RetrogeneDB ID:

retro_hsap_92

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:8:88885011..88886199(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000176566
Aliases:DCAF4L2, WDR21C
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:DCAF4
Ensembl ID:ENSG00000119599
Aliases:DCAF4, WDR21, WDR21A
Description:DDB1 and CUL4 associated factor 4 [Source:HGNC Symbol;Acc:20229]


Retrocopy-Parental alignment summary:






>retro_hsap_92
ATGGAGAGCAAAAGACCGCGACTGCTCGAGGAAGCAGACAAGCAGAAAAAGACAGTCAGAGTGGGACTCAATGCACCTTC
CATGCTACGAAAGAACCAGCTAGGTTTCCTCAGATTCGCCAACTATTGCCGTATAGCTCGCGAGCTGCGTGTAAGCTGCA
TGCAGAGGAAAAAGGTCCAGATTCATAGCTGGGATCCCTCCTCTTTGGCAAGCGACCGATTTAACCGCATACTGGCGAAT
ACCAACACTGACCAGCTCTTCACAGTGAACCAAGTCGAAGCTGGAGGCTCCAAGTACGGCATCATCACCATGCGAGGCCT
GACGACCCCTGAGCTCCGGGTATACCCGCACAAAACCCTCTACGTCCCTAATCGGAAGGTGAATTCTATGTGCTGGGCCT
CACTGAATCACTTGGATTCCCACCTTCTGCTGTGCTTCGTGGGACTTGCAGATACTCCAAGCTGTGCCGTGCTGCTCCCA
GCGTCGCTGTTCATAGGTAGCTTCCCAGGAATGCGTCGGCCTGGCATGCTTTGCAGTTTCCAGATCCCTGATGCCTGGTC
CTGTGCCTGGTCCCTGAGCATCCACGCGTATCACTCTTTCAGTACAGGCTTGTCTCAGCAGGTCCTGTTGACCAACGTGG
TGACGGGACACCAGCAGTCATTTGGGACTAGCAGTGATGTCTTGGCCCAGCAGTTTGCAATCATGACTCCTTTGCTGTTT
AATGGCTGTCGCTCTGGGGAGATCTTTGGCATTGATCTGCGCTGTGGAAATCAAGGCAGCGGGTGGAAGGCCATTTGCCT
GTCCCATGATTCAGCAGTGACTTCTCTGCAAATCCTCCAAGATGGCCAATTCCTGGTGTCATCAGACATGACTGGAACTA
TCAAGCTGTGGGACTTGAGGGCCACTAAATGTGTAACACAGTACGAAGGTCATGTGAATAACTCCGCCTACCTACCCGTG
CATGTGAACGAAGAAGAAGGAGTCGTGGCGGCCGTGGGCCAGGACTGCTACACGAGAATCTGGAGCCTCCGTCATGGCCA
CCTGCTCACAACCATACCCTCCCCATACCCCGCCTCGGAGAACGACATTCCCAGTGTGGCCTTCTCTTCTCGCCTCGGGG
GCTTCCGAGGAGCACCAGGGCTGCTCATGGCTGTCCGGGAGGACCTTTATTGTTTCTCCTACGGTTAA

ORF - retro_hsap_92 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 74.62 %
Parental protein coverage: 79.6 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMESKRLRLLQEEDRRKKIARMGFNASSMLRKSQLGFLNVTNYCHLAHELRLSCMERKKVQIRSMDPSALA
MESKR.RLL.E.D..KK..R.G.NA.SMLRK.QLGFL...NYC..A.ELR.SCM.RKKVQI.S.DPS.LA
RetrocopyMESKRPRLLEEADKQKKTVRVGLNAPSMLRKNQLGFLRFANYCRIARELRVSCMQRKKVQIHSWDPSSLA
ParentalSDRFNLILADTNSDRLFTVNDVKVGGSKYGIINLQSLKTPTLKVFMHENLYFTNRKVNSVCWASLNHLDS
SDRFN.ILA.TN.D.LFTVN.V..GGSKYGII....L.TP.L.V..H..LY..NRKVNS.CWASLNHLDS
RetrocopySDRFNRILANTNTDQLFTVNQVEAGGSKYGIITMRGLTTPELRVYPHKTLYVPNRKVNSMCWASLNHLDS
ParentalHILLCLMGLAETPGCATLLPASLFVNSHPGIDRPGMLCSFRIPGAWSCAWSLNIQANNCFSTGLSRRVLL
H.LLC..GLA.TP.CA.LLPASLF..S.PG..RPGMLCSF.IP.AWSCAWSL.I.A...FSTGLS..VLL
RetrocopyHLLLCFVGLADTPSCAVLLPASLFIGSFPGMRRPGMLCSFQIPDAWSCAWSLSIHAYHSFSTGLSQQVLL
ParentalTNVVTGHRQSFGTNSDVLAQQFALMAPLLFNGCRSGEIFAIDLRCGNQGKGWKATRLFHDSAVTSVRILQ
TNVVTGH.QSFGT.SDVLAQQFA.M.PLLFNGCRSGEIF.IDLRCGNQG.GWKA..L.HDSAVTS..ILQ
RetrocopyTNVVTGHQQSFGTSSDVLAQQFAIMTPLLFNGCRSGEIFGIDLRCGNQGSGWKAICLSHDSAVTSLQILQ
ParentalDEQYLMASDMAGKIKLWDLRTTKCVRQYEGHVNEYAYLPLHVHEEEGILVAVGQDCYTRIWSLHDARLLR
D.Q.L..SDM.G.IKLWDLR.TKCV.QYEGHVN..AYLP.HV.EEEG...AVGQDCYTRIWSL....LL.
RetrocopyDGQFLVSSDMTGTIKLWDLRATKCVTQYEGHVNNSAYLPVHVNEEEGVVAAVGQDCYTRIWSLRHGHLLT
ParentalTIPSPYPASKADIPSVAFSSRLGGSRGAPGLLMAVGQDLYCYSY
TIPSPYPAS..DIPSVAFSSRLGG.RGAPGLLMAV..DLYC.SY
RetrocopyTIPSPYPASENDIPSVAFSSRLGGFRGAPGLLMAVREDLYCFSY

