RetrogeneDB ID:

retro_hsap_1677

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:16:34404064..34404613(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000261461
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:UBE2M
Ensembl ID:ENSG00000130725
Aliases:UBE2M, UBC-RS2, UBC12, hUbc12
Description:ubiquitin-conjugating enzyme E2M [Source:HGNC Symbol;Acc:12491]


Retrocopy-Parental alignment summary:






>retro_hsap_1677
ATGATCAAGCTGTTCTCGCTGAAGCAGCAGAAGAAGGAGGAGTAGTCGGCGGGAGGCACCAAGCGCAGCAGCAAGAAGGC
GTCGGCGGCGCAGCTGCGGATCCAGAAGGACATAAACGAGCTGAACCTGCCCAAGACGTGTGATATCAGCTTCTCAGATC
CAGACGACCTCCTCAACTTCAAGTTGGTCATCTGTCCTGATGAGGGCTTCTACAAGAGTGGGAAGTTTGTGTTCAGTTTT
AAGGTGGGCCAGGGTTACCCGCATGATCCCCCCAAGGTGAAGTGTGAGACAATGGTCTATCACCCCAACATTGAAATCGA
GGGCAACGTCTGCCTCAACATCCTCAGAGAGAACTGGAAGCCAGTCCTTACGATAAACTCCATAATTTATGGCCTGCAGT
ATCTCTACTTGGAGCCCAACCCCGAGGACCCACTGAACAAGAAGGCCGCAGAGGTCCTGCAGAACAACCGGCAGCTGTTG
GAGCAGAACGTGCAGCCATCCATGCGGGATGGCTACATAGGCTCCACCTACTTCGAGCGCTGCCTGAAA

ORF - retro_hsap_1677 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 93.99 %
Parental protein coverage: 100. %
Number of stop codons detected: 1
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMIKLFSLKQQKKEEESAGGTKGSSKKASAAQLRIQKDINELNLPKTCDISFSDPDDLLNFKLVICPDEGF
MIKLFSLKQQKKEE.SAGGTK.SSKKASAAQLRIQKDINELNLPKTCDISFSDPDDLLNFKLVICPDEGF
RetrocopyMIKLFSLKQQKKEE*SAGGTKRSSKKASAAQLRIQKDINELNLPKTCDISFSDPDDLLNFKLVICPDEGF
ParentalYKSGKFVFSFKVGQGYPHDPPKVKCETMVYHPNIDLEGNVCLNILREDWKPVLTINSIIYGLQYLFLEPN
YKSGKFVFSFKVGQGYPHDPPKVKCETMVYHPNI..EGNVCLNILRE.WKPVLTINSIIYGLQYL.LEPN
RetrocopyYKSGKFVFSFKVGQGYPHDPPKVKCETMVYHPNIEIEGNVCLNILRENWKPVLTINSIIYGLQYLYLEPN
ParentalPEDPLNKEAAEVLQNNRRLFEQNVQRSMRGGYIGSTYFERCLK
PEDPLNK.AAEVLQNNR.L.EQNVQ.SMR.GYIGSTYFERCLK
RetrocopyPEDPLNKKAAEVLQNNRQLLEQNVQPSMRDGYIGSTYFERCLK

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 .02 RPM 32 .16 RPM
bodymap2_adrenal 0 .02 RPM 27 .70 RPM
bodymap2_brain 0 .05 RPM 47 .79 RPM
bodymap2_breast 0 .06 RPM 25 .70 RPM
bodymap2_colon 0 .02 RPM 31 .27 RPM
bodymap2_heart 0 .70 RPM 36 .65 RPM
bodymap2_kidney 0 .17 RPM 27 .28 RPM
bodymap2_liver 0 .02 RPM 14 .24 RPM
bodymap2_lung 0 .19 RPM 36 .62 RPM
bodymap2_lymph_node 0 .15 RPM 29 .84 RPM
bodymap2_ovary 0 .04 RPM 27 .30 RPM
bodymap2_prostate 0 .17 RPM 44 .17 RPM
bodymap2_skeletal_muscle 0 .67 RPM 62 .02 RPM
bodymap2_testis 0 .08 RPM 35 .80 RPM
bodymap2_thyroid 0 .04 RPM 27 .55 RPM
bodymap2_white_blood_cells 0 .04 RPM 25 .36 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_1677 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_1677 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_1677 retrocopy 5' end.

Lab - click to see more details

retro_hsap_1677 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_1677 has 1 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Gorilla gorilla retro_ggor_27
Parental genes homology:
Parental genes homology involve 4 parental genes, and 5 retrocopies.

Species Parental gene accession Retrocopies number
Homo sapiens ENSG00000130725 1 retrocopy
retro_hsap_1677 ,
Homo sapiens ENSG000001841822 retrocopies
retro_hsap_2439, retro_hsap_2773,
Gorilla gorilla ENSGGOG000000133571 retrocopy
retro_ggor_27,
Mus musculus ENSMUSG000000055751 retrocopy
retro_mmus_2868,

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 = 0.24 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .15 RPM
CEU_NA11843 0 .20 RPM
CEU_NA11930 0 .07 RPM
CEU_NA12004 0 .08 RPM
CEU_NA12400 0 .07 RPM
CEU_NA12751 0 .05 RPM
CEU_NA12760 0 .09 RPM
CEU_NA12827 0 .14 RPM
CEU_NA12872 0 .05 RPM
CEU_NA12873 0 .06 RPM
FIN_HG00183 0 .03 RPM
FIN_HG00277 0 .04 RPM
FIN_HG00315 0 .06 RPM
FIN_HG00321 0 .09 RPM
FIN_HG00328 0 .09 RPM
FIN_HG00338 0 .02 RPM
FIN_HG00349 0 .23 RPM
FIN_HG00375 0 .05 RPM
FIN_HG00377 0 .05 RPM
FIN_HG00378 0 .04 RPM
GBR_HG00099 0 .03 RPM
GBR_HG00111 0 .02 RPM
GBR_HG00114 0 .08 RPM
GBR_HG00119 0 .00 RPM
GBR_HG00131 0 .03 RPM
GBR_HG00133 0 .10 RPM
GBR_HG00134 0 .07 RPM
GBR_HG00137 0 .08 RPM
GBR_HG00142 0 .00 RPM
GBR_HG00143 0 .03 RPM
TSI_NA20512 0 .08 RPM
TSI_NA20513 0 .02 RPM
TSI_NA20518 0 .17 RPM
TSI_NA20532 0 .03 RPM
TSI_NA20538 0 .05 RPM
TSI_NA20756 0 .00 RPM
TSI_NA20765 0 .10 RPM
TSI_NA20771 0 .20 RPM
TSI_NA20786 0 .03 RPM
TSI_NA20798 0 .03 RPM
YRI_NA18870 0 .10 RPM
YRI_NA18907 0 .03 RPM
YRI_NA18916 0 .08 RPM
YRI_NA19093 0 .03 RPM
YRI_NA19099 0 .24 RPM
YRI_NA19114 0 .03 RPM
YRI_NA19118 0 .08 RPM
YRI_NA19213 0 .12 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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