SLC1A4 (solute carrier family 1 member 4) - Rat Genome Database

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Gene: SLC1A4 (solute carrier family 1 member 4) Homo sapiens
Analyze
Symbol: SLC1A4
Name: solute carrier family 1 member 4
RGD ID: 1345199
HGNC Page HGNC
Description: Enables L-amino acid transmembrane transporter activity and chloride channel activity. Involved in amino acid transport and cognition. Located in centrosome. Part of membrane. Is active in plasma membrane.
Type: protein-coding
RefSeq Status: REVIEWED
Also known as: alanine/serine/cysteine/threonine transporter 1; ASCT-1; ASCT1; glutamate/neutral amino acid transporter; neutral amino acid transporter A; SATT; solute carrier family 1 (glutamate/neutral amino acid transporter), member 4; SPATCCM
RGD Orthologs
Mouse
Rat
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl264,988,477 - 65,023,865 (+)EnsemblGRCh38hg38GRCh38
GRCh38264,988,479 - 65,023,865 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh37265,215,613 - 65,250,999 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36265,070,098 - 65,104,503 (+)NCBINCBI36hg18NCBI36
Build 34265,128,244 - 65,162,648NCBI
Celera265,061,957 - 65,097,385 (+)NCBI
Cytogenetic Map2p14NCBI
HuRef264,949,345 - 64,984,802 (+)NCBIHuRef
CHM1_1265,146,566 - 65,181,989 (+)NCBICHM1_1
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-schisandrin B  (ISO)
1,2-dimethylhydrazine  (ISO)
17alpha-ethynylestradiol  (ISO)
17beta-estradiol  (EXP,ISO)
2,2',4,4',5,5'-hexachlorobiphenyl  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,3,7,8-Tetrachlorodibenzofuran  (ISO)
3,3',4,4',5-pentachlorobiphenyl  (ISO)
3,4-methylenedioxymethamphetamine  (ISO)
3-chloropropane-1,2-diol  (ISO)
4-hydroxyphenyl retinamide  (ISO)
6-propyl-2-thiouracil  (ISO)
acrylamide  (EXP)
aflatoxin B1  (EXP,ISO)
AM-251  (EXP)
andrographolide  (ISO)
aristolochic acid  (EXP)
arsenite(3-)  (ISO)
benzo[a]pyrene  (EXP,ISO)
benzo[a]pyrene diol epoxide I  (EXP)
beta-naphthoflavone  (ISO)
bisphenol A  (EXP,ISO)
bromobenzene  (ISO)
cadmium dichloride  (EXP)
cannabidiol  (ISO)
carbamazepine  (EXP)
chlordecone  (ISO)
chloroacetaldehyde  (EXP)
chlorpyrifos  (ISO)
cidofovir anhydrous  (EXP)
cisplatin  (EXP,ISO)
clodronic acid  (EXP)
clofibrate  (ISO)
cobalt dichloride  (ISO)
cocaine  (ISO)
copper atom  (EXP)
copper(0)  (EXP)
copper(II) sulfate  (EXP)
coumestrol  (EXP)
crocidolite asbestos  (EXP)
Cuprizon  (ISO)
cyclosporin A  (EXP,ISO)
dexamethasone  (ISO)
diazinon  (ISO)
dibutyl phthalate  (ISO)
diclofenac  (ISO)
diethyl maleate  (ISO)
dioxygen  (EXP)
dorsomorphin  (EXP)
endosulfan  (ISO)
Enterolactone  (EXP)
ethanol  (ISO)
ethyl methanesulfonate  (EXP)
fluoranthene  (ISO)
formaldehyde  (EXP)
genistein  (EXP)
ibuprofen  (EXP)
indole-3-methanol  (ISO)
lamivudine  (EXP)
lead diacetate  (ISO)
lucanthone  (EXP)
mercury dibromide  (EXP)
metformin  (ISO)
methyl methanesulfonate  (EXP)
methylmercury chloride  (EXP)
mitomycin C  (ISO)
motexafin gadolinium  (EXP)
N-methyl-4-phenylpyridinium  (EXP)
N-nitrosodiethylamine  (ISO)
ochratoxin A  (EXP)
orphenadrine  (ISO)
paracetamol  (EXP,ISO)
paraquat  (ISO)
perfluorononanoic acid  (EXP)
perfluorooctane-1-sulfonic acid  (EXP,ISO)
phenformin  (ISO)
phenobarbital  (ISO)
phenylmercury acetate  (EXP)
pirinixic acid  (EXP,ISO)
potassium chromate  (ISO)
potassium dichromate  (ISO)
progesterone  (EXP)
propiconazole  (ISO)
resveratrol  (EXP)
rotenone  (ISO)
S-(1,2-dichlorovinyl)-L-cysteine  (EXP)
SB 431542  (EXP)
silicon dioxide  (EXP)
sodium arsenite  (EXP,ISO)
succimer  (ISO)
sunitinib  (EXP)
tert-butyl hydroperoxide  (EXP)
testosterone  (ISO)
tetrachloromethane  (ISO)
tetracycline  (ISO)
thapsigargin  (EXP)
thifluzamide  (EXP)
toluene  (ISO)
Triptolide  (ISO)
tunicamycin  (EXP)
valproic acid  (EXP)
vanadium atom  (EXP)
vanadium(0)  (EXP)
vinclozolin  (ISO)
vorinostat  (EXP)
zidovudine  (EXP)
zinc acetate  (EXP)
zinc atom  (EXP)
