RetrogeneDB ID:

retro_hsap_3186

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:5:68629733..68630076(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000215006
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:CHCHD2
Ensembl ID:ENSG00000106153
Aliases:CHCHD2, C7orf17
Description:coiled-coil-helix-coiled-coil-helix domain containing 2 [Source:HGNC Symbol;Acc:21645]


Retrocopy-Parental alignment summary:






>retro_hsap_3186
ATGCCGCGTGGAAGCCGAAGCCGCACCTCCCGCATGGCCCCTCCGGCCAGCCAGGCCCCCTCAGATGAGAGCTGCACCCA
GGCCAGTACCAGTCGTTCAGCCACCAGCAGCGGCACCCCCATCTGTAGTTGGCTCTTCTGCTGCTGCGCCCCGGCAGCCA
GGTCTGATGGCCCAGATGGCAACCACTGCAGCTGGCGTGGCTGTGGGCTCTGCTGTGGGTCACGCCATTACTGGGGCTTT
CAGGGGAGGAAGTAATGCTGAGCCTGCGAGGCCTGACATCACTTACCAGGAGCCTCAGGGAACCCAGCCGGCACAGCAGC
AGCAGCCTTGCTTCTATGAGATC

ORF - retro_hsap_3186 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 89.92 %
Parental protein coverage: 78.15 %
Number of stop codons detected: 0
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalMPRGSRSRTSRMAPPASRAP-QMRAAPRPAPVAQPPAAAPPSAVGSSAAAPRQPGLMAQMATTAAGVAVG
MPRGSRSRTSRMAPPAS.AP.QMRAAPRP.PV.QPPAAAPPS.VGSSAAAPRQPGLMAQMATTAAGVAVG
RetrocopyMPRGSRSRTSRMAPPASQAP>QMRAAPRPVPVVQPPAAAPPSVVGSSAAAPRQPGLMAQMATTAAGVAVG
ParentalSAVGHTLGHAITGGFSGGSNAEPARPDITYQEPQGTQPAQQQQPCLYEI
SAVGH....AITG.F.GGSNAEPARPDITYQEPQGTQPAQQQQPC.YEI
RetrocopySAVGH----AITGAFRGGSNAEPARPDITYQEPQGTQPAQQQQPCFYEI

