Slc23a4 (solute carrier family 23 member 4) - Rat Genome Database

Send us a Message



Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Gene: Slc23a4 (solute carrier family 23 member 4) Rattus norvegicus
Analyze
No known orthologs.
Symbol: Slc23a4 (Ensembl: RGD1565367)
Name: solute carrier family 23 member 4 (Ensembl:similar to Solute carrier family 23, member 2 (Sodium-dependent vitamin C transporter 2))
RGD ID: 1565367
Description: Predicted to enable transmembrane transporter activity. Predicted to be involved in transmembrane transport. Predicted to be located in plasma membrane.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: LOC312226; RGD1565367; similar to Solute carrier family 23, member 2 (Sodium-dependent vitamin C transporter 2); similar to Solute carrier family 23, member 2 (Sodium-dependent vitamin C transporter 2) (mSVCT2) (Na+/L-ascorbic acid transporter 2) (Yolk sac permease-like molecule 2); SNBT1; sodium-dependent nucleobase transporter 1; solute carrier family 23 member 2-like
RGD Orthologs
Alliance Orthologs
More Info homologs ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8464,598,429 - 64,646,168 (-)NCBIGRCr8
mRatBN7.2463,631,292 - 63,679,687 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl463,631,834 - 63,678,987 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx468,589,600 - 68,636,538 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0464,505,215 - 64,552,155 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0462,907,726 - 62,954,656 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0462,480,058 - 62,526,724 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl462,480,600 - 62,526,724 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0462,208,285 - 62,262,195 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4462,337,411 - 62,401,000 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera458,682,468 - 58,729,396 (-)NCBICelera
Cytogenetic Map4q22NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

