RetrogeneDB ID:

retro_ptro_3283

Retrocopy
location
Organism:Chimpanzee (Pan troglodytes)
Coordinates:Y:947831..949487(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:GLUD2
Ensembl ID:ENSPTRG00000002711
Aliases:None
Description:Pan troglodytes glutamate dehydrogenase 2 (GLUD2), nuclear gene encoding mitochondrial protein, mRNA. [Source:RefSeq mRNA;Acc:NM_001009004]


Retrocopy-Parental alignment summary:






>retro_ptro_3283
GGCGAAGCCCTGCGGCTCTCCCGGGTTGGCCCGGTGCCCTGGGTTCGGCGGCCGCCCACTCAGCCGCGTTGCTGGGCCGG
GCCGGGGGATAGCCCACCGCCGCCCGCAGCCGGGGCTCGTATTGGCCGCCCGGCGCCACTACAGCGAAGAGGTGGCCGAA
CGCGAGGACGACCCCAGCTTCTTCAAAACGGTGGAGGGCTTCTTCAATCGTGGCGCCAGCATCGTGCAGGACAAGCTGGT
GGAGGACCTGAGGACCCGGGAGAGTGAGGAGCAGAAGCGGAACCGGGTGGGCGGCATCTTTCGGATCATCAATCCCTGCA
ACCACATGCTGAGTGTCTCCTTCCGCATCCGGCGCGACGACAGCTCCTGGGAGGTCACCAAAGGCTACCCGGCCCAGCAC
AGCCAGCACCGCATGCCCTGCAATGGAGGTGTCCATTACAGCACTGATGTGAGTATAGATGAAGTAAAAGCTTTGGCTTC
TCTGATGACATGCAAGTGTGCAGTGGTTGGTGTGTCGTTCTGGGGTGCTAAAGCTGGTGTTAAGATCAGTCCCAAGTACT
ATACCAATAATGAATTGGAAAAGATCACAAGGAGGTTCACCATAGAGCTAGCAAAGAAAGGCTTTATTGGTTGTGGCATT
GATGTGCCTGCTCCAGACATGAGCACAGGTGAGCTGGAGATGTCCTGGATCGCTGATGCCTATGCCAGCACCATAGGGCA
CTACGATATTAATGCACACGCCTGTGTTATTGGTAAACCCATCAGCCAAGGGGGAATCCATGGACGCATCTCTGCTACTG
GCCATGGTGTCTTCCATGGGATTGAAAATTTCATCAATGAAGCTTCTTACATGAGCATTTTAGGAATGACATCAGGGTTT
GGAGGTAAAACATTTTTCGTTCAGGGATTTGGTAATGCGGGCCTCCACTCTATGAGATATTTACATCGTTTTGGTGCTAA
ATGTATTGCTGTTGGTAAGTCTGATGGGAGTATATGGAATCCAGATGGTATTGACCCAAAGGAATTGGAAGACTTCAAAT
TGCAACATGGGTCCATTGTGGGCTTCCCCAAGGTAAAGCCCTATGAAGGAAGCATCTTGGAGCCCTACTGTGACATACTG
ATCCCAGCTGCCAGTGAGAAGCAGTTGAGCAAATCCAATGAATCCAGAGTCAAAGCCAAGATCATTGCTGAAGGTGACAA
TGGGCCAACAACCCCAGAAGCTGACAAGATCTTCCTGGAGAGAAACATTATGGTTATTCCAGATCTCTACATGAATGCTG
GAGGAGTGACAGTATCTTACTTTGAGTGGCTGAAGAATCTAAAGCATGTCAGCTATGGCCGTTTGACCTTCAAATATGAA
AGGAATTCTAACTACCACTTGTTCATGTCTGTTGAAGAGACTTTAGAAAGAAAATGTGGAAAGCATGGTGGAACTATTCC
CATTGTACCCACGGCAGAGTTCCAAGACAGGATATCGGGTGCATCTGAGAAAGACATCATGCACTCCGGCTTGGTGTGCA
CAATGGAGCATTCTGCCAGGCAAATCATGCACACAGCCAGGAAGTATAAACTGGGATGGACCTGAGAGCAGCTGCCTATG
TCAATACCATTGAGAAAGTCTTCAAAGTGTACAATGAAGCTGGTGCGACCTTCACA

