RetrogeneDB ID:

retro_ptro_126

Retrocopy
location
Organism:Chimpanzee (Pan troglodytes)
Coordinates:4:166585000..166586881(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSPTRG00000016563
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:TKT
Ensembl ID:ENSPTRG00000015024
Aliases:None
Description:Pan troglodytes transketolase (TKT), mRNA. [Source:RefSeq mRNA;Acc:NM_001009097]


Retrocopy-Parental alignment summary:






>retro_ptro_126
ATCATGGCCAACGACGCCAAGCCCGACGTGAAGACCGTGCAGGTGCTGCGGGACACAGCCAACCGCCTGCGGATCCATTC
CATCAGGGCCACGTGTGCCTCTGGTTCTGGCCAGCTCACGTCGTGCTGCAGTGCAGCGGAGGTCGTGTCTGTCCTCTTCT
TCCACACGATGAAGTATAAACAGACAGACCCAGAACACCCGGACAACGACCGGTTCATCCTCTCCAGGGGACATGCTGCT
CCTATCCTCTATGCTGCTTGGGTGGAGGTGGGTGACATCAGTGAATCTGACTTGCTGAACCTGAGGAAACTTCACAGCGA
CTTGGAGAGACACCCTACCCCCCGATTGCCGTTTGTTGACGTGGCAACAGGGTCCCTAGGTCAAGGATTAGGTGCTGCAT
GTGGAATGGCTTATACTGGCAAGTACCTTGACAAGGCCAGCTACCGGGTGTTCTGCCTTATGGGAGATGGCGAATCCTCA
GAAGGCTCTGTGTGGGAGGCTTTTGCTTTTGCCTCCCACTACAACTTGGACAATCTCGTGGCGGTCTTCGACGTGAACCG
CTTGGGACAAAGTGGCCCTGCACCCCTTGAGCATGGCGCAGACATCTACCAGAATTGCTGTGAAGCCTTTGGATGGAATA
CTTACTTAGTGGATGGCCATGATGTGGAGGCCTTGTGCCAAGCATTTTGGCAAGCAAGTCAAGTGAAGAACAAGCCTACT
GCTATAGTTGCCAAGACCTTCAAAGGTCGGGGTATTCCAAATATTGAGGATGCAGAAAATTGGCATGGAAAGCCAGTGCC
AAAAGAAAGAGCAGATGCAATTGTCAAATTAATTGAGAGTCAGATACAGACCAATGAGAATCTCATACCAAAATCGCCTG
TGGAAGACTCACCTCAAATAAGCATCACAGATATAAAAATGACCTCCCCACCTGCTTACAAAGTTGGTGACAAGATAGCT
ACTCAGAAAACATATGGTTTGGCTCTGGCTAAACTGGGCCGTGCAAATGAAAGAGTTATTGTTCTGAGTGGTGACACGAT
GAACTCCACCTTTTCTGAGATATTCAGGAAAGAACACCCTGAGCGTTTCATAGAGTGTATTATTGCTGAACAAAACATGG
TAAGTGTGGCACTAGGCTGTGCTACACGTGGTCGAACCATTGCTTTTGCTGGTGCTTTTGCTGCCTTTTTTACTAGAGCA
TTTGATCAGCTCCGAATGGGAGCCATTTCTCAAGCCAATATCAACCTTATTGGTTCCCACTGTGGGGTATCCACTGGAGA
AGATGGAGTCTCCCAGATGGCCCTGGAGGATCTAGCCATGTTCCGAAGCATTCCCAATTGTACTGTTTTCTATCCAAGTG
ATGCCATCTCGACAGAGCATGCTATTTATCTAGCCGCCAATACCAAGGGAATGTGCTTCATTCGAACCAGCCAACCAGAA
ACTGCAGTTATTTATACCCCACAAGAAAATTTTGAGATTGGCCAGGCCAAGGTGGTCCGCCATAGTGTCAATGATAAAGT
CACAGTAATTGGAGCTGGAGTTACTCTCCATGAAGCCTTAGCAGCTGCTGACCATCTTTCTCAACAAGGTATTTCTGTCC
GTGTCATCGACCCATTTACCATTAAACCCCTGGATGCCGCCACCATCATCTCCAGTGCAAAAGCCACAGGCGGCCGAGTT
ATCACAGTGGAGGATCACTACAGGGAAGGTGGCATTGGAGAAGCTGTTTGTGCAGCTGTCTCCAGGGAGCCTGATATCCT
TGTTCATCAACTGGCAGTGTCAGGAGTGCCTCAACGTGGGAAAACTAGTGAATTGCTGGATATGTTTGGAATCAGTACCA
GATACATTATAGCAGCCGTAACACTTACTTTAATGAAGTAA

