RetrogeneDB ID:

retro_ptro_777

Retrocopy
location
Organism:Chimpanzee (Pan troglodytes)
Coordinates:12:89663200..89664565(-)
Located in intron of:ENSPTRG00000005284
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:GALNT12
Ensembl ID:ENSPTRG00000021180
Aliases:None
Description:UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 12 (GalNAc-T12) [Source:HGNC Symbol;Acc:19877]


Retrocopy-Parental alignment summary:






>retro_ptro_777
TGTAAGTCCCAGAAGTTCAACTATAGGACACTTCCTACCACCTCTGTTATCATTGCTTTCTATAACGAAGCCTGGTCGAC
TTTGCTCCGTACCATTCACAGTGTTTTAGAAACTTCTCCTGCAGTTCTTTTGAAAGAGATCATCTTGGTGGATGACTTGA
GTGACAGAGTTTATTTGAAGACACAACTTGAAACTTACATCAGCAATCTTGATAGAGTACGCTTGATTAGGACCAATAAG
CGAGAGGGGCTGGTTAGGGCCCGTCTGATTGGGGCCACTTTCGCCACTGGGGACGTCCTCACTTTCCTGGATTGTCACTG
TGAGTGTAATTCCGGTTGGCTGGAACCGCTTTTGGAAAGGATTGGGAGAGATGAAACAGCAGTTGTGTGTCCTGTTATAG
ACACAATTGATTGGAATACTTTTGAATTCTATATGCAGACAGGGGAGCCCATGATTGGTGGGTTTGACTGGCGTTTAACA
TTTCAGTGGCATTCTGTCCCCAAACAGGAAAGGGACAGGCGGATATCAAGAATTGACCCCATCAGATCACCTACCATGGC
TGGAGGACTGTTTGCTGTCAGCAAGAAATATTTTCAGTACCTTGGAACGTATGACACAGGAATGGAAGTGTGGGGAGGTG
AAAACCTTGAGCTGTCTTTTAGGGTGTGGCAGTGTGGTGGCAAATTGGAGATCCACCCGTGTTCCCACGTGGGCCATGTG
TTCCCCAAGCGGGCACCATATGCTCGCCCCAATTTCCTACAGAATACTGCTCGGGCAGCAGAAGTTTGGATGGATGAGTA
CAAAGAGCACTTCTACAATAGAAACCCTCCAGCAAGAAAAGAAGCTTATGGTGATATTTCTGAAAGAAAATTACTACGAG
AGCGGTTGAGATGCAAGAGCTTTGACTGGTATTTGAAAAACGTTTTTCCTAATTTACATGTTCCAGAGGATAGACCAGGC
TGGCATGGGGCTATTCGCAGTAGAGGGATCTCGTCTGAATGTTTAGATTATAATTCTCCTGACAACAACCCCACAGGTGC
TAACCTTTCACTGTTTGGATGCCATGGTCAAGGAGGCAATCAATTCTTTGAATATACTTCAAACAAAGAAATAAGGTTTA
ATTCTGTGACAGAGTTATGTGCAGAGGTACCTGAGCAAAAAAATTATGTAGGAATGCAAAATTGTCCCAAAGATGGGTTC
CCTGTACCAGCAAACATTATTTGGCATTTTAAAGAAGATGGAACTATTTTTCACCCACACTCAGGACTGTGTCTTAGTGC
TTATCGGACACCGGAGGGCCGACCTGATGTACAAATGAGAACTTGTGATGCTCTAGATAAAAATCAAATTTGGAGTTTTG
AGAAA

