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






(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
RNA Polymerase II actvity near the 5' end of retro_hsap_759 was not detected
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
No TSS is located nearby retro_hsap_759 retrocopy 5' end.
retro_hsap_759 was not experimentally validated.


Parental genes homology:
Parental genes homology involve 18 parental genes, and 18 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000184661 retrocopy
Bos taurus ENSBTAG000000010591 retrocopy
Canis familiaris ENSCAFG000000192861 retrocopy
Callithrix jacchus ENSCJAG000000111851 retrocopy
Equus caballus ENSECAG000000185091 retrocopy
Homo sapiens ENSG00000067829 1 retrocopy
retro_hsap_759 ,
Latimeria chalumnae ENSLACG000000073651 retrocopy
Loxodonta africana ENSLAFG000000069041 retrocopy
Macropus eugenii ENSMEUG000000139341 retrocopy
Myotis lucifugus ENSMLUG000000044571 retrocopy
Mustela putorius furoENSMPUG000000087811 retrocopy
Mus musculus ENSMUSG000000020101 retrocopy
Nomascus leucogenys ENSNLEG000000135401 retrocopy
Otolemur garnettii ENSOGAG000000067351 retrocopy
Pteropus vampyrus ENSPVAG000000131631 retrocopy
Rattus norvegicus ENSRNOG000000372841 retrocopy
Sus scrofa ENSSSCG000000127831 retrocopy
Tursiops truncatus ENSTTRG000000117281 retrocopy

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