RetrogeneDB ID:

retro_hsap_759

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:11:21305326..21306491(+)
Located in intron of:ENSG00000165973
Retrocopy
information
Ensembl ID:ENSG00000225477
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:IDH3G
Ensembl ID:ENSG00000067829
Aliases:IDH3G, H-IDHG
Description:isocitrate dehydrogenase 3 (NAD+) gamma [Source:HGNC Symbol;Acc:5386]


Retrocopy-Parental alignment summary:






>retro_hsap_759
TTGGTATTGAAGATGCTGACAGTAGCCAGTGGCTCTGTGAAGGCAATTTTCCAACCTACCATTCTTGGCTACTCCTGGGA
TATTTTACTTGGCTGTGAGATCCCCCTGAGAAGCTTCTCTTTTTCTCACACAATTCCTCCATCAGCGAAGTGTGGTGGGC
AGCACACAGTGACTATGATTCCTGGAGATGGCACTGGGACTGAACTTATGCTGCCTGTCAAGATTATGTTCAGACATGTG
TGTGTGCCTGTGGACTTTGAGGGAATGTCAGTGACCTCCACCTCTGCCTCACATGAAGAGGAAATTCATAATGCCATCAT
GGCAGTTCATTGAAACCGTGTGGCTTTGAAGAGTAGCGTTAAAACTGACGACACCCTGCCACCATCATACAAATCCTTCA
ACAACATGTTGCATACCACCCTAGATCTCTATGCCAGTGTCATTCATTTAAAAAATTTGCCAAACGTGGAGACCTGGCAC
AAAGATGTAGACATCCTAGTTGTTTGGGAAAACACAGAGGGTGAGTATAGCAATCTGGAGCATGAGAGTGTGAAAGGAGT
GACAGAGAGCCTAAAGATCATGACTAAGGCCAAGTCTTTGTGCATTGCTGAATATGCCTTCCAGCTGGCCCAGAAGATGG
GATGCAAAAAAGTGATGGCTGTGCACAAGGTCAACATCACGAAACTGGGAGATGGTCTCTTCCTCCAGTGCTGTGGGGGA
GGTGGCATCCCGCTATCCTCAGCTCACCTTAGAAGACATGATTGTGGAGAATGCCACAATGCAGTGAGTATCCCAGCCCC
AACAGTTTGATGTCATGGTAATGCTCAGTCTTTATGGCAATGTTATCAACAGTGTCTGCACAGGTTTGATTGGTGGGGCA
GGCCTTGTGCCTGGAGCCAACTATGTCTATATGTATGCAGTGTTTGAGACAGCTTCAAGGCAATGTGACAATTTAGTCAA
TACAAATCTGGCAAACCCTACCGCCATGCTGCTGGCAATTTGTATCATGCTGGATTACCTCAAACTCCACTCCTATGCCA
CCCACATTAATACTGCAGTCTTGGCATCCTTGGACAACAAAAGTGTCCACACTGCAGACCTTGGAGGCCAGGGTACCACA
TTGGACATCATTCAAAACATCATAGACCACATTTGAAATGTCAAT