zinc(0)  (EXP)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

References

Additional References at PubMed
PMID:7896285   PMID:8101838   PMID:8125298   PMID:8340364   PMID:8603078   PMID:8910405   PMID:10933718   PMID:11268453   PMID:11824937   PMID:12050356   PMID:12477932   PMID:12584318  
PMID:14502423   PMID:15489334   PMID:15815621   PMID:16344560   PMID:16820059   PMID:16897601   PMID:17081065   PMID:17106422   PMID:18195088   PMID:18442140   PMID:18638388   PMID:19086053  
PMID:19581412   PMID:19946888   PMID:20424473   PMID:20458337   PMID:21757002   PMID:22020285   PMID:22286219   PMID:22623531   PMID:22916037   PMID:24808181   PMID:24816252   PMID:25798074  
PMID:25930971   PMID:26041762   PMID:26138499   PMID:26186194   PMID:26590417   PMID:26638075   PMID:27193218   PMID:27909246   PMID:28298427   PMID:28514442   PMID:28807674   PMID:29180619  
PMID:29955039   PMID:30280653   PMID:30639242   PMID:31995728   PMID:32238831   PMID:34079125  


Genomics

Comparative Map Data
SLC1A4
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl264,988,477 - 65,023,865 (+)EnsemblGRCh38hg38GRCh38
GRCh38264,988,479 - 65,023,865 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh37265,215,613 - 65,250,999 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36265,070,098 - 65,104,503 (+)NCBINCBI36hg18NCBI36
Build 34265,128,244 - 65,162,648NCBI
Celera265,061,957 - 65,097,385 (+)NCBI
Cytogenetic Map2p14NCBI
HuRef264,949,345 - 64,984,802 (+)NCBIHuRef
CHM1_1265,146,566 - 65,181,989 (+)NCBICHM1_1
Slc1a4
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391120,252,180 - 20,282,713 (-)NCBIGRCm39mm39
GRCm39 Ensembl1120,252,180 - 20,282,713 (-)Ensembl
GRCm381120,302,180 - 20,332,713 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1120,302,180 - 20,332,713 (-)EnsemblGRCm38mm10GRCm38
MGSCv371120,202,183 - 20,232,716 (-)NCBIGRCm37mm9NCBIm37
MGSCv361120,202,208 - 20,232,674 (-)NCBImm8
Celera1122,451,521 - 22,482,559 (-)NCBICelera
Cytogenetic Map11A3.1NCBI
cM Map1112.97NCBI
Slc1a4
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21494,530,801 - 94,560,190 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl1494,529,084 - 94,560,418 (-)Ensembl
Rnor_6.014104,582,884 - 104,612,417 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl14104,581,190 - 104,612,597 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.014104,317,800 - 104,345,829 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.414101,123,740 - 101,153,790 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.114101,142,950 - 101,173,001 (-)NCBI
Celera1493,550,109 - 93,578,743 (-)NCBICelera
Cytogenetic Map14q22NCBI
Slc1a4
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495542419,474,082 - 19,499,592 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495542419,474,082 - 19,499,592 (-)NCBIChiLan1.0ChiLan1.0
SLC1A4
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.12A66,177,835 - 66,212,249 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2A66,176,925 - 66,209,615 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v02A65,051,025 - 65,086,917 (+)NCBIMhudiblu_PPA_v0panPan3
SLC1A4
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11064,482,840 - 64,508,288 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1064,483,060 - 64,505,747 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1064,369,739 - 64,394,932 (+)NCBI
ROS_Cfam_1.01065,493,157 - 65,518,318 (+)NCBI
UMICH_Zoey_3.11065,172,083 - 65,197,216 (+)NCBI
UNSW_CanFamBas_1.01065,480,918 - 65,503,851 (+)NCBI
UU_Cfam_GSD_1.01065,774,013 - 65,799,174 (+)NCBI
Slc1a4
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440629218,780,757 - 18,810,279 (-)NCBI
SpeTri2.0NW_0049364919,761,002 - 9,790,535 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SLC1A4
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl376,938,105 - 76,970,508 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1376,938,102 - 76,970,519 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2380,747,982 - 80,754,397 (-)NCBISscrofa10.2Sscrofa10.2susScr3
