RetrogeneDB ID:

retro_hsap_3724

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:7:43806888..43807195(+)
Located in intron of:ENSG00000106605
Retrocopy
information
Ensembl ID:ENSG00000229497
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:VMA21
Ensembl ID:ENSG00000160131
Aliases:VMA21, MEAX, XMEA
Description:VMA21 vacuolar H+-ATPase homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:22082]


Retrocopy-Parental alignment summary:






>retro_hsap_3724
GTGGAGCACCCAGATAAAGTGGCGCTGAACGCACTGCAGCCTCCTAAGTTCGGAAAAGAAAGCTCATTAGCATCTACACT
GAAGACGCTCCTGTTCTTCACAGCTTTAATGATCACTGTTCCTATCGGGTTATTTATATTTCACAACTAAATCTTATATA
TCTGGAGGCGCCCTTGGGATATCCAATAAGGACAGCTGTTTTTATGCTGCTATTGTTGCCGTGGTCACCGGCCATGTGGT
GCTGGCCCTCTTTATGTATGTGGTCTGGAATGAAGGCTCATGACAGTGACATGAAGGCAAACAGGAT

ORF - retro_hsap_3724 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 73.79 %
Parental protein coverage: 100. %
Number of stop codons detected: 2
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalMERPDKAALNALQPPEFRNESSLASTLKTLLFFTALMITVPIGLY-FTTKSYIFEG-ALGMSNRDSYFYA
.E.PDK.ALNALQPP.F..ESSLASTLKTLLFFTALMITVPIGL....T......G.ALG.SN.DS.FYA
RetrocopyVEHPDKVALNALQPPKFGKESSLASTLKTLLFFTALMITVPIGLF>YFTTKSYISGGALGISNKDSCFYA
ParentalAIVAVVAVHVVLALFVYVAWNEGSRQWREGKQD
AIVAVV..HVVLALF.YV.WNEGS.Q..EGKQD
RetrocopyAIVAVVTGHVVLALFMYVVWNEGS*Q*HEGKQD

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 63 .39 RPM
bodymap2_adrenal 0 .04 RPM 56 .48 RPM
bodymap2_brain 0 .00 RPM 78 .85 RPM
bodymap2_breast 0 .00 RPM 75 .37 RPM
bodymap2_colon 0 .00 RPM 38 .79 RPM
bodymap2_heart 0 .00 RPM 26 .51 RPM
bodymap2_kidney 0 .00 RPM 62 .33 RPM
bodymap2_liver 0 .00 RPM 20 .15 RPM
bodymap2_lung 0 .00 RPM 44 .50 RPM
bodymap2_lymph_node 0 .00 RPM 49 .67 RPM
bodymap2_ovary 0 .02 RPM 82 .95 RPM
bodymap2_prostate 0 .00 RPM 47 .86 RPM
bodymap2_skeletal_muscle 0 .00 RPM 21 .68 RPM
bodymap2_testis 0 .06 RPM 73 .83 RPM
bodymap2_thyroid 0 .00 RPM 69 .26 RPM
bodymap2_white_blood_cells 0 .00 RPM 67 .84 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity may be related with retro_hsap_3724 in 1 libraries
ENCODE library ID Target ChIP-Seq Peak coordinates
ENCFF002CXQ POLR2A 7:43806096..43806746

EST - click to see more details

No EST(s) were mapped for retro_hsap_3724 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_3724 retrocopy 5' end.

Lab - click to see more details

retro_hsap_3724 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_3724 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pongo abelii retro_pabe_3133
Macaca mulatta retro_mmul_1693
Parental genes homology:
Parental genes homology involve 11 parental genes, and 12 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000062961 retrocopy
retro_btau_1106,
Callithrix jacchus ENSCJAG000000039161 retrocopy
retro_cjac_150,
Dasypus novemcinctus ENSDNOG000000084261 retrocopy
retro_dnov_504,
Homo sapiens ENSG00000160131 1 retrocopy
retro_hsap_3724 ,
Macaca mulatta ENSMMUG000000090341 retrocopy
retro_mmul_1693,
Mus musculus ENSMUSG000000731312 retrocopies
retro_mmus_116, retro_mmus_3675,
Nomascus leucogenys ENSNLEG000000137111 retrocopy
retro_nleu_1971,
Oryctolagus cuniculus ENSOCUG000000152011 retrocopy
retro_ocun_443,
Pongo abelii ENSPPYG000000208201 retrocopy
retro_pabe_3133,
Rattus norvegicus ENSRNOG000000497441 retrocopy
retro_rnor_2843,
Ictidomys tridecemlineatus ENSSTOG000000111791 retrocopy
retro_itri_500,

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 = 0.1 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .00 RPM
CEU_NA11843 0 .00 RPM
CEU_NA11930 0 .10 RPM
CEU_NA12004 0 .00 RPM
CEU_NA12400 0 .04 RPM
CEU_NA12751 0 .02 RPM
CEU_NA12760 0 .00 RPM
CEU_NA12827 0 .00 RPM
CEU_NA12872 0 .03 RPM
CEU_NA12873 0 .00 RPM
FIN_HG00183 0 .05 RPM
FIN_HG00277 0 .04 RPM
FIN_HG00315 0 .03 RPM
FIN_HG00321 0 .03 RPM
FIN_HG00328 0 .02 RPM
FIN_HG00338 0 .00 RPM
FIN_HG00349 0 .03 RPM
FIN_HG00375 0 .02 RPM
FIN_HG00377 0 .03 RPM
FIN_HG00378 0 .02 RPM
GBR_HG00099 0 .03 RPM
GBR_HG00111 0 .02 RPM
GBR_HG00114 0 .03 RPM
GBR_HG00119 0 .05 RPM
GBR_HG00131 0 .00 RPM
GBR_HG00133 0 .00 RPM
GBR_HG00134 0 .00 RPM
GBR_HG00137 0 .03 RPM
GBR_HG00142 0 .03 RPM
GBR_HG00143 0 .00 RPM
TSI_NA20512 0 .00 RPM
TSI_NA20513 0 .00 RPM
TSI_NA20518 0 .03 RPM
TSI_NA20532 0 .03 RPM
TSI_NA20538 0 .00 RPM
TSI_NA20756 0 .00 RPM
TSI_NA20765 0 .00 RPM
TSI_NA20771 0 .03 RPM
TSI_NA20786 0 .03 RPM
TSI_NA20798 0 .00 RPM
YRI_NA18870 0 .00 RPM
YRI_NA18907 0 .03 RPM
YRI_NA18916 0 .00 RPM
YRI_NA19093 0 .03 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 .04 RPM

Indel association:

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



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