RetrogeneDB ID:

retro_hsap_4178

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:9:71223986..71226897(+)
Located in intron of:ENSG00000226337
Retrocopy
information
Ensembl ID:ENSG00000224025
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:DSE
Ensembl ID:ENSG00000111817
Aliases:DSE, DSEP, DSEPI, EDSMC2, SART-2, SART2
Description:dermatan sulfate epimerase [Source:HGNC Symbol;Acc:21144]


Retrocopy-Parental alignment summary:






>retro_hsap_4178
GGATGTTTTGAAGATGCTTTGGCTGCCTTGGAGATTTGGAGATCTGATGCCACGATGAGGACTCACACACAGGGGTGCTC
CCAGTGTGTTTTTCATATATTTGCTTTGCATTGTGTCAGCCTACATCACCGACGAGAACCCAGAAGTCATGATTCCCTTC
ACCAATGCCAGCCACAACAGCCACCCCATGCTGTACTTCAGGGCAGAGGTGGCGGAGCTGCAGCTCAGGGCGGCCAGCTG
GCAGGAGCACATTGCAGCCCGCCTCACGGAGGATGTGCACACGATGCTGTGCAGCCCCTTGGAATACCTCCCTCCCTGGG
ATCCCAAGGATTACAGTGCCCGCTAGAACGAAATCTATGGAAACAACTTGGGTGTCTTGGCAATGTTCTGTGTGCTGTAT
CCTGAGGACACTGAAGCCCAAGACATGGCCAAAGTCTACATGGAGAGGATGGCAGTGCAGCCTATTTGGTTGGTGAAAGA
TGCTCCTTGGGATGAGGTCCCGCTTGCTCACTCCCTGGTTGGTTTTGCCACTGCTTATGACTTCTTGCACAACTACCTGA
GCAAGACACAACAGAAGAAGTTTCTTGAAGTGATTGCCAGTGCCTCAGGGTATATGTATGAAAATTCATACAGGAGAGGA
CGGGGATTTCAATACCTGCACAATCATCAGCCCACCAACTGCATGGCTTTGCTCACAGGAAGCCTAGTACTGACGAATCA
AGGATATCTTCAAGAATCCTGCTTATGGACCAAACAAGTTCTGACCATCATGGAGAAATCTCTGGTCTTGCTCAGGGAGA
TGATGGATGGCTCCCTCTATGAAAGAGTTGTGTATGGAAGCTACACCACTAGATCACTCTTCCAATACATGTTTCTCATC
CAGAGGCACTTCATGTTGGCCATCCGTGGCTTAAACAACACTTTGCATTTATGTATAGAACCATCCTGCCAGGGTTTCAA
AGGACTGTGGCTATTGAGGACTCAAATTACAACTGATTTTATGGTCCAGAAAGCCAATTAGTTTTCCTTGATAAATTTAT
CATGCGTAACAGCAGTGGTAACTGGCTAGCTGACCAAATCAGAAGGAACTGTGTGGTGGAAGGTCCAGGAACACTGTCCA
AAGGGCAGCGCCGGTGCACTCTGCACACAGAATTTCTCTGGTATGATGCCAGCTTGAAATCAGTTCCTCCTCCAGACTTT
GGCACCCCTACGCTGCATTATTTTGAAGACTGGGTGTCGTGACTTGAAGTGCACTACCTGCTGAAATCAATAAATCTTTC
CTCTCTTTCAAGTCTGGAAAACCGGGGGGACATGCAATATGTGACATTGTCCACAGAAACAAATACAAAGATTGGATCAA
AGGATGGAGAAATTTTAGGACAGGGCATGAACATTATGATCAAAACTCATTTACTTTTGCTCCCAGTTGTGTGCCTTTCG
TTATTGAGGCTCTGTACAGGCCAAAGTACACCTTCTTCAACAATGTTTTGATGTTTTCCGCAGCTGTGTCGAAGAGCTGC
TTTTCTCCCTGGAAGGGTCAAGTCACAGAACACTGTTCATCAAAATGGTCTAAATACCAGCATGACCTGGCAGCTAGCTG
TCAGGGGAGAGTGGTTGCAGCAGAGGAGAAAAATGGGGTGGTTTTCATCTGAGGAGAAGGTGTGGGAGCTTATAACCTCC
AGCTCAACCTGAAGAATGTTCAGAGGAATCTGATCCTCCTACATCCACAGCTGCTTCTCCTTGTAGACCAAATACACCTG
GGAGAGGAGAGTCCCCTGGAGACAGCAGCGAGCTTCTTCCACAATGTGGATGTTCCTTTTGAGGAGACTGTGGTAGATGG
TGTCCATGGGGCTTTCATCAGGTAGAGAAATGGTCTCTATAAAAAGTACTGGATGGACAATACTGGCTACGGCAAGAAAG
CAATATTTGCATCAGTGACATATCCTGGGAGCTATCCCTACAATGGGACAAACTATGTGAATGTCACCATGCACCTCTGA
AGTCCCATCACCAGGCCAGCTTACCTCTTCATAGGGTCACTATAGATGTTCAGAGCTTCACCATCCACAGAGACTCTCAG
CAACTGGATGTGTTCATAGCCACCAGAGAACATGCCTACGCAATGTACCTGTGGACAGGTGAGGCCGCAGGACAGTCTGC
CTTTGCACAGGTCATTGCTGATCATCACAAAATTCTGTTTGACCAGAATTCAGCCATCAAGAGCAGCATTGTCCCTGAGG
TGAAGGACTATGCTGCTATTGTGGAACAGAACCTGCAGCATTTTAAGCCAGTGTTTCAGCTGGAGAAGCAGATACTCTCC
TGAGTCCAGAACCAGCTAGCTTTAGGAAGACTGCTGACCGGCTGCTGAGATTTTCAGATAAGAGACAGGCTGAAGAGGCC
ATCGACAGGATTTTTGCCGTAACACAGCAACAGCAGCAGCAAAGCAAGTCAAAGAAAAACCGAAGGGCAGGCGAATGCTA
TAAATCTGTGGATGCTGTCCCTGATATTTTTGCACAGATTGAGGTCAATGAGAAAAAGATTAGACAGAAAGCTCAGATTC
AGGCACAGAAAGAACTACCCATAAATGAAGATGAAGAAATGAAAAACCTCTTAGATTTTGCAGATATAACATATGAGAAA
CATAAAAATGGGGCTTGAGGAAAGGCCGGGTTGGACAGGCATGGATGGTGACAACTACTCGTAGCAGGGCCTCATCACTA
TCTGCTTCCTATACCAGATTGTTCCTCATCCTGAACATTGCTATTTTCTTTGTCATGTTGGCAATACAACTGACTTTTTC
CAGAGGGCCCACAACCTTTTTCCAGAGGGCCAAAGATGTCTTTATGCAGTTCTTCTAACAGATAGCTGTATTTTATTGTG
GTTGTACTCTTCTTGTTCCCAATCACAGTGT

