RetrogeneDB ID:

retro_hsap_36

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:14:50360454..50360982(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000165527
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:ARF3
Ensembl ID:ENSG00000134287
Aliases:None
Description:ADP-ribosylation factor 3 [Source:HGNC Symbol;Acc:654]


Retrocopy-Parental alignment summary:






>retro_hsap_36
ATGGGGAAGGTGCTATCCAAAATCTTCGGGAACAAGGAAATGCGGATCCTCATGTTGGGCCTGGACGCGGCCGGCAAGAC
AACAATCCTGTACAAGTTGAAGCTGGGCCAGTCGGTGACCACCATTCCCACTGTGGGTTTCAACGTGGAGACGGTGACTT
ACAAAAATGTCAAGTTCAACGTATGGGATGTGGGCGGCCAGGACAAGATCCGGCCGCTCTGGCGGCATTACTACACTGGG
ACCCAAGGTCTCATCTTCGTAGTGGACTGCGCCGACCGCGACCGCATCGATGAGGCTCGCCAGGAGCTGCACCGCATTAT
CAATGACCGGGAGATGAGGGACGCCATAATCCTCATCTTCGCCAACAAGCAGGACCTGCCCGATGCCATGAAACCCCACG
AGATCCAGGAGAAACTGGGCCTGACCCGGATTCGGGACAGGAACTGGTATGTGCAGCCCTCCTGTGCCACCTCAGGGGAC
GGACTCTATGAGGGGCTCACATGGTTAACCTCTAACTACAAATCTTAA

ORF - retro_hsap_36 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 69.54 %
Parental protein coverage: 96.13 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalGNLLKSLIGKKEMRILMVGLDAAGKTTILYKLKLGEIVTTIPTIGFNVETVEYKNISFTVWDVGGQDKIR
G..L....G.KEMRILM.GLDAAGKTTILYKLKLG..VTTIPT.GFNVETV.YKN..F.VWDVGGQDKIR
RetrocopyGKVLSKIFGNKEMRILMLGLDAAGKTTILYKLKLGQSVTTIPTVGFNVETVTYKNVKFNVWDVGGQDKIR
ParentalPLWRHYFQNTQGLIFVVDSNDRERVNEAREELMRMLAEDELRDAVLLVFANKQDLPNAMNAAEITDKLGL
PLWRHY...TQGLIFVVD..DR.R..EAR.EL.R.....E.RDA..L.FANKQDLP.AM...EI..KLGL
RetrocopyPLWRHYYTGTQGLIFVVDCADRDRIDEARQELHRIINDREMRDAIILIFANKQDLPDAMKPHEIQEKLGL
ParentalHSLRHRNWYIQATCATSGDGLYEGLDWLANQLKN
...R.RNWY.Q..CATSGDGLYEGL.WL....K.
RetrocopyTRIRDRNWYVQPSCATSGDGLYEGLTWLTSNYKS

