RetrogeneDB ID:

retro_hsap_4059

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:8:56962599..56963775(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000236814
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:PSMC6
Ensembl ID:ENSG00000100519
Aliases:PSMC6, CADP44, HEL-S-73, P44, SUG2, p42
Description:proteasome (prosome, macropain) 26S subunit, ATPase, 6 [Source:HGNC Symbol;Acc:9553]


Retrocopy-Parental alignment summary:






>retro_hsap_4059
CTTCTCATCATGGCGGACCCTAGAGATAAGGCGCTTAGGGACTACCGCAAGAAGGTGCTTGAGCACAAGGAGATCGATGG
CCGTCTTAAGGAGTTAAGGGAACAATTAAAAGAACTTACCAAGCAGTATGAAAAGTCTGAAAATGATCTGAAGGCCCTAC
GAAGTGTTGGGCAGATTGTGGGTGAAGTGTTTAAACAGTTAACTGAAGAAAAATTCATTGTTAAAGCTACCAATGGACCA
AGATATGTTGTGGGTTGTCGTCGACAGCTTGACAAAAGTAAGCTGAAGCCAGGAACAAGAGTTGCTTTGGATATGACTAC
ACTAACTATCATGAGATATTTGCCAAGAGAGGTGGATCCACTGATTTATAACATGTCTCATGAGGACCCTGAGAATGTTT
CTTATTCTGAGATTGGAGGGCTATCAGAACAGATCCGGGAATTAAGAGAGGTGATAGAATTACCTCTTACAAACCCAGAG
TTATTTCAGCGTGTAGGAATAATACCTCCAAAAGGCTGTTTGTTATATGGACCACCAGGTACGGGAAAAACACTCTTGGC
ACGAGCCATTGCTAGCCAGCTGGACTGCAATTTCTTAAAGGTTGTATCTAGTTCTATTGTAGACAAGTACATTGGTGAAA
GTGCTCATTTGATCAGAGAAATGTTTAATTATGCTAGAGATCATCAACCATGCATCATTTTTATGGATGAAATAGATGCT
ATTGGTGGTCGTCGGTTTTCTGAGGGTACTTCAGCTGACAGAGAGATTCAGAGAACGTTAACGGAGTTACTGAATCAAAT
GGATGGATTTGATACTCTGCATAGAGTTAAAATGATCATGGCTACAAACAGACCAGATACACTGGATCCTGCTTTGCTGT
GTCCAGGAAGATTAGATAGAAAAATACATATTGATTTGCCAAATGAACAAACAAGATTAGACATACTGAAAATCCATGCA
GGTCCCATTACAAAGCATGGTGAAATAGATTATGAAGCAATTGTGAAGCTTTCAGATGGCTTTAATGGAGCAGACCTGAG
AAATGTTTGTACTGAAGCAGGTATGTTCGCAATTCGTGCTGATCATGATTTTGTAGTACAGGAAGACTTCATGAAAGCAG
TCAGAAAAGTGGCTGATTCTAAGAAGCTGGAGGCTAAATTGGACTACAAACCTGTG

ORF - retro_hsap_4059 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 96.94 %
Parental protein coverage: 97.27 %
Number of stop codons detected: 0
Number of frameshifts detected: 0


Retrocopy - Parental Gene Alignment:

ParentalLLIMADPRDKALQDYRKKLLEHKEIDGRLKELREQLKELTKQYEKSENDLKALQSVGQIVGEVLKQLTEE
LLIMADPRDKAL.DYRKK.LEHKEIDGRLKELREQLKELTKQYEKSENDLKAL.SVGQIVGEV.KQLTEE
RetrocopyLLIMADPRDKALRDYRKKVLEHKEIDGRLKELREQLKELTKQYEKSENDLKALRSVGQIVGEVFKQLTEE
ParentalKFIVKATNGPRYVVGCRRQLDKSKLKPGTRVALDMTTLTIMRYLPREVDPLVYNMSHEDPGNVSYSEIGG
KFIVKATNGPRYVVGCRRQLDKSKLKPGTRVALDMTTLTIMRYLPREVDPL.YNMSHEDP.NVSYSEIGG
RetrocopyKFIVKATNGPRYVVGCRRQLDKSKLKPGTRVALDMTTLTIMRYLPREVDPLIYNMSHEDPENVSYSEIGG
ParentalLSEQIRELREVIELPLTNPELFQRVGIIPPKGCLLYGPPGTGKTLLARAVASQLDCNFLKVVSSSIVDKY
LSEQIRELREVIELPLTNPELFQRVGIIPPKGCLLYGPPGTGKTLLARA.ASQLDCNFLKVVSSSIVDKY
RetrocopyLSEQIRELREVIELPLTNPELFQRVGIIPPKGCLLYGPPGTGKTLLARAIASQLDCNFLKVVSSSIVDKY
ParentalIGESARLIREMFNYARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQMDGFDTLHRVKMIM
IGESA.LIREMFNYARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTL.ELLNQMDGFDTLHRVKMIM
RetrocopyIGESAHLIREMFNYARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLTELLNQMDGFDTLHRVKMIM
ParentalATNRPDTLDPALLRPGRLDRKIHIDLPNEQARLDILKIHAGPITKHGEIDYEAIVKLSDGFNGADLRNVC
ATNRPDTLDPALL.PGRLDRKIHIDLPNEQ.RLDILKIHAGPITKHGEIDYEAIVKLSDGFNGADLRNVC
RetrocopyATNRPDTLDPALLCPGRLDRKIHIDLPNEQTRLDILKIHAGPITKHGEIDYEAIVKLSDGFNGADLRNVC
ParentalTEAGMFAIRADHDFVVQEDFMKAVRKVADSKKLESKLDYKPV
TEAGMFAIRADHDFVVQEDFMKAVRKVADSKKLE.KLDYKPV
RetrocopyTEAGMFAIRADHDFVVQEDFMKAVRKVADSKKLEAKLDYKPV

