RetrogeneDB ID:

retro_hsap_3033

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:4:37997117..37997824(-)
Located in intron of:ENSG00000065882
Retrocopy
information
Ensembl ID:ENSG00000251332
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:PSME2
Ensembl ID:ENSG00000100911
Aliases:PSME2, PA28B, PA28beta, REGbeta
Description:proteasome (prosome, macropain) activator subunit 2 (PA28 beta) [Source:HGNC Symbol;Acc:9569]


Retrocopy-Parental alignment summary:






>retro_hsap_3033
GCCAAGCCTTGTGGTGGGTGCCTGAGCAGGGAGGCCCACACCCAGGTACATGTCTTCAGGCAAGAGCTTTTCCAAGAAGC
CAAGGAATTCCTCTACAGATTCTTGCCACAGAAAATCATATACCCACATAGGCCTTGCAAAAGGATTCCCTCATTGTAGC
TGCCTGACCTCCCTCCGGGCCCCACTGGACATCCCCATCCCAGAACCCCCACCCAAGGATGAGGTAGAAACAGAGAGGCA
AGAGAAGAAAGAAGTCCTTGAGTGTGGATTTCTCCCTGGGAATGAGAAGGTCCTGTCGCTGCTTGCCATGGTTAAGCCAG
AAGTCTGGATTCTCAAAGAGAAATGCATTCTGGTGATCACATGGATCCAGCACCTGATCCCCAAGACTGAGGATGCAAAT
GATTTGGGGTAGCAATCCAGGAGAAGGTGCTGGAGAGGGTGAATGCAGTTAAGACCAAAGTGCAAGCCGTCCAGACAACC
ATTTCCAAATACTTCTCAGAACACGGGGATGCTGTGGCCAAGGCCTCCAAGGAGACCCATGTAATGGATTACCAGGCGTT
GGTGCAAAAGTGAGATAAGACAGCCTATGGGGAGGTCAAGGCCAGGGTACTGGACCTGAAGGCCTTCTGTGCTGAGCTTT
ATCATATCATCAGCACCAACCTGGAGAAAACCGCAACCCAAAAGGTGAAGAGAAACCATCTGTGTAC

ORF - retro_hsap_3033 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 80.17 %
Parental protein coverage: 99.58 %
Number of stop codons detected: 1
Number of frameshifts detected 4


Retrocopy - Parental Gene Alignment:

ParentalAKPCGVRLSGEARKQVEVFRQNLFQEAEEFLYRFLPQKIIYLNQ-LLQEDSLNVAD-LTSLRAPLDIPIP
AKPCG..LS.EA..QV.VFRQ.LFQEA.EFLYRFLPQKIIY.....LQ.DSL.VA..LTSLRAPLDIPIP
RetrocopyAKPCGGCLSREAHTQVHVFRQELFQEAKEFLYRFLPQKIIYPHR<ALQKDSLIVAA<LTSLRAPLDIPIP
ParentalDPPPKDDEMETDKQEKKEVHKCGFLPGNEKVLSLLALVKPEVWTLKEKCILVITWIQHLIPKIEDGND-F
.PPPKD.E.ET..QEKKEV..CGFLPGNEKVLSLLA.VKPEVW.LKEKCILVITWIQHLIPK.ED.ND.F
RetrocopyEPPPKD-EVETERQEKKEVLECGFLPGNEKVLSLLAMVKPEVWILKEKCILVITWIQHLIPKTEDAND<F
ParentalGVAIQEKVLERVNAVKTKVEAFQTTISKYFSERGDAVAKASKETHVMDYRALVHERDEAAYGELRAMVLD
GVAIQEKVLERVNAVKTKV.A.QTTISKYFSE.GDAVAKASKETHVMDY.ALV...D..AYGE..A.VLD
RetrocopyGVAIQEKVLERVNAVKTKVQAVQTTISKYFSEHGDAVAKASKETHVMDYQALVQK*DKTAYGEVKARVLD
ParentalLRAFYAELYHIISSNLEKIV-NPKGEEKPSMY
L.AF.AELYHIIS.NLEK...NPKGEEKPS.Y
RetrocopyLKAFCAELYHIISTNLEKTA<NPKGEEKPSVY

