRP007412_kidney 1 .62 RPM 181 .91 RPM
SRP007412_liver 1 .41 RPM 385 .87 RPM
SRP007412_testis 0 .63 RPM 163 .13 RPM

ChIP-Seq - click to see more details

Pan troglodytes was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_ptro_331 retrocopy.

TSS - click to see more details

Pan troglodytes was not studied using FANTOM5 data.

Lab - click to see more details

retro_ptro_331 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ptro_331 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_217
Gorilla gorilla retro_ggor_287
Parental genes homology:
Parental genes homology involve 6 parental genes, and 6 retrocopies.

Species Parental gene accession Retrocopies number
Homo sapiens ENSG000001670041 retrocopy
retro_hsap_217,
Gorilla gorilla ENSGGOG000000234401 retrocopy
retro_ggor_287,
Myotis lucifugus ENSMLUG000000093801 retrocopy
retro_mluc_2352,
Otolemur garnettii ENSOGAG000000042981 retrocopy
retro_ogar_1750,
Procavia capensis ENSPCAG000000129051 retrocopy
retro_pcap_409,
Pan troglodytes ENSPTRG00000007002 1 retrocopy
retro_ptro_331 ,


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