RetrogeneDB ID:

retro_hsap_51

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:4:118005439..118006549(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000174599
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:TRAM1
Ensembl ID:ENSG00000067167
Aliases:TRAM1, PNAS8, TRAM, TRAMP
Description:translocation associated membrane protein 1 [Source:HGNC Symbol;Acc:20568]


Retrocopy-Parental alignment summary:






>retro_hsap_51
ATGGGGCTCCGTAAGAAGAGCACCAAGAACCCCCCCGTTCTCAGCCAGGAATTCATCCTGCAGAATCATGCGGACATCGT
CTCCTGCGTGGGGATGTTCTTCCTGCTGGGGCTTGTGTTCGAGGGAACAGCAGAAGCATCCATCGTGTTTCTCACTCTTC
AGCACAGTGTTGCTGTCCCTGCAGCAGAGGAACAAGCCACGGGCTCAAAGTCCCTCTATTATTATGGTGTCAAAGATTTG
GCCACGGTTTTCTTCTACATGCTGGTGGCAATCATTATTCATGCCACAATTCAGGAATATGTGTTGGATAAAATTAACAA
GAGAATGCAGTTCACCAAAGCGAAACAAAACAAGTTTAACGAGTCTGGTCAGTTTAGTGTGTTCTACTTTTTTTCTTGTA
TTTGGGGCACATTCATTTTAATCTCTGAAAACTGCCTGTCAGACCCAACTCTTATATGGAAGGCTCGTCCCCATAGCATG
ATGACATTTCAAATGAAGTTTTTCTACATATCCCAGTTGGCTTACTGGTTTCATGCTTTTCCTGAACTCTACTTCCAGAA
AACCAAAAAACAAGACATCCCTCGTCAACTTGTCTACATTGGTCTTCACCTCTTCCACATTACTGGAGCTTATCTCTTGT
ACTTGAATCATTTGGGACTTCTTCTTTTGGTACTGCATTATTTTGTTGAATTACTTTCCCACATGTGCGGCCTGTTTTAC
TTTAGTGATGAAAAGTACCAGAAAGGCATATCTCTGTGGGCCATTGTGTTTATCTTGGGTAGACTTGTGACTTTAATTGT
TTCCGTACTCACTGTTGGGTTTCACCTGGCTGGATCGCAGAATCGGAATCCTGATGCCCTTACTGGAAATGTAAATGTGT
TGGCAGCTAAAATTGCTGTTCTGTCGTCCAGTTGCACGATCCAAGCCTACGTAACATGGAACTTAATTACTCTCTGGCTT
CAGAGGTGGGTAGAAGATTCTAATATTCAGGCCTCATGTATGAAAAAGAAACGGTCGAGATCTTCTAAAAAAAGAACAGA
AAACGGAGTGGGAGTGGAAACTTCAAATAGAGTAGACTGTCCGCCAAAGAGGAAAGAGAAATCTTCATAA

