RetrogeneDB ID:

retro_hsap_1828

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:17:33923845..33924147(-)
Located in intron of:ENSG00000006125
Retrocopy
information
Ensembl ID:ENSG00000267592
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:TMEM160
Ensembl ID:ENSG00000130748
Aliases:None
Description:transmembrane protein 160 [Source:HGNC Symbol;Acc:26042]


Retrocopy-Parental alignment summary:






>retro_hsap_1828
CTCCGCTTCCGGAGGTCGCTACTGCTGCCTCAGTGGCCCCGGAGCGGGGGCGCCCAGGGGTCCTTCGCCCCCGGCCACGG
CCCCCACAACGGGGCTTCGCCGCCACCTGTGTCCGAGCTGGACCGTGCAGGCGCCAGGCTCCTCTCCGAAAGGCGCACGA
GACAGCTTTCTTCTCCTGGTTCCACAATGGCCTCCTGGCATAGGGCATCGGGGTTATCTCCTTCATGCAGAGTGACATGG
ATCACGAAGCAGCATATGGCTTCTTCCTGCTGGGCGGCCTGTGTGCGGTGTGGGGCAGCGCC

ORF - retro_hsap_1828 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 80.39 %
Parental protein coverage: 53.19 %
Number of stop codons detected: 1
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalLRFRRSLLPPQRPRSGGARGSFAPGHGPRAGASPPPVSELDRADAWLLR-KAHETAFL-SWFRNGLLASG
LRFRRSLL.PQ.PRSGGA.GSFAPGHGP..GASPPPVSELDRA.A.LL..K.....FL.SWF.NGLLA.G
RetrocopyLRFRRSLLLPQWPRSGGAQGSFAPGHGPHNGASPPPVSELDRAGARLLS>KGARDSFL>SWFHNGLLA*G
ParentalIGVISFMQSDMGREAAYGFFLLGGLCVVWGSA
IGVISFMQSDM..EAAYGFFLLGGLC.VWGSA
RetrocopyIGVISFMQSDMDHEAAYGFFLLGGLCAVWGSA

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 .04 RPM 2 .80 RPM
bodymap2_adrenal 0 .02 RPM 2 .17 RPM
bodymap2_brain 0 .02 RPM 4 .85 RPM
bodymap2_breast 0 .00 RPM 3 .87 RPM
bodymap2_colon 0 .00 RPM 3 .19 RPM
bodymap2_heart 0 .00 RPM 2 .31 RPM
bodymap2_kidney 0 .04 RPM 4 .22 RPM
bodymap2_liver 0 .00 RPM 2 .51 RPM
bodymap2_lung 0 .16 RPM 5 .38 RPM
bodymap2_lymph_node 0 .00 RPM 4 .39 RPM
bodymap2_ovary 0 .00 RPM 0 .27 RPM
bodymap2_prostate 0 .00 RPM 3 .34 RPM
bodymap2_skeletal_muscle 0 .18 RPM 2 .69 RPM
bodymap2_testis 0 .04 RPM 0 .32 RPM
bodymap2_thyroid 0 .00 RPM 1 .64 RPM
bodymap2_white_blood_cells 0 .00 RPM 5 .36 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity may be related with retro_hsap_1828 in 1 libraries
ENCODE library ID Target ChIP-Seq Peak coordinates
ENCFF002CMI POLR2A 17:33923456..33924388

EST - click to see more details

No EST(s) were mapped for retro_hsap_1828 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_1828 retrocopy 5' end.

Lab - click to see more details

retro_hsap_1828 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_1828 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_1165
Gorilla gorilla retro_ggor_2165
Pongo abelii retro_pabe_1498
Parental genes homology:
Parental genes homology involve 7 parental genes, and 7 retrocopies.

Species Parental gene accession Retrocopies number
Echinops telfairi ENSETEG000000179971 retrocopy
retro_etel_2100,
Homo sapiens ENSG00000130748 1 retrocopy
retro_hsap_1828 ,
Gorilla gorilla ENSGGOG000000134101 retrocopy
retro_ggor_2165,
Oryctolagus cuniculus ENSOCUG000000230971 retrocopy
retro_ocun_1750,
Pongo abelii ENSPPYG000000101661 retrocopy
retro_pabe_1498,
Pan troglodytes ENSPTRG000000112001 retrocopy
retro_ptro_1165,
Rattus norvegicus ENSRNOG000000153041 retrocopy
retro_rnor_1176,

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 = 0.14 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .00 RPM
CEU_NA11843 0 .00 RPM
CEU_NA11930 0 .03 RPM
CEU_NA12004 0 .00 RPM
CEU_NA12400 0 .04 RPM
CEU_NA12751 0 .00 RPM
CEU_NA12760 0 .00 RPM
CEU_NA12827 0 .05 RPM
CEU_NA12872 0 .00 RPM
CEU_NA12873 0 .06 RPM
FIN_HG00183 0 .00 RPM
FIN_HG00277 0 .07 RPM
FIN_HG00315 0 .00 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 .00 RPM
FIN_HG00378 0 .00 RPM
GBR_HG00099 0 .03 RPM
GBR_HG00111 0 .00 RPM
GBR_HG00114 0 .03 RPM
GBR_HG00119 0 .02 RPM
GBR_HG00131 0 .06 RPM
GBR_HG00133 0 .05 RPM
GBR_HG00134 0 .02 RPM
GBR_HG00137 0 .11 RPM
GBR_HG00142 0 .14 RPM
GBR_HG00143 0 .00 RPM
TSI_NA20512 0 .06 RPM
TSI_NA20513 0 .05 RPM
TSI_NA20518 0 .00 RPM
TSI_NA20532 0 .03 RPM
TSI_NA20538 0 .05 RPM
TSI_NA20756 0 .00 RPM
TSI_NA20765 0 .04 RPM
TSI_NA20771 0 .00 RPM
TSI_NA20786 0 .03 RPM
TSI_NA20798 0 .00 RPM
YRI_NA18870 0 .03 RPM
YRI_NA18907 0 .10 RPM
YRI_NA18916 0 .04 RPM
YRI_NA19093 0 .03 RPM
YRI_NA19099 0 .03 RPM
YRI_NA19114 0 .03 RPM
YRI_NA19118 0 .02 RPM
YRI_NA19213 0 .07 RPM
YRI_NA19214 0 .10 RPM
YRI_NA19223 0 .06 RPM

Indel association:

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



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