RetrogeneDB ID:

retro_hsap_26

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:X:49644910..49646227(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000242013
Aliases:USP27X, USP22L, USP27
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:USP22
Ensembl ID:ENSG00000124422
Aliases:USP22, USP3L
Description:ubiquitin specific peptidase 22 [Source:HGNC Symbol;Acc:12621]


Retrocopy-Parental alignment summary:






>retro_hsap_26
ATGTGTAAGGACTATGTATATGACAAAGACATTGAGCAAATTGCCAAAGAAGAGCAAGGAGAAGCTTTGAAATTACAAGC
CTCCACCTCAACAGAGGTTTCTCACCAGCAGTGTTCAGTGCCAGGCCTTGGTGAGAAATTCCCAACCTGGGAAACAACCA
AACCAGAATTAGAACTGCTGGGGCACAACCCGAGGAGAAGAAGAATCACCTCCAGCTTTACGATCGGTTTAAGAGGACTC
ATCAATCTTGGCAACACGTGCTTTATGAACTGCATTGTCCAGGCCCTCACCCACACGCCGATACTGAGAGATTTCTTTCT
CTCTGACAGGCACCGATGTGAGATGCCGAGTCCCGAGTTGTGTCTGGTCTGTGAGATGTCGTCGCTGTTTCGGGAGTTGT
ATTCTGGAAACCCGTCTCCTCATGTGCCCTATAAGTTACTGCACCTGGTGTGGATACATGCCCGCCATTTAGCAGGGTAC
AGGCAACAGGATGCCCACGAGTTCCTCATTGCAGCGTTAGATGTCCTGCACAGGCACTGCAAAGGTGATGATGTCGGGAA
GGCGGCCAACAATCCCAACCACTGTAACTGCATCATAGACCAAATCTTCACAGGTGGCCTGCAGTCTGATGTCACCTGTC
AAGCCTGCCATGGCGTCTCCACCACGATAGACCCATGCTGGGACATTAGTTTGGACTTGCCTGGCTCTTGCACCTCCTTC
TGGCCCATGAGCCCAGGGAGGGAGAGCAGTGTGAACGGGGAAAGCCACATACCAGGAATCACCACCCTCACGGACTGCTT
GCGGAGGTTTACGAGGCCAGAGCACTTAGGAAGCAGTGCCAAAATCAAATGTGGTAGTTGCCAAAGCTACCAGGAATCTA
CCAAACAGCTCACAATGAATAAATTACCTGTCGTTGCCTGTTTTCATTTCAAACGGTTTGAACATTCAGCGAAACAGAGG
CGCAAGATCACTACATACATTTCCTTTCCTCTGGAGCTGGATATGACGCCGTTTATGGCCTCAAGTAAAGAGAGCAGAAT
GAATGGACAATTGCAGCTGCCAACCAATAGTGGAAACAACGAAAATAAGTATTCCTTGTTTGCTGTGGTTAATCACCAAG
GAACCTTGGAGAGTGGCCACTATACCAGCTTCATCCGGCACCACAAGGACCAGTGGTTCAAGTGTGATGATGCCGTCATC
ACTAAGGCCAGTATTAAGGACGTACTGGACAGTGAAGGGTATTTACTGTTCTATCACAAACAGGTGCTAGAACATGAGTC
AGAAAAAGTGAAAGAAATGAACACACAAGCCTACTGA

