RetrogeneDB ID:

retro_hsap_1498

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:15:51236800..51238193(+)
Located in intron of:ENSG00000081014
Retrocopy
information
Ensembl ID:ENSG00000259378
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:DCAF13
Ensembl ID:ENSG00000164934
Aliases:DCAF13, GM83, WDSOF1
Description:DDB1 and CUL4 associated factor 13 [Source:HGNC Symbol;Acc:24535]


Retrocopy-Parental alignment summary:






>retro_hsap_1498
CAGTGGACAGAACTCACAGCAAAGAGCTCGTGGAGTCCGGCCAGAAGAGCAACCAAGATGAGGATGAAGATACTGAGCCA
GAATCTGGACAATTATGTCTGTGAAACCAAGTTGGACTTACAGAGAGTTCCAAGAAACTATGATCCTACCTTACATCCTT
TTGAGGTCCCATGAGAATATGTAAGAGCTTTAAATGCTACCAAAATGGAATGAGTATTTGCAAAACCATTCCTTGCTTTG
CTGGATGGTCACCAAGATGGAGTCAGTTGCTTGGCAAAGCATCCAAAGAACCTGGCTACTGTCCTTTCTGGGGCGTGTGA
TGGAGAGGTTAGAATTTGGAACCTGACTCAACAGAAATGTATCCATACAATACAAGCACATGAAGGCTTTGTATAAGGAA
TACGTACTCACTTTTGTGGGACTTCTTTTTTCACCGTTGGTGGTGACAAAACTGTGAAACAATGGAAAATGGATGGGCCA
GGCTATGGAGATGAGGAAGAACCATTACATACAACATTAGGAAAGACAGTGTATACTGGGGTTTATCATCACTGTAAAGA
AGCTGTTTTTGCCACATGTGGACAGCAAGTAGACATTTGGGATGAACAAAGAACTAATCCTGTATGTTCAATGACCTGGG
GATTTGACAGTGTAAGTAGTGTTAAATTTAACCCAATCGAGACATTTCTCTTGGGAAGTTTGTGCGTCTGACAGGAATAT
AGTACTGTACAACATGAGGCAAGCTACTCCTTTGAAAAAGGTTATATTAGATATGAGAACAAATACAGTTTGTTGGAACC
CTATGGAAGCTTTCATTTTTACGGCAGCAAATGAAGACTATAACTTACATACTTTTGATATGTGTGCACTGGACACTCCT
GTAATGTTCCATATGGATCATGTATCTGCAGTGCTTGACATGGATTACCCTCCCACTGGGAAAGAGCTTGTGTCTGCTAG
TTTCGATAAAGCTATTTGTATCTTTCCTATAGACAAAAGTTGAAGCAGGGAGGTATATCACACAAAGCGAATGCAACATG
TTATCTGTGTAAAATGCACTTCTGACAGCAAGTATATTATGTGTGGATCTGATGAAATGAACATTTGCCTGTGGAAAGCT
AATGCTTCTGAAAAATTTGGTGTGCTTACATCATGAGAAAAAGCAGCTAAGGATTATAACTAGAAATTGAAGGAGAAATT
TCAGCATCATCCTGATATAAAATGTATAGCTTGTCATTGACATCTACCAAAATCTATCTACAGCCAGATTCAGGAACAGT
GCATCATGAAAGAAGCTCGTCGAAGAAAGGAAGTGAATCGTATTAAACACAGCAAGCCTGGATCTGTGCCAATTGTGTCA
GAGAAGAAGAAACATGTAGGGGCAGTTGTAAAA