SLC1A4
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11441,999,216 - 42,032,326 (-)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl1441,999,064 - 42,032,288 (-)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366604569,848,255 - 69,881,833 (+)NCBIVero_WHO_p1.0
Slc1a4
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247628,532,550 - 8,558,912 (-)NCBIHetGla_female_1.0hetGla2

Position Markers
RH70537  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh37265,248,091 - 65,248,211UniSTSGRCh37
Build 36265,101,595 - 65,101,715RGDNCBI36
Celera265,094,477 - 65,094,597RGD
Cytogenetic Map2p15-p13UniSTS
HuRef264,981,887 - 64,982,007UniSTS
GeneMap99-GB4 RH Map2201.61UniSTS
D2S1652E  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh37265,250,716 - 65,250,849UniSTSGRCh37
Build 36265,104,220 - 65,104,353RGDNCBI36
Celera265,097,102 - 65,097,235RGD
Cytogenetic Map2p15-p13UniSTS
HuRef264,984,519 - 64,984,652UniSTS
WI-14351  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh37265,250,812 - 65,250,940UniSTSGRCh37
Build 36265,104,316 - 65,104,444RGDNCBI36
Celera265,097,198 - 65,097,326RGD
Cytogenetic Map2p15-p13UniSTS
HuRef264,984,615 - 64,984,743UniSTS
GeneMap99-GB4 RH Map2201.61UniSTS
Whitehead-RH Map2272.2UniSTS
RH69014  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh37265,248,308 - 65,248,493UniSTSGRCh37
Build 36265,101,812 - 65,101,997RGDNCBI36
Celera265,094,694 - 65,094,879RGD
Cytogenetic Map2p15-p13UniSTS
HuRef264,982,104 - 64,982,289UniSTS
GeneMap99-GB4 RH Map2203.29UniSTS
NCBI RH Map2349.4UniSTS
RH16636  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh37265,250,759 - 65,250,915UniSTSGRCh37
Build 36265,104,263 - 65,104,419RGDNCBI36
Celera265,097,145 - 65,097,301RGD
Cytogenetic Map2p15-p13UniSTS
HuRef264,984,562 - 64,984,718UniSTS
GeneMap99-GB4 RH Map2203.65UniSTS
NCBI RH Map2349.4UniSTS
D2S2933  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh37265,228,746 - 65,228,895UniSTSGRCh37
Build 36265,082,250 - 65,082,399RGDNCBI36
Celera265,075,131 - 65,075,280RGD
Cytogenetic Map2p15-p13UniSTS
HuRef264,962,516 - 64,962,665UniSTS
D2S421E  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh37265,245,211 - 65,245,367UniSTSGRCh37
Build 36265,098,715 - 65,098,871RGDNCBI36
Celera265,091,597 - 65,091,753RGD
Cytogenetic Map2p15-p13UniSTS
HuRef264,979,007 - 64,979,163UniSTS
D2S2566  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh37265,248,478 - 65,248,597UniSTSGRCh37
Build 36265,101,982 - 65,102,101RGDNCBI36
Celera265,094,864 - 65,094,983RGD
Cytogenetic Map2p15-p13UniSTS
HuRef264,982,274 - 64,982,393UniSTS
TNG Radiation Hybrid Map241294.0UniSTS
GeneMap99-GB4 RH Map2202.76UniSTS
GeneMap99-G3 RH Map22535.0UniSTS
D2S2858  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh37265,249,803 - 65,249,938UniSTSGRCh37
Build 36265,103,307 - 65,103,442RGDNCBI36
Celera265,096,189 - 65,096,324RGD
Cytogenetic Map2p15-p13UniSTS
HuRef264,983,599 - 64,983,734UniSTS
TNG Radiation Hybrid Map241304.0UniSTS
GeneMap99-G3 RH Map22527.0UniSTS
D2S1651E  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh37265,250,699 - 65,250,888UniSTSGRCh37
Build 36265,104,203 - 65,104,392RGDNCBI36
Celera265,097,085 - 65,097,274RGD
Cytogenetic Map2p15-p13UniSTS
HuRef264,984,502 - 64,984,691UniSTS
GeneMap99-GB4 RH Map2203.65UniSTS
NCBI RH Map2349.4UniSTS
SLC1A4  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh37265,245,312 - 65,245,807UniSTSGRCh37
Celera265,091,698 - 65,092,193UniSTS
HuRef264,979,108 - 64,979,603UniSTS

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:2103
Count of miRNA genes:1027
Interacting mature miRNAs:1234
Transcripts:ENST00000234256, ENST00000471551, ENST00000480594, ENST00000493121, ENST00000531327
Prediction methods: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.