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 29 .74 RPM 222 .28 RPM
bodymap2_adrenal 36 .74 RPM 202 .28 RPM
bodymap2_brain 9 .21 RPM 477 .85 RPM
bodymap2_breast 21 .67 RPM 155 .62 RPM
bodymap2_colon 16 .53 RPM 182 .88 RPM
bodymap2_heart 8 .92 RPM 43 .75 RPM
bodymap2_kidney 23 .35 RPM 192 .83 RPM
bodymap2_liver 13 .03 RPM 55 .17 RPM
bodymap2_lung 32 .05 RPM 215 .07 RPM
bodymap2_lymph_node 35 .18 RPM 138 .22 RPM
bodymap2_ovary 17 .83 RPM 206 .47 RPM
bodymap2_prostate 25 .17 RPM 152 .09 RPM
bodymap2_skeletal_muscle 21 .01 RPM 17 .62 RPM
bodymap2_testis 21 .00 RPM 221 .73 RPM
bodymap2_thyroid 16 .95 RPM 265 .03 RPM
bodymap2_white_blood_cells 64 .67 RPM 309 .73 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity may be related with retro_hsap_36 in 52 libraries
ENCODE library ID Target ChIP-Seq Peak coordinates
ENCFF001VKU POLR2A 14:50359215..50360263
ENCFF002CFW POLR2A 14:50359310..50360442
ENCFF002CFX POLR2A 14:50359317..50360285
ENCFF002CGN POLR2A 14:50359419..50360032
ENCFF002CHO POLR2A 14:50358989..50361061
ENCFF002CIH POLR2A 14:50359697..50360022
ENCFF002CIH POLR2A 14:50359459..50359724
ENCFF002CIO POLR2A 14:50359397..50360427
ENCFF002CJE POLR2A 14:50359322..50360353
ENCFF002CJZ POLR2A 14:50359258..50360341
ENCFF002CKX POLR2A 14:50359403..50360032
ENCFF002CLM POLR2A 14:50359797..50359932
ENCFF002CMI POLR2A 14:50359368..50360492
ENCFF002COJ POLR2A 14:50359604..50360040
ENCFF002CPG POLR2A 14:50359455..50359748
ENCFF002CPG POLR2A 14:50359686..50360004
ENCFF002CPH POLR2A 14:50359425..50359815
ENCFF002CPH POLR2A 14:50359645..50360035
ENCFF002CQA POLR2A 14:50359446..50359774
ENCFF002CQA POLR2A 14:50359765..50360008
ENCFF002CQC POLR2A 14:50359419..50360032
ENCFF002CQE POLR2A 14:50359394..50360036
ENCFF002CQG POLR2A 14:50359467..50360013
ENCFF002CQI POLR2A 14:50359415..50360025
ENCFF002CQK POLR2A 14:50359384..50360051
ENCFF002CQM POLR2A 14:50359424..50360038
ENCFF002CQO POLR2A 14:50359360..50360388
ENCFF002CRK POLR2A 14:50359352..50359876
ENCFF002CRK POLR2A 14:50359560..50360084
ENCFF002CRO POLR2A 14:50359390..50359810
ENCFF002CRO POLR2A 14:50359742..50359948
ENCFF002CSY POLR2A 14:50358981..50360515
ENCFF002CUP POLR2A 14:50359667..50359947
ENCFF002CUQ POLR2A 14:50359404..50360036
ENCFF002CVF POLR2A 14:50359747..50359902
ENCFF002CVF POLR2A 14:50359409..50359825
ENCFF002CVJ POLR2A 14:50359400..50360354
ENCFF002CXM POLR2A 14:50359584..50360074
ENCFF002CXN POLR2A 14:50359334..50359830
ENCFF002CXN POLR2A 14:50359610..50360106
ENCFF002CXO POLR2A 14:50359733..50359910
ENCFF002CXO POLR2A 14:50359522..50359672
ENCFF002CXP POLR2A 14:50359696..50359982
ENCFF002CXR POLR2A 14:50359439..50359771
ENCFF002CXR POLR2A 14:50359670..50359995
ENCFF002CZC POLR2A 14:50359373..50360064
ENCFF002CZD POLR2A 14:50359393..50360060
ENCFF002CZQ POLR2A 14:50359674..50360004
ENCFF002CZQ POLR2A 14:50359442..50359763
ENCFF002CZW POLR2A 14:50359261..50360273
ENCFF002CZY POLR2A 14:50359378..50360049
ENCFF002DAE POLR2A 14:50359555..50359633
ENCFF002DAE POLR2A 14:50359782..50359881
ENCFF002DAH POLR2A 14:50359691..50359975
ENCFF002DAK POLR2A 14:50359342..50359842
ENCFF002DAK POLR2A 14:50359543..50360043
ENCFF002DAS POLR2A 14:50359364..50359840
ENCFF002DAS POLR2A 14:50359593..50360069
ENCFF002DAV POLR2A 14:50359339..50359883
ENCFF002DAV POLR2A 14:50359772..50359919
ENCFF002DAY POLR2A 14:50359278..50359914
ENCFF002DAY POLR2A 14:50359520..50360156
ENCFF002DBB POLR2A 14:50359503..50359703
ENCFF002DBB POLR2A 14:50359774..50359974
ENCFF002DBE POLR2A 14:50359693..50359967
ENCFF002DBO POLR2A 14:50359432..50360035
ENCFF002DBP POLR2A 14:50359464..50359746
ENCFF002DBP POLR2A 14:50359696..50359983
ENCFF002DBQ POLR2A 14:50359515..50359713
ENCFF002DBQ POLR2A 14:50359758..50359897
ENCFF002DBT POLR2A 14:50359585..50359677
ENCFF002DBT POLR2A 14:50359804..50359897