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 .06 RPM 53 .91 RPM
bodymap2_adrenal 0 .33 RPM 76 .11 RPM
bodymap2_brain 0 .19 RPM 94 .58 RPM
bodymap2_breast 0 .04 RPM 64 .24 RPM
bodymap2_colon 0 .29 RPM 98 .92 RPM
bodymap2_heart 0 .04 RPM 85 .79 RPM
bodymap2_kidney 0 .56 RPM 120 .61 RPM
bodymap2_liver 0 .04 RPM 78 .90 RPM
bodymap2_lung 0 .00 RPM 126 .37 RPM
bodymap2_lymph_node 0 .11 RPM 94 .57 RPM
bodymap2_ovary 0 .15 RPM 67 .18 RPM
bodymap2_prostate 0 .07 RPM 109 .97 RPM
bodymap2_skeletal_muscle 0 .05 RPM 96 .85 RPM
bodymap2_testis 0 .43 RPM 123 .05 RPM
bodymap2_thyroid 0 .15 RPM 76 .40 RPM
bodymap2_white_blood_cells 0 .12 RPM 95 .11 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity may be related with retro_hsap_3186 in 39 libraries
ENCODE library ID Target ChIP-Seq Peak coordinates
ENCFF002CFW POLR2A 5:68628381..68628878
ENCFF002CFX POLR2A 5:68628383..68628878
ENCFF002CGN POLR2A 5:68628385..68628855
ENCFF002CHO POLR2A 5:68628324..68628925
ENCFF002CIH POLR2A 5:68628571..68628870
ENCFF002CIO POLR2A 5:68628360..68628886
ENCFF002CJZ POLR2A 5:68628371..68628905
ENCFF002CKX POLR2A 5:68628375..68628871
ENCFF002CLM POLR2A 5:68628292..68628832
ENCFF002CMI POLR2A 5:68628363..68628888
ENCFF002COJ POLR2A 5:68628348..68628784
ENCFF002CPG POLR2A 5:68628542..68628859
ENCFF002CPH POLR2A 5:68628364..68628754
ENCFF002CQA POLR2A 5:68628397..68628892
ENCFF002CQC POLR2A 5:68628395..68628852
ENCFF002CQE POLR2A 5:68628389..68628854
ENCFF002CQG POLR2A 5:68628391..68628834
ENCFF002CQI POLR2A 5:68628408..68628839
ENCFF002CQK POLR2A 5:68628362..68628879
ENCFF002CQM POLR2A 5:68628396..68628832
ENCFF002CQO POLR2A 5:68628372..68628874
ENCFF002CRK POLR2A 5:68628310..68628834
ENCFF002CRK POLR2A 5:68628510..68629034
ENCFF002CRO POLR2A 5:68628371..68628791
ENCFF002CSY POLR2A 5:68628282..68628955
ENCFF002CUQ POLR2A 5:68628361..68628869
ENCFF002CXM POLR2A 5:68628337..68628827
ENCFF002CXN POLR2A 5:68628422..68628918
ENCFF002CXO POLR2A 5:68628354..68628778
ENCFF002CXP POLR2A 5:68628468..68628738
ENCFF002CZC POLR2A 5:68628373..68628905
ENCFF002CZD POLR2A 5:68628426..68628889
ENCFF002CZQ POLR2A 5:68628476..68628768
ENCFF002CZQ POLR2A 5:68628558..68629008
ENCFF002CZW POLR2A 5:68628351..68628795
ENCFF002CZW POLR2A 5:68628624..68628812
ENCFF002CZY POLR2A 5:68628354..68628898
ENCFF002DAK POLR2A 5:68628310..68628810
ENCFF002DAK POLR2A 5:68628509..68629009
ENCFF002DAY POLR2A 5:68628380..68629016
ENCFF002DBO POLR2A 5:68628398..68628839
ENCFF002DBP POLR2A 5:68628415..68628804
ENCFF002DBT POLR2A 5:68628388..68628758

EST - click to see more details

No EST(s) were mapped for retro_hsap_3186 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_155355937 libraries694 libraries197 libraries1 library0 libraries

