RetrogeneDB ID:

retro_pabe_3758

Retrocopy
location
Organism:Orangutan (Pongo abelii)
Coordinates:X:52564455..52565199(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:TPMT
Ensembl ID:ENSPPYG00000016263
Aliases:None
Description:thiopurine S-methyltransferase [Source:RefSeq peptide;Acc:NP_001125496]


Retrocopy-Parental alignment summary:






>retro_pabe_3758
ATGGATGGTACGAGAACTTCACTTGATATTGAATAGTACCCAGATACTGAGGTGCAAAAAAAACAAGTACTAACTCAGCA
AGAATGGCAAGACAAGTGGGTGAACTGAAATATTGGTTTTCGTCAAAAACAAGGACATCAGATATCAAAGCAGCATTTAG
ATACTTTTCTTAAAGGCAAGAGTGGAGTGAGGGTATTTTTTCCTCTGTGTGGAAAAGCAGTTGAGATGAAATATTTTGCA
GACTGGGGACACAGTGTACTTGGTGTGGAAATCACCAAGTACTTGGTGTGGGATATGAGATTTTTTTTTACAGAGCAGAA
TCTTTCTTACTCAGAAGAGCCAATCACCAAAATTCCTGGAGCCAAAGTGTTTAAGAGTTCTTTGGGGAACATTTCATTGT
ACTGTTGCTGTATTTTTTATCCTCCTAGAGCAAATATTGGCAAATTTGACAGGATTTAGGATAGAAGAGCATTAGTTGCC
ATTAATCCAGCTGATCACAAATGCTATGCAGTTATAATGTCGTCCAACCTGGGTAAAGGGTTTCAGTACCTCATGTGTGT
TCTTTCTTGTGATCCAACTAAACATGCAGGCCCACTATTTTGTGTTCTACTTGCTGAAATTGAAAGACTGTTCAGTACAG
TGTGTAATATTTGTTGTCTTGAGAAGGTTGATGCTTTTGAGGAATGACATAAAAGTTTTGGAATTGACCACATTTTTAAA
AGGTTATAACTACTTACAGAAAAG

ORF - retro_pabe_3758 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 71.77 %
Parental protein coverage: 100. %
Number of stop codons detected: 5
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMDGIRTSLDIEEYSDTEVQKNQVLTLEEWQDKWVNGNTAFHQEQGHRLLKKHLDTFLKGESGLRVFFPLC
MDG.RTSLDIE.Y.DTEV...QVLT..EWQDKWVN.N..F.Q.QGH...K.HLDTFLKG.SG.RVFFPLC
RetrocopyMDGTRTSLDIE*YPDTEVXXXQVLTQQEWQDKWVN*NIGFRQKQGHQISKQHLDTFLKGKSGVRVFFPLC
ParentalGKAVEMKWFADRGHSVVGVEISEL---GIREFFTEQNLSYSEEPVTEIPGTKIFKSSSGNISLYCCSIFD
GKAVEMK.FAD.GHSV.GVEI........R...TEQNLSYSEEP.T.IPG.K.FKSS.GNISLYCC.IF.
RetrocopyGKAVEMKYFADWGHSVLGVEITKYLVWDMRXXXTEQNLSYSEEPITKIPGAKVFKSSLGNISLYCCCIFY
ParentalLPRTNIGKFDMIWDRGALVAINPGDRKCYADTMLSLLGKKFQYLLCVLSYDPTKHPGPPFYVPHAEIERL
.PR.NIGKFD.I.DR.ALVAINP.D.KCYA..M.S.LGK.FQYL.CVLS.DPTKH.GP.F.V..AEIERL
RetrocopyPPRANIGKFDRI*DRRALVAINPADHKCYAVIMSSNLGKGFQYLMCVLSCDPTKHAGPLFCVLLAEIERL
ParentalFGKICNIHCLEKVDAFEERHKSWGIDYLFEKLYLLTEK
F...CNI.CLEKVDAFEE.HKS.GID..F..L.LLTEK
RetrocopyFSTVCNICCLEKVDAFEE*HKSFGIDHIFKRL*LLTEK

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 21 .84 RPM
SRP007412_cerebellum 0 .00 RPM 13 .50 RPM
SRP007412_heart 0 .00 RPM 6 .86 RPM
SRP007412_kidney 0 .00 RPM 38 .35 RPM
SRP007412_liver 0 .00 RPM 15 .97 RPM
Pongo abelii was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_pabe_3758 retrocopy.
Pongo abelii was not studied using FANTOM5 data.
retro_pabe_3758 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_pabe_3758 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_4835
Pan troglodytes retro_ptro_3217
Gorilla gorilla retro_ggor_3014

Parental genes homology:
Parental genes homology involve 14 parental genes, and 61 retrocopies.

Species Parental gene accession Retrocopies number
Choloepus hoffmanni ENSCHOG0000000867627 retrocopies
Callithrix jacchus ENSCJAG000000069062 retrocopies
Cavia porcellus ENSCPOG000000052951 retrocopy
Dasypus novemcinctus ENSDNOG000000048421 retrocopy
Homo sapiens ENSG000001373644 retrocopies
Gorilla gorilla ENSGGOG000000161554 retrocopies
Loxodonta africana ENSLAFG000000116321 retrocopy
Macaca mulatta ENSMMUG000000166273 retrocopies
Mus musculus ENSMUSG000000213761 retrocopy
Nomascus leucogenys ENSNLEG000000015484 retrocopies
Oryctolagus cuniculus ENSOCUG000000038542 retrocopies
Otolemur garnettii ENSOGAG000000077382 retrocopies
Pongo abelii ENSPPYG00000016263 4 retrocopies
Pan troglodytes ENSPTRG000000177565 retrocopies



Copyright © RetrogeneDB 2014-2017