ORF - retro_hsap_4178 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 87.51 %
Parental protein coverage: 99.9 %
Number of stop codons detected: 7
Number of frameshifts detected 7


Retrocopy - Parental Gene Alignment:

ParentalGSFEDGLAALEIWRSDATMRTHT-RGAPSVFFIYLLCFVSAYITDENPEVMIPFTNANYDSHPMLYFSRA
G.FED.LAALEIWRSDATMRTHT.RGAPSVFFIYLLC.VSAYITDENPEVMIPFTNA...SHPMLYF.RA
RetrocopyGCFEDALAALEIWRSDATMRTHT>RGAPSVFFIYLLCIVSAYITDENPEVMIPFTNASHNSHPMLYF-RA
ParentalEVAELQLRAASSHEHIAARLTEAVHTMLSSPLEYLPPWDPKDYSARWNEIFGNNLGALAMFCVLYPENIE
EVAELQLRAAS..EHIAARLTE.VHTML.SPLEYLPPWDPKDYSAR.NEI.GNNLG.LAMFCVLYPE..E
RetrocopyEVAELQLRAASWQEHIAARLTEDVHTMLCSPLEYLPPWDPKDYSAR*NEIYGNNLGVLAMFCVLYPEDTE
ParentalARDMAKDYMERMAAQPSWLVKDAPWDEVPLAHSLVGFATAYDFLYNYLSKTQQEKFLEVIANASGYMYET
A.DMAK.YMERMA.QP.WLVKDAPWDEVPLAHSLVGFATAYDFL.NYLSKTQQ.KFLEVIA.ASGYMYE.
RetrocopyAQDMAKVYMERMAVQPIWLVKDAPWDEVPLAHSLVGFATAYDFLHNYLSKTQQKKFLEVIASASGYMYEN
ParentalSYRRGWGFQYLHNHQPTNCMALLTGSLVLMNQGYLQEAYLWTKQVLTIMEKSLVLLREVTDGSLYEGVAY
SYRRG.GFQYLHNHQPTNCMALLTGSLVL.NQGYLQE..LWTKQVLTIMEKSLVLLRE..DGSLYE.V.Y
RetrocopySYRRGRGFQYLHNHQPTNCMALLTGSLVLTNQGYLQESCLWTKQVLTIMEKSLVLLREMMDGSLYERVVY
ParentalGSYTTRSLFQYMFLVQRHF-NINHFGHPWLKQHFAFMYRTILPGFQRTVAIADSNYNWFYGPESQLVFLD
GSYTTRSLFQYMFL.QRHF....H...PWLKQHFAFMYRTILPGFQRTVAI.DSNYN.FYGPESQLVFLD
RetrocopyGSYTTRSLFQYMFLIQRHF<HVGH---PWLKQHFAFMYRTILPGFQRTVAIEDSNYN*FYGPESQLVFLD
ParentalKFVMRNGSGNWLADQIRRNRVVEGPGTPSKGQRWCTLHTEFLWYDGSLKSVPPPDFGTPTLHYFEDW-GV
KF.MRN.SGNWLADQIRRN.VVEGPGT.SKGQR.CTLHTEFLWYD.SLKSVPPPDFGTPTLHYFEDW.GV
RetrocopyKFIMRNSSGNWLADQIRRNCVVEGPGTLSKGQRRCTLHTEFLWYDASLKSVPPPDFGTPTLHYFEDW<GV
ParentalVTYGSALPAEINRSFLSFKSGKLGGRAIYDIVHRNKYKDWIKGWRNFNAGHEHPDQNSFTFAPNGVPFIT
VT..SALPAEIN.SFLSFKSGK.GG.AI.DIVHRNKYKDWIKGWRNF..GHEH.DQNSFTFAP..VPF..