ORF - retro_ptro_126 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 67.75 %
Parental protein coverage: 98.15 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalGHSHPTSCCSAAEIMAVLFFHTMRYKSQDPRNPHNDRFVLSKGHAAPILYAVWAEAGFLAEAELLNLRKI
G....TSCCSAAE...VLFFHTM.YK..DP..P.NDRF.LS.GHAAPILYA.W.E.G...E..LLNLRK.
RetrocopyGSGQLTSCCSAAEVVSVLFFHTMKYKQTDPEHPDNDRFILSRGHAAPILYAAWVEVGDISESDLLNLRKL
ParentalSSDLDGHPVPKQAFTDVATGSLGQGLGAACGMAYTGKYFDKASYRVYCLLGDGELSEGSVWEAMAFASIY
.SDL..HP.P...F.DVATGSLGQGLGAACGMAYTGKY.DKASYRV.CL.GDGE.SEGSVWEA.AFAS.Y
RetrocopyHSDLERHPTPRLPFVDVATGSLGQGLGAACGMAYTGKYLDKASYRVFCLMGDGESSEGSVWEAFAFASHY
ParentalKLDNLVAILDINRLGQSDPAPLQHQMDIYQKRCEAFGWHAIIVDGHSVEELCKAFGQA---KHQPTAIIA
.LDNLVA..D.NRLGQS.PAPL.H..DIYQ..CEAFGW....VDGH.VE.LC.AF.QA...K..PTAI.A
RetrocopyNLDNLVAVFDVNRLGQSGPAPLEHGADIYQNCCEAFGWNTYLVDGHDVEALCQAFWQASQVKNKPTAIVA
ParentalKTFKGRGITGVEDKESWHGKPLPKNMAEQIIQEIYSQIQSKKKILATPPQEDAPSVDIANIRMPSLPSYK
KTFKGRGI...ED.E.WHGKP.PK..A..I...I.SQIQ.........P.ED.P...I..I.M.S.P.YK
RetrocopyKTFKGRGIPNIEDAENWHGKPVPKERADAIVKLIESQIQTNENLIPKSPVEDSPQISITDIKMTSPPAYK
ParentalVGDKIATRKAYGQALAKLGHASDRIIALDGDTKNSTFSEIFKKEHPDRFIECYIAEQNMVSIAVGCATRN
VGDKIAT.K.YG.ALAKLG.A..R.I.L.GDT.NSTFSEIF.KEHP.RFIEC.IAEQNMVS.A.GCATR.
RetrocopyVGDKIATQKTYGLALAKLGRANERVIVLSGDTMNSTFSEIFRKEHPERFIECIIAEQNMVSVALGCATRG
ParentalRTVPFCSTFAAFFTRAFDQIRMAAISESNINLCGSHCGVSIGEDGPSQMALEDLAMFRSVPTSTVFYPSD
RT..F...FAAFFTRAFDQ.RM.AIS..NINL.GSHCGVS.GEDG.SQMALEDLAMFRS.P..TVFYPSD
RetrocopyRTIAFAGAFAAFFTRAFDQLRMGAISQANINLIGSHCGVSTGEDGVSQMALEDLAMFRSIPNCTVFYPSD
ParentalGVATEKAVELAANTKGICFIRTSRPENAIIYNNNEDFQVGQAKVILKSKDDQVTVIGAGVTLHEALAAAE
...TE.A..LAANTKG.CFIRTS.PE.A.IY...E.F..GQAKV...S..D.VTVIGAGVTLHEALAAA.
RetrocopyAISTEHAIYLAANTKGMCFIRTSQPETAVIYTPQENFEIGQAKVVRHSVNDKVTVIGAGVTLHEALAAAD
ParentalLLKKEKINIRVLDPFTIKPLDRKLILDSARATKGRILTVEDHYYEGGIGEAVSSAVVGEPGITVTHLAVN
.L....I..RV.DPFTIKPLD...I..SA.AT.GR..TVEDHY.EGGIGEAV..AV..EP.I.V..LAV.
RetrocopyHLSQQGISVRVIDPFTIKPLDAATIISSAKATGGRVITVEDHYREGGIGEAVCAAVSREPDILVHQLAVS
ParentalRVPRSGKPAELLKMFGIDKDAIAQAV
.VP..GK..ELL.MFGI....I..AV
RetrocopyGVPQRGKTSELLDMFGISTRYIIAAV

