RTP3 (receptor transporter protein 3) - Rat Genome Database

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Gene: RTP3 (receptor transporter protein 3) Homo sapiens
Analyze
Symbol: RTP3
Name: receptor transporter protein 3
RGD ID: 1353966
HGNC Page HGNC:15572
Description: Predicted to enable olfactory receptor binding activity. Involved in detection of chemical stimulus involved in sensory perception of bitter taste and protein targeting to membrane. Located in cytoplasm.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: 3CxxC-type zinc finger protein 3; LTM1; receptor (chemosensory) transporter protein 3; receptor transporting protein 3; receptor-transporting protein 3; TMEM7; transmembrane protein 7; Z3CXXC3; zinc finger, 3CxxC-type 3
RGD Orthologs
Mouse
Rat
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38346,497,976 - 46,500,950 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl346,494,611 - 46,500,950 (+)EnsemblGRCh38hg38GRCh38
GRCh37346,539,466 - 46,542,440 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36346,514,489 - 46,517,443 (+)NCBINCBI36Build 36hg18NCBI36
Build 34346,514,488 - 46,517,443NCBI
Celera346,477,225 - 46,480,179 (+)NCBICelera
Cytogenetic Map3p21.31NCBI
HuRef346,581,734 - 46,584,688 (+)NCBIHuRef
CHM1_1346,489,673 - 46,492,627 (+)NCBICHM1_1
T2T-CHM13v2.0346,514,086 - 46,517,060 (+)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component
cytoplasm  (IBA,IDA)
membrane  (IEA)

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. GOAs Human GO annotations GOA_HUMAN data from the GO Consortium
2. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:11896456   PMID:12477932   PMID:15550249   PMID:16271481   PMID:16720576   PMID:17693185   PMID:20175129   PMID:21873635   PMID:33961781  


Genomics

Comparative Map Data
RTP3
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38346,497,976 - 46,500,950 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl346,494,611 - 46,500,950 (+)EnsemblGRCh38hg38GRCh38
GRCh37346,539,466 - 46,542,440 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36346,514,489 - 46,517,443 (+)NCBINCBI36Build 36hg18NCBI36
Build 34346,514,488 - 46,517,443NCBI
Celera346,477,225 - 46,480,179 (+)NCBICelera
Cytogenetic Map3p21.31NCBI
HuRef346,581,734 - 46,584,688 (+)NCBIHuRef
CHM1_1346,489,673 - 46,492,627 (+)NCBICHM1_1
T2T-CHM13v2.0346,514,086 - 46,517,060 (+)NCBIT2T-CHM13v2.0
Rtp3
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm399110,814,003 - 110,818,781 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl9110,814,003 - 110,819,651 (-)EnsemblGRCm39 Ensembl
GRCm389110,984,935 - 110,990,265 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl9110,984,935 - 110,990,583 (-)EnsemblGRCm38mm10GRCm38
MGSCv379110,887,442 - 110,892,217 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv369110,829,754 - 110,834,529 (-)NCBIMGSCv36mm8
Celera9110,708,362 - 110,712,918 (-)NCBICelera
Cytogenetic Map9F2NCBI
cM Map960.79NCBI
Rtp3
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr88119,847,947 - 119,853,549 (-)NCBIGRCr8
mRatBN7.28110,970,154 - 110,975,000 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl8110,970,160 - 110,974,699 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx8116,584,100 - 116,588,641 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.08114,783,312 - 114,787,853 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.08112,626,130 - 112,630,671 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.08119,260,609 - 119,265,501 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl8119,260,618 - 119,265,157 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.08118,603,373 - 118,608,250 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.48115,388,088 - 115,392,602 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.18115,408,106 - 115,411,353 (-)NCBI
Celera8110,252,497 - 110,257,013 (-)NCBICelera
Cytogenetic Map8q32NCBI
Rtp3
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0NW_00495542025,545,752 - 25,550,044 (-)NCBIChiLan1.0ChiLan1.0
RTP3
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2246,454,390 - 46,457,386 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1346,459,160 - 46,462,156 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0346,397,231 - 46,400,221 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1347,502,087 - 47,505,062 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl347,502,087 - 47,505,062 (+)Ensemblpanpan1.1panPan2
RTP3
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12042,197,170 - 42,202,569 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2042,197,409 - 42,202,543 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2042,112,722 - 42,118,575 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02042,679,115 - 42,684,967 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2042,679,112 - 42,684,937 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12041,920,361 - 41,926,216 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02042,321,768 - 42,327,639 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02042,602,656 - 42,608,519 (-)NCBIUU_Cfam_GSD_1.0
Rtp3
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405118200,844,289 - 200,859,809 (+)NCBIHiC_Itri_2
SpeTri2.0NW_004936596392,885 - 408,892 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
RTP3
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.11329,471,568 - 29,476,277 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21332,699,153 - 32,702,415 (-)NCBISscrofa10.2Sscrofa10.2susScr3
RTP3
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1227,925,733 - 7,930,132 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl227,926,804 - 7,931,187 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_023666041159,220,334 - 159,223,643 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Rtp3
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462473074,605,692 - 74,609,946 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in RTP3
20 total Variants

