RetrogeneDB ID:

retro_hsap_2114

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:2:65432242..65433121(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000172974
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:VDAC2
Ensembl ID:ENSG00000165637
Aliases:VDAC2, POR
Description:voltage-dependent anion channel 2 [Source:HGNC Symbol;Acc:12672]


Retrocopy-Parental alignment summary:






>retro_hsap_2114
ATGGCGACCCACGGACAGACTTGCGCGCGTCCAATGTGTATTCCTCCATCATATGCTGACCTTGGCAAAGCTGCCAGAGA
TATTTTCAACAAAGGATTTGGTTTTGGGTTGGTGAAACTGGATGTGAAAACAAAGTCTTGCAGTGGCGTGGAATTTTCAA
CGTCCGGTTCATCTAATACAGACACTGGTAAAGTTACTGGGACCCTGGAGACCAAATACAAGTGGTGTGAGTATGGTCTG
ACTTTCACAGAAAAGTGGAACACTGATAACACTCTGGGAACAGAAATCGCAATTGAAGACCAGATTTGTCAAGGTTTGAA
ACTGACATTTGATACTACCTTCTCACCAAACACAGGAAAGAAAAGTGGTAAAATCAAGTCTTACAAGAGGGAGTGTATAA
ACCTTGGTTGTGATGTTGACTTTGATTTTGCTGGACCTGCAATCCATGGTTCAGCTGTCTTTGGTTATGAGGGCTGGCTT
GCTGGCTACCAGATGACCTTTGACAGTGCCAAATCAAAGCTGACAAGGAATAACTTTGCAGTGGGCTACAGGACTGGGGA
CTTCCAGCTACACACTAATGTCAATGATGGGACAGAATTTGGAGGATCAATTTATCAGAAAGTTTGTGAAGATCTTGACA
CTTCAGTAAACCTTGCTTGGACATCAGGTACCAACTGCACTCGTTTTGGCATTGCAGCTAAATATCAGTTGGATCCCACT
GCTTCCATTTCTGCAAAAGTCAACAACTCTAGCTTAATTGGAGTAGGCTATACTCAGACTCTGAGGCCTGGTGTGAAGCT
TACACTCTCTGCTCTGGTAGACGGGAAGAGCATTAATGCTGGAGGCCACAAGGTTGGGCTCGCCCTGGAGTTGGAGGCT

ORF - retro_hsap_2114 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 99.66 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMATHGQTCARPMCIPPSYADLGKAARDIFNKGFGFGLVKLDVKTKSCSGVEFSTSGSSNTDTGKVTGTLE
MATHGQTCARPMCIPPSYADLGKAARDIFNKGFGFGLVKLDVKTKSCSGVEFSTSGSSNTDTGKVTGTLE
RetrocopyMATHGQTCARPMCIPPSYADLGKAARDIFNKGFGFGLVKLDVKTKSCSGVEFSTSGSSNTDTGKVTGTLE
ParentalTKYKWCEYGLTFTEKWNTDNTLGTEIAIEDQICQGLKLTFDTTFSPNTGKKSGKIKSSYKRECINLGCDV
TKYKWCEYGLTFTEKWNTDNTLGTEIAIEDQICQGLKLTFDTTFSPNTGKKSGKIK.SYKRECINLGCDV
RetrocopyTKYKWCEYGLTFTEKWNTDNTLGTEIAIEDQICQGLKLTFDTTFSPNTGKKSGKIK-SYKRECINLGCDV
ParentalDFDFAGPAIHGSAVFGYEGWLAGYQMTFDSAKSKLTRNNFAVGYRTGDFQLHTNVNDGTEFGGSIYQKVC
DFDFAGPAIHGSAVFGYEGWLAGYQMTFDSAKSKLTRNNFAVGYRTGDFQLHTNVNDGTEFGGSIYQKVC
RetrocopyDFDFAGPAIHGSAVFGYEGWLAGYQMTFDSAKSKLTRNNFAVGYRTGDFQLHTNVNDGTEFGGSIYQKVC
ParentalEDLDTSVNLAWTSGTNCTRFGIAAKYQLDPTASISAKVNNSSLIGVGYTQTLRPGVKLTLSALVDGKSIN
EDLDTSVNLAWTSGTNCTRFGIAAKYQLDPTASISAKVNNSSLIGVGYTQTLRPGVKLTLSALVDGKSIN
RetrocopyEDLDTSVNLAWTSGTNCTRFGIAAKYQLDPTASISAKVNNSSLIGVGYTQTLRPGVKLTLSALVDGKSIN
ParentalAGGHKVGLALELEA
AGGHKVGLALELEA
RetrocopyAGGHKVGLALELEA

