RetrogeneDB ID:

retro_hsap_104

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:2:120979499..120980552(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000226479
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:TMEM185A
Ensembl ID:ENSG00000155984
Aliases:TMEM185A, CXorf13, FAM11A, FRAXF, ee3
Description:transmembrane protein 185A [Source:HGNC Symbol;Acc:17125]


Retrocopy-Parental alignment summary:






>retro_hsap_104
ATGAACCCCAGGGGCCTGTTCCAGGACTTCAACCCCAGTAAGTTTCTCATCTACACCTGCCTGCTGCTCTTCTCGGTGCT
GCTGCCCCTCCGCCTGGACGGCATCATCCAATGGAGCTACTGGGCCGTCTTTGCCCCCATATGGCTGTGGAAGCTTCTAG
TCGTCGCAGGCGCCTCCGTGGGCGCGGGCGTTTGGGCCCGCAACCCTCGCTACCGCACCGAGGGAGAGGCCTGTGTGGAG
TTCAAAGCCATGCTGATCGCTGTGGGCATCCACCTGCTGCTGCTCATGTTCGAAGTCCTGGTCTGCGACAGGGTGGAGAG
GGGCACCCACTTCTGGCTGCTGGTCTTCATGCCTCTCTTCTTCGTGTCCCCCGTGTCCGTGGCTGCCTGCGTCTGGGGCT
TTCGACACGATAGGTCGCTGGAGCTGGAGATCCTGTGCTCGGTCAACATCCTGCAGTTCATCTTCATCGCCCTAAAGCTG
GACAGGATTATTCACTGGCCGTGGCTGGTGGTGTTTGTGCCCCTGTGGATCCTCATGTCGTTCCTTTGCCTGGTCGTCCT
CTATTACATCGTCTGGTCCCTCCTGTTCCTGCGGTCCCTGGATGTGGTTGCCGAGCAGCGGAGAACACACGTGACCATGG
CTATCAGTTGGATAACGATTGTCGTGCCTCTGCTCACTTTTGAGGTCCTGCTGGTTCACAGATTGGATGGCCACAATACA
TTCTCCTACGTCTCCATATTTGTCCCCCTTTGGCTTTCCTTACTAACTTTAATGGCCACAACATTTAGGCGAAAGGGGGG
CAATCATTGGTGGTTTGGCATTCGCAGAGACTTCTGTCAGTTTCTGCTTGAAATTTTCCCATTTTTAAGAGAATATGGGA
ACATTTCATATGATCTCCATCACGAAGATAGTGAAGATGCTGAAGAAACATCAGTTCCAGAAGCTCCGAAAATTGCTCCA
ATATTTGGAAAGAAGGCCAGAGTAGTTATAACCCAGAGCCCTGGGAAATACGTTCCCCCCCCTCCCAAGTTAAATATTGA
TATGCCAGATTAA

