RetrogeneDB ID:

retro_hsap_1333

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:14:50066711..50067278(+)
Located in intron of:ENSG00000165501
Retrocopy
information
Ensembl ID:ENSG00000258568
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:RHOQ
Ensembl ID:ENSG00000119729
Aliases:None
Description:ras homolog family member Q [Source:HGNC Symbol;Acc:17736]


Retrocopy-Parental alignment summary:






>retro_hsap_1333
ATGGCTCACGGGCCCGGCGCGCTGATGCTCAAGTGCGTGGTGGTCGGCGACGGGGCGGTGGGCAAGACGTGCCTACTCAT
GAGCTGTGCCAACGACGCCTTCCCGGAGGAGTACGTGCCCACCGTCTTCGACCACTACACAGTCAGCGTCACCGTGGGGG
GCAAGCAGTACCTCCTAGGACTCTATAACACCGCCGGACAGGAAGACTATGACCATCTGAGGCCTTTATCTTACCCAATG
ACCGACGTCTTCCTTATATGCTTCTCGGTGGTAAATCCAGCCTCATTTCAAAATGTGAGGGAGGAGTGGGTACCGGAACT
TAAGGAATACGCACCAAATGTACCCTTTTTATTAATAGGAGCTCAGATTGATCTCCGAGATGACCCCAAAACTTTAGCAA
GACTGAGTGATATGAAAGAAAAACCTATATGTGTGGAACAAGGACAGAAACTAGCAAAAGAGATAGGAGCATGCTGCTAT
GTGGAATGTTCAGCTTTAACCCAGAAGGGATTGAAGACTGTTTTTGATGAGGCTATCATAGCCATTTTAACTCCAAAGAA
ACACACT

ORF - retro_hsap_1333 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 96.3 %
Parental protein coverage: 92.2 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMAHGPGALMLKCVVVGDGAVGKTCLLMSYANDAFPEEYVPTVFDHYAVSVTVGGKQYLLGLYDTAGQEDY
MAHGPGALMLKCVVVGDGAVGKTCLLMS.ANDAFPEEYVPTVFDHY.VSVTVGGKQYLLGLY.TAGQEDY
RetrocopyMAHGPGALMLKCVVVGDGAVGKTCLLMSCANDAFPEEYVPTVFDHYTVSVTVGGKQYLLGLYNTAGQEDY
ParentalDRLRPLSYPMTDVFLICFSVVNPASFQNVKEEWVPELKEYAPNVPFLLIGTQIDLRDDPKTLARLNDMKE
D.LRPLSYPMTDVFLICFSVVNPASFQNV.EEWVPELKEYAPNVPFLLIG.QIDLRDDPKTLARL.DMKE
RetrocopyDHLRPLSYPMTDVFLICFSVVNPASFQNVREEWVPELKEYAPNVPFLLIGAQIDLRDDPKTLARLSDMKE
ParentalKPICVEQGQKLAKEIGACCYVECSALTQKGLKTVFDEAIIAILTPKKHT
KPICVEQGQKLAKEIGACCYVECSALTQKGLKTVFDEAIIAILTPKKHT
RetrocopyKPICVEQGQKLAKEIGACCYVECSALTQKGLKTVFDEAIIAILTPKKHT