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 sensory system visual system adipose tissue appendage entire extraembryonic component pharyngeal arch
High
Medium 697 1347 716 221 972 133 2779 906 3324 104 1169 492 98 98 2245 1
Low 1739 1610 1010 403 950 332 1577 1286 409 311 291 1121 77 1 1106 543 5 2
Below cutoff 2 34 29 5 1 4

Sequence

Nucleotide Sequences
RefSeq Transcripts NG_053002 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_001193493 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_001348406 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_001348407 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_003038 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AB026689 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AC007386 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AH006680 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK126636 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK223486 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK295687 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK298472 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK313052 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK315986 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC007350 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC026216 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC072423 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BI553783 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH471053 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CR990382 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  DA214889 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  DA218921 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  L14595 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  L19444 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENST00000234256   ⟹   ENSP00000234256
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl264,989,399 - 65,023,865 (+)Ensembl
RefSeq Acc Id: ENST00000471551
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl264,988,490 - 65,018,127 (+)Ensembl
RefSeq Acc Id: ENST00000480594
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl264,999,448 - 65,023,863 (+)Ensembl
RefSeq Acc Id: ENST00000493121
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl264,988,477 - 65,016,554 (+)Ensembl
RefSeq Acc Id: ENST00000531327   ⟹   ENSP00000431942
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl264,988,490 - 65,021,394 (+)Ensembl
RefSeq Acc Id: NM_001193493   ⟹   NP_001180422
RefSeq Status: REVIEWED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38264,988,479 - 65,023,865 (+)NCBI
GRCh37265,215,579 - 65,250,999 (+)ENTREZGENE
HuRef264,949,345 - 64,984,802 (+)ENTREZGENE
CHM1_1265,146,566 - 65,181,989 (+)NCBI
Sequence:
RefSeq Acc Id: NM_001348406   ⟹   NP_001335335
RefSeq Status: REVIEWED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38264,988,479 - 65,023,865 (+)NCBI
Sequence:
RefSeq Acc Id: NM_001348407   ⟹   NP_001335336
RefSeq Status: REVIEWED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38264,988,479 - 65,023,865 (+)NCBI
Sequence:
RefSeq Acc Id: NM_003038   ⟹   NP_003029
RefSeq Status: REVIEWED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38264,989,399 - 65,023,865 (+)NCBI
GRCh37265,215,579 - 65,250,999 (+)ENTREZGENE
Build 36265,070,098 - 65,104,503 (+)NCBI Archive
HuRef264,949,345 - 64,984,802 (+)ENTREZGENE
CHM1_1265,147,470 - 65,181,989 (+)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_001180422   ⟸   NM_001193493
- Peptide Label: isoform 2 precursor
- UniProtKB: P43007 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: NP_003029   ⟸   NM_003038
- Peptide Label: isoform 1
- UniProtKB: P43007 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: NP_001335335   ⟸   NM_001348406
- Peptide Label: isoform 3 precursor
- Sequence:
RefSeq Acc Id: NP_001335336   ⟸   NM_001348407
- Peptide Label: isoform 3 precursor
- Sequence:
RefSeq Acc Id: ENSP00000431942   ⟸   ENST00000531327
