RetrogeneDB ID:

retro_ptro_37

Retrocopy
location
Organism:Chimpanzee (Pan troglodytes)
Coordinates:12:7782087..7783869(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSPTRG00000042397
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:PTPN6
Ensembl ID:ENSPTRG00000004601
Aliases:None
Description:protein tyrosine phosphatase, non-receptor type 6 [Source:HGNC Symbol;Acc:9658]


Retrocopy-Parental alignment summary:






>retro_ptro_37
ATGACATCGCGGAGATGGTTTCACCCAAATATCACTGGTGTGGAGGCAGAAAACCTACTGTTGACAAGAGGAGTTGATGG
CAGTTTTTTGGCAAGGCCTAGTAAAAGTAACCCTGGAGACTTCACACTTTCCGTTAGAAGAAATGGAGCTGTCACCCACA
TCAAGATTCAGAACACTGGTGATTACTATGACCTGTATGGAGGGGAGAAATTTGCCACTTTGGCTGAGTTGGTCCAGTAT
TACATGGAACATCACGGGCAATTAAAAGAGAAGAATGGAGATGTCATTGAGCTTAAATATCCTCTGAACTGTGCAGATCC
TACCTCTGAAAGGTGGTTTCATGGACACCTCTCTGGGAAAGAAGCAGAGAAATTATTAACTGAAAAAGGAAAACATGGTA
GTTTTCTTGTACGAGAGAGCCAGAGCCACCCTGGAGATTTTGTTCTTTCTGTGCGCACTGGTGATGACAAAGGGGAGAGC
AATGACGGCAAGTCTAAAGTGACCCATGTTATGATTCGCTGTCAGGAACTGAAATACGACGTTGGTGGAGGAGAACGGTT
TGATTCTTTGACAGATCTTGTGGAACATTATAAGAAGAATCCTATGGTGGAAACATTGGGTACAGTACTACAACTCAAGC
AGCCCCTTAACACGACTCGTATAAATGCTGCTGAAATAGAAAGCAGAGTTCGAGAACTAAGCAAATTAGCTGAGACCACA
GATAAAGTCAAACAAGGCTTTTGGGAAGAATTTGAGACACTACAACAACAGGAGTGCAAACTTCTCTACAGCCGAAAAGA
GGGTCAAAGGCAAGAAAACAAAAACAAAAATAGATATAAAAACATCCTGCCCTTTGATCATACCAGGGTTGTCCTACACG
ATGGTGATCCCAATGAGCCTGTTTCAGATTACATCAATGCAAATATCATCATGCCTGAATTTGAAACCAAGTGCAACAAT
TCAAAGCCCAAAAAGAGTTACATTGCCACACAAGGCTGCCTGCAAAACACGGTGAATGACTTTTGGCGGATGGTGTTCCA
AGAAAACTCCCGAGTGATTGTCATGACAACGAAAGAAGTGGAGAGAGGAAAGAGTAAATGTGTCAAATACTGGCCTGATG
AGTATGCTCTAAAAGAATATGGCGTCATGCGTGTTAGGAACGTCAAAGAAAGCGCCGCTCATGACTATACGCTAAGAGAA
CTTAAACTTTCAAAGGTTGGACAAGGGAATACGGAGAGAACGGTCTGGCAATACCACTTTCGGACCTGGCCGGACCACGG
CGTACCCAGCGACCCCGGGGGCGTGCTGGACTTCCTGGAGGAGGTGCACCATAAGCAGGAGAGCATCATGGATGCAGGGC
CGGTCGTGGTGCACTGCAGTGCTGGAATTGGCCGGACAGGGACGTTCATTGTGATTGATATTCTTATTGACATCATCAGA
GAGAAAGGTGTTGACTGCGATATTGACGTTCCCAAAACCATCCAGATGGTGCGGTCTCAGAGGTCAGGGATGGTCCAGAC
AGAAGCACAGTACCGATTTATCTATATGGCGGTCCAGCATTATATTGAAACACTACAGCGCAGGATTGAAGAAGAGCAGA
AAAGCAAGAGGAAAGGGCACGAATATACAAATATTAAGTATTCTCTAGCGGACCAGACGAGTGGAGATCAGAGCCCCCTC
CCGCCTTGTACTCCAACGCCACCCTGTGCAGAAATGAGAGAAGACAGTGCTAGAGTCTATGAAAACGTGGGCCTGATGCA
ACAGCAGAAAAGTTTCAGATGA

