Slc10a4 (solute carrier family 10, member 4) - Rat Genome Database

Send us a Message
Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Search RGD Grant Resources Citing RGD About Us Contact Us
Genes Variants Community Projects QTLs Strains Markers Genome Information Ontologies Cell Lines References Download Submit Data
OntoMate (Literature Search) JBrowse (Genome Browser) Synteny Browser (VCMap) Variant Visualizer Multi-Ontology Enrichment (MOET) Gene-Ortholog Location Finder (GOLF) InterViewer (Protein-Protein Interactions) PhenoMiner (Quatitative Phenotypes) Gene Annotator OLGA (Gene List Generator) AllianceMine GViewer (Genome Viewer)
Aging & Age-Related Disease Behavioral & Substance Use Disorder Cancer & Neoplastic Disease Cardiovascular Disease Coronavirus Disease Developmental Disease Diabetes Hematologic Disease Immune & Inflammatory Disease Infectious Disease Liver Disease Neurological Disease Obesity & Metabolic Syndrome Renal Disease Respiratory Disease Sensory Organ Disease
Find Models Genetic Models Autism Models Rat PhenoMiner (Quantitative Phenotypes) Chinchilla PhenoMiner Expected Ranges (Quantitative Phenotype) PhenoMiner Term Comparison Hybrid Rat Diversity Panel Phenotypes Phenotypes in Other Animal Models Animal Husbandry Strain Medical Records Phylogenetics Strain Availability Calendar Rats 101 Submissions Photo Archive
Pathways
Rat Community Forum Directory of Rat Laboratories Video Tutorials News RGD Publications RGD Presentations Archive Nomenclature Guidelines Resource Links Laboratory Resources Employment Resources
Advanced Search (OLGA)
Gene: Slc10a4 (solute carrier family 10, member 4) Rattus norvegicus
Analyze
Symbol: Slc10a4
Name: solute carrier family 10, member 4
RGD ID: 1309536
Description: Predicted to enable bile acid:sodium symporter activity. Predicted to be involved in bile acid and bile salt transport and regulation of neurotransmitter loading into synaptic vesicle. Predicted to act upstream of or within adult behavior and response to xenobiotic stimulus. Predicted to be located in plasma membrane. Predicted to be active in several cellular components, including dopaminergic synapse; serotonergic synapse; and synaptic vesicle membrane. Orthologous to human SLC10A4 (solute carrier family 10 member 4); INTERACTS WITH 6-propyl-2-thiouracil; bisphenol A; copper atom.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: bile acid transporter Slc10a4; LOC305309; Na(+)/bile acid cotransporter 4; sodium/bile acid cotransporter 4; solute carrier family 10 (sodium/bile acid cotransporter family), member 4; solute carrier family 10 member 4
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
GRCr81435,552,170 - 35,557,884 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1435,552,170 - 35,557,884 (-)EnsemblGRCr8
mRatBN7.21435,198,149 - 35,203,863 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1435,197,886 - 35,203,729 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx1435,562,389 - 35,567,613 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01436,867,146 - 36,872,370 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01435,355,472 - 35,360,696 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.01437,764,839 - 37,770,059 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1437,764,839 - 37,770,059 (-)Ensemblrn6Rnor6.0
Rnor_5.01437,575,344 - 37,580,564 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41437,603,484 - 37,608,704 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1434,453,572 - 34,458,796 (-)NCBICelera
RGSC_v3.11437,605,918 - 37,611,139 (-)NCBI
Cytogenetic Map14p11NCBI
JBrowse:




Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

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. GOA pipeline RGD automated data pipeline
3. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:18355966   PMID:21742018   PMID:23022458   PMID:25176177  