RetrocopyVT-*SALPAEINKSFLSFKSGKPGGHAICDIVHRNKYKDWIKGWRNFRTGHEHYDQNSFTFAPSCVPFVI
ParentalEALYGPKYTFFNNVLMFSPAVSKSCFSPWVGQVTEDCSSKWSKYKHDLAASCQGRVVAAEEKNGVVFIRG
EALY.PKYTFFNNVLMFS.AVSKSCFSPW.GQVTE.CSSKWSKY.HDLAASCQGRVVAAEEKNGVVFI.G
RetrocopyEALYRPKYTFFNNVLMFSAAVSKSCFSPWKGQVTEHCSSKWSKYQHDLAASCQGRVVAAEEKNGVVFI*G
ParentalEGVGAYNPQLNLKNVQRNLILLHPQLLLLVDQIHLGEESPLETAASFFHNVDVPFEETVVDGVHGAFIRQ
EGVGAYN.QLNLKNVQRNLILLHPQLLLLVDQIHLGEESPLETAASFFHNVDVPFEETVVDGVHGAFIR.
RetrocopyEGVGAYNLQLNLKNVQRNLILLHPQLLLLVDQIHLGEESPLETAASFFHNVDVPFEETVVDGVHGAFIR*
ParentalRDGLYKMYWMDDTGYSEKATFASVTYPRGYPYNGTNYVNVTMHLRSPITRAAYLFIGP-SIDVQSFTVHG
R.GLYK.YWMD.TGY..KA.FASVTYP..YPYNGTNYVNVTMHL.SPITR.AYLFIG...IDVQSFT.H.
RetrocopyRNGLYKKYWMDNTGYGKKAIFASVTYPGSYPYNGTNYVNVTMHL*SPITRPAYLFIGS<TIDVQSFTIHR
ParentalDSQQLDVFIATSKHAYATYLWTGEATGQSAFAQVIADRHKILFDRNSAIKSSIVPEVKDYAAIVEQNLQH
DSQQLDVFIAT..HAYA.YLWTGEA.GQSAFAQVIAD.HKILFD.NSAIKSSIVPEVKDYAAIVEQNLQH
RetrocopyDSQQLDVFIATREHAYAMYLWTGEAAGQSAFAQVIADHHKILFDQNSAIKSSIVPEVKDYAAIVEQNLQH
ParentalFKPVFQLLEKQILSRVRN-TASFRKTAERLLRFSDKRQTEEAIDRIFAISQQQQQQSKSKKNRRAGKRYK
FKPVFQ.LEKQILS.V.N..ASFRKTA.RLLRFSDKRQ.EEAIDRIFA..QQQQQQSKSKKNRRAG..YK
RetrocopyFKPVFQ-LEKQILS*VQN<PASFRKTADRLLRFSDKRQAEEAIDRIFAVTQQQQQQSKSKKNRRAGECYK
ParentalFVDAVPDIFAQIEVNEKKIRQKAQILAQKELPIDEDEEMKDLLDFADVTYEKHKNG-GLIKGRFGQARMV
.VDAVPDIFAQIEVNEKKIRQKAQI.AQKELPI.EDEEMK.LLDFAD.TYEKHKNG.GL.KGR.GQA.MV
RetrocopySVDAVPDIFAQIEVNEKKIRQKAQIQAQKELPINEDEEMKNLLDFADITYEKHKNG<GLRKGRVGQAWMV
ParentalTTTHSRAPSLSASYTRLFLILNIAIFFVMLAMQLT-YFQRAQSL--HGQRCLYAVLLIDSCILLWLYSSC
TTT.SRA.SLSASYTRLFLILNIAIFFVMLA.QLT..FQRA..L...GQRCLYAVLL.DSCILLWLYSSC
RetrocopyTTTRSRASSLSASYTRLFLILNIAIFFVMLAIQLT<FFQRAHNLFPEGQRCLYAVLLTDSCILLWLYSSC
ParentalSQSQC
SQSQC
RetrocopySQSQC