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 .99 RPM 155 .90 RPM
bodymap2_adrenal 0 .29 RPM 75 .55 RPM
bodymap2_brain 0 .19 RPM 72 .38 RPM
bodymap2_breast 1 .01 RPM 302 .16 RPM
bodymap2_colon 0 .54 RPM 144 .05 RPM
bodymap2_heart 0 .24 RPM 302 .02 RPM
bodymap2_kidney 0 .19 RPM 77 .34 RPM
bodymap2_liver 0 .06 RPM 19 .35 RPM
bodymap2_lung 0 .42 RPM 151 .11 RPM
bodymap2_lymph_node 0 .33 RPM 86 .67 RPM
bodymap2_ovary 0 .25 RPM 84 .18 RPM
bodymap2_prostate 0 .35 RPM 204 .17 RPM
bodymap2_skeletal_muscle 0 .75 RPM 148 .10 RPM
bodymap2_testis 0 .89 RPM 70 .38 RPM
bodymap2_thyroid 0 .38 RPM 100 .73 RPM
bodymap2_white_blood_cells 0 .98 RPM 84 .19 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity may be related with retro_hsap_1333 in 50 libraries
ENCODE library ID Target ChIP-Seq Peak coordinates
ENCFF001VKU POLR2A 14:50065189..50066060
ENCFF002CFW POLR2A 14:50065146..50066117
ENCFF002CFW POLR2A 14:50066532..50066962
ENCFF002CFX POLR2A 14:50065159..50066111
ENCFF002CFX POLR2A 14:50066684..50066877
ENCFF002CGN POLR2A 14:50065440..50066115
ENCFF002CHO POLR2A 14:50064879..50066217
ENCFF002CHO POLR2A 14:50066354..50066999
ENCFF002CIH POLR2A 14:50065534..50066006
ENCFF002CIH POLR2A 14:50065534..50066008
ENCFF002CIO POLR2A 14:50065102..50066147
ENCFF002CJE POLR2A 14:50065093..50066211
ENCFF002CJZ POLR2A 14:50065084..50066254
ENCFF002CJZ POLR2A 14:50066735..50066987
ENCFF002CKX POLR2A 14:50065176..50066083
ENCFF002CLM POLR2A 14:50065463..50066003
ENCFF002CMI POLR2A 14:50065157..50066203
ENCFF002COJ POLR2A 14:50065464..50065900
ENCFF002CPG POLR2A 14:50065588..50065930
ENCFF002CPH POLR2A 14:50065527..50065917
ENCFF002CQA POLR2A 14:50065619..50065901
ENCFF002CQC POLR2A 14:50065496..50065994
ENCFF002CQC POLR2A 14:50065496..50065999
ENCFF002CQE POLR2A 14:50065146..50066100
ENCFF002CQG POLR2A 14:50065513..50065882
ENCFF002CQI POLR2A 14:50065498..50065980
ENCFF002CQK POLR2A 14:50065108..50066097
ENCFF002CQM POLR2A 14:50065158..50066080
ENCFF002CQO POLR2A 14:50065115..50066071
ENCFF002CRK POLR2A 14:50065450..50065974
ENCFF002CSY POLR2A 14:50064939..50066237
ENCFF002CUP POLR2A 14:50065755..50065970
ENCFF002CUP POLR2A 14:50066472..50066788
ENCFF002CUQ POLR2A 14:50065579..50066054
ENCFF002CVF POLR2A 14:50065667..50066083
ENCFF002CVJ POLR2A 14:50065658..50066022
ENCFF002CXM POLR2A 14:50065464..50065954
ENCFF002CXN POLR2A 14:50065473..50065969
ENCFF002CXO POLR2A 14:50065597..50065824
ENCFF002CXP POLR2A 14:50065587..50065871
ENCFF002CXR POLR2A 14:50065502..50065934
ENCFF002CZC POLR2A 14:50065137..50066209
ENCFF002CZD POLR2A 14:50065167..50066174
ENCFF002CZQ POLR2A 14:50065510..50065880
ENCFF002CZW POLR2A 14:50065156..50066154
ENCFF002CZY POLR2A 14:50065109..50066022
ENCFF002DAE POLR2A 14:50065567..50065877
ENCFF002DAH POLR2A 14:50065589..50065873
ENCFF002DAK POLR2A 14:50065463..50065963
ENCFF002DAS POLR2A 14:50065460..50065936
ENCFF002DAV POLR2A 14:50065723..50065910
ENCFF002DAY POLR2A 14:50065411..50066047
ENCFF002DBB POLR2A 14:50065598..50065798
ENCFF002DBE POLR2A 14:50065527..50065877
ENCFF002DBO POLR2A 14:50065143..50066035
ENCFF002DBO POLR2A 14:50066635..50067019
ENCFF002DBP POLR2A 14:50065473..50065974
ENCFF002DBP POLR2A 14:50066658..50066988
ENCFF002DBQ POLR2A 14:50065550..50065920

EST - click to see more details

No EST(s) were mapped for retro_hsap_1333 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_1333 retrocopy 5' end.

