Tmem47 (transmembrane protein 47) - Rat Genome Database

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Gene: Tmem47 (transmembrane protein 47) Rattus norvegicus
Analyze
Symbol: Tmem47
Name: transmembrane protein 47
RGD ID: 1564799
Description: Predicted to be involved in cell-cell adhesion. Predicted to be located in adherens junction and plasma membrane. Predicted to be active in cell-cell junction. Orthologous to human TMEM47 (transmembrane protein 47); INTERACTS WITH 17alpha-ethynylestradiol; 2,3,7,8-tetrachlorodibenzodioxine; 3,3',4,4',5-pentachlorobiphenyl.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: hypothetical protein LOC501569; LOC501569; RGD1564799; similar to transmembrane 4 superfamily member 10
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Black Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8X49,338,532 - 49,365,026 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 EnsemblX49,338,326 - 49,521,541 (+)EnsemblGRCr8
mRatBN7.2X45,421,405 - 45,447,900 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 EnsemblX45,421,405 - 45,447,900 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_UtxX46,784,980 - 46,811,486 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0X50,251,798 - 50,278,304 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0X47,917,000 - 47,943,508 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0X48,779,110 - 48,805,644 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX48,779,110 - 48,805,644 (+)Ensemblrn6Rnor6.0
Rnor_5.0X48,984,317 - 49,010,851 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4X67,522,289 - 67,549,061 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
CeleraX46,067,701 - 46,094,193 (+)NCBICelera
Cytogenetic MapXq21NCBI
JBrowse:




Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
17alpha-ethynylestradiol  (EXP)
17beta-estradiol  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
3,3',4,4',5-pentachlorobiphenyl  (EXP)
3-chloropropane-1,2-diol  (EXP)
4-hydroxyphenyl retinamide  (ISO)
5-aza-2'-deoxycytidine  (ISO)
6-propyl-2-thiouracil  (EXP)
acetamide  (EXP)
acrylamide  (EXP)
aflatoxin B1  (ISO)
amitrole  (EXP)
antirheumatic drug  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
benzo[a]pyrene  (EXP,ISO)
benzo[a]pyrene diol epoxide I  (ISO)
bisphenol A  (EXP,ISO)
cadmium dichloride  (EXP)
camptothecin  (ISO)
carbamazepine  (ISO)
CGP 52608  (ISO)
choline  (ISO)
cisplatin  (ISO)
cobalt dichloride  (ISO)
crocidolite asbestos  (ISO)
Cuprizon  (EXP)
cyclosporin A  (ISO)
DDE  (ISO)
DDT  (EXP)
diallyl trisulfide  (ISO)
diethyl phthalate  (EXP)
disodium selenite  (ISO)
dorsomorphin  (ISO)
doxorubicin  (ISO)
endosulfan  (EXP)
epoxiconazole  (ISO)
ethanol  (ISO)
etoposide  (ISO)
folic acid  (ISO)
ketoconazole  (ISO)
L-methionine  (ISO)
lipopolysaccharide  (ISO)
methapyrilene  (EXP)
methimazole  (EXP)
miconazole  (ISO)
mitoxantrone  (ISO)
nickel atom  (ISO)
oxaliplatin  (EXP)
ozone  (ISO)
paracetamol  (ISO)
perfluorohexanesulfonic acid  (ISO)
perfluorooctane-1-sulfonic acid  (ISO)
phenobarbital  (ISO)
pirinixic acid  (ISO)
progesterone  (ISO)
resveratrol  (ISO)
S-(1,2-dichlorovinyl)-L-cysteine  (ISO)
SB 431542  (ISO)
silicon dioxide  (ISO)
sodium arsenate  (ISO)
sodium arsenite  (ISO)
sulfadimethoxine  (EXP)
sunitinib  (ISO)
temozolomide  (ISO)
testosterone  (EXP)
thioacetamide  (EXP)
titanium dioxide  (ISO)
topotecan  (EXP)
trichloroethene  (ISO)
trichostatin A  (ISO)
valproic acid  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component
adherens junction  (IEA)
cell-cell junction  (IBA,IEA,ISO)
membrane  (IEA)
plasma membrane  (IEA,ISO)

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
2. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
3. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:17195181  


