RetrogeneDB ID:

retro_hsap_7

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:2:130737688..130738453(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000222014
Aliases:RAB6C, WTH3
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:RAB6A
Ensembl ID:ENSG00000175582
Aliases:RAB6A, RAB6
Description:RAB6A, member RAS oncogene family [Source:HGNC Symbol;Acc:9786]


Retrocopy-Parental alignment summary:






>retro_hsap_7
ATGTCCGCGGGCGGAGACTTCGGGAATCCGCTGAGGAAATTCAAGCTGGTGTTCCTGGGGGAGCAAAGCGTTGCAAAGAC
ATCTTTGATCACCAGATTCAGGTATGACAGTTTTGACAACACCTATCAGGCAATAATTGGCATTGACTTTTTATCAAAAA
CTATGTACTTGGAGGATGGAACAATCGGGCTTCGGCTGTGGGATACGGCGGGTCAGGAACGTCTCCGTAGCCTCATTCCC
AGGTACATCCGTGATTCTGCTGCAGCTGTAGTAGTTTACGATATCACAAATGTTAACTCATTCCAGCAAACTACAAAGTG
GATTGATGATGTCAGAACAGAAAGAGGAAGTGATGTTATCATCACGCTAGTAGGAAATAGAACAGATCTTGCTGACAAGA
GGCAAGTGTCAGTTGAGGAGGGAGAGAGGAAAGCCAAAGGGCTGAATGTTACGTTTATTGAAACTAGGGCAAAAGCTGGA
TACAATGTAAAGCAGCTCTTTCGACGTGTAGCAGCAGCTTTGCCGGGAATGGAAAGCACACAGGACGGAAGCAGAGAAGA
CATGAGTGACATAAAACTGGAAAAGCCTCAGGAGCAAACAGTCAGCGAAGGGGGTTGTTCCTGCTACTCTCCCATGTCAT
CTTCAACCCTTCCTCAGAAGCCCCCTTACTCTTTCATTGACTGCAGTGTGAATATTGGCTTGAACCTTTTCCCTTCATTA
ATAACGTTTTGCAATTCATCATTGCTGCCTGTCTCGTGGAGGTGA

ORF - retro_hsap_7 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 91.35 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMSTGGDFGNPLRKFKLVFLGEQSVGKTSLITRFMYDSFDNTYQATIGIDFLSKTMYLEDRTIRLQLWDTA
MS.GGDFGNPLRKFKLVFLGEQSV.KTSLITRF.YDSFDNTYQA.IGIDFLSKTMYLED.TI.L.LWDTA
RetrocopyMSAGGDFGNPLRKFKLVFLGEQSVAKTSLITRFRYDSFDNTYQAIIGIDFLSKTMYLEDGTIGLRLWDTA
ParentalGQERFRSLIPSYIRDSAAAVVVYDITNVNSFQQTTKWIDDVRTERGSDVIIMLVGNKTDLADKRQVSIEE
GQER.RSLIP.YIRDSAAAVVVYDITNVNSFQQTTKWIDDVRTERGSDVII.LVGN.TDLADKRQVS.EE
RetrocopyGQERLRSLIPRYIRDSAAAVVVYDITNVNSFQQTTKWIDDVRTERGSDVIITLVGNRTDLADKRQVSVEE
ParentalGERKAKELNVMFIETSAKAGYNVKQLFRRVAAALPGMESTQDRSREDMIDIKLEKPQEQPVSEGGCSC
GERKAK.LNV.FIET.AKAGYNVKQLFRRVAAALPGMESTQD.SREDM.DIKLEKPQEQ.VSEGGCSC
RetrocopyGERKAKGLNVTFIETRAKAGYNVKQLFRRVAAALPGMESTQDGSREDMSDIKLEKPQEQTVSEGGCSC

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 .08 RPM 201 .09 RPM
bodymap2_adrenal 0 .02 RPM 124 .29 RPM
bodymap2_brain 1 .27 RPM 412 .85 RPM
bodymap2_breast 0 .14 RPM 149 .15 RPM
bodymap2_colon 0 .29 RPM 215 .85 RPM
bodymap2_heart 0 .00 RPM 111 .02 RPM
bodymap2_kidney 0 .00 RPM 189 .56 RPM
bodymap2_liver 0 .00 RPM 133 .80 RPM
bodymap2_lung 0 .00 RPM 202 .90 RPM
bodymap2_lymph_node 0 .00 RPM 149 .61 RPM
bodymap2_ovary 0 .00 RPM 170 .85 RPM
bodymap2_prostate 0 .07 RPM 197 .93 RPM
bodymap2_skeletal_muscle 0 .00 RPM 111 .15 RPM
bodymap2_testis 0 .06 RPM 151 .84 RPM
bodymap2_thyroid 0 .11 RPM 186 .84 RPM
bodymap2_white_blood_cells 0 .00 RPM 188 .96 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity may be related with retro_hsap_7 in 2 libraries
ENCODE library ID Target ChIP-Seq Peak coordinates
ENCFF002DBO POLR2A 2:130737298..130737682
ENCFF002DBP POLR2A 2:130737329..130737659

EST - click to see more details

No EST(s) were mapped for retro_hsap_7 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_112157976 libraries39 libraries429 libraries294 libraries91 libraries
TSS #2 TSS_1121581743 libraries80 libraries6 libraries0 libraries0 libraries

The graphical summary, for retro_hsap_7 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_7 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_7 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 7 parental genes, and 16 retrocopies.

Species Parental gene accession Retrocopies number
Choloepus hoffmanni ENSCHOG000000009921 retrocopy
retro_chof_859,
Homo sapiens ENSG00000175582 1 retrocopy
retro_hsap_7 ,
Mus musculus ENSMUSG000000307041 retrocopy
retro_mmus_2400,
Nomascus leucogenys ENSNLEG000000170981 retrocopy
retro_nleu_200,
Ochotona princeps ENSOPRG000000103556 retrocopies
retro_opri_1082, retro_opri_1085, retro_opri_1095, retro_opri_1118, retro_opri_247, retro_opri_858,
Pongo abelii ENSPPYG000000036633 retrocopies
retro_pabe_2097, retro_pabe_2191, retro_pabe_3537,
Ictidomys tridecemlineatus ENSSTOG000000234973 retrocopies
retro_itri_1743, retro_itri_1827, retro_itri_1885,

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 = 0.08 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 .02 RPM
FIN_HG00349 0 .03 RPM
FIN_HG00375 0 .00 RPM
FIN_HG00377 0 .05 RPM
FIN_HG00378 0 .00 RPM
GBR_HG00099 0 .00 RPM
GBR_HG00111 0 .00 RPM
GBR_HG00114 0 .00 RPM
GBR_HG00119 0 .02 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 .02 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 .03 RPM
YRI_NA18907 0 .00 RPM
YRI_NA18916 0 .00 RPM
YRI_NA19093 0 .00 RPM
YRI_NA19099 0 .03 RPM
YRI_NA19114 0 .08 RPM
YRI_NA19118 0 .02 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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