RetrogeneDB ID:

retro_hsap_2387

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:2:217475067..217475682(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000235444
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:PSMB3
Ensembl ID:ENSG00000108294
Aliases:PSMB3, HC10-II
Description:proteasome (prosome, macropain) subunit, beta type, 3 [Source:HGNC Symbol;Acc:9540]


Retrocopy-Parental alignment summary:






>retro_hsap_2387
ATGTCTATTATGTCCTATAACGGAGGAGCCATCATGGCCATGAAGGGGAAGAACCGTGTGGCCATCGCTGCAGACAGGCA
CTTCGGGATCCAGGCCCAGATGGTGACCACGGACTTCCAGGAGATCTTTCCCATGGGTGGTTGGTTGTACATCGGTCTGG
CCGGGCTTGCCACTGACGTCCAGAGAGTTGCCCAGTGCCTCAAGTTCCAGCTGAACCTATATGAGTTGAAGGAAGGTCAG
CAGATCAAACCTTATACCTTCACGAGCATGGTGGCCAACTTCTTGTATGAGAAACATTTTGGCCCCTACTACACTGATCC
AGTCATTGCTGGTTTGGACCTGAAGACCTTTAAGCCCTTCAGTTGCTCTCTAGACCTCATCGGCTTCCCCATGGTGACTG
ATGACTTTGTGGTCAATGGCAGCTATGCCGAACAAATGTACGGAATGTGTGAGTCCCTCTGGGAACCCAACATGGATCCA
GAACACCCGTTTGAAACCATCTCCCCAGCCATGCTGAATGCTGTGGACTGGGGTGCAGGGTCAGGCATGGGAGTCATCAT
CCACATCACCAAGAAGGACAAAATCACCACCAGGACACTGAAGGCCCAAATGGAC

ORF - retro_hsap_2387 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 84.88 %
Parental protein coverage: 100.0 %
Number of stop codons detected: 0
Number of frameshifts detected: 0


Retrocopy - Parental Gene Alignment:

ParentalMSIMSYNGGAVMAMKGKNCVAIAADRRFGIQAQMVTTDFQKIFPMGDRLYIGLAGLATDVQTVAQRLKFR
MSIMSYNGGA.MAMKGKN.VAIAADR.FGIQAQMVTTDFQ.IFPMG..LYIGLAGLATDVQ.VAQ.LKF.
RetrocopyMSIMSYNGGAIMAMKGKNRVAIAADRHFGIQAQMVTTDFQEIFPMGGWLYIGLAGLATDVQRVAQCLKFQ
ParentalLNLYELKEGRQIKPYTLMSMVANLLYEKRFGPYYTEPVIAGLDPKTFKPFICSLDLIGCPMVTDDFVVSG
LNLYELKEG.QIKPYT..SMVAN.LYEK.FGPYYT.PVIAGLD.KTFKPF.CSLDLIG.PMVTDDFVV.G
RetrocopyLNLYELKEGQQIKPYTFTSMVANFLYEKHFGPYYTDPVIAGLDLKTFKPFSCSLDLIGFPMVTDDFVVNG
ParentalTCAEQMYGMCESLWEPNMDPDHLFETISQAMLNAVDRDAVSGMGVIVHIIEKDKITTRTLKARMD
..AEQMYGMCESLWEPNMDP.H.FETIS.AMLNAVD..A.SGMGVI.HI..KDKITTRTLKA.MD
RetrocopySYAEQMYGMCESLWEPNMDPEHPFETISPAMLNAVDWGAGSGMGVIIHITKKDKITTRTLKAQMD

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 42 .96 RPM
bodymap2_adrenal 0 .00 RPM 71 .01 RPM
bodymap2_brain 0 .00 RPM 25 .60 RPM
bodymap2_breast 0 .00 RPM 35 .95 RPM
bodymap2_colon 0 .00 RPM 29 .06 RPM
bodymap2_heart 0 .02 RPM 30 .96 RPM
bodymap2_kidney 0 .04 RPM 48 .02 RPM
bodymap2_liver 0 .25 RPM 59 .32 RPM
bodymap2_lung 0 .00 RPM 55 .47 RPM
bodymap2_lymph_node 0 .00 RPM 50 .60 RPM
bodymap2_ovary 0 .00 RPM 34 .49 RPM
bodymap2_prostate 0 .00 RPM 40 .03 RPM
bodymap2_skeletal_muscle 0 .00 RPM 69 .46 RPM
bodymap2_testis 0 .00 RPM 33 .65 RPM
bodymap2_thyroid 0 .00 RPM 34 .57 RPM
bodymap2_white_blood_cells 0 .00 RPM 61 .94 RPM