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 0 .00 RPM 124 .66 RPM
SRP007412_cerebellum 0 .00 RPM 79 .26 RPM
SRP007412_heart 0 .12 RPM 9 .33 RPM
SRP007412_kidney 0 .13 RPM 133 .01 RPM
SRP007412_liver 0 .03 RPM 113 .55 RPM
SRP007412_testis 310 .25 RPM 13 .17 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_126 retrocopy.

TSS - click to see more details

Pan troglodytes was not studied using FANTOM5 data.

Lab - click to see more details

retro_ptro_126 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ptro_126 has 6 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_47
Macaca mulatta retro_mmul_74
Mus musculus retro_mmus_220
Oryctolagus cuniculus retro_ocun_62
Bos taurus retro_btau_176
Equus caballus retro_ecab_6
Parental genes homology:
Parental genes homology involve 19 parental genes, and 22 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000037581 retrocopy
retro_btau_176,
Callithrix jacchus ENSCJAG000000072531 retrocopy
retro_cjac_2128,
Cavia porcellus ENSCPOG000000000721 retrocopy
retro_cpor_45,
Dipodomys ordii ENSDORG000000013921 retrocopy
retro_dord_329,
Homo sapiens ENSG000001639311 retrocopy
retro_hsap_47,
Macropus eugenii ENSMEUG000000053123 retrocopies
retro_meug_1397, retro_meug_160, retro_meug_796,
Myotis lucifugus ENSMLUG000000009431 retrocopy
retro_mluc_67,
Macaca mulatta ENSMMUG000000144331 retrocopy
retro_mmul_74,
Mus musculus ENSMUSG000000219571 retrocopy
retro_mmus_220,
Oryctolagus cuniculus ENSOCUG000000159042 retrocopies
retro_ocun_319, retro_ocun_62,
Otolemur garnettii ENSOGAG000000169111 retrocopy
retro_ogar_5,
Ochotona princeps ENSOPRG000000098911 retrocopy
retro_opri_10,
Pan troglodytes ENSPTRG00000015024 1 retrocopy
retro_ptro_126 ,
Pteropus vampyrus ENSPVAG000000162831 retrocopy
retro_pvam_352,
Rattus norvegicus ENSRNOG000000160641 retrocopy
retro_rnor_146,
Sarcophilus harrisii ENSSHAG000000173491 retrocopy
retro_shar_827,
Sus scrofa ENSSSCG000000214081 retrocopy
retro_sscr_996,
Tupaia belangeri ENSTBEG000000121141 retrocopy
retro_tbel_3510,
Takifugu rubripes ENSTRUG000000030091 retrocopy
retro_trub_23,


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