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:20042597   PMID:29845779  


Genomics

Variants

.
Variants in Slc23a4
278 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:83
Count of miRNA genes:67
Interacting mature miRNAs:71
Transcripts:ENSRNOT00000038950
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
619616Bp79Blood pressure QTL 790.0292arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)4521460278882945Rat
2303168Bp330Blood pressure QTL 3304.250.017arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)45214602146446691Rat
1358203Stl19Serum triglyceride level QTL 192.80.002blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)4521829465958103Rat
631261Tcas3Tongue tumor susceptibility QTL 36.88tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)41081417091360527Rat
2316958Gluco58Glucose level QTL 5810blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)411320076180699135Rat
6909122Insul22Insulin level QTL 224.63blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)42690728575585128Rat
6909128Pancm4Pancreatic morphology QTL 411.35pancreas mass (VT:0010144)pancreas wet weight (CMO:0000626)42690728575585128Rat
8655906Rf60Renal function QTL 603.8blood creatinine amount (VT:0005328)creatinine clearance (CMO:0000765)42949419581006281Rat
12798520Anxrr55Anxiety related response QTL 554.450.01locomotor behavior trait (VT:0001392)number of rearing movements with lid-pushing in an experimental apparatus (CMO:0002715)432583980114627242Rat
8552782Vie1Viral induced encephalitis QTL 126.4brain integrity trait (VT:0010579)encephalitis incidence/prevalence measurement (CMO:0002361)43443048482490359Rat
8552801Bw143Body weight QTL 1437.3body mass (VT:0001259)change in body weight to body weight ratio (CMO:0002216)43443048482490359Rat
8552809Vie5Viral induced encephalitis QTL 525.3brain integrity trait (VT:0010579)encephalitis incidence/prevalence measurement (CMO:0002361)43443048482490359Rat
8655961Kidm43Kidney mass QTL 4318kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)436303261103194984Rat
1358352Srcrt3Stress Responsive Cort QTL 32.29blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)438465774146803430Rat
61475Aia2Adjuvant induced arthritis QTL 25.8joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)43950527573892441Rat
1331807Rf31Renal function QTL 312.988urine potassium amount (VT:0010539)urine potassium level (CMO:0000128)43952426474726312Rat
1300139Hrtrt6Heart rate QTL 62.85heart pumping trait (VT:2000009)heart rate (CMO:0000002)439524264116179656Rat
61445Strs3Sensitivity to stroke QTL 33cerebrum integrity trait (VT:0010549)post-insult time to onset of cerebrovascular lesion (CMO:0002343)44043338885433388Rat
8694439Bw168Body weight QTL 1689.570.001retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)44043341485433414Rat
6893678Bw108Body weight QTL 1082.60.006body mass (VT:0001259)body weight (CMO:0000012)44345797688457976Rat
1576305Emca6Estrogen-induced mammary cancer QTL 65.8mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)444463720155883716Rat
1354612Foco1Food consumption QTL 18.87eating behavior trait (VT:0001431)food intake rate (CMO:0000427)444463908148090542Rat
1354660Salc1Saline consumption QTL 111.26drinking behavior trait (VT:0001422)saline drink intake rate (CMO:0001627)444463908148090542Rat
2312567Glom19Glomerulus QTL 191.90.006kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)445456990146803430Rat
1298082Stresp4Stress response QTL 4blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)450119848146803430Rat
4889969Bss96Bone structure and strength QTL 964.9tibia size trait (VT:0100001)tibia cortical bone volume (CMO:0001725)45664777678882945Rat
4889972Bss97Bone structure and strength QTL 975.6tibia size trait (VT:0100001)tibia total bone volume (CMO:0001724)45664777678882945Rat
5685009Bmd86Bone mineral density QTL 863.7tibia mineral mass (VT:1000283)bone mineral density (CMO:0001226)45664777678882945Rat
5685012Bmd87Bone mineral density QTL 875.1tibia mineral mass (VT:1000283)bone mineral content (CMO:0001554)45664777678882945Rat
70200Alc18Alcohol consumption QTL 189.2drinking behavior trait (VT:0001422)ethanol intake volume to total fluid intake volume ratio (CMO:0001591)456647873149491524Rat
1641833Alc21Alcohol consumption QTL 218.60.0001drinking behavior trait (VT:0001422)ethanol drink intake rate (CMO:0001407)456698790126192555Rat
634311Sach7Saccharin preference QTL 7taste sensitivity trait (VT:0001986)saccharin intake volume to total fluid intake volume ratio (CMO:0001601)45711443281266970Rat
631546Bp86Blood pressure QTL 863.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)45711443291360801Rat
61336Bp21Blood pressure QTL 214.6arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)45711470578881294Rat
1358363Sradr3Stress Responsive Adrenal Weight QTL 36.19adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)457486946102486946Rat
1558651Swd3Spike wave discharge measurement QTL 34.620.000024brain electrophysiology trait (VT:0010557)brain spike-and-wave discharge frequency (CMO:0001742)45843213392991462Rat
631671Iddm11Insulin dependent diabetes mellitus QTL 113.60.0012blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)45863587778886137Rat
738009Sach4Saccharine consumption QTL 44.90.000016consumption behavior trait (VT:0002069)saccharin intake volume to total fluid intake volume ratio (CMO:0001601)459948935154902892Rat
738016Alc16Alcohol consumption QTL 163.60.00015consumption behavior trait (VT:0002069)ethanol drink intake rate to body weight ratio (CMO:0001616)459948935154902892Rat
738031Alc14Alcohol consumption QTL 147.60.00003consumption behavior trait (VT:0002069)ethanol drink intake rate to body weight ratio (CMO:0001616)459948935154902892Rat
1578657Bss12Bone structure and strength QTL 128.9femur morphology trait (VT:0000559)femoral neck cross-sectional area (CMO:0001697)460220938105220938Rat
1578658Bss13Bone structure and strength QTL 138femur strength trait (VT:0010010)femoral neck polar moment of inertia (CMO:0001670)460220938105220938Rat
2300179Bmd50Bone mineral density QTL 505.90.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)460928534105928534Rat
1549843Bw53Body weight QTL 530.0001body mass (VT:0001259)body weight gain (CMO:0000420)461697658103194791Rat
1549839Bw52Body weight QTL 520.0001body mass (VT:0001259)body weight gain (CMO:0000420)461697658115089733Rat
61418Pia5Pristane induced arthritis QTL 54.5joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)462277855128289560Rat
6478743Anxrr40Anxiety related response QTL 400.83076defecation behavior trait (VT:0010462)defecation rate (CMO:0000998)462753847107753847Rat
6478772Anxrr49Anxiety related response QTL 490.15488defecation behavior trait (VT:0010462)defecation rate (CMO:0000998)462753847107753847Rat
6478684Anxrr30Anxiety related response QTL 300.00087defecation behavior trait (VT:0010462)defecation rate (CMO:0000998)462753847107753847Rat
631651Bp124Blood pressure QTL 1243arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)462879517107879517Rat
7394826Bw126Body weight QTL 1260.002body mass (VT:0001259)body weight gain (CMO:0000420)46293326987483707Rat
8552807Vie4Viral induced encephalitis QTL 47.3brain integrity trait (VT:0010579)encephalitis incidence/prevalence measurement (CMO:0002361)46293350882490359Rat
70192BpQTLcluster5Blood pressure QTL cluster 54.183arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)462933508114921294Rat
70192BpQTLcluster5Blood pressure QTL cluster 54.183arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)462933508114921294Rat
70192BpQTLcluster5Blood pressure QTL cluster 54.183arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)462933508114921294Rat
70192BpQTLcluster5Blood pressure QTL cluster 54.183arterial blood pressure trait (VT:2000000)percent change in mean arterial blood pressure (CMO:0002035)462933508114921294Rat
70192BpQTLcluster5Blood pressure QTL cluster 54.183arterial blood pressure trait (VT:2000000)percent change in systolic blood pressure (CMO:0000747)462933508114921294Rat
70192BpQTLcluster5Blood pressure QTL cluster 54.183arterial blood pressure trait (VT:2000000)absolute change in pulse pressure (CMO:0001882)462933508114921294Rat
70192BpQTLcluster5Blood pressure QTL cluster 54.183arterial blood pressure trait (VT:2000000)absolute change in mean arterial blood pressure (CMO:0000533)462933508114921294Rat