ORF - retro_hsap_759 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 64.62 %
Parental protein coverage: 98.47 %
Number of stop codons detected: 3
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalMALKVATVAGSAAKAVLGPALLCRPWEVLGAHEVPSRNIFSEQTIPPSAKYGGRHTVTMIPGDGIGPELM
..LK..TVA....KA...P..L...W..L...E.P.R......TIPPSAK.GG.HTVTMIPGDG.G.ELM
RetrocopyLVLKMLTVASGSVKAIFQPTILGYSWDILLGCEIPLRSFSFSHTIPPSAKCGGQHTVTMIPGDGTGTELM
ParentalLHVKSVFRHACVPVDFEEVHVSSNA--DEEDIRNAIMAIRRNRVALKGNIETNHNLPPSHKSRNNILRTS
L.VK..FRH.CVPVDFE...V.S.....EE.I.NAIMA...NRVALK....T...LPPS.KS.NN.L.T.
RetrocopyLPVKIMFRHVCVPVDFEGMSVTSTSASHEEEIHNAIMAVH*NRVALKSSVKTDDTLPPSYKSFNNMLHTT
ParentalLDLYANVIHCKSLPGVVTRHKDIDILIVRENTEGEYSSLEHESVAGVVESLKIITKAKSLRIAEYAFKLA
LDLYA.VIH.K.LP.V.T.HKD.DIL.V.ENTEGEYS.LEHESV.GV.ESLKI.TKAKSL.IAEYAF.LA
RetrocopyLDLYASVIHLKNLPNVETWHKDVDILVVWENTEGEYSNLEHESVKGVTESLKIMTKAKSLCIAEYAFQLA
ParentalQESGRKKVTAVHKANIMKLGDGLFLQCCR-EVAARYPQITFENMIVDNTTMQLVSRPQQFDVMVMPNLYG
Q..G.KKV.AVHK.NI.KLGDGLFLQCC..EVA.RYPQ.T.E.MIV.N.TMQ.VS.PQQFDVMVM..LYG
RetrocopyQKMGCKKVMAVHKVNITKLGDGLFLQCCG>EVASRYPQLTLEDMIVENATMQ*VSQPQQFDVMVMLSLYG
ParentalNIVNNVCAGLVGGPGLVAGANYGHVYAVFETATRNTGKSIANKNIANPTATLLASCMMLDHLKLHSYATS
N..N.VC.GL.GG.GLV.GANY...YAVFETA.R.......N.N.ANPTA.LLA.C.MLD.LKLHSYAT.
RetrocopyNVINSVCTGLIGGAGLVPGANYVYMYAVFETASRQC-DNLVNTNLANPTAMLLAICIMLDYLKLHSYATH
ParentalIRKAVLASMDNENMHTPDIGGQGTTSEAIQDVIRHIRVIN
I..AVLAS.DN...HT.D.GGQGTT...IQ..I.HI...N
RetrocopyINTAVLASLDNKSVHTADLGGQGTTLDIIQNIIDHI*NVN

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
bodymap2_adipose 0 .00 RPM 29 .80 RPM
bodymap2_adrenal 0 .00 RPM 29 .93 RPM
bodymap2_brain 0 .00 RPM 21 .96 RPM
bodymap2_breast 0 .00 RPM 22 .08 RPM
bodymap2_colon 0 .00 RPM 17 .38 RPM
bodymap2_heart 0 .00 RPM 25 .53 RPM
bodymap2_kidney 0 .00 RPM 32 .22 RPM
bodymap2_liver 0 .00 RPM 14 .26 RPM
bodymap2_lung 0 .00 RPM 25 .05 RPM
bodymap2_lymph_node 0 .00 RPM 25 .73 RPM
bodymap2_ovary 0 .00 RPM 29 .49 RPM
bodymap2_prostate 0 .00 RPM 32 .87 RPM
bodymap2_skeletal_muscle 0 .00 RPM 53 .60 RPM
bodymap2_testis 1 .51 RPM 26 .24 RPM
bodymap2_thyroid 0 .00 RPM 26 .67 RPM
bodymap2_white_blood_cells 0 .00 RPM 33 .82 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_759 was not detected

EST - click to see more details

1 EST(s) were mapped to retro_hsap_759 retrocopy
EST ID Start End Identity Match Mis-match Score
DB050592 21305242 21305804 100 562 0 562

TSS - click to see more details

No TSS is located nearby retro_hsap_759 retrocopy 5' end.

Lab - click to see more details

retro_hsap_759 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_759 has 7 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_534
Mus musculus retro_mmus_134
Oryctolagus cuniculus retro_ocun_80
Bos taurus retro_btau_1194
Sus scrofa retro_sscr_662
Canis familiaris retro_cfam_1023
Equus caballus retro_ecab_941
Parental genes homology:
Parental genes homology involve 18 parental genes, and 18 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000184661 retrocopy
retro_amel_1892,
Bos taurus ENSBTAG000000010591 retrocopy
retro_btau_1194,
Canis familiaris ENSCAFG000000192861 retrocopy
retro_cfam_1023,
Callithrix jacchus ENSCJAG000000111851 retrocopy
retro_cjac_1597,
Equus caballus ENSECAG000000185091 retrocopy
retro_ecab_941,
Homo sapiens ENSG00000067829 1 retrocopy
retro_hsap_759 ,
Latimeria chalumnae ENSLACG000000073651 retrocopy
retro_lcha_17,
Loxodonta africana ENSLAFG000000069041 retrocopy
retro_lafr_560,
Macropus eugenii ENSMEUG000000139341 retrocopy
retro_meug_203,
Myotis lucifugus ENSMLUG000000044571 retrocopy
retro_mluc_396,
Mustela putorius furoENSMPUG000000087811 retrocopy
retro_mputfur_644,
Mus musculus ENSMUSG000000020101 retrocopy
retro_mmus_134,
Nomascus leucogenys ENSNLEG000000135401 retrocopy
retro_nleu_394,
Otolemur garnettii ENSOGAG000000067351 retrocopy
retro_ogar_25,
Pteropus vampyrus ENSPVAG000000131631 retrocopy
retro_pvam_373,
Rattus norvegicus ENSRNOG000000372841 retrocopy
retro_rnor_209,
Sus scrofa ENSSSCG000000127831 retrocopy
retro_sscr_662,
Tursiops truncatus ENSTTRG000000117281 retrocopy
retro_ttru_848,

