RetrogeneDB ID:

retro_hsap_330

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:1:240333469..240334591(+)
Located in intron of:ENSG00000155816
Retrocopy
information
Ensembl ID:ENSG00000223694
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:ADH5
Ensembl ID:ENSG00000197894
Aliases:ADH5, ADH-3, ADHX, FALDH, FDH, GSH-FDH, GSNOR
Description:alcohol dehydrogenase 5 (class III), chi polypeptide [Source:HGNC Symbol;Acc:253]


Retrocopy-Parental alignment summary:






>retro_hsap_330
ATGGTGAACCAGGTTATCAAGTGCAAGGCTGCAGTTGCCTGGGAGGCTGGAAAGCCTCTCTCCGTAGAGGAGATAGAGGT
GGCACCCCTAAAGGCTCGTGAAGTTTGAATCAAGATCATTGCCACTGCAGTTTGCCATACCAATGCCTATACCCTGAGCA
GAGCTGATCCTGAGGGTTGTTTTCCAGTGATCTTGGGACATGAAGGTGCTGGAATTGTGGGAAGTGTTGGTGAGGGAGTT
GCTAAGCTGAAGGCGGGTGATAACTGTCATCCCATTTTACATCCCACAGTGTGGAGAATGCAAATTTTGTCTAAATCCTA
AAACTAACCTTGCCAGAATATAAGAGTCACTCAAGGGAAAGGATTAGTGCCAGATGGTACCAGCAGATTTACTTGCAAAG
GAAAGACAATTTTACATTACATGGGAACCAGCACATTTTCTGAATGCACAGTTGTGGCTGATATCTCTGTTGCTAAAATA
GATTCTTTAGCACCTTTGGATAAAGTCTGCCTTCTAGGTTGTGGCATTTCAGCTGGTTATGGTGCTGCTGTGAACACTGT
CAAGGTGGGGCCTGGCTCTGTTTGGGCCGTCTTTGGCCTGGGAGGAGTTGGATTGACAGTTATCGTGGGCGGTAAAGTGG
CTGGTGCATCCCGGATCATTGGTGTGGACATCCATCAAGATAAATTTCCAAGGGCTAAAGAGTTTGGAGCCACTGAATGT
ATGAACCGTCAGGATTTTAGTCAACCCATCCAGGAAGTGCTCATTGAGCGGACTGATGGAGGAGTGGACTACTCCTTTGA
ATGTATTAGGAATGTCAAGGTCGTGAGAGCAGCACTTGAGGCATGTCAGCAGGGCTGGGGCGTCAGTGTGGTGGTTGGAG
TAGCTGCTTCAGGTCAAGAAATTGCCACTCATCCATTCCAGCTGGTAACAGGTCGCACATGGAAAGGCACTGCCTTTGGA
GGGTGAAAGAGTGTAGAAAGTGTCCCAAAGTTGGTATCTGAATATGTGTCTAAAAAGATAAAAGTTGATGAATTTGTGAC
TCACAATCTGTCTTTTGATGAAATTAACAAAGCCTTTGAACTGTTGCATTCTGGAAAAAGCATTCGAACTGTTGTGAAGA
TT

ORF - retro_hsap_330 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 89.1 %
Parental protein coverage: 100. %
Number of stop codons detected: 2
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalMANEVIKCKAAVAWEAGKPLSIEEIEVAPPKAHEVRIKIIATAVCHTDAYTLSGADPEGCFPVILGHEGA
M.N.VIKCKAAVAWEAGKPLS.EEIEVAP.KA.EV.IKIIATAVCHT.AYTLS.ADPEGCFPVILGHEGA
RetrocopyMVNQVIKCKAAVAWEAGKPLSVEEIEVAPLKAREV*IKIIATAVCHTNAYTLSRADPEGCFPVILGHEGA
ParentalGIVESVGEGVTKLKAGD-TVIPLYIPQCGECKFCLNPKTNL-CQKIRVTQGKGLMPDGTSRFTCKGKTIL
GIV.SVGEGV.KLKAGD.TVIP.YIPQCGECKFCLNPKTNL.CQ.IRVTQGKGL.PDGTSRFTCKGKTIL
RetrocopyGIVGSVGEGVAKLKAGD>TVIPFYIPQCGECKFCLNPKTNL<CQNIRVTQGKGLVPDGTSRFTCKGKTIL
ParentalHYMGTSTFSEYTVVADISVAKIDPLAPLDKVCLLGCGISTGYGAAVNTAKLEPGSVCAVFGLGGVGLAVI
HYMGTSTFSE.TVVADISVAKID.LAPLDKVCLLGCGIS.GYGAAVNT.K..PGSV.AVFGLGGVGL.VI
RetrocopyHYMGTSTFSECTVVADISVAKIDSLAPLDKVCLLGCGISAGYGAAVNTVKVGPGSVWAVFGLGGVGLTVI
ParentalMGCKVAGASRIIGVDINKDKFARAKEFGATECINPQDFSKPIQEVLIEMTDGGVDYSFECIGNVKVMRAA
.G.KVAGASRIIGVDI..DKF.RAKEFGATEC.N.QDFS.PIQEVLIE.TDGGVDYSFECI.NVKV.RAA
RetrocopyVGGKVAGASRIIGVDIHQDKFPRAKEFGATECMNRQDFSQPIQEVLIERTDGGVDYSFECIRNVKVVRAA
ParentalLEACHKGWGVSVVVGVAASGEEIATRPFQLVTGRTWKGTAFGGWKSVESVPKLVSEYMSKKIKVDEFVTH
LEAC..GWGVSVVVGVAASG.EIAT.PFQLVTGRTWKGTAFGG.KSVESVPKLVSEY.SKKIKVDEFVTH
RetrocopyLEACQQGWGVSVVVGVAASGQEIATHPFQLVTGRTWKGTAFGG*KSVESVPKLVSEYVSKKIKVDEFVTH
ParentalNLSFDEINKAFELMHSGKSIRTVVKI
NLSFDEINKAFEL.HSGKSIRTVVKI
RetrocopyNLSFDEINKAFELLHSGKSIRTVVKI