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 3p21.31-21.2(chr3:45879883-50749922)x4 copy number gain See cases [RCV000133650] Chr3:45879883..50749922 [GRCh38]
Chr3:45921375..50787353 [GRCh37]
Chr3:45896379..50762357 [NCBI36]
Chr3:3p21.31-21.2
pathogenic
GRCh37/hg19 3p22.2-21.31(chr3:37028313-49929220)x3 copy number gain See cases [RCV000240519] Chr3:37028313..49929220 [GRCh37]
Chr3:3p22.2-21.31
likely pathogenic
GRCh37/hg19 3p26.3-q29(chr3:61892-197851986)x3 copy number gain See cases [RCV000511055] Chr3:61892..197851986 [GRCh37]
Chr3:3p26.3-q29
pathogenic
GRCh37/hg19 3p26.3-q29(chr3:61892-197851986) copy number gain See cases [RCV000512358] Chr3:61892..197851986 [GRCh37]
Chr3:3p26.3-q29
pathogenic
GRCh37/hg19 3p26.3-q29(chr3:61495-197838262)x3 copy number gain not provided [RCV000742138] Chr3:61495..197838262 [GRCh37]
Chr3:3p26.3-q29
pathogenic
GRCh37/hg19 3p26.3-q29(chr3:60174-197948027)x3 copy number gain not provided [RCV000742133] Chr3:60174..197948027 [GRCh37]
Chr3:3p26.3-q29
pathogenic
GRCh37/hg19 3p21.31-21.1(chr3:45153770-53878616) copy number gain not provided [RCV000767704] Chr3:45153770..53878616 [GRCh37]
Chr3:3p21.31-21.1
pathogenic
NM_031440.2(RTP3):c.518C>G (p.Pro173Arg) single nucleotide variant not specified [RCV004292418] Chr3:46500718 [GRCh38]
Chr3:46542208 [GRCh37]
Chr3:3p21.31
uncertain significance
NM_031440.2(RTP3):c.256A>G (p.Met86Val) single nucleotide variant not specified [RCV004298893] Chr3:46500456 [GRCh38]
Chr3:46541946 [GRCh37]
Chr3:3p21.31
uncertain significance
NC_000003.11:g.(?_45435946)_(49137751_?)dup duplication Diffuse cerebral and cerebellar atrophy - intractable seizures - progressive microcephaly syndrome [RCV003116297] Chr3:45435946..49137751 [GRCh37]
Chr3:3p21.31
uncertain significance
GRCh37/hg19 3p21.31(chr3:44948482-49115809)x1 copy number loss not provided [RCV002279744] Chr3:44948482..49115809 [GRCh37]
Chr3:3p21.31
pathogenic
NM_031440.2(RTP3):c.161A>C (p.Gln54Pro) single nucleotide variant not specified [RCV004074859] Chr3:46500361 [GRCh38]
Chr3:46541851 [GRCh37]
Chr3:3p21.31
uncertain significance
NM_031440.2(RTP3):c.644G>C (p.Cys215Ser) single nucleotide variant not specified [RCV004188932] Chr3:46500844 [GRCh38]
Chr3:46542334 [GRCh37]
Chr3:3p21.31
uncertain significance
NM_031440.2(RTP3):c.694A>G (p.Ile232Val) single nucleotide variant not specified [RCV004204128] Chr3:46500894 [GRCh38]
Chr3:46542384 [GRCh37]
Chr3:3p21.31
uncertain significance
NM_031440.2(RTP3):c.229G>A (p.Glu77Lys) single nucleotide variant not specified [RCV004140423] Chr3:46500429 [GRCh38]
Chr3:46541919 [GRCh37]
Chr3:3p21.31
likely benign
NM_031440.2(RTP3):c.151G>A (p.Ala51Thr) single nucleotide variant not specified [RCV004214155] Chr3:46498213 [GRCh38]
Chr3:46539703 [GRCh37]
Chr3:3p21.31
uncertain significance
NM_031440.2(RTP3):c.532A>G (p.Arg178Gly) single nucleotide variant not specified [RCV004131866] Chr3:46500732 [GRCh38]
Chr3:46542222 [GRCh37]
