RetrogeneDB ID:

retro_hsap_2175

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:2:169971689..169972045(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000235995
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:UBE2V1
Ensembl ID:ENSG00000244687
Aliases:UBE2V1, CIR1, CROC-1, CROC1, UBE2V, UEV-1, UEV1, UEV1A
Description:ubiquitin-conjugating enzyme E2 variant 1 [Source:HGNC Symbol;Acc:12494]


Retrocopy-Parental alignment summary:






>retro_hsap_2175
GCCACCACAGGCTTGGGAGTAAAAGTCCCTCAGAATTTCCAACTGTTGGAAGAACTGGAACAAGGTTAGAAAGGAGTAGG
TGATGGCACAGGTGGCTGGGGTGTAGAAGACGATGAAGACATGATACTTACAAGATGGACAGAGATGGTAACTGGGCCTC
CAAGAACAACTGATGAAAACCGAATATACAGCCTTAAAATAAAATGTGGACCTAAATACCCAGAAGGACCCCACTTTGTA
AGATTTTTCACAAAAATTAATATGAATGGAGTTAAGAGTTCTAATGGAGTGGTAGACCAAGAGCCATATCAGTGCTAGCA
AAATGGCAGAATTCATAGAGCATCAAAGTGGTTCTG

ORF - retro_hsap_2175 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 82.5 %
Parental protein coverage: 80.95 %
Number of stop codons detected: 2
Number of frameshifts detected: 1


Retrocopy - Parental Gene Alignment:

ParentalATTGSGVKVPRNFRLLEELEEGQKGVGDGTVSWGLEDDEDMTLTRWTGMIIGPPRTIYENRIYSLKIECG
ATTG.GVKVP.NF.LLEELE.G.KGVGDGT..WG.EDDEDM.LTRWT.M..GPPRT..ENRIYSLKI.CG
RetrocopyATTGLGVKVPQNFQLLEELEQG*KGVGDGTGGWGVEDDEDMILTRWTEMVTGPPRTTDENRIYSLKIKCG
ParentalPKYPEAPPFVRFVTKINMNGVNSSNGVVD-PRAISVLAKWQNSYSIKVVL
PKYPE.P.FVRF.TKINMNGV.SSNGVVD.PRAISVLAKWQNS.SIKVVL
RetrocopyPKYPEGPHFVRFFTKINMNGVKSSNGVVD<PRAISVLAKWQNS*SIKVVL

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 .00 RPM 6 .24 RPM
bodymap2_adrenal 0 .00 RPM 8 .47 RPM
bodymap2_brain 0 .00 RPM 6 .77 RPM
bodymap2_breast 0 .00 RPM 5 .80 RPM
bodymap2_colon 0 .00 RPM 4 .68 RPM
bodymap2_heart 0 .00 RPM 2 .31 RPM
bodymap2_kidney 0 .00 RPM 2 .79 RPM
bodymap2_liver 0 .00 RPM 1 .16 RPM
bodymap2_lung 0 .00 RPM 4 .64 RPM
bodymap2_lymph_node 0 .00 RPM 3 .97 RPM
bodymap2_ovary 0 .00 RPM 4 .24 RPM
bodymap2_prostate 0 .00 RPM 2 .68 RPM
bodymap2_skeletal_muscle 0 .00 RPM 2 .02 RPM
bodymap2_testis 0 .00 RPM 9 .11 RPM
bodymap2_thyroid 0 .00 RPM 4 .84 RPM
bodymap2_white_blood_cells 0 .00 RPM 2 .03 RPM

ChIP-Seq - click to see more details

RNA Polymerase II activity near the 5' end of retro_hsap_2175 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_2175 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_2175 retrocopy 5' end.

