Slc5a4 (solute carrier family 5 member 4) - Rat Genome Database

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Gene: Slc5a4 (solute carrier family 5 member 4) Rattus norvegicus
Analyze
Symbol: Slc5a4
Name: solute carrier family 5 member 4
RGD ID: 1306923
Description: Enables proton transmembrane transporter activity. Acts upstream of or within proton transmembrane transport. Predicted to be active in plasma membrane. Orthologous to human SLC5A4 (solute carrier family 5 member 4); INTERACTS WITH acrylamide; bisphenol A; cadmium dichloride.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: LOC103690052; LOC294341; low affinity sodium-glucose cotransporter; low affinity sodium-glucose cotransporter-like; Slc5a4a; solute carrier family 5 (glucose activated ion channel), member 4; solute carrier family 5 (low affinity glucose cotransporter), member 4; solute carrier family 5 (low affinity glucose cotransporter), member 4a; solute carrier family 5, member 4; solute carrier family 5, member 4a
RGD Orthologs
Human
Mouse
Bonobo
Dog
Pig
Green Monkey
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr82012,475,096 - 12,518,186 (-)NCBIGRCr8
mRatBN7.22012,475,644 - 12,518,738 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl2012,475,644 - 12,518,738 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx2013,174,399 - 13,217,606 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.02012,535,325 - 12,578,533 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.02013,007,106 - 13,050,314 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.02013,415,039 - 13,458,110 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl2013,415,039 - 13,458,110 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.02015,500,218 - 15,529,128 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42012,876,032 - 12,919,116 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.12012,876,263 - 12,919,254 (-)NCBI
Celera2013,968,710 - 14,011,331 (-)NCBICelera
Cytogenetic Map20p12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. Mouse SGLT3a generates proton-activated currents but does not transport sugar. Barcelona S, etal., Am J Physiol Cell Physiol. 2012 Apr 15;302(8):C1073-82. doi: 10.1152/ajpcell.00436.2011. Epub 2012 Feb 1.
2. 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.
3. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
4. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions

Genomics

Comparative Map Data
Slc5a4
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr82012,475,096 - 12,518,186 (-)NCBIGRCr8
mRatBN7.22012,475,644 - 12,518,738 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl2012,475,644 - 12,518,738 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx2013,174,399 - 13,217,606 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.02012,535,325 - 12,578,533 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.02013,007,106 - 13,050,314 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.02013,415,039 - 13,458,110 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl2013,415,039 - 13,458,110 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.02015,500,218 - 15,529,128 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42012,876,032 - 12,919,116 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.12012,876,263 - 12,919,254 (-)NCBI
Celera2013,968,710 - 14,011,331 (-)NCBICelera
Cytogenetic Map20p12NCBI
SLC5A4
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh382232,218,464 - 32,355,063 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl2232,218,464 - 32,255,347 (-)EnsemblGRCh38hg38GRCh38
GRCh372232,614,451 - 32,651,334 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 362230,944,463 - 30,981,318 (-)NCBINCBI36Build 36hg18NCBI36
Build 342230,939,018 - 30,975,873NCBI
Celera2216,416,726 - 16,453,537 (-)NCBICelera
Cytogenetic Map22q12.3NCBI
HuRef2215,572,136 - 15,608,952 (-)NCBIHuRef
CHM1_12232,573,814 - 32,610,685 (-)NCBICHM1_1
T2T-CHM13v2.02232,682,547 - 32,819,011 (-)NCBIT2T-CHM13v2.0
Slc5a4a
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391075,983,285 - 76,025,099 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1075,983,285 - 76,025,099 (+)EnsemblGRCm39 Ensembl
GRCm381076,147,451 - 76,189,265 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1076,147,451 - 76,189,265 (+)EnsemblGRCm38mm10GRCm38
MGSCv371075,610,196 - 75,652,010 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361075,591,167 - 75,632,981 (+)NCBIMGSCv36mm8
Celera1077,191,382 - 77,233,195 (+)NCBICelera
Cytogenetic Map10C1NCBI
cM Map1038.71NCBI
SLC5A4
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v22342,149,974 - 42,203,754 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan12244,850,803 - 44,904,590 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v02213,229,789 - 13,267,477 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.12231,084,256 - 31,120,946 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2231,084,256 - 31,120,946 (-)Ensemblpanpan1.1panPan2
SLC5A4
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12624,966,469 - 25,026,600 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2624,966,989 - 25,026,867 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2624,835,603 - 24,893,297 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02625,353,171 - 25,413,321 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2625,353,660 - 25,413,330 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12625,052,077 - 25,112,170 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02625,314,968 - 25,375,049 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02625,376,375 - 25,424,932 (-)NCBIUU_Cfam_GSD_1.0
SLC5A4
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1448,708,047 - 48,741,440 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11448,708,047 - 48,741,440 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21452,153,405 - 52,322,914 (-)NCBISscrofa10.2Sscrofa10.2susScr3
SLC5A4
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11915,043,810 - 15,080,535 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1915,044,069 - 15,079,766 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_023666045110,907,424 - 110,949,182 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0

