RetrogeneDB ID:

retro_hsap_28

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:11:3848792..3849368(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000177105
Aliases:RHOG, ARHG
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:RAC1
Ensembl ID:ENSG00000136238
Aliases:RAC1, Rac-1, TC-25, p21-Rac1
Description:ras-related C3 botulinum toxin substrate 1 (rho family, small GTP binding protein Rac1) [Source:HGNC Symbol;Acc:9801]


Retrocopy-Parental alignment summary:






>retro_hsap_28
ATGCAGAGCATCAAGTGCGTGGTGGTGGGTGATGGGGCTGTGGGCAAGACGTGCCTGCTCATCTGCTACACAACTAACGC
TTTCCCCAAAGAGTACATCCCCACCGTGTTCGACAATTACAGCGCGCAGAGCGCAGTTGACGGGCGCACAGTGAACCTGA
ACCTGTGGGACACTGCGGGCCAGGAGGAGTATGACCGCCTCCGTACACTCTCCTACCCTCAGACCAACGTTTTCGTCATC
TGTTTCTCCATTGCCAGTCCGCCGTCCTATGAGAACGTGCGGCACAAGTGGCATCCAGAGGTGTGCCACCACTGCCCTGA
TGTGCCCATCCTGCTGGTGGGCACCAAGAAGGACCTGAGAGCCCAGCCTGACACCCTACGGCGCCTCAAGGAGCAGGGCC
AGGCGCCCATCACACCGCAGCAGGGCCAGGCACTGGCCAAGCAGATCCACGCTGTGCGCTACCTCGAATGCTCAGCCCTG
CAACAGGATGGTGTCAAGGAAGTGTTCGCCGAGGCTGTCCGGGCTGTGCTCAACCCCACGCCGATCAAGCGTGGGCGGTC
CTGCATCCTCTTGTGA

ORF - retro_hsap_28 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 71.88 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMQAIKCVVVGDGAVGKTCLLISYTTNAFPGEYIPTVFDNYSANVMVDGKPVNLGLWDTAGQEDYDRLRPL
MQ.IKCVVVGDGAVGKTCLLI.YTTNAFP.EYIPTVFDNYSA...VDG..VNL.LWDTAGQE.YDRLR.L
RetrocopyMQSIKCVVVGDGAVGKTCLLICYTTNAFPKEYIPTVFDNYSAQSAVDGRTVNLNLWDTAGQEEYDRLRTL
ParentalSYPQTDVFLICFSLVSPASFENVRAKWYPEVRHHCPNTPIILVGTKLDLRDDKDTIEKLKEKKLTPITYP
SYPQT.VF.ICFS..SP.S.ENVR.KW.PEV.HHCP..PI.LVGTK.DLR...DT...LKE....PIT..
RetrocopySYPQTNVFVICFSIASPPSYENVRHKWHPEVCHHCPDVPILLVGTKKDLRAQPDTLRRLKEQGQAPITPQ
ParentalQGLAMAKEIGAVKYLECSALTQRGLKTVFDEAIRAVLCPPPVKKRKRKCLLL
QG.A.AK.I.AV.YLECSAL.Q.G.K.VF.EA.RAVL.P.P..KR.R.C.LL
RetrocopyQGQALAKQIHAVRYLECSALQQDGVKEVFAEAVRAVLNPTPI-KRGRSCILL

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 18 .05 RPM 299 .08 RPM
bodymap2_adrenal 21 .76 RPM 316 .19 RPM
bodymap2_brain 10 .15 RPM 421 .92 RPM
bodymap2_breast 8 .02 RPM 323 .35 RPM
bodymap2_colon 8 .02 RPM 312 .24 RPM
bodymap2_heart 4 .62 RPM 153 .30 RPM
bodymap2_kidney 7 .30 RPM 226 .02 RPM
bodymap2_liver 4 .22 RPM 109 .86 RPM
bodymap2_lung 35 .09 RPM 367 .58 RPM
bodymap2_lymph_node 27 .94 RPM 226 .96 RPM
bodymap2_ovary 10 .76 RPM 345 .11 RPM
bodymap2_prostate 11 .78 RPM 336 .25 RPM
bodymap2_skeletal_muscle 16 .26 RPM 296 .79 RPM
bodymap2_testis 7 .52 RPM 223 .28 RPM
bodymap2_thyroid 6 .27 RPM 299 .27 RPM
bodymap2_white_blood_cells 95 .58 RPM 226 .06 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity may be related with retro_hsap_28 in 2 libraries
ENCODE library ID Target ChIP-Seq Peak coordinates
ENCFF002CHO POLR2A 11:3848652..3849480
ENCFF002CIO POLR2A 11:3848767..3849311

