RetrogeneDB ID:

retro_hsap_3753

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:7:78115846..78116345(+)
Located in intron of:ENSG00000187391
Retrocopy
information
Ensembl ID:ENSG00000226230
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:UFC1
Ensembl ID:ENSG00000143222
Aliases:UFC1, HSPC155
Description:ubiquitin-fold modifier conjugating enzyme 1 [Source:HGNC Symbol;Acc:26941]


Retrocopy-Parental alignment summary:






>retro_hsap_3753
ATGGCAGATGAGGCCACCTGACATGTTGTGTCTGAGACTCTGGCACTGAAGACTAATGCAGGACCCCGAGATTGGGAGTT
GTGGGTGCAGTGATTGAAGGAGGAATATCAGTCCCTTATCTGGTATGTGGAGAACAACAACAATGGCGACAACGATGGTT
CCAACTGGAGTCCAGCAAGGTAGGGACTCGGTGGTTTGGAAAATGTTGGTATATCCATGGCCTCCTGCAATGTGAGTTTG
ACGTCAAGTTTGAAATTCCTATCATGTATCTTACTACTGCCCTAGAAATTGCTGTCCCTGAGCTCGACAGAAAGACAGCA
AAGATGTACAGAGGTGGCACAATTGCCTGACAGATCATTTCAAATCTTTGTGGGCCAGGAACGTACCCAAATTTGAACTA
GCTCATTTCATGGCTCTGGGGCCGGGTCCATGGCTGGCAGTGGAAATCCCTGATCTGATTCAGAAGAGGGTATTCCAGCA
CAAAGAGAAATGTAACCAA

ORF - retro_hsap_3753 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 81.07 %
Parental protein coverage: 100. %
Number of stop codons detected: 2
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalMADEATRRVVSEIPVLKTNAGPRDRELWVQRLKEEYQSLIRYVENNKNADND-WFRLESNKEGTRWFGKC
MADEAT..VVSE...LKTNAGPRD.ELWVQ.LKEEYQSLI.YVENN.N.DND.WF.LES.K.GTRWFGKC
RetrocopyMADEAT*HVVSETLALKTNAGPRDWELWVQ*LKEEYQSLIWYVENNNNGDND<WFQLESSKVGTRWFGKC
ParentalWYIHDLLKYEFDIEFDIPITYPTTAPEIAVPELDGKTAKMYRGGKI-CLTDHFKPLWARNVPKFGLAHLM
WYIH.LL..EFD..F.IPI.Y.TTA.EIAVPELD.KTAKMYRGG.I.CLTDHFK.LWARNVPKF.LAH.M
RetrocopyWYIHGLLQCEFDVKFEIPIMYLTTALEIAVPELDRKTAKMYRGGTI<CLTDHFKSLWARNVPKFELAHFM
ParentalALGLGPWLAVEIPDLIQKGVIQHKEKCNQ
ALG.GPWLAVEIPDLIQK.V.QHKEKCNQ
RetrocopyALGPGPWLAVEIPDLIQKRVFQHKEKCNQ

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 50 .85 RPM
bodymap2_adrenal 0 .00 RPM 74 .88 RPM
bodymap2_brain 0 .07 RPM 46 .18 RPM
bodymap2_breast 0 .00 RPM 52 .92 RPM
bodymap2_colon 0 .00 RPM 68 .51 RPM
bodymap2_heart 0 .00 RPM 30 .66 RPM
bodymap2_kidney 0 .00 RPM 57 .82 RPM
bodymap2_liver 0 .00 RPM 34 .41 RPM
bodymap2_lung 0 .00 RPM 67 .25 RPM
bodymap2_lymph_node 0 .00 RPM 70 .44 RPM
bodymap2_ovary 0 .00 RPM 91 .97 RPM
bodymap2_prostate 0 .00 RPM 86 .46 RPM
bodymap2_skeletal_muscle 0 .00 RPM 44 .54 RPM
bodymap2_testis 0 .00 RPM 61 .22 RPM
bodymap2_thyroid 0 .00 RPM 61 .03 RPM
bodymap2_white_blood_cells 0 .00 RPM 77 .37 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_3753 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_3753 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_3753 retrocopy 5' end.

Lab - click to see more details

retro_hsap_3753 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_3753 has 5 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_2547
Gorilla gorilla retro_ggor_2525
Pongo abelii retro_pabe_3164
Macaca mulatta retro_mmul_1727
Callithrix jacchus retro_cjac_3146
Parental genes homology:
Parental genes homology involve 23 parental genes, and 35 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000155451 retrocopy
retro_amel_1221,
Callithrix jacchus ENSCJAG000000053033 retrocopies
retro_cjac_2546, retro_cjac_3146, retro_cjac_4122,
Danio rerio ENSDARG000000223401 retrocopy
retro_drer_22,
Dasypus novemcinctus ENSDNOG000000137331 retrocopy
retro_dnov_1943,
Echinops telfairi ENSETEG000000157304 retrocopies
retro_etel_1042, retro_etel_562, retro_etel_714, retro_etel_83,
Felis catus ENSFCAG000000098291 retrocopy
retro_fcat_1217,
Homo sapiens ENSG00000143222 1 retrocopy
retro_hsap_3753 ,
Gorilla gorilla ENSGGOG000000074861 retrocopy
retro_ggor_2525,
Loxodonta africana ENSLAFG000000269691 retrocopy
retro_lafr_473,
Macropus eugenii ENSMEUG000000044171 retrocopy
retro_meug_423,
Myotis lucifugus ENSMLUG000000045431 retrocopy
retro_mluc_716,
Macaca mulatta ENSMMUG000000226322 retrocopies
retro_mmul_1727, retro_mmul_2273,
Mustela putorius furoENSMPUG000000142431 retrocopy
retro_mputfur_854,
Nomascus leucogenys ENSNLEG000000140491 retrocopy
retro_nleu_1893,
Oryctolagus cuniculus ENSOCUG000000023891 retrocopy
retro_ocun_1304,
Otolemur garnettii ENSOGAG000000266794 retrocopies
retro_ogar_1385, retro_ogar_2156, retro_ogar_3496, retro_ogar_496,
Ochotona princeps ENSOPRG000000109063 retrocopies
retro_opri_319, retro_opri_509, retro_opri_773,
Pongo abelii ENSPPYG000000006101 retrocopy
retro_pabe_3164,
Pan troglodytes ENSPTRG000000015721 retrocopy
retro_ptro_2547,
Pteropus vampyrus ENSPVAG000000055192 retrocopies
retro_pvam_1161, retro_pvam_814,
Sus scrofa ENSSSCG000000063631 retrocopy
retro_sscr_171,
Tupaia belangeri ENSTBEG000000162761 retrocopy
retro_tbel_2810,
Tarsius syrichta ENSTSYG000000108241 retrocopy
retro_tsyr_1751,

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 = 0.05 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 .04 RPM
CEU_NA12751 0 .00 RPM
CEU_NA12760 0 .00 RPM
CEU_NA12827 0 .05 RPM
CEU_NA12872 0 .00 RPM
CEU_NA12873 0 .00 RPM
FIN_HG00183 0 .00 RPM
FIN_HG00277 0 .00 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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