Variants

.
Variants in Slc5a4
869 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:112
Count of miRNA genes:78
Interacting mature miRNAs:82
Transcripts:ENSRNOT00000001750, ENSRNOT00000072183
Prediction methods:Microtar, 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 (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1354642Despr15Despair related QTL 150.0027locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)20124159021Rat
1600382Edcs3Endometrial carcinoma susceptibility QTL33.50.003uterus morphology trait (VT:0001120)percentage of study population developing endometrioid carcinoma during a period of time (CMO:0001759)20125159026Rat
2317851Alcrsp22Alcohol response QTL 223.20.05response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)20127339237Rat
1641893Alcrsp7Alcohol response QTL 7response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)20127339237Rat
8694189Bw153Body weight QTL 1533.130.001body mass (VT:0001259)body weight gain (CMO:0000420)20129191651Rat
9590275Scort15Serum corticosterone level QTL 153.480.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)20129191651Rat
7411650Foco23Food consumption QTL 2320.70.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)20129191651Rat
9590109Sffal8Serum free fatty acids level QTL 85.320.01blood free fatty acid amount (VT:0001553)plasma free fatty acids level (CMO:0000546)20129191651Rat
9589155Insul32Insulin level QTL 326.380.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)20129191651Rat
6893685Bw111Body weight QTL 1112.70.004body mass (VT:0001259)body weight (CMO:0000012)20132578807Rat
7411668Foco32Food consumption QTL 3280.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)20136600972Rat
9590252Scort12Serum corticosterone level QTL 1220.460.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)20136600972Rat
2305926Iddm37Insulin dependent diabetes mellitus QTL 376blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)20152784246527842Rat
1641915Colcr9Colorectal carcinoma resistance QTL 92.970.0024intestine integrity trait (VT:0010554)benign colorectal tumor number (CMO:0001795)20153065546530655Rat
1598816Memor12Memory QTL 122.4exploratory behavior trait (VT:0010471)average horizontal distance between subject and target during voluntary locomotion in an experimental apparatus (CMO:0002674)20260683647606836Rat
2317057Aia27Adjuvant induced arthritis QTL 272.83joint integrity trait (VT:0010548)right rear ankle joint diameter (CMO:0002150)20289259726381954Rat
61432Cia1Collagen induced arthritis QTL 1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)20362165614101050Rat
4889857Pur27Proteinuria QTL 2712.20.001urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)20460660717617956Rat
1558640Prcs2Prostate cancer susceptibility QTL 23.3prostate integrity trait (VT:0010571)percentage of study population developing ventral prostate tumorous lesions during a period of time (CMO:0000943)20460660717617956Rat
70154Insul2Insulin level QTL 23.75blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)20669170617489458Rat
1581577Pur15Proteinuria QTL 154.380.0002urine total protein amount (VT:0000032)urine protein excretion rate (CMO:0000759)20804241017617956Rat
4889870Pur30Proteinuria QTL 30190.005urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)20804241029322208Rat
631265Iresp1Immunoglobin response QTL18.3blood anti-double stranded DNA antibody amount (VT:0004762)serum anti-DNA antibody level (CMO:0001533)20903971913461775Rat
7411652Foco24Food consumption QTL 240.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)201175751554435887Rat
9590092Insglur9Insulin/glucose ratio QTL 918.380.001blood insulin amount (VT:0001560)calculated plasma insulin level (CMO:0002170)201175751554435887Rat


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

circulatory system endocrine system exocrine system hepatobiliary system nervous system reproductive system
High
Medium
Low 2
Below cutoff 2 1 1 1 1 9

