RetrogeneDB ID:

retro_hsap_1474

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:15:31712330..31712860(+)
Located in intron of:ENSG00000169926
Retrocopy
information
Ensembl ID:ENSG00000259179
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:UBE2C
Ensembl ID:ENSG00000175063
Aliases:UBE2C, UBCH10, dJ447F3.2
Description:ubiquitin-conjugating enzyme E2C [Source:HGNC Symbol;Acc:15937]


Retrocopy-Parental alignment summary:






>retro_hsap_1474
GTGGTCTCCCAAGACCATAACCCAGCAGCCACTAGTGTCGTCGCCACCCATAAAAGAGCCGAGCTGAGTGGGGGTGCTGC
CCAGAATCCTGTGGGCAAAAGACTACAGCAGGAGCTGATGACCCTCATGATATCTGGTGACAAAGGGATTTCTGCTTTCC
TTGAATCAGACAACCTTTTCAAATGGGTAGGGACCATCCATGGAGCAGCTGGCACAGTGTATGAAGACCTGAGGTATAAG
CTCTTGCTAGAGTTCCCCAGTGGCTACCCTTACAATGAGCCCACAGTGAAGTTCCTCACATCCTGCTACCACCCCAACAT
AGACACCCAGGGTAACATATGCCTGGATATCTGGAAAGACAAGTCGTCTGTACTGTATGGCATCAGGACCATTCTGGTCT
CCATCCAGAGCCTGCTAGGAGAACCCAACATTGATAGCCCTTTGAACATGCATGCTGTTGAGTTCTGGAAAAACCCTACA
GCTTTTACCTTCAAGAAACCTATTCAAAGCAGGTTACCAGCCAGGACCCC

ORF - retro_hsap_1474 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 81.11 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalMASQNRDPAATSVAAARKGAEPSGGAARGPVGKRLQQELMTLMMSGDKGISAFPESDNLFKWVGTIHGAA
..SQ...PAATSV.A..K.AE.SGGAA..PVGKRLQQELMTLM.SGDKGISAF.ESDNLFKWVGTIHGAA
RetrocopyVVSQDHNPAATSVVATHKRAELSGGAAQNPVGKRLQQELMTLMISGDKGISAFLESDNLFKWVGTIHGAA
ParentalGTVYEDLRYKLSLEFPSGYPYNAPTVKFLTPCYHPNVDTQGNICLDILKEKWSALYDVRTILLSIQSLLG
GTVYEDLRYKL.LEFPSGYPYN.PTVKFLT.CYHPN.DTQGNICLDI.K.K.S.LY..RTIL.SIQSLLG
RetrocopyGTVYEDLRYKLLLEFPSGYPYNEPTVKFLTSCYHPNIDTQGNICLDIWKDKSSVLYGIRTILVSIQSLLG
ParentalEPNIDSPLNTHAAELWKN-PTAFKKYLQETYSKQVTSQEP
EPNIDSPLN.HA.E.WKN.P..F..YLQETYSKQVTSQ.P
RetrocopyEPNIDSPLNMHAVEFWKN<PYSF--YLQETYSKQVTSQDP

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 1 .25 RPM
bodymap2_adrenal 0 .04 RPM 1 .13 RPM
bodymap2_brain 0 .02 RPM 0 .02 RPM
bodymap2_breast 0 .00 RPM 0 .80 RPM
bodymap2_colon 0 .00 RPM 2 .49 RPM
bodymap2_heart 0 .00 RPM 0 .39 RPM
bodymap2_kidney 0 .00 RPM 0 .17 RPM
bodymap2_liver 0 .06 RPM 0 .17 RPM
bodymap2_lung 0 .00 RPM 1 .37 RPM
bodymap2_lymph_node 0 .00 RPM 2 .65 RPM
bodymap2_ovary 0 .00 RPM 0 .54 RPM
bodymap2_prostate 0 .00 RPM 0 .43 RPM
bodymap2_skeletal_muscle 0 .00 RPM 0 .22 RPM
bodymap2_testis 0 .00 RPM 6 .81 RPM
bodymap2_thyroid 0 .00 RPM 0 .73 RPM
bodymap2_white_blood_cells 0 .00 RPM 0 .37 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_1474 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_1474 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_1474 retrocopy 5' end.

Lab - click to see more details

retro_hsap_1474 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_1474 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Gorilla gorilla retro_ggor_1130
Macaca mulatta retro_mmul_170
Parental genes homology:
Parental genes homology involve 16 parental genes, and 64 retrocopies.

Species Parental gene accession Retrocopies number
Cavia porcellus ENSCPOG000000141022 retrocopies
retro_cpor_1007, retro_cpor_211,
Dipodomys ordii ENSDORG000000117744 retrocopies
retro_dord_157, retro_dord_386, retro_dord_421, retro_dord_84,
Homo sapiens ENSG00000175063 3 retrocopies
retro_hsap_1474 , retro_hsap_1922, retro_hsap_2935,
Gorilla gorilla ENSGGOG000000260613 retrocopies
retro_ggor_1130, retro_ggor_1402, retro_ggor_2035,
Macropus eugenii ENSMEUG0000000717714 retrocopies
retro_meug_1021, retro_meug_1128, retro_meug_1203, retro_meug_1398, retro_meug_1435, retro_meug_145, retro_meug_1476, retro_meug_1504, retro_meug_1575, retro_meug_1773, retro_meug_1808, retro_meug_2034, retro_meug_334, retro_meug_645,
Myotis lucifugus ENSMLUG000000067154 retrocopies
retro_mluc_2164, retro_mluc_2220, retro_mluc_600, retro_mluc_636,
Macaca mulatta ENSMMUG000000210234 retrocopies
retro_mmul_1345, retro_mmul_170, retro_mmul_1951, retro_mmul_777,
Monodelphis domestica ENSMODG000000136616 retrocopies
retro_mdom_1549, retro_mdom_1552, retro_mdom_1732, retro_mdom_1970, retro_mdom_2020, retro_mdom_415,
Mus musculus ENSMUSG000000014035 retrocopies
retro_mmus_1344, retro_mmus_1593, retro_mmus_1770, retro_mmus_2881, retro_mmus_3512,
Otolemur garnettii ENSOGAG000000049893 retrocopies
retro_ogar_2347, retro_ogar_249, retro_ogar_3067,
Ochotona princeps ENSOPRG000000142844 retrocopies
retro_opri_1009, retro_opri_1055, retro_opri_222, retro_opri_50,
Pongo abelii ENSPPYG000000110714 retrocopies
retro_pabe_1155, retro_pabe_1221, retro_pabe_1589, retro_pabe_2519,
Pan troglodytes ENSPTRG000000135641 retrocopy
retro_ptro_38,
Pteropus vampyrus ENSPVAG000000003691 retrocopy
retro_pvam_423,
Rattus norvegicus ENSRNOG000000151315 retrocopies
retro_rnor_1390, retro_rnor_2131, retro_rnor_2470, retro_rnor_719, retro_rnor_864,
Tursiops truncatus ENSTTRG000000159871 retrocopy
retro_ttru_1752,

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 ) 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 .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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