RetrogeneDB ID:

retro_hsap_2801

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:3:72925886..72927253(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000240135
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:PSMD12
Ensembl ID:ENSG00000197170
Aliases:None
Description:proteasome (prosome, macropain) 26S subunit, non-ATPase, 12 [Source:HGNC Symbol;Acc:9557]


Retrocopy-Parental alignment summary:






>retro_hsap_2801
ATGGCAGACGGCCACTTGCAGCAGGCTGACGGGCGCATATTCAAAATGGAAGTGGACTACAACGCCACGGTAGATCAGTG
CCTACCCGAGTGTGAGAAGCTGGCCAAGGAAGGAAGACTTCAAGAAGTCATGGAAACCCTTCTCTCTTTGGAAAAACAGA
CTCGTACTGCTTCTGATATGGGGTCAACATCCCAAATCTTAGTTGCAGTAGTGAAGATGTGCTATGAGGCTAAAGAATGG
GATTTACTTAATGAAAATATTACACTTTTGTCCAAAAGGCGGAGTCAGTTAATACAAGCTGTTGCCAAAATGGTTCAATA
GTACTGTATTTATGTTGAGGAAATCACAGACCTTCCTATCAAACTTCAATTAACTGATACTCTATGAATGGTTACCGAAG
GCAAGATTTATGTTGAAATTGAGTGTGCTCGACTGACTAAAACATTAGCAACTATAAAAGAACAAAATGGTGATGTGAAA
GAGGCAGCCTCCGTTTATAGGAGCTACAGGTGGAAACCTATGGATCAATGTAAAAGAAAGAGCAAGTGGAATTTATTTTG
GAGCAAATGAGGCTCTGCCTAGCTGTAAAGGATTACATTCGAACATAAATCATCAGTAAGAAAATTAATACCAAGTTTTT
CCAGGAAGAAAATACAGCGAAATTAAAGTTGAAGTACGATAATTTAATGACTCAGCTGGATGAACATGAGGGATCCTATT
TGTTTATTTGTAAGCACTACAGAGCAATATATAATACTCCCTGTATACAGGCAGAAAGTGAAAAATGGCAGCAGGCTATG
AAGAGTGTTGTACCCTATGTTACCCTGGCTCCTTTTGACAATGAACAGTCAGATTTGGTTCACTGAATAAGTGGTGACAA
GAAGTCAGAAGAAATTCCCAAATACAAGGATCTTCTAAAGCTTTTTACCACAATGGAGTTGATGCGTTGGTCCACACTTG
TGGAGGACTATGGAATGGAATTAAGAAAAGGTTCCGTTGGCAGTCCTGCAACTGATGCTTTTGGTTCTACAGAGGAAGGC
GAAAAAAGGTGGAAAGATTTGAATAACAGAGTTGTTGAACATAATATTAGAATAATGGCCAAGTATTATACTCGGATGAC
AATGAAAAGGATGGTACAGCTTCTGGATCTATCTGTTGATGAGTCCGAAGCCTTTCTCTCAAATCTAGTAGTTAACAAGA
CCATATTTGCTAAAGTAGACAGATTAGCAGGAATTAACAACTTCCAGAGACCCAAGGATCCAAATAATTTATGAAATGAC
TGGTCTCAGAAACTGAACTCATTAATGTCTCTAGTTAACAAAACTACACATCTCATAGCTAAAGAGGAGATGATACATAA
TCTACAA

