RetrogeneDB ID:

retro_hsap_4720

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:X:79965426..79966204(+)
Located in intron of:ENSG00000165288
Retrocopy
information
Ensembl ID:ENSG00000225715
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:PSMA1
Ensembl ID:ENSG00000129084
Aliases:PSMA1, HC2, HEL-S-275, NU, PROS30
Description:proteasome (prosome, macropain) subunit, alpha type, 1 [Source:HGNC Symbol;Acc:9530]


Retrocopy-Parental alignment summary:






>retro_hsap_4720
TTTAGAAACCAGTATGACAATGATATCATTGTCTGGAGCAGGATTCATCAAACTGAATATGCAATGGAAGCTGTTAAACA
AGGTTCAGCCACAGTTGGTCTGAAATCAAAAACCCATGCAGTATTGGTTGCATTGAAAAGGGCACCATCGGAGCTTGCAG
CTCATCAGAAAAAAATTCTCCATATTGACAAACATATTGGTATCTCAATTGCAGGGCTTACTGATGATGGTAAACTGTTA
CGTAATTTTATGTGCCAGGAGTGTTTCGATTCCAGATTTGTATCTGATAGACCACTTCCTGTGTCTTCTCTTGTATCTCT
AATTGGAAGCAAGACCCAAATATCAACACAACAATATGGCTGGAGACCATATGGTGTTAGGCTACTTACTGCTGGTTATA
ATGATATGGGCCTCACATTTTCCAAACCTGGTCATCTGCTGACTATTTTGACTACAGAGCTACGTCCACTGGGGCCCATT
CTCAGTCAGCTCGTACTTACTTGGAGAGACATATGTCTAAATTTATGGAATACAATTTAAATGAACTGGTTAAACATGGT
CTGCATGCCTGAAGAGAGACAATTCCTGCAGAACAGGACATAACTACAAAAATGTTTCCATTGGAATTGCTGGTAATAAT
TTGGAGTTTACAATCTATCATGATGATGATGATGTGTCTCCAATCCTGGAAGGTCTTGAAGAAAGGCCACAGAGAAAGGC
AAAGCCTGCTCAACCTGCTGATTAACCAGCAGAAAAGGCTGATGAACCAATGGAACAT

ORF - retro_hsap_4720 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 83.02 %
Parental protein coverage: 99.62 %
Number of stop codons detected: 2
Number of frameshifts detected: 2


Retrocopy - Parental Gene Alignment:

ParentalFRNQYDNDVTVWSPQGRIHQIEYAMEAVKQGSATVGLKSKTHAVLVALKRAQSELAAHQKKILHVDNHIG
FRNQYDND..VWS...RIHQ.EYAMEAVKQGSATVGLKSKTHAVLVALKRA.SELAAHQKKILH.D.HIG
RetrocopyFRNQYDNDIIVWS---RIHQTEYAMEAVKQGSATVGLKSKTHAVLVALKRAPSELAAHQKKILHIDKHIG
ParentalISIAGLTADARLLCNFMRQECLDSRFVFDRPLPVSRLVSLIGSKTQIPTQRYGRRPYGVGLLIAGYDDM-
ISIAGLT.D..LL.NFM.QEC.DSRFV.DRPLPVS.LVSLIGSKTQI.TQ.YG.RPYGV.LL.AGY.DM.
RetrocopyISIAGLTDDGKLLRNFMCQECFDSRFVSDRPLPVSSLVSLIGSKTQISTQQYGWRPYGVRLLTAGYNDM<
ParentalGPHIFQTCPSANYFDCRAMSIGARSQSARTYLERHMSEFMECNLNELVKHGLRALRETLPAEQDLTT-KN
GPHIFQT..SA.YFD.RA.S.GA.SQSARTYLERHMS.FME.NLNELVKHGL.A.RET.PAEQD.TT.KN
RetrocopyGPHIFQTWSSADYFDYRATSTGAHSQSARTYLERHMSKFMEYNLNELVKHGLHA*RETIPAEQDITT<KN
ParentalVSIGIVGKDLEFTIY-DDDDVSPFLEGLEERPQRKAQPAQPADEPAEKADEPMEH
VSIGI.G..LEFTIY.DDDDVSP.LEGLEERPQRKA.PAQPAD.PAEKADEPMEH
RetrocopyVSIGIAGNNLEFTIYHDDDDVSPILEGLEERPQRKAKPAQPAD*PAEKADEPMEH