Genomics

Comparative Map Data
Slc10a4
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81435,552,170 - 35,557,884 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1435,552,170 - 35,557,884 (-)EnsemblGRCr8
mRatBN7.21435,198,149 - 35,203,863 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1435,197,886 - 35,203,729 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx1435,562,389 - 35,567,613 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01436,867,146 - 36,872,370 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01435,355,472 - 35,360,696 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.01437,764,839 - 37,770,059 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1437,764,839 - 37,770,059 (-)Ensemblrn6Rnor6.0
Rnor_5.01437,575,344 - 37,580,564 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41437,603,484 - 37,608,704 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1434,453,572 - 34,458,796 (-)NCBICelera
RGSC_v3.11437,605,918 - 37,611,139 (-)NCBI
Cytogenetic Map14p11NCBI
SLC10A4
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38448,483,343 - 48,489,526 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl448,483,343 - 48,489,526 (+)Ensemblhg38GRCh38
GRCh37448,485,360 - 48,491,543 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36448,180,206 - 48,185,921 (+)NCBIBuild 36Build 36hg18NCBI36
Build 34448,326,376 - 48,332,092NCBI
Celera448,934,151 - 48,940,332 (+)NCBICelera
Cytogenetic Map4p11NCBI
HuRef447,805,548 - 47,811,582 (+)NCBIHuRef
CHM1_1448,484,515 - 48,490,696 (+)NCBICHM1_1
T2T-CHM13v2.0448,450,381 - 48,456,560 (+)NCBIT2T-CHM13v2.0
Slc10a4
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39573,164,247 - 73,170,298 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl573,164,226 - 73,170,298 (+)EnsemblGRCm39 EnsemblGRCm39
GRCm38573,006,904 - 73,012,955 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl573,006,883 - 73,012,955 (+)Ensemblmm10GRCm38
MGSCv37573,398,143 - 73,404,194 (+)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv36573,286,039 - 73,292,090 (+)NCBIMGSCv36mm8
Celera570,259,481 - 70,265,532 (+)NCBICelera
Cytogenetic Map5C3.2NCBI
cM Map538.44NCBI
Slc10a4
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495544719,189,262 - 19,194,412 (-)Ensembl
ChiLan1.0NW_00495544719,189,516 - 19,194,982 (-)NCBIChiLan1.0ChiLan1.0
SLC10A4
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2379,375,193 - 79,381,360 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1479,636,679 - 79,642,846 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0473,663,681 - 73,669,852 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1484,391,103 - 84,402,422 (-)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl484,391,103 - 84,402,422 (-)EnsemblpanPan2panpan1.1
SLC10A4
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11344,293,956 - 44,299,529 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1344,277,094 - 44,299,732 (+)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha1344,247,450 - 44,253,276 (+)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.01344,898,294 - 44,903,727 (+)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1344,898,966 - 44,903,921 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.11344,572,619 - 44,578,253 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01344,105,676 - 44,113,317 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01344,987,655 - 44,993,299 (+)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Slc10a4
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440528531,795,835 - 31,801,849 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493648214,496,386 - 14,502,957 (+)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_00493648214,496,386 - 14,502,313 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SLC10A4
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl838,378,872 - 38,385,863 (+)EnsemblsusScr11Sscrofa11.1
Sscrofa11.1838,378,878 - 38,385,748 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2840,414,352 - 40,419,674 (+)NCBISscrofa10.2Sscrofa10.2susScr3
SLC10A4
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1271,763,028 - 1,769,246 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl271,762,568 - 1,769,056 (-)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_02366604747,765,658 - 47,771,896 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Slc10a4
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462476118,489,683 - 18,495,507 (-)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_00462476118,489,636 - 18,495,607 (-)NCBIHetGla 1.0HetGla 1.0hetGla2
Slc10a4
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v11129,817,231 - 29,823,262 (+)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Slc10a4
52 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:72
Count of miRNA genes:66
Interacting mature miRNAs:68
Transcripts:ENSRNOT00000029721
Prediction methods:Microtar, Miranda, Rnahybrid, Targetscan
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
631528Scl11Serum cholesterol level QTL 114.9blood cholesterol amount (VT:0000180)blood total cholesterol level (CMO:0000051)141787564536079022Rat
7411573Bw139Body weight QTL 1394.70.001body mass (VT:0001259)body weight gain (CMO:0000420)14140068101Rat
9589814Gluco67Glucose level QTL 674.540.001blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)14140068101Rat
731183Pia20Pristane induced arthritis QTL 203.55joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)14939329839411170Rat
1300154Bp189Blood pressure QTL 1893.04arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)143123808072970315Rat
70187Pancm5Pancreatic morphology QTL 516.7pancreas mass (VT:0010144)pancreas weight to body weight ratio (CMO:0000630)143067446985041098Rat
2324617Coatc2Coat color QTL 20.001coat/hair pigmentation trait (VT:0010463)pigmented coat/hair area to total coat/hair area ratio (CMO:0001810)143112133339507682Rat
631523Pia13Pristane induced arthritis QTL 133.3joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1433424686102238540Rat
1358296Ael3Aortic elastin QTL 33.70.00051aorta elastin amount (VT:0003905)aortic elastin14862139853621398Rat
61420Pia6Pristane induced arthritis QTL 64.9joint integrity trait (VT:0010548)arthritic paw count (CMO:0001460)141891545442433608Rat
7387267Uae42Urinary albumin excretion QTL 420.61urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)142252151767521517Rat
631839Niddm37Non-insulin dependent diabetes mellitus QTL 373.37blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1411334716100078267Rat
2313397Coatc1Coat color QTL1coat/hair pigmentation trait (VT:0010463)coat/hair color measurement (CMO:0001808)141889519263895192Rat
631262Tcas4Tongue tumor susceptibility QTL 47.29tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)141790672654251504Rat
634352Apr6Acute phase response QTL 63.7blood interleukin-6 amount (VT:0008595)plasma interleukin-6 level (CMO:0001927)14141415516Rat
2302045Pia39Pristane induced arthritis QTL 394.90.001blood immunoglobulin amount (VT:0002460)serum immunoglobulin G2a level (CMO:0002116)14862139853621398Rat


