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

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Gene: SLC1A4 (solute carrier family 1 member 4) Canis lupus familiaris
Analyze
Symbol: SLC1A4
Name: solute carrier family 1 member 4
RGD ID: 12057403
Description: ENCODES a protein that exhibits L-cystine transmembrane transporter activity (ortholog); L-serine transmembrane transporter activity (ortholog); INVOLVED IN L-cystine transport (ortholog); L-serine transport (ortholog); serine import across plasma membrane (ortholog); PARTICIPATES IN argininosuccinic aciduria pathway; carbamoyl phosphate synthetase I deficiency pathway; citrullinemia pathway; ASSOCIATED WITH autism spectrum disorder (ortholog); genetic disease (ortholog); microcephaly (ortholog); FOUND IN dendrite (ortholog); neuronal cell body (ortholog); plasma membrane (ortholog)
Type: protein-coding
RefSeq Status: MODEL
Previously known as: alanine/serine/cysteine/threonine transporter 1; ASCT1; neutral amino acid transporter A
RGD Orthologs
Human
Mouse
Rat
Chinchilla
Bonobo
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: CanFam3.1 - Dog CanFam3.1 Assembly
Position:
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 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.01065,493,157 - 65,518,318 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1065,492,613 - 65,518,315 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.11065,172,083 - 65,197,216 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01065,480,918 - 65,503,851 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01065,774,013 - 65,799,174 (+)NCBIUU_Cfam_GSD_1.0
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

Cellular Component

References
Additional References at PubMed
PMID:22131312   PMID:22301074   PMID:30032202  


Genomics

Comparative Map Data
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 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.01065,493,157 - 65,518,318 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1065,492,613 - 65,518,315 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.11065,172,083 - 65,197,216 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01065,480,918 - 65,503,851 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01065,774,013 - 65,799,174 (+)NCBIUU_Cfam_GSD_1.0
SLC1A4
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38264,988,479 - 65,023,865 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl264,988,477 - 65,023,865 (+)EnsemblGRCh38hg38GRCh38
GRCh37265,215,613 - 65,250,999 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36265,070,098 - 65,104,503 (+)NCBINCBI36Build 36hg18NCBI36
Build 34265,128,244 - 65,162,648NCBI
Celera265,061,957 - 65,097,385 (+)NCBICelera
Cytogenetic Map2p14NCBI
HuRef264,949,345 - 64,984,802 (+)NCBIHuRef
CHM1_1265,146,566 - 65,181,989 (+)NCBICHM1_1
T2T-CHM13v2.0264,998,100 - 65,033,490 (+)NCBIT2T-CHM13v2.0
Slc1a4
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391120,252,180 - 20,282,713 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1120,252,180 - 20,282,713 (-)EnsemblGRCm39 Ensembl
GRCm381120,302,180 - 20,332,713 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1120,302,180 - 20,332,713 (-)EnsemblGRCm38mm10GRCm38
MGSCv371120,202,183 - 20,232,716 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361120,202,208 - 20,232,674 (-)NCBIMGSCv36mm8
Celera1122,451,521 - 22,482,559 (-)NCBICelera
Cytogenetic Map11A3.1NCBI
cM Map1112.97NCBI
Slc1a4
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81498,718,646 - 98,761,672 (-)NCBIGRCr8
mRatBN7.21494,530,801 - 94,560,190 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1494,529,084 - 94,560,418 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1498,877,394 - 98,907,056 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.014100,117,664 - 100,147,323 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01496,585,031 - 96,614,695 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
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 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
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
NHGRI_mPanPan1-v21261,377,645 - 61,412,341 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan12A61,380,650 - 61,416,291 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v02A65,051,025 - 65,086,917 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.12A66,177,835 - 66,212,249 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2A66,176,925 - 66,209,615 (+)Ensemblpanpan1.1panPan2
Slc1a4
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440629218,780,757 - 18,810,279 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049364919,760,952 - 9,790,536 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049364919,761,002 - 9,790,535 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SLC1A4
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl376,938,107 - 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 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1441,999,064 - 42,032,288 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604569,848,255 - 69,881,833 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Slc1a4
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247628,532,063 - 8,558,994 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046247628,532,550 - 8,558,912 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in SLC1A4
265 total Variants