Chr3:3p21.31
uncertain significance
NM_031440.2(RTP3):c.298C>G (p.Leu100Val) single nucleotide variant not specified [RCV004213165] Chr3:46500498 [GRCh38]
Chr3:46541988 [GRCh37]
Chr3:3p21.31
uncertain significance
NM_031440.2(RTP3):c.245G>T (p.Gly82Val) single nucleotide variant not specified [RCV004080616] Chr3:46500445 [GRCh38]
Chr3:46541935 [GRCh37]
Chr3:3p21.31
uncertain significance
NM_031440.2(RTP3):c.217A>G (p.Met73Val) single nucleotide variant not specified [RCV004123571] Chr3:46500417 [GRCh38]
Chr3:46541907 [GRCh37]
Chr3:3p21.31
uncertain significance
NM_031440.2(RTP3):c.366T>G (p.Ile122Met) single nucleotide variant not specified [RCV004073949] Chr3:46500566 [GRCh38]
Chr3:46542056 [GRCh37]
Chr3:3p21.31
uncertain significance
NM_031440.2(RTP3):c.319A>G (p.Thr107Ala) single nucleotide variant not specified [RCV004164671] Chr3:46500519 [GRCh38]
Chr3:46542009 [GRCh37]
Chr3:3p21.31
uncertain significance
NM_031440.2(RTP3):c.186G>C (p.Trp62Cys) single nucleotide variant not specified [RCV004074612] Chr3:46500386 [GRCh38]
Chr3:46541876 [GRCh37]
Chr3:3p21.31
uncertain significance
NM_031440.2(RTP3):c.302T>C (p.Phe101Ser) single nucleotide variant not specified [RCV004446927] Chr3:46500502 [GRCh38]
Chr3:46541992 [GRCh37]
Chr3:3p21.31
uncertain significance
NM_031440.2(RTP3):c.467C>T (p.Ala156Val) single nucleotide variant not specified [RCV004446928] Chr3:46500667 [GRCh38]
Chr3:46542157 [GRCh37]
Chr3:3p21.31
uncertain significance
NM_031440.2(RTP3):c.265T>C (p.Phe89Leu) single nucleotide variant not specified [RCV004446926] Chr3:46500465 [GRCh38]
Chr3:46541955 [GRCh37]
Chr3:3p21.31
uncertain significance
NM_031440.2(RTP3):c.338G>A (p.Arg113Lys) single nucleotide variant not specified [RCV004661146] Chr3:46500538 [GRCh38]
Chr3:46542028 [GRCh37]
Chr3:3p21.31
uncertain significance
NM_031440.2(RTP3):c.506C>T (p.Thr169Ile) single nucleotide variant not specified [RCV004661147] Chr3:46500706 [GRCh38]
Chr3:46542196 [GRCh37]
Chr3:3p21.31
uncertain significance
NM_031440.2(RTP3):c.517C>G (p.Pro173Ala) single nucleotide variant not specified [RCV004661148] Chr3:46500717 [GRCh38]
Chr3:46542207 [GRCh37]
Chr3:3p21.31
uncertain significance
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:21
Count of miRNA genes:21
Interacting mature miRNAs:21
Transcripts:ENST00000296142
Prediction methods:Miranda, Rnahybrid
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 (GRCh38)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1298487BFD1_HBody fluid distribution QTL 1 (human)3.94Body fluid distributionimpedance ratio33638071262380712Human
1298489RA4_HRheumatoid arthritis QTL 4 (human)0.0283Joint/bone inflammationrheumatoid arthritis33638071262380712Human
1643509BW293_HBody Weight QTL 293 (human)1.42Body weightBMI33638071262380712Human
2316061GLUCO194_HGlucose level QTL 194 (human)0.02Glucose level32338077449380774Human
2289308BW392_HBody weight QTL 392 (human)1.42Body weightBMI33638071262380712Human