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 131 .99 RPM
bodymap2_adrenal 0 .00 RPM 120 .26 RPM
bodymap2_brain 0 .19 RPM 83 .77 RPM
bodymap2_breast 0 .00 RPM 163 .62 RPM
bodymap2_colon 0 .00 RPM 203 .20 RPM
bodymap2_heart 0 .00 RPM 114 .35 RPM
bodymap2_kidney 0 .00 RPM 141 .74 RPM
bodymap2_liver 0 .00 RPM 125 .92 RPM
bodymap2_lung 0 .00 RPM 87 .41 RPM
bodymap2_lymph_node 0 .00 RPM 87 .42 RPM
bodymap2_ovary 0 .00 RPM 184 .77 RPM
bodymap2_prostate 0 .00 RPM 291 .74 RPM
bodymap2_skeletal_muscle 0 .00 RPM 101 .23 RPM
bodymap2_testis 0 .04 RPM 164 .42 RPM
bodymap2_thyroid 0 .00 RPM 153 .04 RPM
bodymap2_white_blood_cells 0 .02 RPM 74 .16 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_330 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_330 retrocopy.

TSS - click to see more details



TSS No. TSS Name TSS expression level (Expr) in TPM range:
no expression 0 < Expr ≤ 1 1 < Expr ≤ 5 5 < Expr ≤ 10 Expr > 10
TSS #1 TSS_91661209 libraries137 libraries755 libraries411 libraries317 libraries

The graphical summary, for retro_hsap_330 TSS expression levels > 0 TPM .
TSS expression levels were studied across 1829 TSS-CAGE libraries, based on FANTOM5 data.
The expression values were visualized using beanplot. If you have any doubts, how to read it, read more in Kampstra P (2008)

Display detail expression values in each library
... or ...
Directly download all expression values

Lab - click to see more details

retro_hsap_330 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_330 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_266
Gorilla gorilla retro_ggor_354
Pongo abelii retro_pabe_359
Parental genes homology:
Parental genes homology involve 12 parental genes, and 22 retrocopies.

Species Parental gene accession Retrocopies number
Canis familiaris ENSCAFG000000130071 retrocopy
retro_cfam_14,
Callithrix jacchus ENSCJAG000000071982 retrocopies
retro_cjac_1029, retro_cjac_2933,
Homo sapiens ENSG00000197894 3 retrocopies
retro_hsap_175, retro_hsap_330 , retro_hsap_3607,
Gorilla gorilla ENSGGOG000000282442 retrocopies
retro_ggor_2434, retro_ggor_354,
Myotis lucifugus ENSMLUG000000027221 retrocopy
retro_mluc_1702,
Macaca mulatta ENSMMUG000000035521 retrocopy
retro_mmul_299,
Mustela putorius furoENSMPUG000000096421 retrocopy
retro_mputfur_1625,
Nomascus leucogenys ENSNLEG000000139463 retrocopies
retro_nleu_1772, retro_nleu_2636, retro_nleu_983,
Pongo abelii ENSPPYG000000149463 retrocopies
retro_pabe_176, retro_pabe_359, retro_pabe_453,
Pan troglodytes ENSPTRG000000163033 retrocopies
retro_ptro_166, retro_ptro_2438, retro_ptro_266,
Sus scrofa ENSSSCG000000091851 retrocopy
retro_sscr_659,
Xenopus tropicalis ENSXETG000000093041 retrocopy
retro_xtro_57,

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 = 0.02 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 .00 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 .02 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).





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