ORF - retro_hsap_51 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 71.39 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMAIRKKSTKSPPVLSHEFVLQNHADIVSCVAMVFLLGLMFEITAKASIIFVTLQYNVTLPATEEQATESV
M..RKKSTK.PPVLS.EF.LQNHADIVSCV.M.FLLGL.FE.TA.ASI.F.TLQ..V..PA.EEQAT.S.
RetrocopyMGLRKKSTKNPPVLSQEFILQNHADIVSCVGMFFLLGLVFEGTAEASIVFLTLQHSVAVPAAEEQATGSK
ParentalSLYYYGIKDLATVFFYMLVAIIIHAVIQEYMLDKINRRMHFSKTKHSKFNESGQLSAFYLFACVWGTFIL
SLYYYG.KDLATVFFYMLVAIIIHA.IQEY.LDKIN.RM.F.K.K..KFNESGQ.S.FY.F.C.WGTFIL
RetrocopySLYYYGVKDLATVFFYMLVAIIIHATIQEYVLDKINKRMQFTKAKQNKFNESGQFSVFYFFSCIWGTFIL
ParentalISENYISDPTILWRAYPHNLMTFQMKFFYISQLAYWLHAFPELYFQKTKKEDIPRQLVYIGLYLFHIAGA
ISEN..SDPT..W.A.PH..MTFQMKFFYISQLAYW.HAFPELYFQKTKK.DIPRQLVYIGL.LFHI.GA
RetrocopyISENCLSDPTLIWKARPHSMMTFQMKFFYISQLAYWFHAFPELYFQKTKKQDIPRQLVYIGLHLFHITGA
ParentalYLLNLNHLGLVLLVLHYFVEFLFHISRLFYFSNEKYQKGFSLWAVLFVLGRLLTLILSVLTVGFGLARAE
YLL.LNHLGL.LLVLHYFVE.L.H...LFYFS.EKYQKG.SLWA..F.LGRL.TLI.SVLTVGF.LA...
RetrocopyYLLYLNHLGLLLLVLHYFVELLSHMCGLFYFSDEKYQKGISLWAIVFILGRLVTLIVSVLTVGFHLAGSQ
ParentalNQKLDFSTGNFNVLAVRIAVLASICVTQAFMMWKFINFQLRRWREHSAFQAPAVKKKPTVTKGRSSKKGT
N...D..TGN.NVLA..IAVL.S.C..QA...W..I...L.RW.E.S..QA...KKK......RSSKK.T
RetrocopyNRNPDALTGNVNVLAAKIAVLSSSCTIQAYVTWNLITLWLQRWVEDSNIQASCMKKK----RSRSSKKRT
ParentalENGVNGTLTSNVADSPRNKKEKSS
ENGV.G..TSN..D.P...KEKSS
RetrocopyENGV-GVETSNRVDCPPKRKEKSS

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 .44 RPM 145 .86 RPM
bodymap2_adrenal 4 .32 RPM 115 .55 RPM
bodymap2_brain 5 .39 RPM 45 .50 RPM
bodymap2_breast 1 .34 RPM 121 .27 RPM
bodymap2_colon 0 .56 RPM 128 .51 RPM
bodymap2_heart 0 .09 RPM 67 .55 RPM
bodymap2_kidney 4 .86 RPM 212 .59 RPM
bodymap2_liver 0 .00 RPM 174 .82 RPM
bodymap2_lung 0 .18 RPM 232 .00 RPM
bodymap2_lymph_node 0 .73 RPM 199 .86 RPM
bodymap2_ovary 2 .66 RPM 142 .19 RPM
bodymap2_prostate 1 .30 RPM 99 .16 RPM
bodymap2_skeletal_muscle 0 .11 RPM 31 .14 RPM
bodymap2_testis 2 .26 RPM 136 .31 RPM
bodymap2_thyroid 4 .76 RPM 180 .76 RPM
bodymap2_white_blood_cells 0 .00 RPM 248 .15 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity may be related with retro_hsap_51 in 8 libraries
ENCODE library ID Target ChIP-Seq Peak coordinates
ENCFF002CFW POLR2A 4:118006557..118006684
ENCFF002CFX POLR2A 4:118006684..118006882
ENCFF002CGN POLR2A 4:118006715..118006898
ENCFF002CJE POLR2A 4:118006623..118006901
ENCFF002CZC POLR2A 4:118006533..118007073
ENCFF002CZD POLR2A 4:118006581..118007091
ENCFF002DAE POLR2A 4:118006647..118006957
ENCFF002DBB POLR2A 4:118006690..118006890

EST - click to see more details

2 EST(s) were mapped to retro_hsap_51 retrocopy
EST ID Start End Identity Match Mis-match Score
BE938736 118005960 118006279 98.8 313 2 305
BE938743 118005960 118006280 99.1 316 2 312

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_139215828 libraries458 libraries510 libraries28 libraries5 libraries
TSS #2 TSS_139216725 libraries454 libraries534 libraries97 libraries19 libraries

