RetrogeneDB ID:

retro_hsap_4906

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:X:135179791..135180507(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000231513
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:E2F6
Ensembl ID:ENSG00000169016
Aliases:E2F6, E2F-6
Description:E2F transcription factor 6 [Source:HGNC Symbol;Acc:3120]


Retrocopy-Parental alignment summary:






>retro_hsap_4906
ATGAGTCAGCAGCAGCCTGCAGGAAAGTTGACTGACCTGCCCATTAACCCGGCGGAGGAGACGGTTCGCCGCCGAGACGC
CACCAATGCGGAGTGCCCACTGCCATCAACAATAAGGATTAATTCCAAAGATGATGTACAACCTGAGTCTAAAAGAGAAA
CTGTAAATATGAAACCTCATAATAAGACATCACTGGCTTGTACAACGCGAAAATTTATAGATATTCTCAAATCGGCTCCT
GGAGGTGTTCTTAGCTTAAGCCAGGTAGCAGCAAAACTGGCAGTGCACAGACGAAGAATATATGACATCATCAGTGTCTT
ACAAGGAGTCAAACTAATTGAAAAAACATCTAAGAACCATATTCAGTGGATTGGACCTGATTTTAATTCTGGAGCAACAC
CCGAAGAAAAGAAGCTAGAGGAGGAAGTTTCCAAATTATCAGCAACAGAAGATGCCTTGGATAAGTTAATTGAAGATTGT
TCTCAGCAACTGTGTGAGTTAACAAATGACAAAGAATTGGGAAAACTAGCATATGTGACGCTTGAAGACATTCACAACTT
GGAACGCTTCCAGGAACAGACCGTTTTTGTCGCTAAATTGCCAGTAGAAATCACACTGGAAATTCCAATTTCTGAAGACT
CTTTCTCATTACGTTTAAGTAACAACGACGGACCTGTTGACGCCTATTTGTGTCTATCGAAGAAGGATTACGAAGC

ORF - retro_hsap_4906 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 54.29 %
Parental protein coverage: 86.83 %
Number of stop codons detected: 0
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalMSQQRPARKLPSLLLDPTEETVRRRCRDPINVEGLLPSKIRINLEDNVQYVSMRKALKVKRPRFDVSLVY
MSQQ.PA.KL..L...P.EETVRRR..D..N.E..LPS.IRIN..D.VQ..S.R.....K.P....SL..
RetrocopyMSQQQPAGKLTDLPINPAEETVRRR--DATNAECPLPSTIRINSKDDVQPESKRETVNMK-PHNKTSLAC
ParentalLTRKFMDLVRSAPGGILDLNKVATKLGVRKRRVYDITNVLDGIDLVEKKSKNHIRWIGSDLSNFGAVPQQ
.TRKF.D...SAPGG.L.L..VA.KL.V..RR.YDI..VL.G..L.EK.SKNHI.WIG.D..N.GA.P..
RetrocopyTTRKFIDILKSAPGGVLSLSQVAAKLAVHRRRIYDIISVLQGVKLIEKTSKNHIQWIGPDF-NSGATPEE
ParentalKKLQEELSDLSAMEDALDELIKDCAQQLFELTDDKENERLAYVTYQDIHSIQAFHEQIVIAVKAPAETRL
KKL.EE.S.LSA.EDALD.LI.DC.QQL.ELT.DKE...LAYVT..DIH....F.EQ.V...K.P.E..L
RetrocopyKKLEEEVSKLSATEDALDKLIEDCSQQLCELTNDKELGKLAYVTLEDIHNLERFQEQTVFVAKLPVEITL
ParentalDVPAPREDSITVHIRSTNGPIDVYLC-EVEQGQTS
..P...EDS.........GP.D.YLC...E.G..S
RetrocopyEIPI-SEDSFSLRLSNNDGPVDAYLC<SIEEGLRS

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 9 .86 RPM
bodymap2_adrenal 0 .00 RPM 12 .65 RPM
bodymap2_brain 0 .05 RPM 11 .88 RPM
bodymap2_breast 0 .00 RPM 10 .29 RPM
bodymap2_colon 0 .00 RPM 8 .64 RPM
bodymap2_heart 0 .00 RPM 17 .89 RPM
bodymap2_kidney 0 .00 RPM 10 .57 RPM
bodymap2_liver 0 .00 RPM 6 .40 RPM
bodymap2_lung 0 .00 RPM 8 .90 RPM
bodymap2_lymph_node 0 .00 RPM 10 .60 RPM
bodymap2_ovary 0 .02 RPM 18 .51 RPM
bodymap2_prostate 0 .00 RPM 11 .57 RPM
bodymap2_skeletal_muscle 0 .00 RPM 15 .75 RPM
bodymap2_testis 0 .66 RPM 19 .66 RPM
bodymap2_thyroid 0 .00 RPM 19 .30 RPM
bodymap2_white_blood_cells 0 .18 RPM 8 .78 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity may be related with retro_hsap_4906 in 2 libraries
ENCODE library ID Target ChIP-Seq Peak coordinates
ENCFF002CXR POLR2A X:135180212..135180648
ENCFF002CZQ POLR2A X:135180449..135180899

EST - click to see more details

No EST(s) were mapped for retro_hsap_4906 retrocopy.

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_1974121782 libraries30 libraries12 libraries3 libraries2 libraries
TSS #2 TSS_1974131810 libraries14 libraries5 libraries0 libraries0 libraries
TSS #3 TSS_1974141797 libraries25 libraries6 libraries1 library0 libraries

The graphical summary, for retro_hsap_4906 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_4906 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_4906 has 1 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Macaca mulatta retro_mmul_87
Parental genes homology:
Parental genes homology involve 12 parental genes, and 19 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000482861 retrocopy
retro_btau_1820,
Callithrix jacchus ENSCJAG000000069101 retrocopy
retro_cjac_178,
Dasypus novemcinctus ENSDNOG000000002581 retrocopy
retro_dnov_187,
Homo sapiens ENSG000001122421 retrocopy
retro_hsap_1749,
Homo sapiens ENSG00000169016 4 retrocopies
retro_hsap_2542, retro_hsap_2547, retro_hsap_2572, retro_hsap_4906 ,
Macropus eugenii ENSMEUG000000079574 retrocopies
retro_meug_1169, retro_meug_860, retro_meug_882, retro_meug_893,
Myotis lucifugus ENSMLUG000000033841 retrocopy
retro_mluc_864,
Macaca mulatta ENSMMUG000000232251 retrocopy
retro_mmul_87,
Nomascus leucogenys ENSNLEG000000141341 retrocopy
retro_nleu_2351,
Pongo abelii ENSPPYG000000126461 retrocopy
retro_pabe_1,
Pan troglodytes ENSPTRG000000116612 retrocopies
retro_ptro_1484, retro_ptro_3272,
Ictidomys tridecemlineatus ENSSTOG000000033161 retrocopy
retro_itri_135,

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 .02 RPM
FIN_HG00338 0 .00 RPM
FIN_HG00349 0 .03 RPM
FIN_HG00375 0 .00 RPM
FIN_HG00377 0 .00 RPM
FIN_HG00378 0 .00 RPM
GBR_HG00099 0 .00 RPM
GBR_HG00111 0 .02 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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