ORF - retro_hsap_2801 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 89.93 %
Parental protein coverage: 100. %
Number of stop codons detected: 6
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalMADGGSERADGRIVKMEVDYSATVDQRLPECAKLAKEGRLQEVIETLLSLEKQTRTASDMVSTSRILVAV
MADG....ADGRI.KMEVDY.ATVDQ.LPEC.KLAKEGRLQEV.ETLLSLEKQTRTASDM.STS.ILVAV
RetrocopyMADGHLQQADGRIFKMEVDYNATVDQCLPECEKLAKEGRLQEVMETLLSLEKQTRTASDMGSTSQILVAV
ParentalVKMCYEAKEWDLLNENIMLLSKRRSQLKQAVAKMVQQCCTYVEEITDLPIKLRLIDTLRMVTEGKIYVEI
VKMCYEAKEWDLLNENI.LLSKRRSQL.QAVAKMVQ..C.YVEEITDLPIKL.L.DTL.MVTEGKIYVEI
RetrocopyVKMCYEAKEWDLLNENITLLSKRRSQLIQAVAKMVQ*YCIYVEEITDLPIKLQLTDTL*MVTEGKIYVEI
ParentalERARLTKTLATIKEQNGDVKEAASILQ-ELQVETYGSMEKKERVEFILEQMRLCLAVKDYIRTQIISKKI
E.ARLTKTLATIKEQNGDVKEAAS....ELQVETYGSM.KKE.VEFILEQMRLCLAVKDYIRT.IISKKI
RetrocopyECARLTKTLATIKEQNGDVKEAASVYR<ELQVETYGSM*KKEQVEFILEQMRLCLAVKDYIRT*IISKKI
ParentalNTKFFQEENTEKLKLKYYNLMIQLDQHEGSYLSICKHYRAIYDTPCIQAESEKWQQALKSVVLYVILAPF
NTKFFQEENT.KLKLKY.NLM.QLD.HEGSYL.ICKHYRAIY.TPCIQAESEKWQQA.KSVV.YV.LAPF
RetrocopyNTKFFQEENTAKLKLKYDNLMTQLDEHEGSYLFICKHYRAIYNTPCIQAESEKWQQAMKSVVPYVTLAPF
ParentalDNEQSDLVHRISGDKKLEEIPKYKDLLKLFTTMELMRWSTLVEDYGMELRKGSLESPATDVFGSTEEGEK
DNEQSDLVH.ISGDKK.EEIPKYKDLLKLFTTMELMRWSTLVEDYGMELRKGS..SPATD.FGSTEEGEK
RetrocopyDNEQSDLVH*ISGDKKSEEIPKYKDLLKLFTTMELMRWSTLVEDYGMELRKGSVGSPATDAFGSTEEGEK
ParentalRWKDLKNRVVEHNIRIMAKYYTRITMKRMAQLLDLSVDESEAFLSNLVVNKTIFAKVDRLAGIINFQRPK
RWKDL.NRVVEHNIRIMAKYYTR.TMKRM.QLLDLSVDESEAFLSNLVVNKTIFAKVDRLAGI.NFQRPK
RetrocopyRWKDLNNRVVEHNIRIMAKYYTRMTMKRMVQLLDLSVDESEAFLSNLVVNKTIFAKVDRLAGINNFQRPK
ParentalDPNNLLNDWSQKLNSLMSLVNKTTHLIAKEEMIHNLQ
DPNNL.NDWSQKLNSLMSLVNKTTHLIAKEEMIHNLQ
RetrocopyDPNNL*NDWSQKLNSLMSLVNKTTHLIAKEEMIHNLQ

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 65 .84 RPM
bodymap2_adrenal 0 .00 RPM 78 .11 RPM
bodymap2_brain 0 .00 RPM 88 .44 RPM
bodymap2_breast 0 .00 RPM 84 .01 RPM
bodymap2_colon 0 .00 RPM 74 .69 RPM
bodymap2_heart 0 .00 RPM 56 .93 RPM
bodymap2_kidney 0 .00 RPM 79 .17 RPM
bodymap2_liver 0 .00 RPM 79 .55 RPM
bodymap2_lung 0 .00 RPM 61 .32 RPM
bodymap2_lymph_node 0 .00 RPM 44 .93 RPM
bodymap2_ovary 0 .00 RPM 69 .86 RPM
bodymap2_prostate 0 .00 RPM 73 .56 RPM
bodymap2_skeletal_muscle 0 .00 RPM 94 .38 RPM
bodymap2_testis 0 .30 RPM 109 .73 RPM
bodymap2_thyroid 0 .00 RPM 101 .48 RPM
bodymap2_white_blood_cells 0 .00 RPM 45 .68 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_2801 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_2801 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_2801 retrocopy 5' end.

Lab - click to see more details

retro_hsap_2801 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_2801 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_1898
Gorilla gorilla retro_ggor_1947
Callithrix jacchus retro_cjac_1400
Parental genes homology:
Parental genes homology involve 9 parental genes, and 10 retrocopies.

Species Parental gene accession Retrocopies number
Callithrix jacchus ENSCJAG000000086912 retrocopies
retro_cjac_1400, retro_cjac_2793,
Homo sapiens ENSG00000197170 1 retrocopy
retro_hsap_2801 ,
Gorilla gorilla ENSGGOG000000147611 retrocopy
retro_ggor_1947,
Loxodonta africana ENSLAFG000000108761 retrocopy
retro_lafr_467,
Nomascus leucogenys ENSNLEG000000012651 retrocopy
retro_nleu_1541,
Pongo abelii ENSPPYG000000085651 retrocopy
retro_pabe_2223,
Pan troglodytes ENSPTRG000000227221 retrocopy
retro_ptro_1898,
Tupaia belangeri ENSTBEG000000147601 retrocopy
retro_tbel_443,
Tarsius syrichta ENSTSYG000000131541 retrocopy
retro_tsyr_1670,

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 = 0.03 RPM Legend:


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 .02 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 .03 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 .03 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 .03 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 .02 RPM

Indel association:

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



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