Legend:
*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide






(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 .08 RPM 41 .51 RPM
bodymap2_adrenal 0 .12 RPM 115 .02 RPM
bodymap2_brain 0 .02 RPM 19 .60 RPM
bodymap2_breast 0 .00 RPM 35 .10 RPM
bodymap2_colon 0 .02 RPM 36 .04 RPM
bodymap2_heart 0 .11 RPM 30 .94 RPM
bodymap2_kidney 0 .33 RPM 92 .94 RPM
bodymap2_liver 0 .08 RPM 69 .10 RPM
bodymap2_lung 0 .09 RPM 95 .73 RPM
bodymap2_lymph_node 0 .00 RPM 77 .28 RPM
bodymap2_ovary 0 .02 RPM 62 .61 RPM
bodymap2_prostate 0 .00 RPM 56 .55 RPM
bodymap2_skeletal_muscle 0 .00 RPM 19 .08 RPM
bodymap2_testis 0 .00 RPM 46 .13 RPM
bodymap2_thyroid 0 .13 RPM 45 .01 RPM
bodymap2_white_blood_cells 0 .24 RPM 122 .04 RPM
RNA Polymerase II actvity near the 5' end of retro_hsap_3033 was not detected
No EST(s) were mapped for retro_hsap_3033 retrocopy.
No TSS is located nearby retro_hsap_3033 retrocopy 5' end.
retro_hsap_3033 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_3033 has 4 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_2046
Gorilla gorilla retro_ggor_2093
Pongo abelii retro_pabe_2512
Macaca mulatta retro_mmul_1940

Parental genes homology:
Parental genes homology involve 10 parental genes, and 30 retrocopies.

Species Parental gene accession Retrocopies number
Callithrix jacchus ENSCJAG000000071673 retrocopies
Homo sapiens ENSG00000100911 4 retrocopies
Homo sapiens ENSG000001314671 retrocopy
Gorilla gorilla ENSGGOG000000160254 retrocopies
Macaca mulatta ENSMMUG000000124734 retrocopies
Mus musculus ENSMUSG000000791971 retrocopy
Nomascus leucogenys ENSNLEG000000152604 retrocopies
Otolemur garnettii ENSOGAG000000165841 retrocopy
Pongo abelii ENSPPYG000000056844 retrocopies
Pan troglodytes ENSPTRG000000061964 retrocopies

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 = 0.12 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .00 RPM
CEU_NA11843 0 .03 RPM
CEU_NA11930 0 .03 RPM
CEU_NA12004 0 .04 RPM
CEU_NA12400 0 .00 RPM
CEU_NA12751 0 .00 RPM
CEU_NA12760 0 .09 RPM
CEU_NA12827 0 .05 RPM
CEU_NA12872 0 .08 RPM
CEU_NA12873 0 .03 RPM
FIN_HG00183 0 .11 RPM
FIN_HG00277 0 .04 RPM
FIN_HG00315 0 .00 RPM
FIN_HG00321 0 .06 RPM
FIN_HG00328 0 .00 RPM
FIN_HG00338 0 .02 RPM
FIN_HG00349 0 .03 RPM
FIN_HG00375 0 .02 RPM
FIN_HG00377 0 .00 RPM
FIN_HG00378 0 .02 RPM
GBR_HG00099 0 .03 RPM
GBR_HG00111 0 .02 RPM
GBR_HG00114 0 .11 RPM
GBR_HG00119 0 .00 RPM
GBR_HG00131 0 .06 RPM
GBR_HG00133 0 .00 RPM
GBR_HG00134 0 .02 RPM
GBR_HG00137 0 .00 RPM
GBR_HG00142 0 .03 RPM
GBR_HG00143 0 .06 RPM
TSI_NA20512 0 .00 RPM
TSI_NA20513 0 .12 RPM
TSI_NA20518 0 .03 RPM
TSI_NA20532 0 .07 RPM
TSI_NA20538 0 .05 RPM
TSI_NA20756 0 .00 RPM
TSI_NA20765 0 .04 RPM
TSI_NA20771 0 .09 RPM
TSI_NA20786 0 .03 RPM
TSI_NA20798 0 .00 RPM
YRI_NA18870 0 .07 RPM
YRI_NA18907 0 .07 RPM
YRI_NA18916 0 .02 RPM
YRI_NA19093 0 .08 RPM
YRI_NA19099 0 .03 RPM
YRI_NA19114 0 .00 RPM
YRI_NA19118 0 .06 RPM
YRI_NA19213 0 .07 RPM
YRI_NA19214 0 .02 RPM
YRI_NA19223 0 .08 RPM


Indel association:

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




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