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 .00 RPM 35 .96 RPM
bodymap2_adrenal 0 .00 RPM 53 .16 RPM
bodymap2_brain 0 .00 RPM 38 .56 RPM
bodymap2_breast 0 .00 RPM 52 .14 RPM
bodymap2_colon 0 .00 RPM 46 .79 RPM
bodymap2_heart 0 .00 RPM 34 .52 RPM
bodymap2_kidney 0 .12 RPM 42 .95 RPM
bodymap2_liver 0 .00 RPM 39 .97 RPM
bodymap2_lung 0 .11 RPM 44 .59 RPM
bodymap2_lymph_node 0 .05 RPM 39 .67 RPM
bodymap2_ovary 0 .00 RPM 44 .86 RPM
bodymap2_prostate 0 .00 RPM 39 .84 RPM
bodymap2_skeletal_muscle 0 .00 RPM 32 .52 RPM
bodymap2_testis 0 .00 RPM 50 .09 RPM
bodymap2_thyroid 0 .09 RPM 53 .03 RPM
bodymap2_white_blood_cells 0 .00 RPM 38 .90 RPM
RNA Polymerase II activity near the 5' end of retro_hsap_4720 was not detected
No EST(s) were mapped for retro_hsap_4720 retrocopy.
No TSS is located nearby retro_hsap_4720 retrocopy 5' end.
retro_hsap_4720 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_4720 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_3137
Pongo abelii retro_pabe_3664
Macaca mulatta retro_mmul_2509

Parental genes homology:
Parental genes homology involve 23 parental genes, and 50 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000024402 retrocopies
Bos taurus ENSBTAG000000065641 retrocopy
Choloepus hoffmanni ENSCHOG0000000539511 retrocopies
Equus caballus ENSECAG000000240861 retrocopy
Felis catus ENSFCAG000000113811 retrocopy
Homo sapiens ENSG00000129084 1 retrocopy
retro_hsap_4720 ,
Gorilla gorilla ENSGGOG000000014161 retrocopy
Macropus eugenii ENSMEUG000000111121 retrocopy
Myotis lucifugus ENSMLUG000000092514 retrocopies
Macaca mulatta ENSMMUG000000164461 retrocopy
Mustela putorius furoENSMPUG000000131994 retrocopies
Mus musculus ENSMUSG000000307511 retrocopy
Nomascus leucogenys ENSNLEG000000177051 retrocopy
Oryctolagus cuniculus ENSOCUG000000004392 retrocopies
Otolemur garnettii ENSOGAG000000116223 retrocopies
Ochotona princeps ENSOPRG000000136771 retrocopy
Pongo abelii ENSPPYG000000034662 retrocopies
Pan troglodytes ENSPTRG000000033851 retrocopy
Sarcophilus harrisii ENSSHAG000000156261 retrocopy
Ictidomys tridecemlineatus ENSSTOG000000062702 retrocopies
Tupaia belangeri ENSTBEG000000120373 retrocopies
Tarsius syrichta ENSTSYG000000038692 retrocopies
Vicugna pacos ENSVPAG000000088203 retrocopies

Expression level across human populations :

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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



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Library Retrogene expression
CEU_NA11831 0 .00 RPM
CEU_NA11843 0 .00 RPM
CEU_NA11930 0 .00 RPM
CEU_NA12004 0 .00 RPM
CEU_NA12400 0 .00 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 .00 RPM
FIN_HG00277 0 .00 RPM
FIN_HG00315 0 .00 RPM
FIN_HG00321 0 .00 RPM
FIN_HG00328 0 .00 RPM
FIN_HG00338 0 .00 RPM
FIN_HG00349 0 .00 RPM
FIN_HG00375 0 .00 RPM
FIN_HG00377 0 .00 RPM
FIN_HG00378 0 .00 RPM
GBR_HG00099 0 .00 RPM
GBR_HG00111 0 .00 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 .00 RPM
GBR_HG00142 0 .00 RPM
GBR_HG00143 0 .00 RPM
TSI_NA20512 0 .00 RPM
TSI_NA20513 0 .00 RPM
TSI_NA20518 0 .00 RPM
TSI_NA20532 0 .00 RPM
TSI_NA20538 0 .00 RPM
TSI_NA20756 0 .00 RPM
TSI_NA20765 0 .00 RPM
TSI_NA20771 0 .00 RPM
TSI_NA20786 0 .00 RPM
TSI_NA20798 0 .00 RPM
YRI_NA18870 0 .00 RPM
YRI_NA18907 0 .00 RPM
YRI_NA18916 0 .00 RPM
YRI_NA19093 0 .00 RPM
YRI_NA19099 0 .00 RPM
YRI_NA19114 0 .00 RPM
YRI_NA19118 0 .00 RPM
YRI_NA19213 0 .00 RPM
YRI_NA19214 0 .00 RPM
YRI_NA19223 0 .00 RPM
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