RetrogeneDB ID:

retro_hsap_2199

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:2:203044017..203044624(+)
Located in intron of:ENSG00000182329
Retrocopy
information
Ensembl ID:ENSG00000227890
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:PSMA2
Ensembl ID:ENSG00000106588
Aliases:PSMA2, HC3, MU, PMSA2, PSC2
Description:proteasome (prosome, macropain) subunit, alpha type, 2 [Source:HGNC Symbol;Acc:9531]


Retrocopy-Parental alignment summary:






>retro_hsap_2199
ATGGCGGAGCGCGGTACGGCTTTTCGCTGACTACATTCAGCCCGTCTGATAAACTTGTCCGGATTGAATATGCTTTGGCT
GCTGTAGCTGGAGGAGCCCTGTCAGTGGGAATTAAAGCGGCAAATGGTGTGGTATTAGCAACCGAGAAAAAACAGAAATT
CATTCTGTATGATGAGCGAAGTGTAGACAAAGTGGAACCAATTACCAAGCACATAGGTTTGGTGTACAGTGGCGTGGGCC
CAGATAACAAAGTGCTTGTGCACACAGCTCGAAACTAGCTCAACAATACTATCTTGTGTACCAAGTGCCCATTCCCACAG
CTCAGCTAGTGCGGAGAGTAGCTTCTGTAATGCAAGAATATACTCAGTCAGGTGGTGTTTGTCCATTTGGAGTTTCTTTA
CTTGTTTGTGGTTGGAATGAGGGACAACCATATTTATTTCAGTCAGATCCATCTGGAGCTTACTTGGCCTGGAAAGCCAC
AGCAGTGGGAAAGAACTATGTGAATGGGGAAACTTCCCTTGAGAAAAGATAAAATGAAGATCTGGAACTTGAAGATGCCA
TTCATACAGCCATGTTAACCCTAAAGGAAAGCTTTGAAGGCCAAATG

ORF - retro_hsap_2199 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 88.78 %
Parental protein coverage: 86.75 %
Number of stop codons detected: 1
Number of frameshifts detected: 2


Retrocopy - Parental Gene Alignment:

ParentalMAERG-YSFSLTTFSPSGKLVQIEYALAAVAGGAPSVGIKAANGVVLATEKKQKSILYDERSVHKVEPIT
MAERG.Y.FSLTTFSPS.KLV.IEYALAAVAGGA.SVGIKAANGVVLATEKKQK.ILYDERSV.KVEPIT
RetrocopyMAERG<YGFSLTTFSPSDKLVRIEYALAAVAGGALSVGIKAANGVVLATEKKQKFILYDERSVDKVEPIT
ParentalKHIGLVYSGMGPDYRVLVHRAR-KLAQQYYLVYQEPIPTAQLVQRVASVMQEYTQSGGVRPFGVSLLICG
KHIGLVYSG.GPD..VLVH.AR.KLAQQYYLVYQ.PIPTAQLV.RVASVMQEYTQSGGV.PFGVSLL.CG
RetrocopyKHIGLVYSGVGPDNKVLVHTAR<KLAQQYYLVYQVPIPTAQLVRRVASVMQEYTQSGGVCPFGVSLLVCG
ParentalWNEGRPYLFQSDPSGAYFAWKATAMGKNYVNGKTFLEKRYNEDLELEDAIHTAILTLKESFEGQM
WNEG.PYLFQSDPSGAY.AWKATA.GKNYVNG.T.LEKR.NEDLELEDAIHTA.LTLKESFEGQM
RetrocopyWNEGQPYLFQSDPSGAYLAWKATAVGKNYVNGETSLEKR*NEDLELEDAIHTAMLTLKESFEGQM

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 17 .51 RPM
bodymap2_adrenal 0 .04 RPM 26 .90 RPM
bodymap2_brain 0 .07 RPM 24 .54 RPM
bodymap2_breast 0 .00 RPM 38 .95 RPM
bodymap2_colon 0 .06 RPM 30 .69 RPM
bodymap2_heart 0 .00 RPM 12 .85 RPM
bodymap2_kidney 0 .00 RPM 34 .74 RPM
bodymap2_liver 0 .02 RPM 27 .06 RPM
bodymap2_lung 0 .00 RPM 21 .01 RPM
bodymap2_lymph_node 0 .00 RPM 22 .15 RPM
bodymap2_ovary 0 .06 RPM 28 .80 RPM
bodymap2_prostate 0 .05 RPM 19 .80 RPM
bodymap2_skeletal_muscle 0 .07 RPM 23 .04 RPM
bodymap2_testis 0 .51 RPM 31 .33 RPM
bodymap2_thyroid 0 .00 RPM 27 .17 RPM
bodymap2_white_blood_cells 0 .00 RPM 18 .78 RPM

ChIP-Seq - click to see more details

RNA Polymerase II activity may be related with retro_hsap_2199 in 1 libraries
ENCODE library ID Target ChIP-Seq Peak coordinates
ENCFF002CVJ POLR2A 2:203042943..203043553

EST - click to see more details

No EST(s) were mapped for retro_hsap_2199 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_117409508 libraries 435 libraries 137 libraries 294 libraries 455 libraries

