RetrogeneDB ID:

retro_hsap_108

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:2:20647226..20647817(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000143878
Aliases:RHOB, ARH6, ARHB, MST081, MSTP081, RHOH6
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:RHOA
Ensembl ID:ENSG00000067560
Aliases:RHOA, ARH12, ARHA, RHO12, RHOH12
Description:ras homolog family member A [Source:HGNC Symbol;Acc:667]


Retrocopy-Parental alignment summary:






>retro_hsap_108
ATGGCGGCCATCCGCAAGAAGCTGGTGGTGGTGGGCGACGGCGCGTGTGGCAAGACGTGCCTGCTGATCGTGTTCAGTAA
GGACGAGTTCCCCGAGGTGTACGTGCCCACCGTCTTCGAGAACTATGTGGCCGACATTGAGGTGGACGGCAAGCAGGTGG
AGCTGGCGCTGTGGGACACGGCGGGCCAGGAGGACTACGACCGCCTGCGGCCGCTCTCCTACCCGGACACCGACGTCATT
CTCATGTGCTTCTCGGTGGACAGCCCGGACTCGCTGGAGAACATCCCCGAGAAGTGGGTCCCCGAGGTGAAGCACTTCTG
TCCCAATGTGCCCATCATCCTGGTGGCCAACAAAAAAGACCTGCGCAGCGACGAGCATGTCCGCACAGAGCTGGCCCGCA
TGAAGCAGGAACCCGTGCGCACGGATGACGGCCGCGCCATGGCCGTGCGCATCCAAGCCTACGACTACCTCGAGTGCTCT
GCCAAGACCAAGGAAGGCGTGCGCGAGGTCTTCGAGACGGCCACGCGCGCCGCGCTGCAGAAGCGCTACGGCTCCCAGAA
CGGCTGCATCAACTGCTGCAAGGTGCTATGA

ORF - retro_hsap_108 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 85.34 %
Parental protein coverage: 98.96 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMAAIRKKLVIVGDGACGKTCLLIVFSKDQFPEVYVPTVFENYVADIEVDGKQVELALWDTAGQEDYDRLR
MAAIRKKLV.VGDGACGKTCLLIVFSKD.FPEVYVPTVFENYVADIEVDGKQVELALWDTAGQEDYDRLR
RetrocopyMAAIRKKLVVVGDGACGKTCLLIVFSKDEFPEVYVPTVFENYVADIEVDGKQVELALWDTAGQEDYDRLR
ParentalPLSYPDTDVILMCFSIDSPDSLENIPEKWTPEVKHFCPNVPIILVGNKKDLRNDEHTRRELAKMKQEPVK
PLSYPDTDVILMCFS.DSPDSLENIPEKW.PEVKHFCPNVPIILV.NKKDLR.DEH.R.ELA.MKQEPV.
RetrocopyPLSYPDTDVILMCFSVDSPDSLENIPEKWVPEVKHFCPNVPIILVANKKDLRSDEHVRTELARMKQEPVR
ParentalPEEGRDMANRIGAFGYMECSAKTKDGVREVFEMATRAALQARRGKKKSGCL
...GR.MA.RI.A..Y.ECSAKTK.GVREVFE.ATRAALQ.R.G....GC.
RetrocopyTDDGRAMAVRIQAYDYLECSAKTKEGVREVFETATRAALQKRYG-SQNGCI