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000072183   ⟹   ENSRNOP00000066926
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl2012,475,644 - 12,518,738 (-)Ensembl
Rnor_6.0 Ensembl2013,415,039 - 13,458,110 (-)Ensembl
RefSeq Acc Id: NM_001106383   ⟹   NP_001099853
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr82012,475,096 - 12,518,186 (-)NCBI
mRatBN7.22012,475,644 - 12,518,738 (-)NCBI
Rnor_6.02013,415,039 - 13,458,110 (-)NCBI
Rnor_5.02015,500,218 - 15,529,128 (-)NCBI
RGSC_v3.42012,876,032 - 12,919,116 (-)RGD
Celera2013,968,710 - 14,011,331 (-)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_001099853 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein D3ZIS0 (Get FASTA)   NCBI Sequence Viewer  
  EDL97160 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000066926
  ENSRNOP00000066926.2
  ENSRNOP00055032196
  ENSRNOP00060034721
  ENSRNOP00065032443
Reference Protein Sequences
RefSeq Acc Id: NP_001099853   ⟸   NM_001106383
- UniProtKB: D3ZIS0 (UniProtKB/TrEMBL),   M0RBI9 (UniProtKB/TrEMBL),   A6JKE4 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000066926   ⟸   ENSRNOT00000072183

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZIS0-F1-model_v2 AlphaFold D3ZIS0 1-671 view protein structure

Transcriptome

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

Promoters
RGD ID:13701524
Promoter ID:EPDNEW_R12047
Type:single initiation site
Name:Slc5a4_1
Description:solute carrier family 5 member 4
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_6.02013,458,043 - 13,458,103EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1306923 AgrOrtholog
BioCyc Gene G2FUF-4179 BioCyc
Ensembl Genes ENSRNOG00000049734 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOG00055023083 UniProtKB/Swiss-Prot
  ENSRNOG00060024183 UniProtKB/Swiss-Prot
  ENSRNOG00065023355 UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000072183 ENTREZGENE
  ENSRNOT00000072183.3 UniProtKB/Swiss-Prot
  ENSRNOT00055039657 UniProtKB/Swiss-Prot
  ENSRNOT00060041868 UniProtKB/Swiss-Prot
  ENSRNOT00065039901 UniProtKB/Swiss-Prot
Gene3D-CATH Sodium/glucose cotransporter UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro Na/Glc_symporter_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Na/solute_symporter UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Na/solute_symporter_CS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:294341 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
NCBI Gene 294341 ENTREZGENE
PANTHER SOLUTE CARRIER FAMILY 5 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SOLUTE CARRIER FAMILY 5 MEMBER 4 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam SSF UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Slc5a4 PhenoGen
PROSITE NA_SOLUT_SYMP_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  NA_SOLUT_SYMP_3 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
RatGTEx ENSRNOG00000049734 RatGTEx
  ENSRNOG00055023083 RatGTEx
  ENSRNOG00060024183 RatGTEx
  ENSRNOG00065023355 RatGTEx
UniProt A6JKE4 ENTREZGENE, UniProtKB/TrEMBL
  D3ZIS0 ENTREZGENE
  M0RBI9 ENTREZGENE
  SC5A4_RAT UniProtKB/Swiss-Prot
UniProt Secondary M0RBI9 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2021-03-09 Slc5a4  solute carrier family 5 member 4  LOC103690052  low affinity sodium-glucose cotransporter-like  Data merged from RGD:9126656 737654 PROVISIONAL
2016-07-05 Slc5a4  solute carrier family 5 member 4  Slc5a4  solute carrier family 5 (glucose activated ion channel), member 4  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2014-08-25 LOC103690052  low affinity sodium-glucose cotransporter-like      Symbol and Name status set to provisional 70820 PROVISIONAL
2013-08-02 Slc5a4  solute carrier family 5 (glucose activated ion channel), member 4  Slc5a4  solute carrier family 5 (low affinity glucose cotransporter), member 4  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2012-10-16 Slc5a4  solute carrier family 5 (low affinity glucose cotransporter), member 4  Slc5a4  solute carrier family 5, member 4  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2012-03-06 Slc5a4  solute carrier family 5, member 4  Slc5a4a  solute carrier family 5 (low affinity glucose cotransporter), member 4a  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2011-02-23 Slc5a4a  solute carrier family 5 (low affinity glucose cotransporter), member 4a  Slc5a4  solute carrier family 5 (low affinity glucose cotransporter), member 4a  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 Slc5a4a  solute carrier family 5, member 4a   Slc5a4a_predicted  solute carrier family 5, member 4a (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Slc5a4a_predicted  solute carrier family 5, member 4a (predicted)      Symbol and Name status set to approved 70820 APPROVED