ORF - retro_ptro_3283 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 85.79 %
Parental protein coverage: 99.1 %
Number of stop codons detected: 1
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalGEALLLSRAGPA-ALGSASADSAALLGWARGQPAAA-PQPGLALAARRHYSEAVADREDDPNFFKMVEGF
GEAL.LSR.GP..ALGSA.A.SAALLG.A.G.P.AA.PQPGL.LAARRHYSE.VA.REDDP.FFK.VEGF
RetrocopyGEALRLSRVGPV<ALGSAAAHSAALLGRAGG*PTAA<PQPGLVLAARRHYSEEVAEREDDPSFFKTVEGF
ParentalFDRGASIVEDKLVEDLRTRESEEQKRNRVRGILRIIKPCNHVLSLSFPIRRDDGSWEVIEGYRAQHSQHR
F.RGASIV.DKLVEDLRTRESEEQKRNRV.GI.RII.PCNH.LS.SF.IRRDD.SWEV..GY.AQHSQHR
RetrocopyFNRGASIVQDKLVEDLRTRESEEQKRNRVGGIFRIINPCNHMLSVSFRIRRDDSSWEVTKGYPAQHSQHR
ParentalTPCKGGIRYSTDVSVDEVKALASLMTYKCAVVDVPFGGAKAGVKINPKNYTDNELEKITRRFTMELAKKG
.PC.GG..YSTDVS.DEVKALASLMT.KCAVV.V.F.GAKAGVKI.PK.YT.NELEKITRRFT.ELAKKG
RetrocopyMPCNGGVHYSTDVSIDEVKALASLMTCKCAVVGVSFWGAKAGVKISPKYYTNNELEKITRRFTIELAKKG
ParentalFIGPGIDVPAPDMSTGEREMSWIADTYASTIGHYDINAHACVTGKPISQGGIHGRISATGRGVFHGIENF
FIG.GIDVPAPDMSTGE.EMSWIAD.YASTIGHYDINAHACV.GKPISQGGIHGRISATG.GVFHGIENF
RetrocopyFIGCGIDVPAPDMSTGELEMSWIADAYASTIGHYDINAHACVIGKPISQGGIHGRISATGHGVFHGIENF
ParentalINEASYMSILGMTPGFGDKTFVVQGFGNVGLHSMRYLHRFGAKCIAVGESEGSIWNPDGIDPKELEDFKL
INEASYMSILGMT.GFG.KTF.VQGFGN.GLHSMRYLHRFGAKCIAVG.S.GSIWNPDGIDPKELEDFKL
RetrocopyINEASYMSILGMTSGFGGKTFFVQGFGNAGLHSMRYLHRFGAKCIAVGKSDGSIWNPDGIDPKELEDFKL
ParentalQHGSILGFPKAKPYEGSILEADCDILIPAASEKQLTKSNAPRVKAKIIAEGANGPTTPEADKIFLERNIM
QHGSI.GFPK.KPYEGSILE..CDILIPAASEKQL.KSN..RVKAKIIAEG.NGPTTPEADKIFLERNIM
RetrocopyQHGSIVGFPKVKPYEGSILEPYCDILIPAASEKQLSKSNESRVKAKIIAEGDNGPTTPEADKIFLERNIM
ParentalVIPDLYLNAGGVTVSYFEWLKNLNHVSYGRLTFKYERDSNYHLLMSVQESLERKFGKHGGTIPIVPTAEF
VIPDLY.NAGGVTVSYFEWLKNL.HVSYGRLTFKYER.SNYHL.MSV.E.LERK.GKHGGTIPIVPTAEF
RetrocopyVIPDLYMNAGGVTVSYFEWLKNLKHVSYGRLTFKYERNSNYHLFMSVEETLERKCGKHGGTIPIVPTAEF
ParentalQDRISGASEKDIVHSGLAYTMERSARQIMRTAMKYNL-GLDLRTAAYVNAIEKVFKVYNEAGVTFT
QDRISGASEKDI.HSGL..TME.SARQIM.TA.KY.L.G.DLR.AAYVN.IEKVFKVYNEAG.TFT
RetrocopyQDRISGASEKDIMHSGLVCTMEHSARQIMHTARKYKL<GMDLRAAAYVNTIEKVFKVYNEAGATFT

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 140 .90 RPM
SRP007412_cerebellum 0 .00 RPM 104 .43 RPM
SRP007412_heart 0 .00 RPM 109 .18 RPM
SRP007412_kidney 0 .05 RPM 315 .57 RPM
SRP007412_liver 0 .13 RPM 455 .56 RPM
SRP007412_testis 0 .11 RPM 31 .30 RPM
Pan troglodytes was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ptro_3283 retrocopy.
Pan troglodytes was not studied using FANTOM5 data.
retro_ptro_3283 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ptro_3283 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 20 parental genes, and 28 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000075402 retrocopies
Canis familiaris ENSCAFG000000160951 retrocopy
Choloepus hoffmanni ENSCHOG000000011011 retrocopy
Callithrix jacchus ENSCJAG000000116331 retrocopy
Dipodomys ordii ENSDORG000000097671 retrocopy
Equus caballus ENSECAG000000073712 retrocopies
Echinops telfairi ENSETEG000000196382 retrocopies
Homo sapiens ENSG000001486721 retrocopy
Gorilla gorilla ENSGGOG000000157701 retrocopy
Loxodonta africana ENSLAFG000000120591 retrocopy
Microcebus murinus ENSMICG000000165261 retrocopy
Monodelphis domestica ENSMODG000000027561 retrocopy
Nomascus leucogenys ENSNLEG000000116581 retrocopy
Otolemur garnettii ENSOGAG000000036411 retrocopy
Procavia capensis ENSPCAG000000086621 retrocopy
Pongo abelii ENSPPYG000000028273 retrocopies
Pan troglodytes ENSPTRG00000002711 4 retrocopies
Ictidomys tridecemlineatus ENSSTOG000000128431 retrocopy
Tarsius syrichta ENSTSYG000000015781 retrocopy
Tursiops truncatus ENSTTRG000000081451 retrocopy



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