ORF - retro_hsap_26 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 84.85 %
Parental protein coverage: 75.43 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalEEQRKAWKMQGVGEKFSTWEPTKRELELLKHNPKRRKITSNCTIGLRGLINLGNTCFMNCIVQALTHTPL
E.........G.GEKF.TWE.TK.ELELL.HNP.RR.ITS..TIGLRGLINLGNTCFMNCIVQALTHTP.
RetrocopyEVSHQQCSVPGLGEKFPTWETTKPELELLGHNPRRRRITSSFTIGLRGLINLGNTCFMNCIVQALTHTPI
ParentalLRDFFLSDRHRCEMQSPSSCLVCEMSSLFQEFYSGHRSPHIPYKLLHLVWTHARHLAGYEQQDAHEFLIA
LRDFFLSDRHRCEM.SP..CLVCEMSSLF.E.YSG..SPH.PYKLLHLVW.HARHLAGY.QQDAHEFLIA
RetrocopyLRDFFLSDRHRCEMPSPELCLVCEMSSLFRELYSGNPSPHVPYKLLHLVWIHARHLAGYRQQDAHEFLIA
ParentalALDVLHRHCKGDDNGKKANNPNHCNCIIDQIFTGGLQSDVTCQVCHGVSTTIDPFWDISLDLPGSSTPFW
ALDVLHRHCKGDD.GK.ANNPNHCNCIIDQIFTGGLQSDVTCQ.CHGVSTTIDP.WDISLDLPGS.T.FW
RetrocopyALDVLHRHCKGDDVGKAANNPNHCNCIIDQIFTGGLQSDVTCQACHGVSTTIDPCWDISLDLPGSCTSFW
ParentalPLSPGSEGNVVNGESHVSGTTTLTDCLRRFTRPEHLGSSAKIKCSGCHSYQESTKQLTMKKLPIVACFHL
P.SPG.E...VNGESH..G.TTLTDCLRRFTRPEHLGSSAKIKC..C.SYQESTKQLTM.KLP.VACFH.
RetrocopyPMSPGRESS-VNGESHIPGITTLTDCLRRFTRPEHLGSSAKIKCGSCQSYQESTKQLTMNKLPVVACFHF
ParentalKRFEHSAKLRRKITTYVSFPLELDMTPFMASSKESRMNGQYQQPTDSLNNDNKYSLFAVVNHQGTLESGH
KRFEHSAK.RRKITTY.SFPLELDMTPFMASSKESRMNGQ.Q.PT.S.NN.NKYSLFAVVNHQGTLESGH
RetrocopyKRFEHSAKQRRKITTYISFPLELDMTPFMASSKESRMNGQLQLPTNSGNNENKYSLFAVVNHQGTLESGH
ParentalYTSFIRQHKDQWFKCDDAIITKASIKDVLDSEGYLLFYHKQFLEYE
YTSFIR.HKDQWFKCDDA.ITKASIKDVLDSEGYLLFYHKQ.LE.E
RetrocopyYTSFIRHHKDQWFKCDDAVITKASIKDVLDSEGYLLFYHKQVLEHE

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 2 .01 RPM 142 .03 RPM
bodymap2_adrenal 3 .19 RPM 120 .32 RPM
bodymap2_brain 7 .08 RPM 229 .64 RPM
bodymap2_breast 1 .36 RPM 121 .64 RPM
bodymap2_colon 3 .29 RPM 94 .15 RPM
bodymap2_heart 1 .61 RPM 115 .49 RPM
bodymap2_kidney 2 .92 RPM 129 .67 RPM
bodymap2_liver 1 .01 RPM 60 .16 RPM
bodymap2_lung 1 .32 RPM 103 .25 RPM
bodymap2_lymph_node 1 .35 RPM 121 .63 RPM
bodymap2_ovary 7 .25 RPM 214 .32 RPM
bodymap2_prostate 3 .52 RPM 100 .73 RPM
bodymap2_skeletal_muscle 1 .87 RPM 236 .02 RPM
bodymap2_testis 2 .47 RPM 107 .67 RPM
bodymap2_thyroid 3 .77 RPM 202 .34 RPM
bodymap2_white_blood_cells 3 .54 RPM 129 .01 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity may be related with retro_hsap_26 in 15 libraries
ENCODE library ID Target ChIP-Seq Peak coordinates
ENCFF002CFW POLR2A X:49643847..49644366
ENCFF002CFX POLR2A X:49643862..49644359
ENCFF002CHO POLR2A X:49643960..49644397
ENCFF002CKX POLR2A X:49644035..49644293
ENCFF002CQC POLR2A X:49643757..49644237
ENCFF002CQE POLR2A X:49643882..49644318
ENCFF002CQK POLR2A X:49643912..49644402
ENCFF002CRO POLR2A X:49643783..49644203
ENCFF002CZD POLR2A X:49643721..49644231
ENCFF002DAE POLR2A X:49643934..49644244
ENCFF002DAH POLR2A X:49644049..49644333
ENCFF002DBB POLR2A X:49644100..49644300
ENCFF002DBO POLR2A X:49644118..49644245
ENCFF002DBP POLR2A X:49644076..49644406
ENCFF002DBQ POLR2A X:49644051..49644421

