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






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 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

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_3283 retrocopy.

TSS - click to see more details

Pan troglodytes was not studied using FANTOM5 data.

Lab - click to see more details

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
retro_btau_1413, retro_btau_1741,
Canis familiaris ENSCAFG000000160951 retrocopy
retro_cfam_747,
Choloepus hoffmanni ENSCHOG000000011011 retrocopy
retro_chof_2002,
Callithrix jacchus ENSCJAG000000116331 retrocopy
retro_cjac_2830,
Dipodomys ordii ENSDORG000000097671 retrocopy
retro_dord_400,
Equus caballus ENSECAG000000073712 retrocopies
retro_ecab_886, retro_ecab_919,
Echinops telfairi ENSETEG000000196382 retrocopies
retro_etel_141, retro_etel_2024,
Homo sapiens ENSG000001486721 retrocopy
retro_hsap_31,
Gorilla gorilla ENSGGOG000000157701 retrocopy
retro_ggor_2954,
Loxodonta africana ENSLAFG000000120591 retrocopy
retro_lafr_504,
Microcebus murinus ENSMICG000000165261 retrocopy
retro_mmur_524,
Monodelphis domestica ENSMODG000000027561 retrocopy
retro_mdom_124,
Nomascus leucogenys ENSNLEG000000116581 retrocopy
retro_nleu_36,
Otolemur garnettii ENSOGAG000000036411 retrocopy
retro_ogar_2757,
Procavia capensis ENSPCAG000000086621 retrocopy
retro_pcap_11,
Pongo abelii ENSPPYG000000028273 retrocopies
retro_pabe_3109, retro_pabe_3213, retro_pabe_79,
Pan troglodytes ENSPTRG00000002711 4 retrocopies
retro_ptro_3162, retro_ptro_3283 , retro_ptro_3285, retro_ptro_3290,
Ictidomys tridecemlineatus ENSSTOG000000128431 retrocopy
retro_itri_737,
Tarsius syrichta ENSTSYG000000015781 retrocopy
retro_tsyr_313,
Tursiops truncatus ENSTTRG000000081451 retrocopy
retro_ttru_950,


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