Lab - click to see more details

retro_hsap_2175 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_2175 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 14 parental genes, and 89 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000273164 retrocopies
retro_btau_1196, retro_btau_1226, retro_btau_1307, retro_btau_415,
Canis familiaris ENSCAFG000000322448 retrocopies
retro_cfam_1005, retro_cfam_1066, retro_cfam_1299, retro_cfam_1340, retro_cfam_1499, retro_cfam_2186, retro_cfam_494, retro_cfam_604,
Callithrix jacchus ENSCJAG0000003698410 retrocopies
retro_cjac_1076, retro_cjac_1952, retro_cjac_2810, retro_cjac_2865, retro_cjac_3081, retro_cjac_3140, retro_cjac_3258, retro_cjac_4089, retro_cjac_462, retro_cjac_974,
Equus caballus ENSECAG000000118583 retrocopies
retro_ecab_1112, retro_ecab_250, retro_ecab_900,
Homo sapiens ENSG00000244687 4 retrocopies
retro_hsap_2175 , retro_hsap_2440, retro_hsap_2884, retro_hsap_4192,
Loxodonta africana ENSLAFG000000273592 retrocopies
retro_lafr_1026, retro_lafr_1221,
Macaca mulatta ENSMMUG000000122286 retrocopies
retro_mmul_1722, retro_mmul_2382, retro_mmul_351, retro_mmul_436, retro_mmul_629, retro_mmul_907,
Mustela putorius furoENSMPUG000000175573 retrocopies
retro_mputfur_1522, retro_mputfur_384, retro_mputfur_834,
Nomascus leucogenys ENSNLEG000000069878 retrocopies
retro_nleu_1554, retro_nleu_1612, retro_nleu_1996, retro_nleu_2206, retro_nleu_2773, retro_nleu_3025, retro_nleu_304, retro_nleu_566,
Otolemur garnettii ENSOGAG0000002589412 retrocopies
retro_ogar_1381, retro_ogar_1391, retro_ogar_153, retro_ogar_1637, retro_ogar_1929, retro_ogar_2027, retro_ogar_2478, retro_ogar_2984, retro_ogar_3172, retro_ogar_3338, retro_ogar_620, retro_ogar_80,
Pan troglodytes ENSPTRG000000136151 retrocopy
retro_ptro_64,
Rattus norvegicus ENSRNOG0000002558021 retrocopies
retro_rnor_1014, retro_rnor_1032, retro_rnor_1291, retro_rnor_1609, retro_rnor_1649, retro_rnor_1650, retro_rnor_1651, retro_rnor_2055, retro_rnor_2282, retro_rnor_2406, retro_rnor_2407, retro_rnor_2412, retro_rnor_2488, retro_rnor_2489, retro_rnor_2490, retro_rnor_2534, retro_rnor_2535, retro_rnor_2905, retro_rnor_819, retro_rnor_881, retro_rnor_991,
Sus scrofa ENSSSCG000000306321 retrocopy
retro_sscr_431,
Ictidomys tridecemlineatus ENSSTOG000000143226 retrocopies
retro_itri_1001, retro_itri_1002, retro_itri_1134, retro_itri_1452, retro_itri_1600, retro_itri_992,

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 = 0.04 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .00 RPM
CEU_NA11843 0 .00 RPM
CEU_NA11930 0 .00 RPM
CEU_NA12004 0 .00 RPM
CEU_NA12400 0 .00 RPM
CEU_NA12751 0 .00 RPM
CEU_NA12760 0 .00 RPM
CEU_NA12827 0 .00 RPM
CEU_NA12872 0 .00 RPM
CEU_NA12873 0 .00 RPM
FIN_HG00183 0 .00 RPM
FIN_HG00277 0 .04 RPM
FIN_HG00315 0 .00 RPM
FIN_HG00321 0 .00 RPM
FIN_HG00328 0 .00 RPM
FIN_HG00338 0 .00 RPM
FIN_HG00349 0 .00 RPM
FIN_HG00375 0 .00 RPM
FIN_HG00377 0 .00 RPM
FIN_HG00378 0 .00 RPM
GBR_HG00099 0 .00 RPM
GBR_HG00111 0 .00 RPM
GBR_HG00114 0 .00 RPM
GBR_HG00119 0 .00 RPM
GBR_HG00131 0 .00 RPM
GBR_HG00133 0 .00 RPM
GBR_HG00134 0 .00 RPM
GBR_HG00137 0 .00 RPM
GBR_HG00142 0 .00 RPM
GBR_HG00143 0 .00 RPM
TSI_NA20512 0 .00 RPM
TSI_NA20513 0 .00 RPM
TSI_NA20518 0 .00 RPM
TSI_NA20532 0 .00 RPM
TSI_NA20538 0 .00 RPM
TSI_NA20756 0 .00 RPM
TSI_NA20765 0 .00 RPM
TSI_NA20771 0 .00 RPM
TSI_NA20786 0 .00 RPM
TSI_NA20798 0 .00 RPM
YRI_NA18870 0 .00 RPM
YRI_NA18907 0 .00 RPM
YRI_NA18916 0 .00 RPM
YRI_NA19093 0 .00 RPM
YRI_NA19099 0 .00 RPM
YRI_NA19114 0 .00 RPM
YRI_NA19118 0 .00 RPM
YRI_NA19213 0 .00 RPM
YRI_NA19214 0 .00 RPM
YRI_NA19223 0 .00 RPM

Indel association:

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



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