ChIP-Seq - click to see more details

RNA Polymerase II activity near the 5' end of retro_hsap_2387 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_2387 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_118650215 libraries 172 libraries 1152 libraries 217 libraries 73 libraries
TSS #2 TSS_118651926 libraries 776 libraries 121 libraries 6 libraries 0 libraries

The graphical summary, for retro_hsap_2387 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_2387 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_2387 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Gorilla gorilla retro_ggor_103
Pongo abelii retro_pabe_2153
Callithrix jacchus retro_cjac_2852
Parental genes homology:
Parental genes homology involve 17 parental genes, and 39 retrocopies.

Species Parental gene accession Retrocopies number
Canis familiaris ENSCAFG000000165872 retrocopies
retro_cfam_135, retro_cfam_532,
Callithrix jacchus ENSCJAG000000082461 retrocopy
retro_cjac_2852,
Equus caballus ENSECAG000000009871 retrocopy
retro_ecab_476,
Erinaceus europaeus ENSEEUG000000152751 retrocopy
retro_eeur_10,
Homo sapiens ENSG00000108294 2 retrocopies
retro_hsap_1121, retro_hsap_2387 ,
Gorilla gorilla ENSGGOG000000070672 retrocopies
retro_ggor_103, retro_ggor_876,
Loxodonta africana ENSLAFG000000022331 retrocopy
retro_lafr_70,
Macropus eugenii ENSMEUG000000041312 retrocopies
retro_meug_1804, retro_meug_551,
Microcebus murinus ENSMICG000000029971 retrocopy
retro_mmur_397,
Macaca mulatta ENSMMUG000000123631 retrocopy
retro_mmul_868,
Monodelphis domestica ENSMODG000000126142 retrocopies
retro_mdom_1722, retro_mdom_1812,
Mus musculus ENSMUSG000000697448 retrocopies
retro_mmus_1449, retro_mmus_1551, retro_mmus_1790, retro_mmus_1938, retro_mmus_2110, retro_mmus_41, retro_mmus_46, retro_mmus_536,
Nomascus leucogenys ENSNLEG000000005943 retrocopies
retro_nleu_1511, retro_nleu_188, retro_nleu_371,
Oryctolagus cuniculus ENSOCUG000000025981 retrocopy
retro_ocun_561,
Pteropus vampyrus ENSPVAG000000022701 retrocopy
retro_pvam_822,
Rattus norvegicus ENSRNOG000000129387 retrocopies
retro_rnor_1016, retro_rnor_2094, retro_rnor_2448, retro_rnor_2537, retro_rnor_2804, retro_rnor_743, retro_rnor_8,
Ictidomys tridecemlineatus ENSSTOG000000142583 retrocopies
retro_itri_527, retro_itri_935, retro_itri_936,

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 = 0.14 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .02 RPM
CEU_NA11843 0 .06 RPM
CEU_NA11930 0 .03 RPM
CEU_NA12004 0 .00 RPM
CEU_NA12400 0 .07 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 .03 RPM
FIN_HG00277 0 .00 RPM
FIN_HG00315 0 .00 RPM
FIN_HG00321 0 .03 RPM
FIN_HG00328 0 .00 RPM
FIN_HG00338 0 .00 RPM
FIN_HG00349 0 .00 RPM
FIN_HG00375 0 .02 RPM
FIN_HG00377 0 .03 RPM
FIN_HG00378 0 .00 RPM
GBR_HG00099 0 .03 RPM
GBR_HG00111 0 .02 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 .03 RPM
GBR_HG00142 0 .03 RPM
GBR_HG00143 0 .00 RPM
TSI_NA20512 0 .00 RPM
TSI_NA20513 0 .00 RPM
TSI_NA20518 0 .06 RPM
TSI_NA20532 0 .00 RPM
TSI_NA20538 0 .14 RPM
TSI_NA20756 0 .06 RPM
TSI_NA20765 0 .02 RPM
TSI_NA20771 0 .03 RPM
TSI_NA20786 0 .00 RPM
TSI_NA20798 0 .03 RPM
YRI_NA18870 0 .00 RPM
YRI_NA18907 0 .00 RPM
YRI_NA18916 0 .02 RPM
YRI_NA19093 0 .00 RPM
YRI_NA19099 0 .00 RPM
YRI_NA19114 0 .00 RPM
YRI_NA19118 0 .04 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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