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 128 .79 RPM 757 .45 RPM
bodymap2_adrenal 93 .89 RPM 649 .43 RPM
bodymap2_brain 44 .44 RPM 361 .28 RPM
bodymap2_breast 60 .04 RPM 744 .74 RPM
bodymap2_colon 71 .89 RPM 587 .60 RPM
bodymap2_heart 23 .08 RPM 237 .02 RPM
bodymap2_kidney 38 .96 RPM 493 .85 RPM
bodymap2_liver 44 .68 RPM 198 .94 RPM
bodymap2_lung 136 .20 RPM 799 .91 RPM
bodymap2_lymph_node 33 .31 RPM 569 .64 RPM
bodymap2_ovary 88 .94 RPM 636 .81 RPM
bodymap2_prostate 98 .45 RPM 587 .31 RPM
bodymap2_skeletal_muscle 31 .68 RPM 593 .82 RPM
bodymap2_testis 54 .45 RPM 544 .03 RPM
bodymap2_thyroid 49 .83 RPM 519 .31 RPM
bodymap2_white_blood_cells 22 .78 RPM 1068 .50 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity may be related with retro_hsap_108 in 50 libraries
ENCODE library ID Target ChIP-Seq Peak coordinates
ENCFF001VKU POLR2A 2:20646455..20650954
ENCFF002CFW POLR2A 2:20646426..20648260
ENCFF002CFX POLR2A 2:20646438..20648135
ENCFF002CGN POLR2A 2:20646686..20647057
ENCFF002CHO POLR2A 2:20646430..20648143
ENCFF002CIH POLR2A 2:20646687..20647060
ENCFF002CIO POLR2A 2:20646659..20647094
ENCFF002CJE POLR2A 2:20646544..20647139
ENCFF002CJE POLR2A 2:20647379..20648015
ENCFF002CJZ POLR2A 2:20646455..20648143
ENCFF002CKX POLR2A 2:20646442..20648278
ENCFF002CLM POLR2A 2:20646689..20647493
ENCFF002CMI POLR2A 2:20646676..20647057
ENCFF002COJ POLR2A 2:20646755..20646985
ENCFF002CPG POLR2A 2:20646704..20647027
ENCFF002CPH POLR2A 2:20646741..20646976
ENCFF002CQA POLR2A 2:20646670..20647034
ENCFF002CQC POLR2A 2:20646667..20647066
ENCFF002CQE POLR2A 2:20646673..20647039
ENCFF002CQG POLR2A 2:20646664..20647065
ENCFF002CQI POLR2A 2:20646684..20647049
ENCFF002CQK POLR2A 2:20646462..20647086
ENCFF002CQM POLR2A 2:20646682..20647063
ENCFF002CQO POLR2A 2:20646627..20647087
ENCFF002CRK POLR2A 2:20646699..20647014
ENCFF002CRO POLR2A 2:20646704..20647044
ENCFF002CSY POLR2A 2:20646363..20648893
ENCFF002CUP POLR2A 2:20646701..20647574
ENCFF002CUQ POLR2A 2:20646446..20647162
ENCFF002CUQ POLR2A 2:20647078..20648194
ENCFF002CVF POLR2A 2:20646679..20647128
ENCFF002CVF POLR2A 2:20647057..20647742
ENCFF002CVJ POLR2A 2:20646438..20648018
ENCFF002CXM POLR2A 2:20646604..20647094
ENCFF002CXN POLR2A 2:20646641..20647137
ENCFF002CXO POLR2A 2:20646639..20647063
ENCFF002CXP POLR2A 2:20646608..20647088
ENCFF002CXR POLR2A 2:20646697..20647006
ENCFF002CZC POLR2A 2:20646520..20647117
ENCFF002CZD POLR2A 2:20646558..20647106
ENCFF002CZW POLR2A 2:20646458..20647168
ENCFF002DAE POLR2A 2:20646732..20647004
ENCFF002DAH POLR2A 2:20646758..20646985
ENCFF002DAK POLR2A 2:20646607..20647107
ENCFF002DAS POLR2A 2:20646776..20646923
ENCFF002DAV POLR2A 2:20646649..20647096
ENCFF002DAY POLR2A 2:20646633..20647184
ENCFF002DBB POLR2A 2:20646766..20647019
ENCFF002DBB POLR2A 2:20647345..20647545
ENCFF002DBE POLR2A 2:20646760..20646970
ENCFF002DBO POLR2A 2:20646709..20647069
ENCFF002DBO POLR2A 2:20646933..20647317
ENCFF002DBP POLR2A 2:20646724..20647023
ENCFF002DBQ POLR2A 2:20646727..20647022
ENCFF002DBT POLR2A 2:20646720..20647019

EST - click to see more details

No EST(s) were mapped for retro_hsap_108 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_11760944 libraries9 libraries91 libraries83 libraries1602 libraries
TSS #2 TSS_1176101097 libraries547 libraries177 libraries7 libraries1 library

The graphical summary, for retro_hsap_108 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_108 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_108 has 6 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_10
Gorilla gorilla retro_ggor_18
Macaca mulatta retro_mmul_977
Bos taurus retro_btau_206
Canis familiaris retro_cfam_186
Equus caballus retro_ecab_112
Parental genes homology:
Parental genes homology involve 24 parental genes, and 47 retrocopies.