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
12 3 53 127 50 47 19 66 19 6 198 142 2 108 23 68 28 8 8

Sequence


Ensembl Acc Id: ENSRNOT00000029721   ⟹   ENSRNOP00000037495
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1435,552,170 - 35,557,884 (-)Ensembl
mRatBN7.2 Ensembl1435,197,886 - 35,203,729 (-)Ensembl
Rnor_6.0 Ensembl1437,764,839 - 37,770,059 (-)Ensembl
RefSeq Acc Id: NM_001008555   ⟹   NP_001008555
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81435,552,170 - 35,557,884 (-)NCBI
mRatBN7.21435,198,149 - 35,203,863 (-)NCBI
Rnor_6.01437,764,839 - 37,770,059 (-)NCBI
Rnor_5.01437,575,344 - 37,580,564 (-)NCBI
RGSC_v3.41437,603,484 - 37,608,704 (-)RGD
Celera1434,453,572 - 34,458,796 (-)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_001008555 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAV80706 (Get FASTA)   NCBI Sequence Viewer  
  AAW30131 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000037495
GenBank Protein Q5PT56 (Get FASTA)   NCBI Sequence Viewer  
RefSeq Acc Id: NP_001008555   ⟸   NM_001008555
- UniProtKB: Q5PT56 (UniProtKB/Swiss-Prot),   F1LQG5 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000037495   ⟸   ENSRNOT00000029721

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q5PT56-F1-model_v2 AlphaFold Q5PT56 1-437 view protein structure

Transcriptome

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


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1309536 AgrOrtholog
BioCyc Gene G2FUF-15860 BioCyc
Ensembl Genes ENSRNOG00000026091 Ensembl, ENTREZGENE
Ensembl Transcript ENSRNOT00000029721 ENTREZGENE
Gene3D-CATH 1.20.1530.20 UniProtKB/Swiss-Prot
InterPro BilAc:Na_symport/Acr3 UniProtKB/Swiss-Prot
  Bilac:Na_transpt UniProtKB/Swiss-Prot
  Na+/solute_symporter_sf UniProtKB/Swiss-Prot
KEGG Report rno:305309 UniProtKB/Swiss-Prot
NCBI Gene 305309 ENTREZGENE
PANTHER PTHR10361 UniProtKB/Swiss-Prot
  PTHR10361:SF41 UniProtKB/Swiss-Prot
Pfam SBF UniProtKB/Swiss-Prot
PhenoGen Slc10a4 PhenoGen
RatGTEx ENSRNOG00000026091 RatGTEx
UniProt F1LQG5 ENTREZGENE, UniProtKB/TrEMBL
  NTCP4_RAT UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2013-08-02 Slc10a4  solute carrier family 10, member 4  Slc10a4  solute carrier family 10 (sodium/bile acid cotransporter family), member 4  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-12-06 Slc10a4  solute carrier family 10 (sodium/bile acid cotransporter family), member 4  Slc10a4_predicted  solute carrier family 10 (sodium/bile acid cotransporter family), member 4 (predicted)  Symbol and Name updated 1559027 APPROVED
2005-01-12 Slc10a4_predicted  solute carrier family 10 (sodium/bile acid cotransporter family), member 4 (predicted)      Symbol and Name status set to approved 70820 APPROVED