RetrogeneDB ID:

retro_ptro_775

Retrocopy
location
Organism:Chimpanzee (Pan troglodytes)
Coordinates:12:85893831..85894389(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:TM2D3
Ensembl ID:ENSPTRG00000007515
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_ptro_775
GCAGTGAAAGTACCGAAATTACACCTTTTATGTTCAAGCAATGGTTTGTGTAGCAGGTATTCTGCAGAATTTATAGACTG
CACAACAAATGTCCTCTGTGTCTATGGGAAGCTAGTCACTTTTGACTGTACAGTGAAACCTTCTGTTGCCTGTGTTGATT
AGGAGTTAAAATCCCAAAGTAACTTTCTCATCAACATGACTTGATTTTGATGGAAGCCTCCAGAAACAGAATATGAATGT
TTCAATTCTACCAGCTGCATGAGGTCCTGTCCTCAACGGCATTATGCTGCCAAATACATGATAAACACATTCATGACTTG
GGTAACTACTTTTTTCAAAATGCTGCACTGAAATTGGGCTGGAGGCTATAAGTGGTCTATTGCTCTGGCTCTAAGCATCA
CCCTTGGTGGCTTTGGAGCAGACCATTTCCACCTCAACCAGTGGCAAGAAGGCCTTGGCAAGCTCTTCAGCTTCAGTGGC
CTGGAAATATGGACACTAATAGACATCTTGCTAATTGGAGTTGGCTACATTGGACCAGCAGATGGCTCTTGATACATT

ORF - retro_ptro_775 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 65.26 %
Parental protein coverage: 76.92 %
Number of stop codons detected: 5
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalSTEIPPYVMKCPSNGLCSRLPADCIDCTTNFSCIYGKPVTFDCAVKPSVTCVDQDFKSQKNFIINMTCRF
....P.....C.SNGLCSR..A..IDCTTN..C.YGK.VTFDC.VKPSV.CVD...KSQ.NF.INMT..F
RetrocopyAVKVPKLHLLCSSNGLCSRYSAEFIDCTTNVLCVYGKLVTFDCTVKPSVACVD*ELKSQSNFLINMT*-F
ParentalCWQLPETDYECTNSTSCMTVSCPRQRYPANCTVRDHVHCLGNRTFPKMLYCNWTGGYKWSTALALSITLG
.W..PET.YEC.NSTSCM..SCP...Y.A..............TF.KML..NW.GGYKWS.ALALSITLG
Retrocopy*WKPPETEYECFNSTSCMR-SCPQRHYAAKYMINTFMTWV--TTFFKMLH*NWAGGYKWSIALALSITLG
ParentalGFGADRFYLGQWREGLGKLFSFGGLGIWTLIDVLLIGVGYVGPADGSLYI
GFGAD.F.L.QW.EGLGKLFSF.GL.IWTLID.LLIGVGY.GPADGS.YI
RetrocopyGFGADHFHLNQWQEGLGKLFSFSGLEIWTLIDILLIGVGYIGPADGS*YI

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 28 .24 RPM
SRP007412_cerebellum 0 .00 RPM 23 .12 RPM
SRP007412_heart 0 .00 RPM 13 .84 RPM
SRP007412_kidney 0 .00 RPM 15 .66 RPM
SRP007412_liver 0 .00 RPM 18 .10 RPM
SRP007412_testis 0 .00 RPM 8 .75 RPM
Pan troglodytes was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ptro_775 retrocopy.
Pan troglodytes was not studied using FANTOM5 data.
retro_ptro_775 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ptro_775 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_1138
Gorilla gorilla retro_ggor_887
Macaca mulatta retro_mmul_884

Parental genes homology:
Parental genes homology involve 8 parental genes, and 8 retrocopies.

Species Parental gene accession Retrocopies number
Callithrix jacchus ENSCJAG000000173401 retrocopy
Homo sapiens ENSG000001842771 retrocopy
Gorilla gorilla ENSGGOG000000115981 retrocopy
Macaca mulatta ENSMMUG000000002771 retrocopy
Mustela putorius furoENSMPUG000000109851 retrocopy
Nomascus leucogenys ENSNLEG000000005291 retrocopy
Pan troglodytes ENSPTRG00000007515 1 retrocopy
retro_ptro_775 ,
Tarsius syrichta ENSTSYG000000045361 retrocopy



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