EST - click to see more details

29 EST(s) were mapped to retro_hsap_36 retrocopy
EST ID Start End Identity Match Mis-match Score
AI940133 50360534 50360708 95.3 164 4 154
AI940136 50360551 50360660 98.1 105 0 100
AW751295 50360566 50360693 97.6 122 3 117
AW751296 50360551 50360666 98.2 107 1 102
BQ315629 50360533 50360696 95.1 159 3 153
BQ315631 50360525 50360735 99.6 203 1 196
BQ315632 50360556 50360725 98.3 164 3 159
BQ315633 50360542 50360724 99.5 175 0 169
BQ315634 50360562 50360720 99.4 157 1 156
BQ315635 50360576 50360724 99.4 147 1 146
BQ315636 50360539 50360735 99 188 2 181
BQ315637 50360536 50360724 99 181 1 175
BQ315638 50360573 50360726 99.4 150 0 147
BQ315639 50360543 50360724 98.3 171 2 164
BQ315640 50360547 50360714 100 163 0 159
BQ315641 50360547 50360724 99.4 164 0 157
BQ315642 50360527 50360724 99.5 190 1 184
BQ315643 50360517 50360715 97.9 183 3 174
BQ315644 50360565 50360724 99.4 158 1 157
BQ315645 50360532 50360724 99.5 186 1 182
BQ315646 50360542 50360724 98.9 173 1 167
BQ315647 50360575 50360724 100 148 0 147
BQ315648 50360551 50360728 99.5 175 1 173
BQ315707 50360529 50360724 100 195 0 195
BQ315714 50360529 50360724 100 195 0 195
BQ315722 50360519 50360693 98.3 169 3 164
BQ315746 50360584 50360735 97.2 138 2 132
BQ315747 50360581 50360717 97 130 1 124
EC481026 50360489 50360592 100 103 0 103

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_38365743 libraries835 libraries246 libraries4 libraries1 library
TSS #2 TSS_38366342 libraries521 libraries735 libraries180 libraries51 libraries
TSS #3 TSS_383691141 libraries544 libraries142 libraries2 libraries0 libraries
TSS #4 TSS_38370919 libraries643 libraries229 libraries30 libraries8 libraries

The graphical summary, for retro_hsap_36 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_36 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_36 has 12 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_5
Gorilla gorilla retro_ggor_161
Pongo abelii retro_pabe_126
Macaca mulatta retro_mmul_174
Callithrix jacchus retro_cjac_300
Mus musculus retro_mmus_147
Rattus norvegicus retro_rnor_272
Oryctolagus cuniculus retro_ocun_132
Bos taurus retro_btau_26
Sus scrofa retro_sscr_82
Canis familiaris retro_cfam_119
Equus caballus retro_ecab_106
Parental genes homology:
Parental genes homology involve 20 parental genes, and 31 retrocopies.