RefSeq Acc Id: ENSP00000234256   ⟸   ENST00000234256

Promoters
RGD ID:6860478
Promoter ID:EPDNEW_H3404
Type:multiple initiation site
Name:SLC1A4_2
Description:solute carrier family 1 member 4
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_H3405  
Experiment Methods:Single-end sequencing.; Paired-end sequencing.
Position:
Human AssemblyChrPosition (strand)Source
GRCh38264,988,479 - 64,988,539EPDNEW
RGD ID:6860480
Promoter ID:EPDNEW_H3405
Type:initiation region
Name:SLC1A4_1
Description:solute carrier family 1 member 4
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_H3404  
Experiment Methods:Single-end sequencing.
Position:
Human AssemblyChrPosition (strand)Source
GRCh38264,989,399 - 64,989,459EPDNEW
RGD ID:6798170
Promoter ID:HG_KWN:32948
Type:CpG-Island
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:CD4+TCell,   CD4+TCell_12Hour,   K562,   Lymphoblastoid,   NB4
Transcripts:NM_001135581,   OTTHUMT00000327464,   OTTHUMT00000327465
Position:
Human AssemblyChrPosition (strand)Source
Build 36265,068,091 - 65,069,202 (+)MPROMDB
RGD ID:6798172
Promoter ID:HG_KWN:32949
Type:CpG-Island
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:CD4+TCell,   CD4+TCell_12Hour,   CD4+TCell_2Hour,   HeLa_S3,   Jurkat,   K562,   Lymphoblastoid,   NB4
Transcripts:OTTHUMT00000251726,   UC002SDG.1,   UC010FCV.1
Position:
Human AssemblyChrPosition (strand)Source
Build 36265,069,546 - 65,070,617 (+)MPROMDB
RGD ID:6798171
Promoter ID:HG_KWN:32951
Type:Non-CpG
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:Lymphoblastoid
Transcripts:OTTHUMT00000327463
Position:
Human AssemblyChrPosition (strand)Source
Build 36265,081,441 - 65,081,941 (+)MPROMDB

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 2p15-14(chr2:63311999-67309291)x1 copy number loss See cases [RCV000054054] Chr2:63311999..67309291 [GRCh38]
Chr2:63539134..67536423 [GRCh37]
Chr2:63392638..67389927 [NCBI36]
Chr2:2p15-14
pathogenic
GRCh38/hg38 2p16.1-11.2(chr2:58279519-83586962)x3 copy number gain See cases [RCV000136053] Chr2:58279519..83586962 [GRCh38]
Chr2:58506654..83814086 [GRCh37]
Chr2:58360158..83667597 [NCBI36]
Chr2:2p16.1-11.2
pathogenic
GRCh38/hg38 2p16.3-11.2(chr2:47620388-86702722)x3 copy number gain See cases [RCV000137586] Chr2:47620388..86702722 [GRCh38]
Chr2:47847527..86929845 [GRCh37]
Chr2:47701031..86783356 [NCBI36]
Chr2:2p16.3-11.2
uncertain significance
GRCh38/hg38 2p14-13.3(chr2:64587095-69876311)x1 copy number loss See cases [RCV000140691] Chr2:64587095..69876311 [GRCh38]
Chr2:64814229..70103443 [GRCh37]
Chr2:64667733..69956947 [NCBI36]
Chr2:2p14-13.3
likely pathogenic
GRCh38/hg38 2p25.1-11.2(chr2:7495123-87705899)x3 copy number gain See cases [RCV000141494] Chr2:7495123..87705899 [GRCh38]
Chr2:7635254..88005418 [GRCh37]
Chr2:7552705..87786533 [NCBI36]
Chr2:2p25.1-11.2
benign
NM_003038.5(SLC1A4):c.766G>A (p.Glu256Lys) single nucleotide variant Spastic tetraplegia, thin corpus callosum, and progressive microcephaly [RCV000412571]|not provided [RCV000505792] Chr2:65010729 [GRCh38]
Chr2:65237863 [GRCh37]
Chr2:2p14
pathogenic
NM_003038.5(SLC1A4):c.1369C>T (p.Arg457Trp) single nucleotide variant Inborn genetic diseases [RCV000623105]|Spastic tetraplegia, thin corpus callosum, and progressive microcephaly [RCV000412526]|not provided [RCV000436990] Chr2:65020916 [GRCh38]
Chr2:65248050 [GRCh37]
Chr2:2p14
pathogenic|likely pathogenic|conflicting interpretations of pathogenicity
NM_003038.5(SLC1A4):c.944_945del (p.Leu315fs) deletion Spastic tetraplegia, thin corpus callosum, and progressive microcephaly [RCV000412627] Chr2:65016583..65016584 [GRCh38]
Chr2:65243717..65243718 [GRCh37]
Chr2:2p14
pathogenic
GRCh37/hg19 2p15-11.2(chr2:62245236-86978895)x3 copy number gain See cases [RCV000448688] Chr2:62245236..86978895 [GRCh37]
Chr2:2p15-11.2
pathogenic
GRCh37/hg19 2p25.3-q37.3(chr2:12771-242783384) copy number gain See cases [RCV000512056] Chr2:12771..242783384 [GRCh37]
Chr2:2p25.3-q37.3
pathogenic
NM_003038.5(SLC1A4):c.1520C>A (p.Ser507Ter) single nucleotide variant Spastic tetraplegia, thin corpus callosum, and progressive microcephaly [RCV001329024]|not specified [RCV000502543] Chr2:65021067 [GRCh38]