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 108 .89 RPM
bodymap2_adrenal 0 .00 RPM 50 .09 RPM
bodymap2_brain 0 .00 RPM 24 .35 RPM
bodymap2_breast 0 .00 RPM 61 .56 RPM
bodymap2_colon 0 .00 RPM 67 .87 RPM
bodymap2_heart 0 .00 RPM 23 .28 RPM
bodymap2_kidney 0 .14 RPM 45 .56 RPM
bodymap2_liver 0 .00 RPM 11 .96 RPM
bodymap2_lung 0 .00 RPM 72 .91 RPM
bodymap2_lymph_node 0 .00 RPM 97 .78 RPM
bodymap2_ovary 0 .00 RPM 103 .03 RPM
bodymap2_prostate 0 .00 RPM 52 .55 RPM
bodymap2_skeletal_muscle 0 .00 RPM 11 .33 RPM
bodymap2_testis 0 .02 RPM 46 .93 RPM
bodymap2_thyroid 0 .00 RPM 29 .58 RPM
bodymap2_white_blood_cells 0 .00 RPM 63 .36 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_4178 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_4178 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_4178 retrocopy 5' end.

Lab - click to see more details

retro_hsap_4178 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_4178 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_2833
Gorilla gorilla retro_ggor_2802
Pongo abelii retro_pabe_3418
Parental genes homology:
Parental genes homology involve 10 parental genes, and 12 retrocopies.

Species Parental gene accession Retrocopies number
Anolis carolinensis ENSACAG000000137911 retrocopy
retro_acar_15,
Callithrix jacchus ENSCJAG000000045301 retrocopy
retro_cjac_1174,
Homo sapiens ENSG00000111817 1 retrocopy
retro_hsap_4178 ,
Gorilla gorilla ENSGGOG000000267462 retrocopies
retro_ggor_1419, retro_ggor_2802,
Nomascus leucogenys ENSNLEG000000131061 retrocopy
retro_nleu_2476,
Pongo abelii ENSPPYG000000169482 retrocopies
retro_pabe_3418, retro_pabe_3517,
Pan troglodytes ENSPTRG000000185291 retrocopy
retro_ptro_2833,
Sorex araneus ENSSARG000000107991 retrocopy
retro_sara_560,
Takifugu rubripes ENSTRUG000000062391 retrocopy
retro_trub_32,
Xenopus tropicalis ENSXETG000000327761 retrocopy
retro_xtro_8,

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 .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 .02 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 .03 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

Indel association:

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





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