Species Parental gene accession Retrocopies number
Anolis carolinensis ENSACAG000000082401 retrocopy
retro_acar_12,
Cavia porcellus ENSCPOG000000250741 retrocopy
retro_cpor_92,
Ciona savignyi ENSCSAVG000000070111 retrocopy
retro_csav_2,
Homo sapiens ENSG000001341081 retrocopy
retro_hsap_361,
Homo sapiens ENSG00000134287 1 retrocopy
retro_hsap_36 ,
Homo sapiens ENSG000001437613 retrocopies
retro_hsap_1008, retro_hsap_1160, retro_hsap_3763,
Homo sapiens ENSG000001683742 retrocopies
retro_hsap_1296, retro_hsap_4221,
Latimeria chalumnae ENSLACG000000190091 retrocopy
retro_lcha_10,
Loxodonta africana ENSLAFG000000042071 retrocopy
retro_lafr_115,
Macropus eugenii ENSMEUG000000050727 retrocopies
retro_meug_1036, retro_meug_1117, retro_meug_1857, retro_meug_29, retro_meug_395, retro_meug_616, retro_meug_946,
Microcebus murinus ENSMICG000000175451 retrocopy
retro_mmur_37,
Monodelphis domestica ENSMODG000000138041 retrocopy
retro_mdom_241,
Mus musculus ENSMUSG000000518531 retrocopy
retro_mmus_147,
Nomascus leucogenys ENSNLEG000000178592 retrocopies
retro_nleu_1348, retro_nleu_94,
Petromyzon marinus ENSPMAG000000005311 retrocopy
retro_pmar_5,
Rattus norvegicus ENSRNOG000000331551 retrocopy
retro_rnor_272,
Rattus norvegicus ENSRNOG000000480891 retrocopy
retro_rnor_2521,
Sarcophilus harrisii ENSSHAG000000036352 retrocopies
retro_shar_25, retro_shar_364,
Tetraodon nigroviridis ENSTNIG000000116851 retrocopy
retro_tnig_19,
Tursiops truncatus ENSTTRG000000046981 retrocopy
retro_ttru_1081,

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 = 92.25 RPM Legend:


Library Retrogene expression
CEU_NA11831 56 .09 RPM
CEU_NA11843 52 .38 RPM
CEU_NA11930 46 .84 RPM
CEU_NA12004 60 .02 RPM
CEU_NA12400 50 .72 RPM
CEU_NA12751 58 .16 RPM
CEU_NA12760 61 .57 RPM
CEU_NA12827 63 .77 RPM
CEU_NA12872 60 .37 RPM
CEU_NA12873 65 .69 RPM
FIN_HG00183 46 .87 RPM
FIN_HG00277 51 .87 RPM
FIN_HG00315 63 .29 RPM
FIN_HG00321 48 .09 RPM
FIN_HG00328 65 .67 RPM
FIN_HG00338 58 .80 RPM
FIN_HG00349 58 .47 RPM
FIN_HG00375 56 .83 RPM
FIN_HG00377 67 .17 RPM
FIN_HG00378 66 .51 RPM
GBR_HG00099 69 .48 RPM
GBR_HG00111 55 .17 RPM
GBR_HG00114 71 .05 RPM
GBR_HG00119 52 .71 RPM
GBR_HG00131 46 .71 RPM
GBR_HG00133 62 .25 RPM
GBR_HG00134 66 .17 RPM
GBR_HG00137 60 .42 RPM
GBR_HG00142 48 .07 RPM
GBR_HG00143 66 .75 RPM
TSI_NA20512 75 .17 RPM
TSI_NA20513 57 .19 RPM
TSI_NA20518 62 .53 RPM
TSI_NA20532 56 .87 RPM
TSI_NA20538 61 .87 RPM
TSI_NA20756 62 .97 RPM
TSI_NA20765 57 .62 RPM
TSI_NA20771 62 .81 RPM
TSI_NA20786 72 .42 RPM
TSI_NA20798 77 .12 RPM
YRI_NA18870 74 .03 RPM
YRI_NA18907 70 .33 RPM
YRI_NA18916 68 .20 RPM
YRI_NA19093 92 .25 RPM
YRI_NA19099 75 .79 RPM
YRI_NA19114 65 .14 RPM
YRI_NA19118 70 .98 RPM
YRI_NA19213 65 .39 RPM
YRI_NA19214 90 .02 RPM
YRI_NA19223 71 .09 RPM

Indel association:

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



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