Chr2:65248201 [GRCh37]
Chr2:2p14
pathogenic|uncertain significance
GRCh37/hg19 2p15-14(chr2:63234780-67908846)x1 copy number loss See cases [RCV000511763] Chr2:63234780..67908846 [GRCh37]
Chr2:2p15-14
pathogenic
GRCh37/hg19 2p15-14(chr2:61701437-65731084)x1 copy number loss See cases [RCV000511169] Chr2:61701437..65731084 [GRCh37]
Chr2:2p15-14
likely pathogenic
GRCh37/hg19 2p25.3-q37.3(chr2:12771-242783384)x3 copy number gain See cases [RCV000511212] Chr2:12771..242783384 [GRCh37]
Chr2:2p25.3-q37.3
pathogenic
NM_003038.5(SLC1A4):c.1035-381_1230-73del deletion Spastic tetraplegia, thin corpus callosum, and progressive microcephaly [RCV000579174] Chr2:65017690..65018472 [GRCh38]
Chr2:65244824..65245606 [GRCh37]
Chr2:2p14
pathogenic
NM_003038.5(SLC1A4):c.40G>A (p.Ala14Thr) single nucleotide variant not provided [RCV000512758] Chr2:64989683 [GRCh38]
Chr2:65216817 [GRCh37]
Chr2:2p14
uncertain significance
NM_003038.5(SLC1A4):c.1182G>A (p.Ala394=) single nucleotide variant not provided [RCV000513113] Chr2:65018218 [GRCh38]
Chr2:65245352 [GRCh37]
Chr2:2p14
conflicting interpretations of pathogenicity|uncertain significance
NM_003038.5(SLC1A4):c.1380G>A (p.Thr460=) single nucleotide variant not provided [RCV000513458] Chr2:65020927 [GRCh38]
Chr2:65248061 [GRCh37]
Chr2:2p14
benign|likely benign|conflicting interpretations of pathogenicity|uncertain significance
NM_003038.5(SLC1A4):c.1364+1G>A single nucleotide variant Spastic tetraplegia, thin corpus callosum, and progressive microcephaly [RCV000714856] Chr2:65018680 [GRCh38]
Chr2:65245814 [GRCh37]
Chr2:2p14
pathogenic
Single allele inversion not provided [RCV000714264] Chr2:40608411..146900718 [GRCh37]
Chr2:2p22.1-q22.3
likely pathogenic
Single allele duplication not provided [RCV000677942] Chr2:63671346..85698002 [GRCh37]
Chr2:2p15-11.2
pathogenic
NM_003038.5(SLC1A4):c.1316G>A (p.Gly439Glu) single nucleotide variant Spastic tetraplegia, thin corpus callosum, and progressive microcephaly [RCV000714857] Chr2:65018631 [GRCh38]
Chr2:65245765 [GRCh37]
Chr2:2p14
uncertain significance
GRCh37/hg19 2p25.3-q37.3(chr2:14238-243048760)x3 copy number gain not provided [RCV000752802] Chr2:14238..243048760 [GRCh37]
Chr2:2p25.3-q37.3
pathogenic
GRCh37/hg19 2p25.3-q37.3(chr2:15672-243101834)x3 copy number gain not provided [RCV000752804] Chr2:15672..243101834 [GRCh37]
Chr2:2p25.3-q37.3
pathogenic
GRCh37/hg19 2p14(chr2:64928527-65810588)x1 copy number loss not provided [RCV000740479] Chr2:64928527..65810588 [GRCh37]
Chr2:2p14
benign
NM_033305.3(VPS13A):c.1758T>C (p.Ala586=) single nucleotide variant not provided [RCV001644203] Chr2:64989664 [GRCh38]
Chr2:65216798 [GRCh37]
Chr2:2p14
benign
NM_001943.5(DSG2):c.1299T>C (p.Asp433=) single nucleotide variant not provided [RCV001709320] Chr2:64989609 [GRCh38]
Chr2:65216743 [GRCh37]
Chr2:2p14
benign
NM_003038.5(SLC1A4):c.65C>T (p.Pro22Leu) single nucleotide variant not provided [RCV000762268] Chr2:64989708 [GRCh38]
Chr2:65216842 [GRCh37]
Chr2:2p14
uncertain significance
NM_003038.5(SLC1A4):c.745C>T (p.Arg249Cys) single nucleotide variant not provided [RCV000762269] Chr2:65010708 [GRCh38]
Chr2:65237842 [GRCh37]
Chr2:2p14
uncertain significance
NM_006096.4(NDRG1):c.64-20dup single nucleotide variant not provided [RCV001707285] Chr2:64989353 [GRCh38]
Chr2:65216487 [GRCh37]
Chr2:2p14
benign
NM_003038.5(SLC1A4):c.1521G>A (p.Ser507=) single nucleotide variant not provided [RCV000906243] Chr2:65021068 [GRCh38]
Chr2:65248202 [GRCh37]
Chr2:2p14
benign
NM_003038.5(SLC1A4):c.1353G>A (p.Val451=) single nucleotide variant not provided [RCV000905828] Chr2:65018668 [GRCh38]
Chr2:65245802 [GRCh37]
Chr2:2p14
benign
NM_003038.5(SLC1A4):c.1450A>G (p.Lys484Glu) single nucleotide variant not provided [RCV000888452] Chr2:65020997 [GRCh38]
Chr2:65248131 [GRCh37]
Chr2:2p14
benign
NM_003038.5(SLC1A4):c.1491C>T (p.Ile497=) single nucleotide variant not provided [RCV000979148] Chr2:65021038 [GRCh38]
Chr2:65248172 [GRCh37]
Chr2:2p14
likely benign