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 reproductive system respiratory system adipose tissue
High
Medium 11 1 1 3 12 4 2
Low 5 5 11 5 6 5 3 6 8 6 4
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSCAFT00000005119   ⟹   ENSCAFP00000004745
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.1 Ensembl1064,483,060 - 64,505,747 (+)Ensembl
RefSeq Acc Id: ENSCAFT00000067773   ⟹   ENSCAFP00000058073
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.1 Ensembl1064,496,275 - 64,505,747 (+)Ensembl
RefSeq Acc Id: ENSCAFT00845036942   ⟹   ENSCAFP00845028925
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
ROS_Cfam_1.0 Ensembl1065,492,613 - 65,518,315 (+)Ensembl
RefSeq Acc Id: ENSCAFT00845037032   ⟹   ENSCAFP00845028998
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
ROS_Cfam_1.0 Ensembl1065,506,308 - 65,518,315 (+)Ensembl
RefSeq Acc Id: XM_038489460   ⟹   XP_038345388
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UMICH_Zoey_3.11065,172,083 - 65,197,216 (+)NCBI
RefSeq Acc Id: XM_038551449   ⟹   XP_038407377
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UU_Cfam_GSD_1.01065,774,013 - 65,799,174 (+)NCBI
RefSeq Acc Id: XM_038615383   ⟹   XP_038471311
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UNSW_CanFamBas_1.01065,480,918 - 65,503,851 (+)NCBI
RefSeq Acc Id: XM_038680770   ⟹   XP_038536698
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
ROS_Cfam_1.01065,493,157 - 65,518,318 (+)NCBI
RefSeq Acc Id: XM_538511   ⟹   XP_538511
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.11064,482,840 - 64,508,288 (+)NCBI
Dog10K_Boxer_Tasha1064,369,739 - 64,394,932 (+)NCBI
Sequence:
Reference Protein Sequences
RefSeq Acc Id: XP_538511   ⟸   XM_538511
- UniProtKB: A0A8C0Q4G4 (UniProtKB/TrEMBL),   A0A8P0S969 (UniProtKB/TrEMBL),   A0A8C0LN80 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSCAFP00000058073   ⟸   ENSCAFT00000067773
RefSeq Acc Id: ENSCAFP00000004745   ⟸   ENSCAFT00000005119
RefSeq Acc Id: XP_038345388   ⟸   XM_038489460
RefSeq Acc Id: XP_038471311   ⟸   XM_038615383
RefSeq Acc Id: XP_038536698   ⟸   XM_038680770
- UniProtKB: A0A8I3S220 (UniProtKB/TrEMBL),   A0A8C0LN80 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038407377   ⟸   XM_038551449
- UniProtKB: A0A8C0LN80 (UniProtKB/TrEMBL),   A0A8C0Q4G4 (UniProtKB/TrEMBL),   A0A8P0S969 (UniProtKB/TrEMBL)
RefSeq Acc Id: ENSCAFP00845028998   ⟸   ENSCAFT00845037032
RefSeq Acc Id: ENSCAFP00845028925   ⟸   ENSCAFT00845036942

Promoters
RGD ID:13685087
Promoter ID:EPDNEW_C3154
Type:single 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_C3155  
Experiment Methods:Single-end sequencing.
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.11064,482,459 - 64,482,519EPDNEW
RGD ID:13685089
Promoter ID:EPDNEW_C3155
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_C3154  
Experiment Methods:Single-end sequencing.
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.11064,482,869 - 64,482,929EPDNEW

Additional Information

Database Acc Id Source(s)
Ensembl Genes ENSCAFG00000003180 Ensembl, UniProtKB/TrEMBL
  ENSCAFG00030016687 UniProtKB/TrEMBL
  ENSCAFG00040005221 UniProtKB/TrEMBL
  ENSCAFG00845020925 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSCAFT00000005119.5 UniProtKB/TrEMBL
  ENSCAFT00000101641.1 UniProtKB/TrEMBL
  ENSCAFT00030030929.1 UniProtKB/TrEMBL
  ENSCAFT00040009780.1 UniProtKB/TrEMBL
  ENSCAFT00040009826.1 UniProtKB/TrEMBL
  ENSCAFT00845036942 ENTREZGENE
  ENSCAFT00845036942.1 UniProtKB/TrEMBL
  ENSCAFT00845037032.1 UniProtKB/TrEMBL
Gene3D-CATH 1.10.3860.10 UniProtKB/TrEMBL
InterPro Na-dicarboxylate_symporter UniProtKB/TrEMBL
  Na-dicarboxylate_symporter_CS UniProtKB/TrEMBL
  Na:dicarbo_symporter_sf UniProtKB/TrEMBL
KEGG Report cfa:481391 UniProtKB/TrEMBL
NCBI Gene SLC1A4 ENTREZGENE
PANTHER NEUTRAL AMINO ACID TRANSPORTER A UniProtKB/TrEMBL
  SODIUM/DICARBOXYLATE SYMPORTER-RELATED UniProtKB/TrEMBL
Pfam SDF UniProtKB/TrEMBL
PRINTS EDTRNSPORT UniProtKB/TrEMBL
PROSITE NA_DICARBOXYL_SYMP_1 UniProtKB/TrEMBL
  NA_DICARBOXYL_SYMP_2 UniProtKB/TrEMBL
Superfamily-SCOP SSF118215 UniProtKB/TrEMBL
UniProt A0A8C0LN80 ENTREZGENE
  A0A8C0Q4G4 ENTREZGENE, UniProtKB/TrEMBL
  A0A8C0Q4Q4_CANLF UniProtKB/TrEMBL
  A0A8I3S220 ENTREZGENE, UniProtKB/TrEMBL
  A0A8I3S231_CANLF UniProtKB/TrEMBL
  A0A8P0S969 ENTREZGENE
UniProt Secondary A0A8P0S969 UniProtKB/TrEMBL
VGNC ID VGNC:46264 ENTREZGENE