EST - click to see more details

1 EST(s) were mapped to retro_hsap_26 retrocopy
EST ID Start End Identity Match Mis-match Score
AW752861 49645430 49645812 99.8 381 1 380

TSS - click to see more details

No TSS is located nearby retro_hsap_26 retrocopy 5' end.

Lab - click to see more details

retro_hsap_26 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_26 has 1 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Mus musculus retro_mmus_239
Parental genes homology:
Parental genes homology involve 9 parental genes, and 9 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000089781 retrocopy
retro_btau_82,
Canis familiaris ENSCAFG000000185231 retrocopy
retro_cfam_125,
Homo sapiens ENSG00000124422 1 retrocopy
retro_hsap_26 ,
Microcebus murinus ENSMICG000000099981 retrocopy
retro_mmur_1,
Mus musculus ENSMUSG000000425061 retrocopy
retro_mmus_239,
Otolemur garnettii ENSOGAG000000158011 retrocopy
retro_ogar_274,
Pan troglodytes ENSPTRG000000088911 retrocopy
retro_ptro_44,
Pteropus vampyrus ENSPVAG000000019341 retrocopy
retro_pvam_905,
Ictidomys tridecemlineatus ENSSTOG000000238141 retrocopy
retro_itri_163,

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 = 1.94 RPM Legend:


Library Retrogene expression
CEU_NA11831 1 .69 RPM
CEU_NA11843 0 .80 RPM
CEU_NA11930 1 .14 RPM
CEU_NA12004 0 .65 RPM
CEU_NA12400 1 .37 RPM
CEU_NA12751 1 .14 RPM
CEU_NA12760 1 .30 RPM
CEU_NA12827 1 .18 RPM
CEU_NA12872 1 .42 RPM
CEU_NA12873 1 .18 RPM
FIN_HG00183 1 .18 RPM
FIN_HG00277 1 .18 RPM
FIN_HG00315 1 .02 RPM
FIN_HG00321 1 .51 RPM
FIN_HG00328 1 .37 RPM
FIN_HG00338 1 .23 RPM
FIN_HG00349 0 .94 RPM
FIN_HG00375 1 .03 RPM
FIN_HG00377 0 .73 RPM
FIN_HG00378 1 .06 RPM
GBR_HG00099 1 .57 RPM
GBR_HG00111 0 .64 RPM
GBR_HG00114 1 .34 RPM
GBR_HG00119 1 .46 RPM
GBR_HG00131 1 .12 RPM
GBR_HG00133 1 .42 RPM
GBR_HG00134 1 .11 RPM
GBR_HG00137 1 .29 RPM
GBR_HG00142 1 .31 RPM
GBR_HG00143 1 .18 RPM
TSI_NA20512 0 .88 RPM
TSI_NA20513 1 .74 RPM
TSI_NA20518 1 .80 RPM
TSI_NA20532 0 .88 RPM
TSI_NA20538 1 .01 RPM
TSI_NA20756 1 .40 RPM
TSI_NA20765 1 .43 RPM
TSI_NA20771 1 .30 RPM
TSI_NA20786 1 .33 RPM
TSI_NA20798 1 .72 RPM
YRI_NA18870 1 .42 RPM
YRI_NA18907 1 .21 RPM
YRI_NA18916 0 .99 RPM
YRI_NA19093 0 .89 RPM
YRI_NA19099 1 .94 RPM
YRI_NA19114 1 .55 RPM
YRI_NA19118 1 .20 RPM
YRI_NA19213 1 .53 RPM
YRI_NA19214 1 .18 RPM
YRI_NA19223 0 .92 RPM

Indel association:

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



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