RetrogeneDB ID:

retro_hsap_1200

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:13:49345314..49345962(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000225131
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_1200
CTTTTCCAGGAGGCTGAGGAATTCCTCTACAGATTCTTGCCACAGAAAATCACATACCTGAATCAGCTCTTGCGAGAGGG
CTCCCTCAGTGTGGCTGACCTGACTTCCCTCCGGGCCCCACTGGACATCCCCAACCCAGACCCTCCACCCAAGGATGATG
AGATGGAAACAGATAAGTAGGAGAAGAAAGAAGTCCCTAAGTGTGGATTTCTCCCTGGGAATAAGAAAGTCCTGTCCCTG
CTTGCCCTGGTTAAGCCAGAATTCTGGACTCTCAAAGAGAAATTCATTCTGGTGATTACATGGATCCAGCACCTAATCCC
CAAGATTGAAGATGGAAATGATTTTGGGGTAGCAATCCAGGAGAAGGTGCTGGAGAGGGTGAATGCTGTCAAGACCAAAG
TGGAAGCTTTCCAGACAACCATTTCCAAGTAATTCTCAGAACGTGGGGATGCTGCGGCCAAGGCCTCCGAGGAGACTCAT
GTAATGGATTACCGGGCCTTGGTGCATGAGCGAGATGAGGCAGCCTATGGGGAGCTCAGGGCCATGGTGCTGGACCTGAG
GGCCTTCTATGCTGAGCTTTATCATATCATCAACAGCAACCTGGAGAAAATTGTCAACCCAAAGGGTGAAAAGAAGCCAT
CTATGTAC

ORF - retro_hsap_1200 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 93.06 %
Parental protein coverage: 90.38 %
Number of stop codons detected: 2
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalLFQEAEEFLYRFLPQKIIYLNQLLQEDSLNVADLTSLRAPLDIPIPDPPPKDDEMETDKQEKKEVHKCGF
LFQEAEEFLYRFLPQKI.YLNQLL.E.SL.VADLTSLRAPLDIP.PDPPPKDDEMETDK.EKKEV.KCGF
RetrocopyLFQEAEEFLYRFLPQKITYLNQLLREGSLSVADLTSLRAPLDIPNPDPPPKDDEMETDK*EKKEVPKCGF
ParentalLPGNEKVLSLLALVKPEVWTLKEKCILVITWIQHLIPKIEDGNDFGVAIQEKVLERVNAVKTKVEAFQTT
LPGN.KVLSLLALVKPE.WTLKEK.ILVITWIQHLIPKIEDGNDFGVAIQEKVLERVNAVKTKVEAFQTT
RetrocopyLPGNKKVLSLLALVKPEFWTLKEKFILVITWIQHLIPKIEDGNDFGVAIQEKVLERVNAVKTKVEAFQTT
ParentalISKYFSERGDAVAKASKETHVMDYRALVHERDEAAYGELRAMVLDLRAFYAELYHIISSNLEKIVNPKGE
ISK.FSERGDA.AKAS.ETHVMDYRALVHERDEAAYGELRAMVLDLRAFYAELYHII.SNLEKIVNPKGE
RetrocopyISK*FSERGDAAAKASEETHVMDYRALVHERDEAAYGELRAMVLDLRAFYAELYHIINSNLEKIVNPKGE
ParentalEKPSMY
.KPSMY
RetrocopyKKPSMY

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 .08 RPM 41 .51 RPM
bodymap2_adrenal 0 .33 RPM 115 .02 RPM
bodymap2_brain 0 .02 RPM 19 .60 RPM
bodymap2_breast 0 .02 RPM 35 .10 RPM
bodymap2_colon 0 .06 RPM 36 .04 RPM
bodymap2_heart 0 .06 RPM 30 .94 RPM
bodymap2_kidney 0 .79 RPM 92 .94 RPM
bodymap2_liver 0 .59 RPM 69 .10 RPM
bodymap2_lung 0 .30 RPM 95 .73 RPM
bodymap2_lymph_node 1 .02 RPM 77 .28 RPM
bodymap2_ovary 0 .12 RPM 62 .61 RPM
bodymap2_prostate 1 .14 RPM 56 .55 RPM
bodymap2_skeletal_muscle 0 .36 RPM 19 .08 RPM
bodymap2_testis 0 .17 RPM 46 .13 RPM
bodymap2_thyroid 0 .09 RPM 45 .01 RPM
bodymap2_white_blood_cells 1 .87 RPM 122 .04 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_1200 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_1200 retrocopy.