ORF - retro_hsap_104 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 88.57 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMNLRGLFQDFNPSKFLIYACLLLFSVLLALRLDGIIQWSYWAVFAPIWLWKLMVIVGASVGTGVWARNPQ
MN.RGLFQDFNPSKFLIY.CLLLFSVLL.LRLDGIIQWSYWAVFAPIWLWKL.V..GASVG.GVWARNP.
RetrocopyMNPRGLFQDFNPSKFLIYTCLLLFSVLLPLRLDGIIQWSYWAVFAPIWLWKLLVVAGASVGAGVWARNPR
ParentalYRAEGETCVEFKAMLIAVGIHLLLLMFEVLVCDRIERGSHFWLLVFMPLFFVSPVSVAACVWGFRHDRSL
YR.EGE.CVEFKAMLIAVGIHLLLLMFEVLVCDR.ERG.HFWLLVFMPLFFVSPVSVAACVWGFRHDRSL
RetrocopyYRTEGEACVEFKAMLIAVGIHLLLLMFEVLVCDRVERGTHFWLLVFMPLFFVSPVSVAACVWGFRHDRSL
ParentalELEILCSVNILQFIFIALRLDKIIHWPWLVVCVPLWILMSFLCLVVLYYIVWSVLFLRSMDVIAEQRRTH
ELEILCSVNILQFIFIAL.LD.IIHWPWLVV.VPLWILMSFLCLVVLYYIVWS.LFLRS.DV.AEQRRTH
RetrocopyELEILCSVNILQFIFIALKLDRIIHWPWLVVFVPLWILMSFLCLVVLYYIVWSLLFLRSLDVVAEQRRTH
ParentalITMALSWMTIVVPLLTFEILLVHKLDGHNAFSSIPIFVPLWLSLITLMATTFGQKGGNHWWFGIRKDFCQ
.TMA.SW.TIVVPLLTFE.LLVH.LDGHN.FS...IFVPLWLSL.TLMATTF..KGGNHWWFGIR.DFCQ
RetrocopyVTMAISWITIVVPLLTFEVLLVHRLDGHNTFSYVSIFVPLWLSLLTLMATTFRRKGGNHWWFGIRRDFCQ
ParentalFLLEIFPFLREYGNISYDLHHEDNEETEETPVPEPPKIAPMFRKKARVVITQSPGKYVLPPPKLNIEMPD
FLLEIFPFLREYGNISYDLHHED.E..EET.VPE.PKIAP.F.KKARVVITQSPGKYV.PPPKLNI.MPD
RetrocopyFLLEIFPFLREYGNISYDLHHEDSEDAEETSVPEAPKIAPIFGKKARVVITQSPGKYVPPPPKLNIDMPD

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 8 .98 RPM 5 .59 RPM
bodymap2_adrenal 11 .20 RPM 5 .04 RPM
bodymap2_brain 5 .93 RPM 4 .81 RPM
bodymap2_breast 9 .55 RPM 4 .84 RPM
bodymap2_colon 7 .08 RPM 5 .39 RPM
bodymap2_heart 8 .22 RPM 7 .03 RPM
bodymap2_kidney 9 .31 RPM 5 .13 RPM
bodymap2_liver 2 .66 RPM 1 .31 RPM
bodymap2_lung 7 .19 RPM 2 .95 RPM
bodymap2_lymph_node 7 .02 RPM 5 .34 RPM
bodymap2_ovary 12 .11 RPM 10 .26 RPM
bodymap2_prostate 9 .11 RPM 6 .62 RPM
bodymap2_skeletal_muscle 8 .77 RPM 0 .91 RPM
bodymap2_testis 14 .54 RPM 9 .88 RPM
bodymap2_thyroid 12 .69 RPM 6 .89 RPM
bodymap2_white_blood_cells 11 .75 RPM 4 .98 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity may be related with retro_hsap_104 in 46 libraries
ENCODE library ID Target ChIP-Seq Peak coordinates
ENCFF002CFW POLR2A 2:120980443..120981326
ENCFF002CFX POLR2A 2:120980458..120981320
ENCFF002CGN POLR2A 2:120980622..120981068
ENCFF002CHO POLR2A 2:120980378..120981566
ENCFF002CIH POLR2A 2:120980851..120980999
ENCFF002CIO POLR2A 2:120980595..120981052
ENCFF002CJE POLR2A 2:120980703..120981074
ENCFF002CJZ POLR2A 2:120980716..120981098
ENCFF002CKX POLR2A 2:120980771..120981078
ENCFF002CKX POLR2A 2:120981051..120981202
ENCFF002CLM POLR2A 2:120980641..120981181
ENCFF002CMI POLR2A 2:120980500..120981342
ENCFF002COJ POLR2A 2:120980689..120981125
ENCFF002CPG POLR2A 2:120980647..120981137
ENCFF002CPH POLR2A 2:120980696..120981086
ENCFF002CQA POLR2A 2:120980592..120981162
ENCFF002CQC POLR2A 2:120980681..120981035
ENCFF002CQC POLR2A 2:120980871..120981351
ENCFF002CQE POLR2A 2:120980671..120981075
ENCFF002CQE POLR2A 2:120980994..120981252
ENCFF002CQG POLR2A 2:120980673..120981015
ENCFF002CQI POLR2A 2:120980708..120981059
ENCFF002CQK POLR2A 2:120980608..120981321
ENCFF002CQM POLR2A 2:120980660..120981058
ENCFF002CQO POLR2A 2:120980586..120981072
ENCFF002CRK POLR2A 2:120980908..120981432
ENCFF002CRO POLR2A 2:120980716..120981136
ENCFF002CSY POLR2A 2:120980641..120981163
ENCFF002CUP POLR2A 2:120980763..120981079
ENCFF002CUQ POLR2A 2:120980676..120981180
ENCFF002CVF POLR2A 2:120980709..120981125
ENCFF002CVJ POLR2A 2:120980746..120981054
ENCFF002CXM POLR2A 2:120980643..120981133
ENCFF002CXN POLR2A 2:120980661..120981157
ENCFF002CXO POLR2A 2:120980678..120981102
ENCFF002CXP POLR2A 2:120980752..120981039
ENCFF002CXR POLR2A 2:120980704..120981014
ENCFF002CZC POLR2A 2:120980562..120981123
ENCFF002CZD POLR2A 2:120980584..120981321
ENCFF002DAE POLR2A 2:120980790..120981100
ENCFF002DAE POLR2A 2:120981036..120981346
ENCFF002DAH POLR2A 2:120980797..120981081
ENCFF002DAK POLR2A 2:120980597..120981097
ENCFF002DAV POLR2A 2:120980597..120981141
ENCFF002DBB POLR2A 2:120980834..120981034
ENCFF002DBE POLR2A 2:120980766..120981049
ENCFF002DBO POLR2A 2:120980625..120981079
ENCFF002DBP POLR2A 2:120980771..120981038
ENCFF002DBQ POLR2A 2:120980743..120981113
ENCFF002DBT POLR2A 2:120980748..120981118