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 6 .06 RPM
bodymap2_adrenal 0 .00 RPM 16 .95 RPM
bodymap2_brain 0 .00 RPM 7 .81 RPM
bodymap2_breast 0 .00 RPM 9 .14 RPM
bodymap2_colon 0 .00 RPM 4 .66 RPM
bodymap2_heart 0 .00 RPM 2 .27 RPM
bodymap2_kidney 0 .00 RPM 9 .27 RPM
bodymap2_liver 0 .00 RPM 4 .06 RPM
bodymap2_lung 0 .00 RPM 4 .83 RPM
bodymap2_lymph_node 0 .00 RPM 5 .57 RPM
bodymap2_ovary 0 .00 RPM 14 .11 RPM
bodymap2_prostate 0 .00 RPM 8 .56 RPM
bodymap2_skeletal_muscle 0 .00 RPM 7 .51 RPM
bodymap2_testis 9 .65 RPM 15 .52 RPM
bodymap2_thyroid 0 .00 RPM 21 .43 RPM
bodymap2_white_blood_cells 0 .00 RPM 5 .06 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity may be related with retro_hsap_92 in 3 libraries
ENCODE library ID Target ChIP-Seq Peak coordinates
ENCFF002CMI POLR2A 8:88886109..88886370
ENCFF002CXN POLR2A 8:88885981..88886477
ENCFF002CXO POLR2A 8:88886025..88886449

EST - click to see more details

3 EST(s) were mapped to retro_hsap_92 retrocopy
EST ID Start End Identity Match Mis-match Score
AI216416 88884930 88885340 100 409 0 409
DB040643 88885031 88885594 100 563 0 563
HY003183 88885156 88885688 100 532 0 532

TSS - click to see more details



TSS No. TSS Name TSS expression level (Expr) in TPM range:
no expression 0 < Expr ≤ 1 1 < Expr ≤ 5 5 < Expr ≤ 10 Expr > 10
TSS #1 TSS_1869751801 libraries12 libraries13 libraries2 libraries1 library
TSS #2 TSS_1869761789 libraries14 libraries19 libraries3 libraries4 libraries
TSS #3 TSS_1869771812 libraries6 libraries10 libraries1 library0 libraries

The graphical summary, for retro_hsap_92 TSS expression levels > 0 TPM .
TSS expression levels were studied across 1829 TSS-CAGE libraries, based on FANTOM5 data.
The expression values were visualized using beanplot. If you have any doubts, how to read it, read more in Kampstra P (2008)

Display detail expression values in each library
... or ...
Directly download all expression values

Lab - click to see more details

retro_hsap_92 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_92 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_2774
Gorilla gorilla retro_ggor_2743
Macaca mulatta retro_mmul_264
Parental genes homology:
Parental genes homology involve 6 parental genes, and 11 retrocopies.

Species Parental gene accession Retrocopies number
Cavia porcellus ENSCPOG000000138781 retrocopy
retro_cpor_293,
Homo sapiens ENSG00000119599 2 retrocopies
retro_hsap_101, retro_hsap_92 ,
Gorilla gorilla ENSGGOG000000038152 retrocopies
retro_ggor_2026, retro_ggor_2743,
Macaca mulatta ENSMMUG000000036252 retrocopies
retro_mmul_152, retro_mmul_264,
Nomascus leucogenys ENSNLEG000000024492 retrocopies
retro_nleu_1912, retro_nleu_833,
Pan troglodytes ENSPTRG000000065072 retrocopies
retro_ptro_2774, retro_ptro_46,

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 ) 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 .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 .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 .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 .00 RPM

Indel association:

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





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