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

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 1 6 6 13 2
Low 2 35 28 18 13 18 1 1 74 26 28 9 1
Below cutoff 8 23 23 23 7 10 9 7

Sequence


RefSeq Acc Id: ENSRNOT00000038950   ⟹   ENSRNOP00000030381
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl463,631,834 - 63,678,987 (-)Ensembl
Rnor_6.0 Ensembl462,480,600 - 62,526,724 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000094379   ⟹   ENSRNOP00000078902
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl463,631,968 - 63,678,987 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000114115   ⟹   ENSRNOP00000095717
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl463,631,834 - 63,672,353 (-)Ensembl
RefSeq Acc Id: NM_001270038   ⟹   NP_001256967
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8464,598,429 - 64,646,168 (-)NCBI
mRatBN7.2463,631,834 - 63,678,987 (-)NCBI
Rnor_6.0462,480,600 - 62,526,724 (-)NCBI
Rnor_5.0462,208,285 - 62,262,195 (-)NCBI
Celera458,682,468 - 58,729,396 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039107520   ⟹   XP_038963448
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8464,598,429 - 64,611,740 (-)NCBI
mRatBN7.2463,631,292 - 63,645,328 (-)NCBI
RefSeq Acc Id: XM_063285989   ⟹   XP_063142059
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8464,598,429 - 64,639,144 (-)NCBI
RefSeq Acc Id: NP_001256967   ⟸   NM_001270038
- UniProtKB: D2KX48 (UniProtKB/TrEMBL),   D4A4K8 (UniProtKB/TrEMBL),   A0A8I6GLA0 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000030381   ⟸   ENSRNOT00000038950
RefSeq Acc Id: XP_038963448   ⟸   XM_039107520
- Peptide Label: isoform X2
RefSeq Acc Id: ENSRNOP00000095717   ⟸   ENSRNOT00000114115
RefSeq Acc Id: ENSRNOP00000078902   ⟸   ENSRNOT00000094379
RefSeq Acc Id: XP_063142059   ⟸   XM_063285989
- Peptide Label: isoform X1