Genomics

Comparative Map Data
Tmem47
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8X49,338,532 - 49,365,026 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 EnsemblX49,338,326 - 49,521,541 (+)EnsemblGRCr8
mRatBN7.2X45,421,405 - 45,447,900 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 EnsemblX45,421,405 - 45,447,900 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_UtxX46,784,980 - 46,811,486 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0X50,251,798 - 50,278,304 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0X47,917,000 - 47,943,508 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0X48,779,110 - 48,805,644 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX48,779,110 - 48,805,644 (+)Ensemblrn6Rnor6.0
Rnor_5.0X48,984,317 - 49,010,851 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4X67,522,289 - 67,549,061 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
CeleraX46,067,701 - 46,094,193 (+)NCBICelera
Cytogenetic MapXq21NCBI
TMEM47
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38X34,627,075 - 34,657,285 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 EnsemblX34,627,075 - 34,657,285 (-)Ensemblhg38GRCh38
GRCh37X34,645,192 - 34,675,402 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36X34,555,102 - 34,585,326 (-)NCBIBuild 36Build 36hg18NCBI36
Build 34X34,404,838 - 34,435,062NCBI
CeleraX38,772,420 - 38,802,641 (-)NCBICelera
Cytogenetic MapXp21.1NCBI
HuRefX32,387,635 - 32,399,815 (-)NCBIHuRef
CHM1_1X34,675,754 - 34,705,981 (-)NCBICHM1_1
T2T-CHM13v2.0X34,221,708 - 34,251,928 (-)NCBIT2T-CHM13v2.0
Tmem47
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39X80,114,250 - 80,141,481 (+)NCBIGRCm39GRCm39mm39
GRCm39 EnsemblX80,114,304 - 80,141,478 (+)EnsemblGRCm39 EnsemblGRCm39
GRCm38X81,070,644 - 81,097,875 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 EnsemblX81,070,698 - 81,097,872 (+)Ensemblmm10GRCm38
MGSCv37X78,315,983 - 78,343,214 (+)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv36X77,323,430 - 77,349,182 (+)NCBIMGSCv36mm8
CeleraX72,328,417 - 72,355,541 (+)NCBICelera
Cytogenetic MapXBNCBI
cM MapX38.38NCBI
Tmem47
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555711,191,700 - 1,222,309 (+)Ensembl
ChiLan1.0NW_0049555711,192,213 - 1,222,057 (+)NCBIChiLan1.0ChiLan1.0
TMEM47
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2X36,475,099 - 36,505,277 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1X36,478,476 - 36,508,636 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0X27,277,397 - 27,307,540 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1X34,807,038 - 34,836,965 (-)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 EnsemblX34,810,272 - 34,836,876 (-)EnsemblpanPan2panpan1.1
TMEM47
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1X29,675,386 - 29,705,941 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 EnsemblX29,675,387 - 29,705,941 (-)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_TashaX34,669,753 - 34,700,160 (-)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.0X29,719,784 - 29,750,211 (-)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 EnsemblX29,719,784 - 29,750,257 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1X29,776,454 - 29,806,855 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0X29,765,071 - 29,795,450 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0X29,874,925 - 29,905,345 (-)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Tmem47
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2X22,149,813 - 22,177,523 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365021,993,749 - 2,018,204 (-)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_0049365021,990,524 - 2,018,707 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
TMEM47
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 EnsemblX30,584,046 - 30,615,232 (-)EnsemblsusScr11Sscrofa11.1
Sscrofa11.1X30,584,044 - 30,615,233 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2X33,945,787 - 33,976,572 (-)NCBISscrofa10.2Sscrofa10.2susScr3
TMEM47
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1X33,172,996 - 33,203,711 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 EnsemblX33,172,990 - 33,203,678 (-)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_02366605635,234,853 - 35,265,637 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Tmem47
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462476221,100,133 - 21,129,895 (+)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_00462476221,100,254 - 21,129,793 (+)NCBIHetGla 1.0HetGla 1.0hetGla2
Tmem47
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v1X40,491,117 - 40,514,285 (+)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Tmem47
84 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:267
Count of miRNA genes:168
Interacting mature miRNAs:197
Transcripts:ENSRNOT00000058434
Prediction methods:Miranda, Pita
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


QTLs in Region (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
738035Stresp1Stress response QTL 14.960.000011stress-related behavior trait (VT:0010451)defensive burying - copingX45182909117740458Rat
631666Iddm5Insulin dependent diabetes mellitus QTL 5blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)X811148653111486Rat
1598837Memor13Memory QTL 133.2exploratory behavior trait (VT:0010471)difference between duration of physical contact or close proximity of test subject and social stimulus during sample phase and test phase (CMO:0002678)X4493088389930883Rat