ORF - retro_ptro_777 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 61.35 %
Parental protein coverage: 97.63 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalCKEKKYDYDNLPRTSVIIAFYNEAWSTLLRTVYSVLETSPDILLEEVILVDDYSDREHLKERLANELSGL
CK..K..Y..LP.TSVIIAFYNEAWSTLLRT..SVLETSP..LL.E.ILVDD.SDR..LK..L....S.L
RetrocopyCKSQKFNYRTLPTTSVIIAFYNEAWSTLLRTIHSVLETSPAVLLKEIILVDDLSDRVYLKTQLETYISNL
ParentalPKVRLIRANKREGLVRARLLGASAARGDVLTFLDCHCECHEGWLEPLLQRIHEEESAVVCPVIDVIDWNT
..VRLIR.NKREGLVRARL.GA..A.GDVLTFLDCHCEC..GWLEPLL.RI...E.AVVCPVID.IDWNT
RetrocopyDRVRLIRTNKREGLVRARLIGATFATGDVLTFLDCHCECNSGWLEPLLERIGRDETAVVCPVIDTIDWNT
ParentalFEYLGNSGEPQIGGFDWRLVFTWHTVPERERIRMRSPVDVIRSPTMAGGLFAVSKKYFEYLGSYDTGMEV
FE.....GEP.IGGFDWRL.F.WH.VP..ER.R..S..D.IRSPTMAGGLFAVSKKYF.YLG.YDTGMEV
RetrocopyFEFYMQTGEPMIGGFDWRLTFQWHSVPKQERDRRISRIDPIRSPTMAGGLFAVSKKYFQYLGTYDTGMEV
ParentalWGGENLEFSFRIWQCGGVLETHPCSHVGHVFPKQAPYSRNKALANSVRAAEVWMDEFKELYYHRNPRARL
WGGENLE.SFR.WQCGG.LE.HPCSHVGHVFPK.APY.R...L.N..RAAEVWMDE.KE..Y.RNP.AR.
RetrocopyWGGENLELSFRVWQCGGKLEIHPCSHVGHVFPKRAPYARPNFLQNTARAAEVWMDEYKEHFYNRNPPARK
ParentalEPFGDVTERKQLRDKLQCKDFKWFLETVYPELHVPEDRPGFFGMLQNKGLTDYCFDYNPPDENQIVGHQV
E..GD..ERK.LR..L.CK.F.W.L..V.P.LHVPEDRPG..G.....G....C.DYN.PD.N...G...
RetrocopyEAYGDISERKLLRERLRCKSFDWYLKNVFPNLHVPEDRPGWHGAIRSRGISSECLDYNSPDNNP-TGANL
ParentalILYLCHGMGQNQFFEYTSQKEIRYNTHQPEGCIAVEAGMDTLIMHLCEE---TAPENQKFILQEDGSLFH
.L..CHG.G.NQFFEYTS.KEIR.N....E.C..V........M..C.......P.N......EDG..FH
RetrocopySLFGCHGQGGNQFFEYTSNKEIRFNS-VTELCAEVPEQKNYVGMQNCPKDGFPVPANIIWHFKEDGTIFH
ParentalEQSKKCVQAARKESSDSFVPLLRDCTNSD-HQKWFFKE
..S..C..A.R.......V...R.C...D..Q.W.F..
RetrocopyPHSGLCLSAYRTPEGRPDVQ-MRTCDALDKNQIWSFEK

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 .48 RPM 3 .24 RPM
SRP007412_cerebellum 2 .08 RPM 13 .77 RPM
SRP007412_heart 1 .46 RPM 0 .50 RPM
SRP007412_kidney 4 .03 RPM 4 .60 RPM
SRP007412_liver 2 .72 RPM 1 .47 RPM
SRP007412_testis 2 .00 RPM 16 .02 RPM
Pan troglodytes was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ptro_777 retrocopy.
Pan troglodytes was not studied using FANTOM5 data.
retro_ptro_777 was not experimentally validated.


Parental genes homology:
Parental genes homology involve 34 parental genes, and 38 retrocopies.

Species Parental gene accession Retrocopies number
Anolis carolinensis ENSACAG000000023021 retrocopy
Ailuropoda melanoleuca ENSAMEG000000045201 retrocopy
Anas platyrhynchos ENSAPLG000000121971 retrocopy
Bos taurus ENSBTAG000000090371 retrocopy
Canis familiaris ENSCAFG000000024941 retrocopy
Cavia porcellus ENSCPOG000000124181 retrocopy
Equus caballus ENSECAG000000165461 retrocopy
Ficedula albicollis ENSFALG000000051881 retrocopy
Felis catus ENSFCAG000000088311 retrocopy
Gorilla gorilla ENSGGOG000000057921 retrocopy
Loxodonta africana ENSLAFG000000220111 retrocopy
Meleagris gallopavo ENSMGAG000000072441 retrocopy
Microcebus murinus ENSMICG000000110751 retrocopy
Myotis lucifugus ENSMLUG000000026301 retrocopy
Macaca mulatta ENSMMUG000000195611 retrocopy
Mustela putorius furoENSMPUG000000065021 retrocopy
Mus musculus ENSMUSG000000397741 retrocopy
Nomascus leucogenys ENSNLEG000000170191 retrocopy
Oryctolagus cuniculus ENSOCUG000000162211 retrocopy
Otolemur garnettii ENSOGAG000000014082 retrocopies
Ochotona princeps ENSOPRG000000060292 retrocopies
Procavia capensis ENSPCAG000000050681 retrocopy
Pongo abelii ENSPPYG000000194371 retrocopy
Pelodiscus sinensis ENSPSIG000000172461 retrocopy
Pan troglodytes ENSPTRG000000198911 retrocopy
Pan troglodytes ENSPTRG00000021180 1 retrocopy
retro_ptro_777 ,
Pteropus vampyrus ENSPVAG000000087741 retrocopy
Rattus norvegicus ENSRNOG000000080993 retrocopies
Sarcophilus harrisii ENSSHAG000000174741 retrocopy
Sus scrofa ENSSSCG000000053791 retrocopy
Ictidomys tridecemlineatus ENSSTOG000000213061 retrocopy
Tupaia belangeri ENSTBEG000000036271 retrocopy
Tarsius syrichta ENSTSYG000000049751 retrocopy
Tursiops truncatus ENSTTRG000000108481 retrocopy



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