ORF - retro_ptro_37 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 58.56 %
Parental protein coverage: 86.38 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalRWFHRDLSGLDAETLLKGRGVHGSFLARPSRKNQGDFSLSVRVGDQVTHIRIQNSGDFYDLYGGEKFATL
RWFH....G..AE.LL..RGV.GSFLARPS..N.GDF.LSVR....VTHI.IQN.GD.YDLYGGEKFATL
RetrocopyRWFHPNITGVEAENLLLTRGVDGSFLARPSKSNPGDFTLSVRRNGAVTHIKIQNTGDYYDLYGGEKFATL
ParentalTELVEYYTQQQGVLQDRDGTIIHLKYPLNCSDPTSERWYHGHMSGGQAETLLQAKGEPWTFLVRESLSQP
.ELV.YY....G.L....G..I.LKYPLNC.DPTSERW.HGH.SG..AE.LL..KG....FLVRES.S.P
RetrocopyAELVQYYMEHHGQLKEKNGDVIELKYPLNCADPTSERWFHGHLSGKEAEKLLTEKGKHGSFLVRESQSHP
ParentalGDFVLSVLSDQPKAGPGS-PLRVTHIKVMCEGGRYTVGGLETFDSLTDLVEHFKKTGIEEASGAFVYLRQ
GDFVLSV.....K.........VTH....C....Y.VGG.E.FDSLTDLVEH.KK....E..G....L.Q
RetrocopyGDFVLSVRTGDDKGESNDGKSKVTHVMIRCQELKYDVGGGERFDSLTDLVEHYKKNPMVETLGTVLQLKQ
ParentalPYYATRVNAADIENRVLELNKKQESEDTAKAGFWEEFESLQKQEVKNLHQRLEGQRPENKGKNRYKNILP
P...TR.NAA.IE.RV.EL.K..E..D..K.GFWEEFE.LQ.QE.K.L..R.EGQR.ENK.KNRYKNILP
RetrocopyPLNTTRINAAEIESRVRELSKLAETTDKVKQGFWEEFETLQQQECKLLYSRKEGQRQENKNKNRYKNILP
ParentalFDHSRVILQGRDSNIPGSDYINANYIKNQLLGPDENA---KTYIASQGCLEATVNDFWQMAWQENSRVIV
FDH.RV.L...D.N.P.SDYINAN.I.........N....K.YIA.QGCL..TVNDFW.M..QENSRVIV
RetrocopyFDHTRVVLHDGDPNEPVSDYINANIIMPEFETKCNNSKPKKSYIATQGCLQNTVNDFWRMVFQENSRVIV
ParentalMTTREVEKGRNKCVPYWPEVGMQRAYGPYSVTNCGEHDTTEYKLRTLQVSPLDNGDLIREIWHYQYLSWP
MTT.EVE.G..KCV.YWP.......YG...V.N..E.....Y.LR.L..S....G...R..W.Y....WP
RetrocopyMTTKEVERGKSKCVKYWPDEYALKEYGVMRVRNVKESAAHDYTLRELKLSKVGQGNTERTVWQYHFRTWP
ParentalDHGVPSEPGGVLSFLDQINQRQESLPHAGPIIVHCSAGIGRTGTIIVIDMLMENISTKGLDCDIDIQKTI
DHGVPS.PGGVL.FL......QES...AGP..VHCSAGIGRTGT.IVID.L...I..KG.DCDID..KTI
RetrocopyDHGVPSDPGGVLDFLEEVHHKQESIMDAGPVVVHCSAGIGRTGTFIVIDILIDIIREKGVDCDIDVPKTI
ParentalQMVRAQRSGMVQTEAQYKFIYVAIAQFIETTKKKLEVLQSQKGQESEYGNITY
QMVR.QRSGMVQTEAQY.FIY.A....IET.....E..Q..K....EY.NI.Y
RetrocopyQMVRSQRSGMVQTEAQYRFIYMAVQHYIETLQRRIEEEQKSKRKGHEYTNIKY

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 24 .95 RPM 3 .84 RPM
SRP007412_cerebellum 33 .63 RPM 9 .43 RPM
SRP007412_heart 40 .57 RPM 4 .02 RPM
SRP007412_kidney 15 .12 RPM 27 .25 RPM
SRP007412_liver 11 .56 RPM 36 .04 RPM
SRP007412_testis 11 .17 RPM 0 .84 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_37 retrocopy.

TSS - click to see more details

Pan troglodytes was not studied using FANTOM5 data.

Lab - click to see more details

retro_ptro_37 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ptro_37 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 2 parental genes, and 3 retrocopies.

Species Parental gene accession Retrocopies number
Pan troglodytes ENSPTRG00000004601 1 retrocopy
retro_ptro_37 ,
Pan troglodytes ENSPTRG000000098842 retrocopies
retro_ptro_361, retro_ptro_813,


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