Markers in Region
TMEM7__5096  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh37346,541,910 - 46,542,609UniSTSGRCh37
Build 36346,516,914 - 46,517,613RGDNCBI36
Celera346,479,650 - 46,480,349RGD
HuRef346,584,159 - 46,584,858UniSTS


Expression

RNA-SEQ Expression

adipose tissue
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
692 986 1542 766 2079 1426 1497 523 754 438 1569 3485 2522 20 875 365 1146 967 94

Sequence


Ensembl Acc Id: ENST00000296142   ⟹   ENSP00000296142
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl346,497,976 - 46,500,950 (+)Ensembl
Ensembl Acc Id: ENST00000684260   ⟹   ENSP00000507138
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl346,494,611 - 46,500,950 (+)Ensembl
RefSeq Acc Id: NM_031440   ⟹   NP_113628
RefSeq Status: VALIDATED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38346,497,976 - 46,500,950 (+)NCBI
GRCh37346,539,485 - 46,542,439 (+)RGD
Build 36346,514,489 - 46,517,443 (+)NCBI Archive
Celera346,477,225 - 46,480,179 (+)RGD
HuRef346,581,734 - 46,584,688 (+)ENTREZGENE
CHM1_1346,489,673 - 46,492,627 (+)NCBI
T2T-CHM13v2.0346,514,086 - 46,517,060 (+)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_113628 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAI31757 (Get FASTA)   NCBI Sequence Viewer  
  AAT70682 (Get FASTA)   NCBI Sequence Viewer  
  CAC37401 (Get FASTA)   NCBI Sequence Viewer  
  EAW64768 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSP00000296142
  ENSP00000296142.3
  ENSP00000507138.1
GenBank Protein Q9BQQ7 (Get FASTA)   NCBI Sequence Viewer  
RefSeq Acc Id: NP_113628   ⟸   NM_031440
- UniProtKB: Q9BQQ7 (UniProtKB/Swiss-Prot),   A2RRP6 (UniProtKB/Swiss-Prot)
- Sequence:
Ensembl Acc Id: ENSP00000296142   ⟸   ENST00000296142
Ensembl Acc Id: ENSP00000507138   ⟸   ENST00000684260

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q9BQQ7-F1-model_v2 AlphaFold Q9BQQ7 1-232 view protein structure

Promoters
RGD ID:6864202
Promoter ID:EPDNEW_H5266
Type:initiation region
Name:RTP3_1
Description:receptor transporter protein 3
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Human AssemblyChrPosition (strand)Source
GRCh38346,497,986 - 46,498,046EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene HGNC:15572 AgrOrtholog
COSMIC RTP3 COSMIC
Ensembl Genes ENSG00000163825 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENST00000296142 ENTREZGENE
  ENST00000296142.4 UniProtKB/Swiss-Prot
  ENST00000684260.1 UniProtKB/Swiss-Prot
GTEx ENSG00000163825 GTEx
HGNC ID HGNC:15572 ENTREZGENE
Human Proteome Map RTP3 Human Proteome Map
InterPro R-trans_p UniProtKB/Swiss-Prot
  Znf-3CxxC UniProtKB/Swiss-Prot
KEGG Report hsa:83597 UniProtKB/Swiss-Prot
NCBI Gene 83597 ENTREZGENE
OMIM 607181 OMIM
PANTHER PTHR14402 UniProtKB/Swiss-Prot
  PTHR14402:SF9 UniProtKB/Swiss-Prot
Pfam zf-3CxxC UniProtKB/Swiss-Prot
PharmGKB PA37981 PharmGKB
SMART zf-3CxxC UniProtKB/Swiss-Prot
UniProt A2RRP6 ENTREZGENE
  Q9BQQ7 ENTREZGENE, UniProtKB/Swiss-Prot
UniProt Secondary A2RRP6 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-05-10 RTP3  receptor transporter protein 3    receptor (chemosensory) transporter protein 3  Symbol and/or name change 5135510 APPROVED