Species Parental gene accession Retrocopies number
Anolis carolinensis ENSACAG000000082971 retrocopy
retro_acar_41,
Anas platyrhynchos ENSAPLG000000146871 retrocopy
retro_apla_10,
Canis familiaris ENSCAFG000000230662 retrocopies
retro_cfam_1652, retro_cfam_186,
Callithrix jacchus ENSCJAG000000039043 retrocopies
retro_cjac_1306, retro_cjac_2010, retro_cjac_411,
Cavia porcellus ENSCPOG000000140731 retrocopy
retro_cpor_514,
Dipodomys ordii ENSDORG000000033823 retrocopies
retro_dord_1, retro_dord_18, retro_dord_538,
Homo sapiens ENSG00000067560 2 retrocopies
retro_hsap_108 , retro_hsap_3632,
Gasterosteus aculeatus ENSGACG000000056701 retrocopy
retro_gacu_9,
Gallus gallus ENSGALG000000038061 retrocopy
retro_ggal_5,
Gadus morhua ENSGMOG000000081881 retrocopy
retro_gmor_18,
Latimeria chalumnae ENSLACG000000169411 retrocopy
retro_lcha_15,
Meleagris gallopavo ENSMGAG000000022801 retrocopy
retro_mgal_2,
Macaca mulatta ENSMMUG000000129621 retrocopy
retro_mmul_977,
Monodelphis domestica ENSMODG000000129812 retrocopies
retro_mdom_19, retro_mdom_294,
Mustela putorius furoENSMPUG000000138405 retrocopies
retro_mputfur_1015, retro_mputfur_140, retro_mputfur_1541, retro_mputfur_1588, retro_mputfur_650,
Mus musculus ENSMUSG000000078159 retrocopies
retro_mmus_178, retro_mmus_191, retro_mmus_2041, retro_mmus_2507, retro_mmus_3728, retro_mmus_3729, retro_mmus_3964, retro_mmus_3965, retro_mmus_3966,
Ornithorhynchus anatinus ENSOANG000000138071 retrocopy
retro_oana_7,
Oreochromis niloticus ENSONIG000000188841 retrocopy
retro_onil_32,
Ochotona princeps ENSOPRG000000096381 retrocopy
retro_opri_590,
Pelodiscus sinensis ENSPSIG000000153281 retrocopy
retro_psin_7,
Rattus norvegicus ENSRNOG000000505193 retrocopies
retro_rnor_127, retro_rnor_2899, retro_rnor_408,
Ictidomys tridecemlineatus ENSSTOG000000045612 retrocopies
retro_itri_39, retro_itri_96,
Takifugu rubripes ENSTRUG000000119441 retrocopy
retro_trub_19,
Tursiops truncatus ENSTTRG000000173702 retrocopies
retro_ttru_27, retro_ttru_339,

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 = 25.74 RPM Legend:


Library Retrogene expression
CEU_NA11831 9 .16 RPM
CEU_NA11843 5 .20 RPM
CEU_NA11930 0 .78 RPM
CEU_NA12004 3 .30 RPM
CEU_NA12400 1 .96 RPM
CEU_NA12751 4 .18 RPM
CEU_NA12760 12 .22 RPM
CEU_NA12827 4 .95 RPM
CEU_NA12872 3 .67 RPM
CEU_NA12873 4 .34 RPM
FIN_HG00183 1 .32 RPM
FIN_HG00277 2 .33 RPM
FIN_HG00315 2 .13 RPM
FIN_HG00321 2 .06 RPM
FIN_HG00328 4 .00 RPM
FIN_HG00338 2 .47 RPM
FIN_HG00349 5 .49 RPM
FIN_HG00375 2 .98 RPM
FIN_HG00377 1 .84 RPM
FIN_HG00378 2 .66 RPM
GBR_HG00099 7 .38 RPM
GBR_HG00111 5 .01 RPM
GBR_HG00114 13 .02 RPM
GBR_HG00119 5 .08 RPM
GBR_HG00131 11 .44 RPM
GBR_HG00133 3 .59 RPM
GBR_HG00134 14 .44 RPM
GBR_HG00137 9 .24 RPM
GBR_HG00142 5 .67 RPM
GBR_HG00143 8 .39 RPM
TSI_NA20512 12 .55 RPM
TSI_NA20513 3 .58 RPM
TSI_NA20518 8 .05 RPM
TSI_NA20532 4 .39 RPM
TSI_NA20538 3 .96 RPM
TSI_NA20756 6 .55 RPM
TSI_NA20765 1 .57 RPM
TSI_NA20771 12 .48 RPM
TSI_NA20786 2 .35 RPM
TSI_NA20798 4 .90 RPM
YRI_NA18870 4 .67 RPM
YRI_NA18907 9 .01 RPM
YRI_NA18916 4 .88 RPM
YRI_NA19093 25 .74 RPM
YRI_NA19099 3 .38 RPM
YRI_NA19114 2 .99 RPM
YRI_NA19118 8 .99 RPM
YRI_NA19213 5 .98 RPM
YRI_NA19214 6 .00 RPM
YRI_NA19223 1 .23 RPM

Indel association:

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





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