Markers in Region
PMC35279P1  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2X45,445,284 - 45,445,578 (+)MAPPERmRatBN7.2
Rnor_6.0X48,803,029 - 48,803,322NCBIRnor6.0
Rnor_5.0X49,008,236 - 49,008,529UniSTSRnor5.0
RGSC_v3.4X67,546,446 - 67,546,739UniSTSRGSC3.4
CeleraX46,091,578 - 46,091,871UniSTS
Cytogenetic MapXq22UniSTS
DXMit112  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2X45,444,497 - 45,444,738 (+)MAPPERmRatBN7.2
Rnor_6.0X48,802,242 - 48,802,482NCBIRnor6.0
Rnor_5.0X49,007,449 - 49,007,689UniSTSRnor5.0
RGSC_v3.4X67,545,659 - 67,545,899UniSTSRGSC3.4
CeleraX46,090,791 - 46,091,031UniSTS
Cytogenetic MapXq22UniSTS
px-7e3  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2X45,445,446 - 45,445,591 (+)MAPPERmRatBN7.2
Rnor_6.0X48,803,191 - 48,803,335NCBIRnor6.0
Rnor_5.0X49,008,398 - 49,008,542UniSTSRnor5.0
RGSC_v3.4X67,546,608 - 67,546,752UniSTSRGSC3.4
CeleraX46,091,740 - 46,091,884UniSTS
Cytogenetic MapXq22UniSTS


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
musculoskeletal system
nervous system
renal system
reproductive system
respiratory system
sensory system
visual system
16 12 67 164 91 90 59 40 59 6 304 140 11 143 81 92 31 17 17

Sequence


Ensembl Acc Id: ENSRNOT00000058434   ⟹   ENSRNOP00000055235
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 EnsemblX49,338,326 - 49,364,936 (+)Ensembl
mRatBN7.2 EnsemblX45,421,405 - 45,447,900 (+)Ensembl
Rnor_6.0 EnsemblX48,779,110 - 48,805,644 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000132790   ⟹   ENSRNOP00000109226
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 EnsemblX49,338,326 - 49,521,541 (+)Ensembl
RefSeq Acc Id: NM_001109317   ⟹   NP_001102787
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X49,338,532 - 49,365,026 (+)NCBI
mRatBN7.2X45,421,405 - 45,447,900 (+)NCBI
Rnor_6.0X48,779,110 - 48,805,644 (+)NCBI
Rnor_5.0X48,984,317 - 49,010,851 (+)NCBI
RGSC_v3.4X67,522,289 - 67,549,061 (+)RGD
CeleraX46,067,701 - 46,094,193 (+)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_001102787 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL96064 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000055235
  ENSRNOP00000055235.2
  ENSRNOP00000109226.1
RefSeq Acc Id: NP_001102787   ⟸   NM_001109317
- UniProtKB: D3ZBB3 (UniProtKB/TrEMBL),   A6IPU9 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000055235   ⟸   ENSRNOT00000058434
Ensembl Acc Id: ENSRNOP00000109226   ⟸   ENSRNOT00000132790

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZBB3-F1-model_v2 AlphaFold D3ZBB3 1-181 view protein structure

Transcriptome

eQTL   View at Phenogen
WGCNA   View at Phenogen
Tissue/Strain Expression   View at Phenogen

Promoters
RGD ID:13701827
Promoter ID:EPDNEW_R12351
Type:initiation region
Name:Tmem47_1
Description:transmembrane protein 47
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0X48,779,111 - 48,779,171EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1564799 AgrOrtholog
BioCyc Gene G2FUF-2374 BioCyc
Ensembl Genes ENSRNOG00000030418 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000058434 ENTREZGENE
  ENSRNOT00000058434.4 UniProtKB/TrEMBL
  ENSRNOT00000132790.1 UniProtKB/TrEMBL
Gene3D-CATH 1.20.140.150 UniProtKB/TrEMBL
InterPro P53_induced UniProtKB/TrEMBL
  PMP22/EMP/MP20/Claudin UniProtKB/TrEMBL
KEGG Report rno:501569 UniProtKB/TrEMBL
NCBI Gene 501569 ENTREZGENE
PANTHER P53_induced UniProtKB/TrEMBL
  TRANSMEMBRANE PROTEIN 47 UniProtKB/TrEMBL
Pfam PMP22_Claudin UniProtKB/TrEMBL
PhenoGen Tmem47 PhenoGen
RatGTEx ENSRNOG00000030418 RatGTEx
UniProt A0ABK0LYA1_RAT UniProtKB/TrEMBL
  A6IPU9 ENTREZGENE, UniProtKB/TrEMBL
  D3ZBB3 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2010-05-05 Tmem47  transmembrane protein 47  RGD1564799  similar to transmembrane 4 superfamily member 10  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 RGD1564799  similar to transmembrane 4 superfamily member 10   RGD1564799_predicted  similar to transmembrane 4 superfamily member 10 (predicted)  'predicted' is removed 2292626 APPROVED
2006-03-07 RGD1564799_predicted  similar to transmembrane 4 superfamily member 10 (predicted)  LOC501569  similar to transmembrane 4 superfamily member 10  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC501569  similar to transmembrane 4 superfamily member 10      Symbol and Name status set to provisional 70820 PROVISIONAL