EST - click to see more details

6 EST(s) were mapped to retro_hsap_28 retrocopy
EST ID Start End Identity Match Mis-match Score
AA057124 3849030 3849184 97.4 152 1 150
AA131346 3849011 3849186 98.9 165 2 163
AA424745 3848862 3849139 98.2 267 5 258
AW404319 3848881 3849079 100 198 0 198
BF992738 3849089 3849219 98.5 128 2 126
BQ317085 3849046 3849150 100 104 0 104

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_14148317 libraries651 libraries739 libraries98 libraries24 libraries

The graphical summary, for retro_hsap_28 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_28 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_28 has 6 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Gorilla gorilla retro_ggor_188
Pongo abelii retro_pabe_21
Macaca mulatta retro_mmul_210
Mus musculus retro_mmus_234
Rattus norvegicus retro_rnor_230
Oryctolagus cuniculus retro_ocun_43
Parental genes homology:
Parental genes homology involve 11 parental genes, and 32 retrocopies.

Species Parental gene accession Retrocopies number
Homo sapiens ENSG000000708316 retrocopies
retro_hsap_2775, retro_hsap_2968, retro_hsap_3028, retro_hsap_3404, retro_hsap_3848, retro_hsap_4013,
Homo sapiens ENSG000001197293 retrocopies
retro_hsap_1333, retro_hsap_2158, retro_hsap_2316,
Homo sapiens ENSG00000136238 6 retrocopies
retro_hsap_1256, retro_hsap_1925, retro_hsap_28 , retro_hsap_3036, retro_hsap_3072, retro_hsap_4910,
Gorilla gorilla ENSGGOG000000267332 retrocopies
retro_ggor_2110, retro_ggor_217,
Mus musculus ENSMUSG000000018472 retrocopies
retro_mmus_1372, retro_mmus_234,
Pan troglodytes ENSPTRG000000189104 retrocopies
retro_ptro_1288, retro_ptro_3044, retro_ptro_3274, retro_ptro_36,
Rattus norvegicus ENSRNOG000000010681 retrocopy
retro_rnor_230,
Ictidomys tridecemlineatus ENSSTOG000000067841 retrocopy
retro_itri_1503,
Tupaia belangeri ENSTBEG000000072724 retrocopies
retro_tbel_1796, retro_tbel_2564, retro_tbel_4296, retro_tbel_9,
Tarsius syrichta ENSTSYG000000016182 retrocopies
retro_tsyr_2027, retro_tsyr_2068,
Xenopus tropicalis ENSXETG000000275931 retrocopy
retro_xtro_1,

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 = 136.01 RPM Legend:


Library Retrogene expression
CEU_NA11831 75 .75 RPM
CEU_NA11843 82 .01 RPM
CEU_NA11930 50 .23 RPM
CEU_NA12004 81 .89 RPM
CEU_NA12400 88 .32 RPM
CEU_NA12751 64 .86 RPM
CEU_NA12760 86 .73 RPM
CEU_NA12827 76 .98 RPM
CEU_NA12872 67 .91 RPM
CEU_NA12873 70 .64 RPM
FIN_HG00183 57 .05 RPM
FIN_HG00277 67 .59 RPM
FIN_HG00315 61 .08 RPM
FIN_HG00321 66 .65 RPM
FIN_HG00328 90 .95 RPM
FIN_HG00338 60 .23 RPM
FIN_HG00349 74 .81 RPM
FIN_HG00375 70 .96 RPM
FIN_HG00377 84 .77 RPM
FIN_HG00378 62 .96 RPM
GBR_HG00099 83 .84 RPM
GBR_HG00111 87 .48 RPM
GBR_HG00114 93 .93 RPM
GBR_HG00119 64 .54 RPM
GBR_HG00131 76 .60 RPM
GBR_HG00133 81 .26 RPM
GBR_HG00134 86 .11 RPM
GBR_HG00137 120 .73 RPM
GBR_HG00142 102 .11 RPM
GBR_HG00143 84 .43 RPM
TSI_NA20512 124 .29 RPM
TSI_NA20513 74 .94 RPM
TSI_NA20518 88 .60 RPM
TSI_NA20532 53 .13 RPM
TSI_NA20538 57 .58 RPM
TSI_NA20756 79 .76 RPM
TSI_NA20765 61 .64 RPM
TSI_NA20771 76 .54 RPM
TSI_NA20786 98 .94 RPM
TSI_NA20798 93 .74 RPM
YRI_NA18870 95 .15 RPM
YRI_NA18907 73 .70 RPM
YRI_NA18916 75 .64 RPM
YRI_NA19093 136 .01 RPM
YRI_NA19099 79 .46 RPM
YRI_NA19114 82 .58 RPM
YRI_NA19118 97 .06 RPM
YRI_NA19213 86 .77 RPM
YRI_NA19214 90 .76 RPM
YRI_NA19223 75 .33 RPM

Indel association:

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



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