The graphical summary, for retro_hsap_51 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_51 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_51 has 1 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_2081
Parental genes homology:
Parental genes homology involve 25 parental genes, and 26 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000063251 retrocopy
retro_amel_78,
Bos taurus ENSBTAG000000075621 retrocopy
retro_btau_24,
Canis familiaris ENSCAFG000000078661 retrocopy
retro_cfam_15,
Callithrix jacchus ENSCJAG000000078931 retrocopy
retro_cjac_168,
Dasypus novemcinctus ENSDNOG000000092962 retrocopies
retro_dnov_27, retro_dnov_906,
Dipodomys ordii ENSDORG000000019011 retrocopy
retro_dord_27,
Equus caballus ENSECAG000000183781 retrocopy
retro_ecab_506,
Echinops telfairi ENSETEG000000184471 retrocopy
retro_etel_674,
Felis catus ENSFCAG000000287751 retrocopy
retro_fcat_136,
Homo sapiens ENSG00000067167 1 retrocopy
retro_hsap_51 ,
Loxodonta africana ENSLAFG000000116251 retrocopy
retro_lafr_9,
Macaca mulatta ENSMMUG000000015161 retrocopy
retro_mmul_235,
Monodelphis domestica ENSMODG000000073161 retrocopy
retro_mdom_308,
Mustela putorius furoENSMPUG000000106161 retrocopy
retro_mputfur_558,
Mus musculus ENSMUSG000000259351 retrocopy
retro_mmus_117,
Nomascus leucogenys ENSNLEG000000113761 retrocopy
retro_nleu_73,
Oryctolagus cuniculus ENSOCUG000000087341 retrocopy
retro_ocun_52,
Otolemur garnettii ENSOGAG000000063791 retrocopy
retro_ogar_2932,
Pongo abelii ENSPPYG000000186601 retrocopy
retro_pabe_169,
Pan troglodytes ENSPTRG000000203341 retrocopy
retro_ptro_2081,
Rattus norvegicus ENSRNOG000000078921 retrocopy
retro_rnor_287,
Sus scrofa ENSSSCG000000061931 retrocopy
retro_sscr_980,
Ictidomys tridecemlineatus ENSSTOG000000055371 retrocopy
retro_itri_38,
Tarsius syrichta ENSTSYG000000138871 retrocopy
retro_tsyr_24,
Tursiops truncatus ENSTTRG000000003281 retrocopy
retro_ttru_24,

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 = 0.56 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .02 RPM
CEU_NA11843 0 .00 RPM
CEU_NA11930 0 .29 RPM
CEU_NA12004 0 .15 RPM
CEU_NA12400 0 .56 RPM
CEU_NA12751 0 .05 RPM
CEU_NA12760 0 .22 RPM
CEU_NA12827 0 .19 RPM
CEU_NA12872 0 .00 RPM
CEU_NA12873 0 .00 RPM
FIN_HG00183 0 .00 RPM
FIN_HG00277 0 .15 RPM
FIN_HG00315 0 .08 RPM
FIN_HG00321 0 .03 RPM
FIN_HG00328 0 .05 RPM
FIN_HG00338 0 .02 RPM
FIN_HG00349 0 .06 RPM
FIN_HG00375 0 .07 RPM
FIN_HG00377 0 .00 RPM
FIN_HG00378 0 .06 RPM
GBR_HG00099 0 .03 RPM
GBR_HG00111 0 .06 RPM
GBR_HG00114 0 .00 RPM
GBR_HG00119 0 .07 RPM
GBR_HG00131 0 .17 RPM
GBR_HG00133 0 .05 RPM
GBR_HG00134 0 .04 RPM
GBR_HG00137 0 .14 RPM
GBR_HG00142 0 .08 RPM
GBR_HG00143 0 .10 RPM
TSI_NA20512 0 .00 RPM
TSI_NA20513 0 .05 RPM
TSI_NA20518 0 .06 RPM
TSI_NA20532 0 .00 RPM
TSI_NA20538 0 .05 RPM
TSI_NA20756 0 .03 RPM
TSI_NA20765 0 .00 RPM
TSI_NA20771 0 .00 RPM
TSI_NA20786 0 .13 RPM
TSI_NA20798 0 .00 RPM
YRI_NA18870 0 .24 RPM
YRI_NA18907 0 .07 RPM
YRI_NA18916 0 .13 RPM
YRI_NA19093 0 .03 RPM
YRI_NA19099 0 .00 RPM
YRI_NA19114 0 .18 RPM
YRI_NA19118 0 .06 RPM
YRI_NA19213 0 .10 RPM
YRI_NA19214 0 .17 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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