Lab - click to see more details

retro_hsap_1333 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_1333 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_910
Pongo abelii retro_pabe_1107
Parental genes homology:
Parental genes homology involve 14 parental genes, and 29 retrocopies.

Species Parental gene accession Retrocopies number
Choloepus hoffmanni ENSCHOG000000005493 retrocopies
retro_chof_2030, retro_chof_457, retro_chof_914,
Callithrix jacchus ENSCJAG000000006851 retrocopy
retro_cjac_2403,
Erinaceus europaeus ENSEEUG000000152261 retrocopy
retro_eeur_129,
Homo sapiens ENSG000000708316 retrocopies
retro_hsap_2775, retro_hsap_2968, retro_hsap_3028, retro_hsap_3404, retro_hsap_3848, retro_hsap_4013,
Homo sapiens ENSG00000119729 3 retrocopies
retro_hsap_1333 , retro_hsap_2158, retro_hsap_2316,
Homo sapiens ENSG000001362386 retrocopies
retro_hsap_1256, retro_hsap_1925, retro_hsap_28, retro_hsap_3036, retro_hsap_3072, retro_hsap_4910,
Loxodonta africana ENSLAFG000000043271 retrocopy
retro_lafr_316,
Microcebus murinus ENSMICG000000091241 retrocopy
retro_mmur_29,
Otolemur garnettii ENSOGAG000000332721 retrocopy
retro_ogar_742,
Pongo abelii ENSPPYG000000124392 retrocopies
retro_pabe_1107, retro_pabe_2195,
Pteropus vampyrus ENSPVAG000000136911 retrocopy
retro_pvam_611,
Rattus norvegicus ENSRNOG000000154151 retrocopy
retro_rnor_473,
Sus scrofa ENSSSCG000000084391 retrocopy
retro_sscr_102,
Tarsius syrichta ENSTSYG000000028371 retrocopy
retro_tsyr_1609,

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 = 1.24 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .34 RPM
CEU_NA11843 0 .43 RPM
CEU_NA11930 0 .52 RPM
CEU_NA12004 0 .46 RPM
CEU_NA12400 0 .46 RPM
CEU_NA12751 0 .51 RPM
CEU_NA12760 0 .67 RPM
CEU_NA12827 0 .61 RPM
CEU_NA12872 0 .65 RPM
CEU_NA12873 0 .73 RPM
FIN_HG00183 0 .60 RPM
FIN_HG00277 0 .44 RPM
FIN_HG00315 0 .39 RPM
FIN_HG00321 0 .66 RPM
FIN_HG00328 0 .59 RPM
FIN_HG00338 0 .30 RPM
FIN_HG00349 0 .43 RPM
FIN_HG00375 0 .46 RPM
FIN_HG00377 0 .35 RPM
FIN_HG00378 0 .83 RPM
GBR_HG00099 0 .55 RPM
GBR_HG00111 0 .45 RPM
GBR_HG00114 0 .55 RPM
GBR_HG00119 0 .53 RPM
GBR_HG00131 0 .43 RPM
GBR_HG00133 0 .34 RPM
GBR_HG00134 0 .57 RPM
GBR_HG00137 0 .44 RPM
GBR_HG00142 0 .58 RPM
GBR_HG00143 0 .70 RPM
TSI_NA20512 0 .51 RPM
TSI_NA20513 0 .73 RPM
TSI_NA20518 0 .42 RPM
TSI_NA20532 0 .78 RPM
TSI_NA20538 1 .24 RPM
TSI_NA20756 0 .61 RPM
TSI_NA20765 0 .66 RPM
TSI_NA20771 0 .57 RPM
TSI_NA20786 0 .24 RPM
TSI_NA20798 0 .37 RPM
YRI_NA18870 0 .81 RPM
YRI_NA18907 0 .35 RPM
YRI_NA18916 0 .80 RPM
YRI_NA19093 0 .39 RPM
YRI_NA19099 0 .45 RPM
YRI_NA19114 0 .60 RPM
YRI_NA19118 0 .70 RPM
YRI_NA19213 0 .88 RPM
YRI_NA19214 0 .79 RPM
YRI_NA19223 0 .72 RPM

Indel association:

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



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