NM_003038.5(SLC1A4):c.765C>T (p.Asn255=) single nucleotide variant not provided [RCV000923829] Chr2:65010728 [GRCh38]
Chr2:65237862 [GRCh37]
Chr2:2p14
benign
NM_003038.5(SLC1A4):c.1313T>C (p.Ile438Thr) single nucleotide variant not provided [RCV000968543] Chr2:65018628 [GRCh38]
Chr2:65245762 [GRCh37]
Chr2:2p14
likely benign
NM_003038.5(SLC1A4):c.1128C>T (p.Thr376=) single nucleotide variant not provided [RCV000927020] Chr2:65018164 [GRCh38]
Chr2:65245298 [GRCh37]
Chr2:2p14
likely benign
NM_003038.5(SLC1A4):c.1455C>T (p.Gly485=) single nucleotide variant not provided [RCV000924418] Chr2:65021002 [GRCh38]
Chr2:65248136 [GRCh37]
Chr2:2p14
likely benign
NM_003038.5(SLC1A4):c.571T>C (p.Tyr191His) single nucleotide variant not provided [RCV000997153] Chr2:65003953 [GRCh38]
Chr2:65231087 [GRCh37]
Chr2:2p14
uncertain significance
NM_003038.5(SLC1A4):c.1029C>T (p.Cys343=) single nucleotide variant not provided [RCV000919843] Chr2:65016668 [GRCh38]
Chr2:65243802 [GRCh37]
Chr2:2p14
likely benign
GRCh37/hg19 2p15-14(chr2:63536353-65793944)x1 copy number loss not provided [RCV000848078] Chr2:63536353..65793944 [GRCh37]
Chr2:2p15-14
pathogenic
NM_003038.5(SLC1A4):c.-1C>T single nucleotide variant not provided [RCV000997152] Chr2:64989643 [GRCh38]
Chr2:65216777 [GRCh37]
Chr2:2p14
uncertain significance
NM_003038.5(SLC1A4):c.1358G>A (p.Trp453Ter) single nucleotide variant Spastic tetraplegia, thin corpus callosum, and progressive microcephaly [RCV001199378] Chr2:65018673 [GRCh38]
Chr2:65245807 [GRCh37]
Chr2:2p14
pathogenic
NM_003038.5(SLC1A4):c.272T>C (p.Leu91Pro) single nucleotide variant Spastic tetraplegia, thin corpus callosum, and progressive microcephaly [RCV000986765] Chr2:64989915 [GRCh38]
Chr2:65217049 [GRCh37]
Chr2:2p14
likely pathogenic
null single nucleotide variant not provided [RCV001672361] Chr2:65001572 [GRCh38]
Chr2:65228706 [GRCh37]
Chr2:2p14
benign
NM_003038.5(SLC1A4):c.1041G>A (p.Ala347=) single nucleotide variant not provided [RCV000940237] Chr2:65018077 [GRCh38]
Chr2:65245211 [GRCh37]
Chr2:2p14
likely benign
NM_003038.5(SLC1A4):c.1206C>T (p.Asn402=) single nucleotide variant not provided [RCV000913439] Chr2:65018242 [GRCh38]
Chr2:65245376 [GRCh37]
Chr2:2p14
benign
NM_003038.5(SLC1A4):c.1357T>C (p.Trp453Arg) single nucleotide variant Spastic tetraplegia, thin corpus callosum, and progressive microcephaly [RCV000985178] Chr2:65018672 [GRCh38]
Chr2:65245806 [GRCh37]
Chr2:2p14
likely pathogenic
NM_003038.5(SLC1A4):c.999C>T (p.Leu333=) single nucleotide variant not provided [RCV000911605] Chr2:65016638 [GRCh38]
Chr2:65243772 [GRCh37]
Chr2:2p14
likely benign
NM_022445.4(TPK1):c.614-13del single nucleotide variant not provided [RCV001721620] Chr2:65018989 [GRCh38]
Chr2:65246123 [GRCh37]
benign
NM_003895.3(SYNJ1):c.3486A>G (p.Pro1162=) deletion not provided [RCV001688882] Chr2:64989252..64989263 [GRCh38]
Chr2:65216386..65216397 [GRCh37]
Chr2:2p14
benign
null single nucleotide variant not provided [RCV001621838] Chr2:65020671 [GRCh38]
Chr2:65247805 [GRCh37]
Chr2:2p14
benign
NM_004837.4(GGPS1):c.782G>A (p.Arg261His) AND MUSCULAR DYSTROPHY, CONGENITAL HEARING LOSS, single nucleotide variant not provided [RCV001638854] Chr2:65010916 [GRCh38]
Chr2:65238050 [GRCh37]
Chr2:2p14
benign
NM_022445.4(TPK1):c.614-13del single nucleotide variant not provided [RCV001721650] Chr2:65016915 [GRCh38]
Chr2:65244049 [GRCh37]
benign
NM_001943.5(DSG2):c.1299T>C (p.Asp433=) single nucleotide variant not provided [RCV001709782] Chr2:65020749 [GRCh38]
Chr2:65247883 [GRCh37]
Chr2:2p14
benign
NM_000744.7(CHRNA4):c.1227T>C (p.Cys409=) single nucleotide variant not provided [RCV001678074] Chr2:65018783 [GRCh38]
Chr2:65245917 [GRCh37]
Chr2:2p14
benign
null single nucleotide variant not provided [RCV001671311] Chr2:65001325 [GRCh38]
Chr2:65228459 [GRCh37]
Chr2:2p14
benign
null single nucleotide variant not provided [RCV001666054] Chr2:65003825 [GRCh38]
Chr2:65230959 [GRCh37]
Chr2:2p14
benign
NM_001193493.2(SLC1A4):c.-134+630del deletion not provided [RCV001539901] Chr2:64989248 [GRCh38]