ORF - retro_hsap_1498 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 86.67 %
Parental protein coverage: 77.72 %
Number of stop codons detected: 7
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalRWAELLADTSWSPAGRATEMKVKMLSRNPDNYVRETKLDLQRVPRNYDPALHPFEVPREYIRALNATKLE
.W.EL.A..SWSPA.RAT.M..K.LS.N.DNYV.ETKLDLQRVPRNYDP.LHPFEVP.EY.RALNATK.E
RetrocopyQWTELTAKSSWSPARRATKMRMKILSQNLDNYVCETKLDLQRVPRNYDPTLHPFEVP*EYVRALNATKME
ParentalRVFAKPFLASLDGHRDGVNCLAKHPEKLATVLSGACDGEVRIWNLTQRNCIRTIQAHEGFVRGICTRFCG
.VFAKPFLA.LDGH.DGV.CLAKHP..LATVLSGACDGEVRIWNLTQ..CI.TIQAHEGFV.GI.T.FCG
Retrocopy*VFAKPFLALLDGHQDGVSCLAKHPKNLATVLSGACDGEVRIWNLTQQKCIHTIQAHEGFV*GIRTHFCG
ParentalTSFFTVGDDKTVKQWKMDGPGYGDEEEPLHTILGKTVYTGIDHHWKEAVFATCGQQVDIWDEQRTNPICS
TSFFTVG.DKTVKQWKMDGPGYGDEEEPLHT.LGKTVYTG..HH.KEAVFATCGQQVDIWDEQRTNP.CS
RetrocopyTSFFTVGGDKTVKQWKMDGPGYGDEEEPLHTTLGKTVYTGVYHHCKEAVFATCGQQVDIWDEQRTNPVCS
ParentalMTWGFDSISSVKFNPIETFLLGS-CASDRNIVLYDMRQATPLKKVILDMRTNTICWNPMEAFIFTAANED
MTWGFDS.SSVKFNPIETFLLGS.CASDRNIVLY.MRQATPLKKVILDMRTNT.CWNPMEAFIFTAANED
RetrocopyMTWGFDSVSSVKFNPIETFLLGS>CASDRNIVLYNMRQATPLKKVILDMRTNTVCWNPMEAFIFTAANED
ParentalYNLYTFDMRALDTPVMVHMDHVSAVLDVDYSPTGKEFVSASFDKSIRIFPVDKSRSREVYHTKRMQHVIC
YNL.TFDM.ALDTPVM.HMDHVSAVLD.DY.PTGKE.VSASFDK.I.IFP.DKS.SREVYHTKRMQHVIC
RetrocopyYNLHTFDMCALDTPVMFHMDHVSAVLDMDYPPTGKELVSASFDKAICIFPIDKS*SREVYHTKRMQHVIC
ParentalVKWTSDSKYIMCGSDEMNIRLWKANASEKLGVLTSREKAAKDYNQKLKEKFQHYPHIKRIARHRHLPKSI
VK.TSDSKYIMCGSDEMNI.LWKANASEK.GVLTS.EKAAKDYN.KLKEKFQH.P.IK.IA.H.HLPKSI
RetrocopyVKCTSDSKYIMCGSDEMNICLWKANASEKFGVLTS*EKAAKDYN*KLKEKFQHHPDIKCIACH*HLPKSI
ParentalYSQIQEQRIMKEARRRKEVNRIKHSKPGSVPLVSEKKKHVVAVVK
YSQIQEQ.IMKEARRRKEVNRIKHSKPGSVP.VSEKKKHV.AVVK
RetrocopyYSQIQEQCIMKEARRRKEVNRIKHSKPGSVPIVSEKKKHVGAVVK

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 21 .91 RPM
bodymap2_adrenal 0 .12 RPM 41 .72 RPM
bodymap2_brain 0 .14 RPM 15 .73 RPM
bodymap2_breast 0 .00 RPM 26 .91 RPM
bodymap2_colon 0 .08 RPM 30 .90 RPM
bodymap2_heart 0 .07 RPM 14 .46 RPM
bodymap2_kidney 0 .04 RPM 45 .43 RPM
bodymap2_liver 0 .09 RPM 20 .09 RPM
bodymap2_lung 0 .18 RPM 14 .59 RPM
bodymap2_lymph_node 0 .13 RPM 24 .67 RPM
bodymap2_ovary 0 .10 RPM 46 .57 RPM
bodymap2_prostate 0 .00 RPM 26 .78 RPM
bodymap2_skeletal_muscle 0 .13 RPM 19 .57 RPM
bodymap2_testis 0 .17 RPM 82 .26 RPM
bodymap2_thyroid 0 .08 RPM 36 .83 RPM
bodymap2_white_blood_cells 0 .00 RPM 28 .80 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_1498 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_1498 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_1498 retrocopy 5' end.