TSS - click to see more details



TSS No. TSS Name TSS expression level (Expr) in TPM range:
no expression 0 < Expr ≤ 1 1 < Expr ≤ 5 5 < Expr ≤ 10 Expr > 10
TSS #1 TSS_33600797 libraries434 libraries474 libraries59 libraries65 libraries

The graphical summary, for retro_hsap_1200 TSS expression levels > 0 TPM .
TSS expression levels were studied across 1829 TSS-CAGE libraries, based on FANTOM5 data.
The expression values were visualized using beanplot. If you have any doubts, how to read it, read more in Kampstra P (2008)

Display detail expression values in each library
... or ...
Directly download all expression values

Lab - click to see more details

retro_hsap_1200 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_1200 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_820
Gorilla gorilla retro_ggor_935
Pongo abelii retro_pabe_1000
Parental genes homology:
Parental genes homology involve 10 parental genes, and 30 retrocopies.

Species Parental gene accession Retrocopies number
Callithrix jacchus ENSCJAG000000071673 retrocopies
retro_cjac_233, retro_cjac_322, retro_cjac_71,
Homo sapiens ENSG00000100911 4 retrocopies
retro_hsap_1200 , retro_hsap_2999, retro_hsap_3033, retro_hsap_3222,
Homo sapiens ENSG000001314671 retrocopy
retro_hsap_245,
Gorilla gorilla ENSGGOG000000160254 retrocopies
retro_ggor_2078, retro_ggor_2093, retro_ggor_2188, retro_ggor_935,
Macaca mulatta ENSMMUG000000124734 retrocopies
retro_mmul_1229, retro_mmul_1919, retro_mmul_1940, retro_mmul_2281,
Mus musculus ENSMUSG000000791971 retrocopy
retro_mmus_145,
Nomascus leucogenys ENSNLEG000000152604 retrocopies
retro_nleu_2086, retro_nleu_2726, retro_nleu_3086, retro_nleu_844,
Otolemur garnettii ENSOGAG000000165841 retrocopy
retro_ogar_61,
Pongo abelii ENSPPYG000000056844 retrocopies
retro_pabe_1000, retro_pabe_2486, retro_pabe_2512, retro_pabe_2669,
Pan troglodytes ENSPTRG000000061964 retrocopies
retro_ptro_2028, retro_ptro_2046, retro_ptro_2172, retro_ptro_820,

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 = 7.4 RPM Legend:


Library Retrogene expression
CEU_NA11831 5 .31 RPM
CEU_NA11843 4 .81 RPM
CEU_NA11930 3 .42 RPM
CEU_NA12004 5 .85 RPM
CEU_NA12400 3 .89 RPM
CEU_NA12751 4 .71 RPM
CEU_NA12760 3 .91 RPM
CEU_NA12827 3 .40 RPM
CEU_NA12872 3 .65 RPM
CEU_NA12873 3 .09 RPM
FIN_HG00183 3 .98 RPM
FIN_HG00277 3 .51 RPM
FIN_HG00315 6 .40 RPM
FIN_HG00321 4 .20 RPM
FIN_HG00328 4 .21 RPM
FIN_HG00338 5 .68 RPM
FIN_HG00349 7 .40 RPM
FIN_HG00375 4 .60 RPM
FIN_HG00377 6 .30 RPM
FIN_HG00378 4 .89 RPM
GBR_HG00099 4 .04 RPM
GBR_HG00111 6 .81 RPM
GBR_HG00114 5 .50 RPM
GBR_HG00119 3 .81 RPM
GBR_HG00131 4 .60 RPM
GBR_HG00133 4 .03 RPM
GBR_HG00134 3 .63 RPM
GBR_HG00137 5 .33 RPM
GBR_HG00142 5 .22 RPM
GBR_HG00143 4 .44 RPM
TSI_NA20512 5 .51 RPM
TSI_NA20513 3 .89 RPM
TSI_NA20518 5 .72 RPM
TSI_NA20532 4 .59 RPM
TSI_NA20538 4 .33 RPM
TSI_NA20756 5 .73 RPM
TSI_NA20765 4 .60 RPM
TSI_NA20771 5 .59 RPM
TSI_NA20786 5 .96 RPM
TSI_NA20798 4 .30 RPM
YRI_NA18870 5 .21 RPM
YRI_NA18907 4 .89 RPM
YRI_NA18916 4 .42 RPM
YRI_NA19093 4 .48 RPM
YRI_NA19099 4 .21 RPM
YRI_NA19114 3 .67 RPM
YRI_NA19118 4 .74 RPM
YRI_NA19213 4 .09 RPM
YRI_NA19214 3 .69 RPM
YRI_NA19223 3 .18 RPM

Indel association:

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



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