The graphical summary, for retro_hsap_3186 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_3186 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_3186 has 1 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_2259
Parental genes homology:
Parental genes homology involve 19 parental genes, and 72 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000160502 retrocopies
retro_amel_500, retro_amel_976,
Bos taurus ENSBTAG000000402952 retrocopies
retro_btau_397, retro_btau_768,
Canis familiaris ENSCAFG000000101781 retrocopy
retro_cfam_1653,
Callithrix jacchus ENSCJAG000000212671 retrocopy
retro_cjac_271,
Erinaceus europaeus ENSEEUG000000128571 retrocopy
retro_eeur_398,
Echinops telfairi ENSETEG000000085981 retrocopy
retro_etel_45,
Homo sapiens ENSG00000106153 8 retrocopies
retro_hsap_116, retro_hsap_1180, retro_hsap_1995, retro_hsap_3063, retro_hsap_3186 , retro_hsap_4057, retro_hsap_4184, retro_hsap_4752,
Gorilla gorilla ENSGGOG000000149388 retrocopies
retro_ggor_2103, retro_ggor_220, retro_ggor_2725, retro_ggor_2807, retro_ggor_2808, retro_ggor_2958, retro_ggor_918, retro_ggor_989,
Myotis lucifugus ENSMLUG000000151511 retrocopy
retro_mluc_345,
Mus musculus ENSMUSG000000704932 retrocopies
retro_mmus_2340, retro_mmus_2536,
Nomascus leucogenys ENSNLEG000000158196 retrocopies
retro_nleu_1250, retro_nleu_1657, retro_nleu_2096, retro_nleu_2108, retro_nleu_555, retro_nleu_770,
Otolemur garnettii ENSOGAG000000100975 retrocopies
retro_ogar_1161, retro_ogar_158, retro_ogar_1848, retro_ogar_2837, retro_ogar_34,
Pongo abelii ENSPPYG000000175434 retrocopies
retro_pabe_131, retro_pabe_139, retro_pabe_1755, retro_pabe_496,
Pan troglodytes ENSPTRG000000192099 retrocopies
retro_ptro_129, retro_ptro_1331, retro_ptro_2065, retro_ptro_2259, retro_ptro_2750, retro_ptro_2838, retro_ptro_3046, retro_ptro_3167, retro_ptro_809,
Sus scrofa ENSSSCG000000077431 retrocopy
retro_sscr_515,
Ictidomys tridecemlineatus ENSSTOG000000105123 retrocopies
retro_itri_1870, retro_itri_670, retro_itri_671,
Tupaia belangeri ENSTBEG0000001290515 retrocopies
retro_tbel_1728, retro_tbel_1891, retro_tbel_2513, retro_tbel_2593, retro_tbel_2596, retro_tbel_2658, retro_tbel_3331, retro_tbel_3764, retro_tbel_3777, retro_tbel_3954, retro_tbel_4082, retro_tbel_4368, retro_tbel_4487, retro_tbel_4728, retro_tbel_817,
Tursiops truncatus ENSTTRG000000151851 retrocopy
retro_ttru_520,
Vicugna pacos ENSVPAG000000061041 retrocopy
retro_vpac_48,

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 = 0.47 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .47 RPM
CEU_NA11843 0 .43 RPM
CEU_NA11930 0 .07 RPM
CEU_NA12004 0 .15 RPM
CEU_NA12400 0 .07 RPM
CEU_NA12751 0 .10 RPM
CEU_NA12760 0 .31 RPM
CEU_NA12827 0 .24 RPM
CEU_NA12872 0 .00 RPM
CEU_NA12873 0 .29 RPM
FIN_HG00183 0 .16 RPM
FIN_HG00277 0 .22 RPM
FIN_HG00315 0 .08 RPM
FIN_HG00321 0 .15 RPM
FIN_HG00328 0 .14 RPM
FIN_HG00338 0 .13 RPM
FIN_HG00349 0 .20 RPM
FIN_HG00375 0 .22 RPM
FIN_HG00377 0 .08 RPM
FIN_HG00378 0 .15 RPM
GBR_HG00099 0 .23 RPM
GBR_HG00111 0 .11 RPM
GBR_HG00114 0 .26 RPM
GBR_HG00119 0 .02 RPM
GBR_HG00131 0 .20 RPM
GBR_HG00133 0 .10 RPM
GBR_HG00134 0 .17 RPM
GBR_HG00137 0 .27 RPM
GBR_HG00142 0 .39 RPM
GBR_HG00143 0 .19 RPM
TSI_NA20512 0 .03 RPM
TSI_NA20513 0 .29 RPM
TSI_NA20518 0 .22 RPM
TSI_NA20532 0 .20 RPM
TSI_NA20538 0 .18 RPM
TSI_NA20756 0 .09 RPM
TSI_NA20765 0 .06 RPM
TSI_NA20771 0 .11 RPM
TSI_NA20786 0 .10 RPM
TSI_NA20798 0 .19 RPM
YRI_NA18870 0 .27 RPM
YRI_NA18907 0 .17 RPM
YRI_NA18916 0 .06 RPM
YRI_NA19093 0 .34 RPM
YRI_NA19099 0 .03 RPM
YRI_NA19114 0 .21 RPM
YRI_NA19118 0 .31 RPM
YRI_NA19213 0 .12 RPM
YRI_NA19214 0 .27 RPM
YRI_NA19223 0 .20 RPM

Indel association:

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



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