Expression level across human populations :
image/svg+xml GBR_HG00142 GBR_HG00099 GBR_HG00114 GBR_HG00143 GBR_HG00131 GBR_HG00137 GBR_HG00133 GBR_HG00119 GBR_HG00111 GBR_HG00134 FIN_HG00378 FIN_HG00338 FIN_HG00349 FIN_HG00375 FIN_HG00315 FIN_HG00277 FIN_HG00328 FIN_HG00321 FIN_HG00377 FIN_HG00183 TSI_NA20756 TSI_NA20538 TSI_NA20798 TSI_NA20532 TSI_NA20765 TSI_NA20518 TSI_NA20513 TSI_NA20512 TSI_NA20771 TSI_NA20786 YRI_NA19114 YRI_NA19099 YRI_NA18870 YRI_NA18907 YRI_NA19223 YRI_NA19214 YRI_NA18916 YRI_NA19093 YRI_NA19118 YRI_NA19213 Toscaniin Italia: Finnish inFinland: British in England and Scotland: Utah Residents (CEPH) with Northernand Western European Ancestry: Yoruba in Ibadan, Nigeria: CEU_NA12760 CEU_NA12827 CEU_NA12872 CEU_NA12751 CEU_NA12873 CEU_NA12400 CEU_NA11930 CEU_NA12004 CEU_NA11831 CEU_NA11843 No expression ( = 0 RPM ) > 0 RPM = 0.03 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .00 RPM
CEU_NA11843 0 .00 RPM
CEU_NA11930 0 .00 RPM
CEU_NA12004 0 .00 RPM
CEU_NA12400 0 .00 RPM
CEU_NA12751 0 .00 RPM
CEU_NA12760 0 .00 RPM
CEU_NA12827 0 .00 RPM
CEU_NA12872 0 .00 RPM
CEU_NA12873 0 .00 RPM
FIN_HG00183 0 .00 RPM
FIN_HG00277 0 .00 RPM
FIN_HG00315 0 .00 RPM
FIN_HG00321 0 .03 RPM
FIN_HG00328 0 .00 RPM
FIN_HG00338 0 .00 RPM
FIN_HG00349 0 .00 RPM
FIN_HG00375 0 .00 RPM
FIN_HG00377 0 .00 RPM
FIN_HG00378 0 .00 RPM
GBR_HG00099 0 .00 RPM
GBR_HG00111 0 .00 RPM
GBR_HG00114 0 .00 RPM
GBR_HG00119 0 .00 RPM
GBR_HG00131 0 .00 RPM
GBR_HG00133 0 .00 RPM
GBR_HG00134 0 .00 RPM
GBR_HG00137 0 .00 RPM
GBR_HG00142 0 .00 RPM
GBR_HG00143 0 .00 RPM
TSI_NA20512 0 .00 RPM
TSI_NA20513 0 .00 RPM
TSI_NA20518 0 .00 RPM
TSI_NA20532 0 .00 RPM
TSI_NA20538 0 .00 RPM
TSI_NA20756 0 .00 RPM
TSI_NA20765 0 .00 RPM
TSI_NA20771 0 .00 RPM
TSI_NA20786 0 .00 RPM
TSI_NA20798 0 .00 RPM
YRI_NA18870 0 .00 RPM
YRI_NA18907 0 .00 RPM
YRI_NA18916 0 .00 RPM
YRI_NA19093 0 .00 RPM
YRI_NA19099 0 .00 RPM
YRI_NA19114 0 .00 RPM
YRI_NA19118 0 .00 RPM
YRI_NA19213 0 .00 RPM
YRI_NA19214 0 .00 RPM
YRI_NA19223 0 .00 RPM

Indel association:

No indels were associated with its genomic coordinates. Based on Kabza et al. 2015 (PubMed).



Copyright © RetrogeneDB 2014-2017