Chr2:65216382 [GRCh37]
Chr2:2p14
benign
NM_003038.5(SLC1A4):c.1141G>A (p.Gly381Arg) single nucleotide variant Spastic tetraplegia, thin corpus callosum, and progressive microcephaly [RCV001199379] Chr2:65018177 [GRCh38]
Chr2:65245311 [GRCh37]
Chr2:2p14
pathogenic
NM_003038.5(SLC1A4):c.240G>C (p.Glu80Asp) single nucleotide variant Microcephaly [RCV001252884] Chr2:64989883 [GRCh38]
Chr2:65217017 [GRCh37]
Chr2:2p14
uncertain significance
NM_003038.5(SLC1A4):c.1281_1284del (p.Val428fs) deletion Spastic tetraplegia, thin corpus callosum, and progressive microcephaly [RCV001334108] Chr2:65018596..65018599 [GRCh38]
Chr2:65245730..65245733 [GRCh37]
Chr2:2p14
pathogenic
NM_003038.5(SLC1A4):c.1277_1278insCC (p.Gly427fs) insertion Spastic tetraplegia, thin corpus callosum, and progressive microcephaly [RCV001334107] Chr2:65018592..65018593 [GRCh38]
Chr2:65245726..65245727 [GRCh37]
Chr2:2p14
pathogenic
NM_003038.5(SLC1A4):c.1365-2A>G single nucleotide variant Spastic tetraplegia, thin corpus callosum, and progressive microcephaly [RCV001334109] Chr2:65020910 [GRCh38]
Chr2:65248044 [GRCh37]
Chr2:2p14
pathogenic
NM_003038.5(SLC1A4):c.312G>C (p.Ser104=) single nucleotide variant not provided [RCV001522381] Chr2:64989955 [GRCh38]
Chr2:65217089 [GRCh37]
Chr2:2p14
benign
NM_032043.3(BRIP1):c.1795-12_1795-10del single nucleotide variant not provided [RCV001715344] Chr2:65004111 [GRCh38]
Chr2:65231245 [GRCh37]
Chr2:2p14
benign
null single nucleotide variant not provided [RCV001666783] Chr2:64989311 [GRCh38]
Chr2:65216445 [GRCh37]
Chr2:2p14
benign
null single nucleotide variant not provided [RCV001695606] Chr2:65016865 [GRCh38]
Chr2:65243999 [GRCh37]
Chr2:2p14
benign
null single nucleotide variant not provided [RCV001615897] Chr2:64989513 [GRCh38]
Chr2:65216647 [GRCh37]
Chr2:2p14
benign
NM_003038.5(SLC1A4):c.1590G>A (p.Ser530=) single nucleotide variant not provided [RCV001522105] Chr2:65021137 [GRCh38]
Chr2:65248271 [GRCh37]
Chr2:2p14
benign
NM_003038.5(SLC1A4):c.1195G>A (p.Val399Ile) single nucleotide variant not provided [RCV001517691] Chr2:65018231 [GRCh38]
Chr2:65245365 [GRCh37]
Chr2:2p14
benign
NM_003895.3(SYNJ1):c.3486A>G (p.Pro1162=) single nucleotide variant not provided [RCV001685341] Chr2:64989514 [GRCh38]
Chr2:65216648 [GRCh37]
Chr2:2p14
benign
NM_003038.5(SLC1A4):c.234C>G (p.Pro78=) single nucleotide variant not provided [RCV001512936] Chr2:64989877 [GRCh38]
Chr2:65217011 [GRCh37]
Chr2:2p14
benign
NM_003038.5(SLC1A4):c.1230-9A>T single nucleotide variant not provided [RCV001455431] Chr2:65018536 [GRCh38]
Chr2:65245670 [GRCh37]
Chr2:2p14
likely benign
NM_003038.5(SLC1A4):c.109G>C (p.Gly37Arg) single nucleotide variant not provided [RCV001516132] Chr2:64989752 [GRCh38]
Chr2:65216886 [GRCh37]
Chr2:2p14
benign

Additional Information

Database Acc Id Source(s)
AGR Gene HGNC:10942 AgrOrtholog
COSMIC SLC1A4 COSMIC
Ensembl Genes ENSG00000115902 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSP00000234256 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSP00000431942 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENST00000234256 ENTREZGENE, UniProtKB/Swiss-Prot
  ENST00000531327 ENTREZGENE, UniProtKB/Swiss-Prot
GTEx ENSG00000115902 GTEx
HGNC ID HGNC:10942 ENTREZGENE
Human Proteome Map SLC1A4 Human Proteome Map
InterPro Na-dicarboxylate_symporter UniProtKB/Swiss-Prot
  Na-dicarboxylate_symporter_CS UniProtKB/Swiss-Prot
  Na:dicarbo_symporter_sf UniProtKB/Swiss-Prot
KEGG Report hsa:6509 UniProtKB/Swiss-Prot
NCBI Gene 6509 ENTREZGENE
OMIM 600229 OMIM
  616657 OMIM
Pfam SDF UniProtKB/Swiss-Prot
PharmGKB PA35829 PharmGKB
PROSITE NA_DICARBOXYL_SYMP_1 UniProtKB/Swiss-Prot
  NA_DICARBOXYL_SYMP_2 UniProtKB/Swiss-Prot
Superfamily-SCOP SSF118215 UniProtKB/Swiss-Prot
UniProt P43007 ENTREZGENE, UniProtKB/Swiss-Prot
UniProt Secondary B7Z3C0 UniProtKB/Swiss-Prot
  D6W5F0 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-02-23 SLC1A4  solute carrier family 1 member 4    solute carrier family 1 (glutamate/neutral amino acid transporter), member 4  Symbol and/or name change 5135510 APPROVED