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 .24 RPM 43 .19 RPM
bodymap2_adrenal 0 .35 RPM 57 .05 RPM
bodymap2_brain 0 .98 RPM 72 .45 RPM
bodymap2_breast 0 .43 RPM 65 .43 RPM
bodymap2_colon 0 .83 RPM 64 .04 RPM
bodymap2_heart 0 .04 RPM 58 .06 RPM
bodymap2_kidney 1 .12 RPM 69 .38 RPM
bodymap2_liver 0 .38 RPM 60 .58 RPM
bodymap2_lung 0 .00 RPM 49 .58 RPM
bodymap2_lymph_node 0 .97 RPM 46 .14 RPM
bodymap2_ovary 0 .33 RPM 73 .17 RPM
bodymap2_prostate 0 .35 RPM 61 .90 RPM
bodymap2_skeletal_muscle 0 .13 RPM 45 .18 RPM
bodymap2_testis 0 .49 RPM 76 .28 RPM
bodymap2_thyroid 0 .38 RPM 89 .56 RPM
bodymap2_white_blood_cells 0 .24 RPM 56 .82 RPM

ChIP-Seq - click to see more details

RNA Polymerase II activity near the 5' end of retro_hsap_4059 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_4059 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_4059 retrocopy 5' end.

Lab - click to see more details

retro_hsap_4059 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_4059 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_2752
Gorilla gorilla retro_ggor_2727
Pongo abelii retro_pabe_3334
Parental genes homology:
Parental genes homology involve 12 parental genes, and 20 retrocopies.

Species Parental gene accession Retrocopies number
Callithrix jacchus ENSCJAG000000071262 retrocopies
retro_cjac_204, retro_cjac_3221,
Cavia porcellus ENSCPOG000000094771 retrocopy
retro_cpor_47,
Homo sapiens ENSG00000100519 2 retrocopies
retro_hsap_1022, retro_hsap_4059 ,
Gorilla gorilla ENSGGOG000000021522 retrocopies
retro_ggor_2727, retro_ggor_808,
Macropus eugenii ENSMEUG000000070843 retrocopies
retro_meug_1700, retro_meug_2090, retro_meug_923,
Monodelphis domestica ENSMODG000000145001 retrocopy
retro_mdom_438,
Nomascus leucogenys ENSNLEG000000125182 retrocopies
retro_nleu_559, retro_nleu_900,
Otolemur garnettii ENSOGAG000000100111 retrocopy
retro_ogar_3101,
Pongo abelii ENSPPYG000000058202 retrocopies
retro_pabe_3334, retro_pabe_858,
Pan troglodytes ENSPTRG000000063522 retrocopies
retro_ptro_2752, retro_ptro_699,
Rattus norvegicus ENSRNOG000000072031 retrocopy
retro_rnor_1480,
Tursiops truncatus ENSTTRG000000038801 retrocopy
retro_ttru_117,

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 = 0.51 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .17 RPM
CEU_NA11843 0 .14 RPM
CEU_NA11930 0 .16 RPM
CEU_NA12004 0 .08 RPM
CEU_NA12400 0 .11 RPM
CEU_NA12751 0 .12 RPM
CEU_NA12760 0 .09 RPM
CEU_NA12827 0 .19 RPM
CEU_NA12872 0 .16 RPM
CEU_NA12873 0 .13 RPM
FIN_HG00183 0 .33 RPM
FIN_HG00277 0 .07 RPM
FIN_HG00315 0 .14 RPM
FIN_HG00321 0 .15 RPM
FIN_HG00328 0 .05 RPM
FIN_HG00338 0 .15 RPM
FIN_HG00349 0 .51 RPM
FIN_HG00375 0 .17 RPM
FIN_HG00377 0 .20 RPM
FIN_HG00378 0 .23 RPM
GBR_HG00099 0 .17 RPM
GBR_HG00111 0 .28 RPM
GBR_HG00114 0 .18 RPM
GBR_HG00119 0 .17 RPM
GBR_HG00131 0 .09 RPM
GBR_HG00133 0 .19 RPM
GBR_HG00134 0 .11 RPM
GBR_HG00137 0 .14 RPM
GBR_HG00142 0 .14 RPM
GBR_HG00143 0 .22 RPM
TSI_NA20512 0 .11 RPM
TSI_NA20513 0 .15 RPM
TSI_NA20518 0 .33 RPM
TSI_NA20532 0 .20 RPM
TSI_NA20538 0 .37 RPM
TSI_NA20756 0 .26 RPM
TSI_NA20765 0 .23 RPM
TSI_NA20771 0 .26 RPM
TSI_NA20786 0 .08 RPM
TSI_NA20798 0 .09 RPM
YRI_NA18870 0 .37 RPM
YRI_NA18907 0 .10 RPM
YRI_NA18916 0 .04 RPM
YRI_NA19093 0 .03 RPM
YRI_NA19099 0 .16 RPM
YRI_NA19114 0 .08 RPM
YRI_NA19118 0 .04 RPM
YRI_NA19213 0 .14 RPM
YRI_NA19214 0 .07 RPM
YRI_NA19223 0 .16 RPM

Indel association:

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



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