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D2KX48-F1-model_v2 AlphaFold D2KX48 1-614 view protein structure

Transcriptome

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

Promoters
RGD ID:13692958
Promoter ID:EPDNEW_R3482
Type:single initiation site
Name:RGD1565367_1
Description:similar to Solute carrier family 23, member 2 (Sodium-dependentvitamin C transporter 2)
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_6.0462,526,772 - 62,526,832EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1565367 AgrOrtholog
BioCyc Gene G2FUF-45259 BioCyc
Ensembl Genes ENSRNOG00000026919 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000038950 ENTREZGENE
  ENSRNOT00000038950.6 UniProtKB/TrEMBL
  ENSRNOT00000094379.1 UniProtKB/TrEMBL
  ENSRNOT00000114115.1 UniProtKB/TrEMBL
InterPro Xan_ur_permease UniProtKB/TrEMBL
  Xant/urac/vitC UniProtKB/TrEMBL
KEGG Report rno:312226 UniProtKB/TrEMBL
NCBI Gene 312226 ENTREZGENE
PANTHER SOLUTE CARRIER FAMILY 23 MEMBER 4 UniProtKB/TrEMBL
  XANTHINE-URACIL / VITAMIN C PERMEASE FAMILY MEMBER UniProtKB/TrEMBL
Pfam Xan_ur_permease UniProtKB/TrEMBL
PhenoGen Slc23a4 PhenoGen
PROSITE XANTH_URACIL_PERMASE UniProtKB/TrEMBL
RatGTEx ENSRNOG00000026919 RatGTEx
UniProt A0A8I5ZLW2_RAT UniProtKB/TrEMBL
  A0A8I6GLA0 ENTREZGENE, UniProtKB/TrEMBL
  D2KX48 ENTREZGENE, UniProtKB/TrEMBL
  D4A4K8 ENTREZGENE
UniProt Secondary D4A4K8 UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2023-09-19 Slc23a4  solute carrier family 23 member 4  RGD1565367  similar to Solute carrier family 23, member 2 (Sodium-dependent vitamin C transporter 2)  Symbol and Name Changed 1299863 APPROVED
2008-04-30 RGD1565367  similar to Solute carrier family 23, member 2 (Sodium-dependent vitamin C transporter 2)   RGD1565367_predicted  similar to Solute carrier family 23, member 2 (Sodium-dependent vitamin C transporter 2) (predicted)  'predicted' is removed 2292626 APPROVED
2006-03-10 RGD1565367_predicted  similar to Solute carrier family 23, member 2 (Sodium-dependent vitamin C transporter 2) (predicted)    similar to Solute carrier family 23, member 2 (Sodium-dependent vitamin C transporter 2) (mSVCT2) (Na+/L-ascorbic acid transporter 2) (Yolk sac permease-like molecule 2) (predicted)  Name updated 1299863 APPROVED
2006-03-07 RGD1565367_predicted  similar to Solute carrier family 23, member 2 (Sodium-dependent vitamin C transporter 2) (mSVCT2) (Na+/L-ascorbic acid transporter 2) (Yolk sac permease-like molecule 2) (predicted)  LOC312226  similar to Solute carrier family 23, member 2 (Sodium-dependent vitamin C transporter 2) (mSVCT2) (Na+/L-ascorbic acid transporter 2) (Yolk sac permease-like molecule 2)  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC312226  similar to Solute carrier family 23, member 2 (Sodium-dependent vitamin C transporter 2) (mSVCT2) (Na+/L-ascorbic acid transporter 2) (Yolk sac permease-like molecule 2)      Symbol and Name status set to provisional 70820 PROVISIONAL