EST - click to see more details

5 EST(s) were mapped to retro_hsap_104 retrocopy
EST ID Start End Identity Match Mis-match Score
AA256930 120979906 120980225 100 319 0 319
BE143874 120979779 120980045 99.7 265 1 264
BF349607 120979557 120980049 95.8 470 3 454
BF800502 120979772 120980109 100 336 0 335
HY301666 120979535 120980044 100 509 0 509

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_111735686 libraries811 libraries315 libraries14 libraries3 libraries
TSS #2 TSS_111736114 libraries127 libraries1099 libraries367 libraries122 libraries
TSS #3 TSS_111737499 libraries795 libraries527 libraries7 libraries1 library
TSS #4 TSS_11173826 libraries1 library30 libraries173 libraries1599 libraries

The graphical summary, for retro_hsap_104 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

Experiment type: PCR amplification
Forward primer: TCGTGCCTCTGCTCACTTTT (20 nt long)
Reverse primer: GCAAAGCCCAAGGAGAGAGT (20 nt long)
Anneling temperature: 56 °C
(Expected) product size: 883
Electrophoresis gel image:
Additional comment: Red arrow indicates PCR product of retrogene in pooled cDNA from 16 human tissues (Clontech). Red number of lane indicates particular retrogene; L - GeneRuler 100 bp DNA Ladder (Thermo Fisher Scientific); N - No template control (water instead of cDNA)

Retrocopy orthology:
Retrocopy retro_hsap_104 has 5 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Gorilla gorilla retro_ggor_189
Pongo abelii retro_pabe_118
Macaca mulatta retro_mmul_310
Mus musculus retro_mmus_358
Rattus norvegicus retro_rnor_6
Parental genes homology:
Parental genes homology involve 26 parental genes, and 26 retrocopies.