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 .60 RPM 50 .25 RPM
bodymap2_adrenal 0 .74 RPM 42 .99 RPM
bodymap2_brain 1 .41 RPM 73 .72 RPM
bodymap2_breast 0 .82 RPM 57 .30 RPM
bodymap2_colon 1 .14 RPM 97 .32 RPM
bodymap2_heart 0 .61 RPM 122 .42 RPM
bodymap2_kidney 0 .60 RPM 68 .33 RPM
bodymap2_liver 0 .34 RPM 24 .97 RPM
bodymap2_lung 0 .62 RPM 58 .23 RPM
bodymap2_lymph_node 0 .27 RPM 47 .16 RPM
bodymap2_ovary 1 .27 RPM 58 .76 RPM
bodymap2_prostate 0 .94 RPM 105 .95 RPM
bodymap2_skeletal_muscle 1 .58 RPM 123 .04 RPM
bodymap2_testis 0 .96 RPM 65 .55 RPM
bodymap2_thyroid 0 .58 RPM 76 .15 RPM
bodymap2_white_blood_cells 0 .39 RPM 40 .16 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_2114 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_2114 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_124386127 libraries124 libraries160 libraries383 libraries1035 libraries

The graphical summary, for retro_hsap_2114 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_2114 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_2114 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 18 parental genes, and 41 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000129752 retrocopies
retro_btau_1252, retro_btau_1389,
Canis familiaris ENSCAFG000000153981 retrocopy
retro_cfam_376,
Callithrix jacchus ENSCJAG000000011451 retrocopy
retro_cjac_2385,
Felis catus ENSFCAG000000269433 retrocopies
retro_fcat_1385, retro_fcat_804, retro_fcat_815,
Homo sapiens ENSG000000786681 retrocopy
retro_hsap_1375,
Homo sapiens ENSG00000165637 1 retrocopy
retro_hsap_2114 ,
Homo sapiens ENSG0000021358513 retrocopies
retro_hsap_1119, retro_hsap_1250, retro_hsap_2250, retro_hsap_2805, retro_hsap_308, retro_hsap_3527, retro_hsap_4287, retro_hsap_458, retro_hsap_4721, retro_hsap_4831, retro_hsap_4872, retro_hsap_4930, retro_hsap_847,
Gorilla gorilla ENSGGOG000000058615 retrocopies
retro_ggor_1677, retro_ggor_1949, retro_ggor_2934, retro_ggor_3036, retro_ggor_425,
Macropus eugenii ENSMEUG000000129951 retrocopy
retro_meug_30,
Myotis lucifugus ENSMLUG000000075002 retrocopies
retro_mluc_1710, retro_mluc_2252,
Mustela putorius furoENSMPUG000000032681 retrocopy
retro_mputfur_354,
Mus musculus ENSMUSG000000217711 retrocopy
retro_mmus_2667,
Otolemur garnettii ENSOGAG000000300391 retrocopy
retro_ogar_2116,
Rattus norvegicus ENSRNOG000000135051 retrocopy
retro_rnor_2652,
Sarcophilus harrisii ENSSHAG000000120481 retrocopy
retro_shar_325,
Tupaia belangeri ENSTBEG000000019464 retrocopies
retro_tbel_1504, retro_tbel_1541, retro_tbel_1885, retro_tbel_4597,
Tarsius syrichta ENSTSYG000000047641 retrocopy
retro_tsyr_14,
Vicugna pacos ENSVPAG000000080681 retrocopy
retro_vpac_156,

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 = 2.53 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .75 RPM
CEU_NA11843 0 .97 RPM
CEU_NA11930 1 .30 RPM
CEU_NA12004 0 .38 RPM
CEU_NA12400 0 .70 RPM
CEU_NA12751 0 .73 RPM
CEU_NA12760 1 .98 RPM
CEU_NA12827 1 .04 RPM
CEU_NA12872 0 .68 RPM
CEU_NA12873 0 .48 RPM
FIN_HG00183 1 .18 RPM
FIN_HG00277 0 .92 RPM
FIN_HG00315 0 .80 RPM
FIN_HG00321 0 .42 RPM
FIN_HG00328 0 .69 RPM
FIN_HG00338 0 .57 RPM
FIN_HG00349 2 .02 RPM
FIN_HG00375 0 .90 RPM
FIN_HG00377 0 .61 RPM
FIN_HG00378 1 .08 RPM
GBR_HG00099 1 .08 RPM
GBR_HG00111 0 .52 RPM
GBR_HG00114 0 .47 RPM
GBR_HG00119 0 .67 RPM
GBR_HG00131 0 .66 RPM
GBR_HG00133 0 .55 RPM
GBR_HG00134 0 .63 RPM
GBR_HG00137 0 .80 RPM
GBR_HG00142 1 .00 RPM
GBR_HG00143 0 .70 RPM
TSI_NA20512 0 .57 RPM
TSI_NA20513 0 .56 RPM
TSI_NA20518 2 .53 RPM
TSI_NA20532 0 .65 RPM
TSI_NA20538 1 .01 RPM
TSI_NA20756 1 .48 RPM
TSI_NA20765 0 .50 RPM
TSI_NA20771 0 .88 RPM
TSI_NA20786 0 .55 RPM
TSI_NA20798 0 .97 RPM
YRI_NA18870 1 .02 RPM
YRI_NA18907 0 .69 RPM
YRI_NA18916 0 .46 RPM
YRI_NA19093 0 .73 RPM
YRI_NA19099 1 .09 RPM
YRI_NA19114 0 .87 RPM
YRI_NA19118 0 .87 RPM
YRI_NA19213 0 .77 RPM
YRI_NA19214 0 .49 RPM
YRI_NA19223 0 .56 RPM

Indel association:

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





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