The graphical summary, for retro_hsap_2199 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_2199 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_2199 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_1670
Pongo abelii retro_pabe_2076
Macaca mulatta retro_mmul_923
Parental genes homology:
Parental genes homology involve 24 parental genes, and 46 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000094333 retrocopies
retro_amel_1029, retro_amel_1336, retro_amel_1379,
Bos taurus ENSBTAG000000009903 retrocopies
retro_btau_296, retro_btau_384, retro_btau_889,
Choloepus hoffmanni ENSCHOG000000006441 retrocopy
retro_chof_893,
Callithrix jacchus ENSCJAG000000077304 retrocopies
retro_cjac_1096, retro_cjac_1868, retro_cjac_2583, retro_cjac_852,
Cavia porcellus ENSCPOG000000131341 retrocopy
retro_cpor_1512,
Dasypus novemcinctus ENSDNOG000000119102 retrocopies
retro_dnov_2202, retro_dnov_724,
Echinops telfairi ENSETEG000000158352 retrocopies
retro_etel_1569, retro_etel_2022,
Homo sapiens ENSG00000106588 2 retrocopies
retro_hsap_2199 , retro_hsap_908,
Gorilla gorilla ENSGGOG000000065381 retrocopy
retro_ggor_735,
Myotis lucifugus ENSMLUG000000100862 retrocopies
retro_mluc_1050, retro_mluc_135,
Macaca mulatta ENSMMUG000000224512 retrocopies
retro_mmul_1114, retro_mmul_923,
Mustela putorius furoENSMPUG000000181451 retrocopy
retro_mputfur_548,
Mus musculus ENSMUSG000000156714 retrocopies
retro_mmus_1104, retro_mmus_1105, retro_mmus_1215, retro_mmus_1320,
Nomascus leucogenys ENSNLEG000000031771 retrocopy
retro_nleu_329,
Oryctolagus cuniculus ENSOCUG000000120921 retrocopy
retro_ocun_774,
Otolemur garnettii ENSOGAG000000168051 retrocopy
retro_ogar_197,
Ochotona princeps ENSOPRG000000117932 retrocopies
retro_opri_135, retro_opri_791,
Pongo abelii ENSPPYG000000176122 retrocopies
retro_pabe_2076, retro_pabe_783,
Pan troglodytes ENSPTRG000000191202 retrocopies
retro_ptro_1670, retro_ptro_628,
Rattus norvegicus ENSRNOG000000499202 retrocopies
retro_rnor_2041, retro_rnor_2769,
Sus scrofa ENSSSCG000000207693 retrocopies
retro_sscr_1082, retro_sscr_419, retro_sscr_440,
Ictidomys tridecemlineatus ENSSTOG000000133341 retrocopy
retro_itri_223,
Tarsius syrichta ENSTSYG000000142992 retrocopies
retro_tsyr_132, retro_tsyr_246,
Tursiops truncatus ENSTTRG000000056491 retrocopy
retro_ttru_356,

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 .04 RPM
CEU_NA11843 0 .00 RPM
CEU_NA11930 0 .03 RPM
CEU_NA12004 0 .08 RPM
CEU_NA12400 0 .04 RPM
CEU_NA12751 0 .07 RPM
CEU_NA12760 0 .00 RPM
CEU_NA12827 0 .00 RPM
CEU_NA12872 0 .03 RPM
CEU_NA12873 0 .10 RPM
FIN_HG00183 0 .00 RPM
FIN_HG00277 0 .11 RPM
FIN_HG00315 0 .03 RPM
FIN_HG00321 0 .00 RPM
FIN_HG00328 0 .00 RPM
FIN_HG00338 0 .06 RPM
FIN_HG00349 0 .03 RPM
FIN_HG00375 0 .05 RPM
FIN_HG00377 0 .08 RPM
FIN_HG00378 0 .06 RPM
GBR_HG00099 0 .06 RPM
GBR_HG00111 0 .00 RPM
GBR_HG00114 0 .05 RPM
GBR_HG00119 0 .02 RPM
GBR_HG00131 0 .03 RPM
GBR_HG00133 0 .05 RPM
GBR_HG00134 0 .02 RPM
GBR_HG00137 0 .05 RPM
GBR_HG00142 0 .03 RPM
GBR_HG00143 0 .03 RPM
TSI_NA20512 0 .00 RPM
TSI_NA20513 0 .05 RPM
TSI_NA20518 0 .08 RPM
TSI_NA20532 0 .00 RPM
TSI_NA20538 0 .05 RPM
TSI_NA20756 0 .09 RPM
TSI_NA20765 0 .00 RPM
TSI_NA20771 0 .00 RPM
TSI_NA20786 0 .00 RPM
TSI_NA20798 0 .03 RPM
YRI_NA18870 0 .14 RPM
YRI_NA18907 0 .03 RPM
YRI_NA18916 0 .04 RPM
YRI_NA19093 0 .03 RPM
YRI_NA19099 0 .03 RPM
YRI_NA19114 0 .03 RPM
YRI_NA19118 0 .02 RPM
YRI_NA19213 0 .00 RPM
YRI_NA19214 0 .02 RPM
YRI_NA19223 0 .04 RPM

Indel association:

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



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