Species Parental gene accession Retrocopies number
Anolis carolinensis ENSACAG000000086371 retrocopy
retro_acar_65,
Ailuropoda melanoleuca ENSAMEG000000093511 retrocopy
retro_amel_8,
Bos taurus ENSBTAG000000068181 retrocopy
retro_btau_1,
Canis familiaris ENSCAFG000000191031 retrocopy
retro_cfam_159,
Cavia porcellus ENSCPOG000000036221 retrocopy
retro_cpor_5,
Dasypus novemcinctus ENSDNOG000000118641 retrocopy
retro_dnov_2451,
Dipodomys ordii ENSDORG000000150271 retrocopy
retro_dord_67,
Equus caballus ENSECAG000000093991 retrocopy
retro_ecab_426,
Felis catus ENSFCAG000000244831 retrocopy
retro_fcat_1116,
Homo sapiens ENSG00000155984 1 retrocopy
retro_hsap_104 ,
Gorilla gorilla ENSGGOG000000242681 retrocopy
retro_ggor_189,
Loxodonta africana ENSLAFG000000030441 retrocopy
retro_lafr_898,
Microcebus murinus ENSMICG000000046391 retrocopy
retro_mmur_106,
Myotis lucifugus ENSMLUG000000013191 retrocopy
retro_mluc_2075,
Macaca mulatta ENSMMUG000000028881 retrocopy
retro_mmul_310,
Mustela putorius furoENSMPUG000000118961 retrocopy
retro_mputfur_46,
Mus musculus ENSMUSG000000731391 retrocopy
retro_mmus_358,
Nomascus leucogenys ENSNLEG000000134871 retrocopy
retro_nleu_2723,
Otolemur garnettii ENSOGAG000000164141 retrocopy
retro_ogar_88,
Procavia capensis ENSPCAG000000091601 retrocopy
retro_pcap_260,
Pongo abelii ENSPPYG000000208091 retrocopy
retro_pabe_118,
Pteropus vampyrus ENSPVAG000000138221 retrocopy
retro_pvam_30,
Rattus norvegicus ENSRNOG000000110471 retrocopy
retro_rnor_6,
Sus scrofa ENSSSCG000000127391 retrocopy
retro_sscr_494,
Ictidomys tridecemlineatus ENSSTOG000000144841 retrocopy
retro_itri_8,
Tursiops truncatus ENSTTRG000000006431 retrocopy
retro_ttru_868,

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 = 15.25 RPM Legend:


Library Retrogene expression
CEU_NA11831 9 .67 RPM
CEU_NA11843 7 .54 RPM
CEU_NA11930 9 .39 RPM
CEU_NA12004 7 .03 RPM
CEU_NA12400 8 .17 RPM
CEU_NA12751 9 .81 RPM
CEU_NA12760 10 .73 RPM
CEU_NA12827 8 .44 RPM
CEU_NA12872 10 .51 RPM
CEU_NA12873 12 .41 RPM
FIN_HG00183 8 .37 RPM
FIN_HG00277 11 .20 RPM
FIN_HG00315 9 .03 RPM
FIN_HG00321 9 .28 RPM
FIN_HG00328 11 .22 RPM
FIN_HG00338 8 .41 RPM
FIN_HG00349 11 .13 RPM
FIN_HG00375 9 .17 RPM
FIN_HG00377 9 .43 RPM
FIN_HG00378 12 .83 RPM
GBR_HG00099 13 .25 RPM
GBR_HG00111 9 .61 RPM
GBR_HG00114 10 .76 RPM
GBR_HG00119 9 .32 RPM
GBR_HG00131 10 .26 RPM
GBR_HG00133 11 .05 RPM
GBR_HG00134 13 .34 RPM
GBR_HG00137 10 .64 RPM
GBR_HG00142 8 .70 RPM
GBR_HG00143 12 .16 RPM
TSI_NA20512 10 .48 RPM
TSI_NA20513 10 .69 RPM
TSI_NA20518 11 .80 RPM
TSI_NA20532 11 .22 RPM
TSI_NA20538 13 .64 RPM
TSI_NA20756 10 .68 RPM
TSI_NA20765 11 .04 RPM
TSI_NA20771 11 .06 RPM
TSI_NA20786 14 .83 RPM
TSI_NA20798 14 .41 RPM
YRI_NA18870 12 .49 RPM
YRI_NA18907 13 .21 RPM
YRI_NA18916 11 .85 RPM
YRI_NA19093 15 .23 RPM
YRI_NA19099 14 .14 RPM
YRI_NA19114 11 .90 RPM
YRI_NA19118 11 .64 RPM
YRI_NA19213 14 .52 RPM
YRI_NA19214 15 .25 RPM
YRI_NA19223 13 .65 RPM

Indel association:

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



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