Lab - click to see more details

retro_hsap_1498 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_1498 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_1017
Gorilla gorilla retro_ggor_1150
Pongo abelii retro_pabe_1249
Parental genes homology:
Parental genes homology involve 12 parental genes, and 18 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000015953 retrocopies
retro_amel_1453, retro_amel_1723, retro_amel_399,
Canis familiaris ENSCAFG000000006633 retrocopies
retro_cfam_1309, retro_cfam_1533, retro_cfam_305,
Callithrix jacchus ENSCJAG000000161812 retrocopies
retro_cjac_3083, retro_cjac_612,
Felis catus ENSFCAG000000272561 retrocopy
retro_fcat_1840,
Homo sapiens ENSG00000164934 1 retrocopy
retro_hsap_1498 ,
Gorilla gorilla ENSGGOG000000151241 retrocopy
retro_ggor_1150,
Myotis lucifugus ENSMLUG000000073751 retrocopy
retro_mluc_2048,
Nomascus leucogenys ENSNLEG000000037911 retrocopy
retro_nleu_1718,
Otolemur garnettii ENSOGAG000000022771 retrocopy
retro_ogar_305,
Pongo abelii ENSPPYG000000188092 retrocopies
retro_pabe_1249, retro_pabe_3211,
Pan troglodytes ENSPTRG000000204931 retrocopy
retro_ptro_1017,
Sarcophilus harrisii ENSSHAG000000065881 retrocopy
retro_shar_507,

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 = 0.16 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .04 RPM
CEU_NA11843 0 .09 RPM
CEU_NA11930 0 .10 RPM
CEU_NA12004 0 .04 RPM
CEU_NA12400 0 .00 RPM
CEU_NA12751 0 .07 RPM
CEU_NA12760 0 .00 RPM
CEU_NA12827 0 .14 RPM
CEU_NA12872 0 .03 RPM
CEU_NA12873 0 .10 RPM
FIN_HG00183 0 .16 RPM
FIN_HG00277 0 .04 RPM
FIN_HG00315 0 .00 RPM
FIN_HG00321 0 .12 RPM
FIN_HG00328 0 .05 RPM
FIN_HG00338 0 .06 RPM
FIN_HG00349 0 .06 RPM
FIN_HG00375 0 .00 RPM
FIN_HG00377 0 .05 RPM
FIN_HG00378 0 .06 RPM
GBR_HG00099 0 .06 RPM
GBR_HG00111 0 .04 RPM
GBR_HG00114 0 .08 RPM
GBR_HG00119 0 .10 RPM
GBR_HG00131 0 .03 RPM
GBR_HG00133 0 .02 RPM
GBR_HG00134 0 .09 RPM
GBR_HG00137 0 .05 RPM
GBR_HG00142 0 .08 RPM
GBR_HG00143 0 .03 RPM
TSI_NA20512 0 .06 RPM
TSI_NA20513 0 .05 RPM
TSI_NA20518 0 .11 RPM
TSI_NA20532 0 .14 RPM
TSI_NA20538 0 .00 RPM
TSI_NA20756 0 .00 RPM
TSI_NA20765 0 .10 RPM
TSI_NA20771 0 .00 RPM
TSI_NA20786 0 .00 RPM
TSI_NA20798 0 .03 RPM
YRI_NA18870 0 .03 RPM
YRI_NA18907 0 .00 RPM
YRI_NA18916 0 .06 RPM
YRI_NA19093 0 .05 RPM
YRI_NA19099 0 .00 RPM
YRI_NA19114 0 .08 RPM
YRI_NA19118 0 .04 RPM
YRI_NA19213 0 .12 RPM
YRI_NA19214 0 .10 RPM
YRI_NA19223 0 .12 RPM

Indel association:

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





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