Slc46a2 (solute carrier family 46, member 2) - Rat Genome Database

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Gene: Slc46a2 (solute carrier family 46, member 2) Mus musculus
Analyze
Symbol: Slc46a2
Name: solute carrier family 46, member 2
RGD ID: 1321414
MGI Page MGI
Description: Predicted to enable cyclic-GMP-AMP transmembrane transporter activity. Acts upstream of or within several processes, including T cell homeostasis; negative regulation of T cell apoptotic process; and thymus development. Located in cell surface. Is expressed in several structures, including foregut gland; hemolymphoid system; and skin. Orthologous to human SLC46A2 (solute carrier family 46 member 2).
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: 5430429N04Rik; Ly11; Ly110; putative thymic stromal co-transporter TSCOT; solute carrier family 46 member 2; thymic stromal cotransporter homolog; thymic stromal cotransporter protein; Tsc; Tscot; TSO-1C; TSO-1C12
RGD Orthologs
Human
Rat
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCm39 - Mouse Genome Assembly GRCm39
Position:
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39459,905,899 - 59,915,056 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl459,905,126 - 59,915,056 (-)EnsemblGRCm39 Ensembl
GRCm38459,905,899 - 59,915,056 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl459,905,126 - 59,915,056 (-)EnsemblGRCm38mm10GRCm38
MGSCv37459,918,771 - 59,927,928 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36459,999,180 - 60,009,110 (-)NCBIMGSCv36mm8
Celera459,822,589 - 59,831,770 (-)NCBICelera
Cytogenetic Map4B3NCBI
cM Map432.81NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

Phenotype Annotations     Click to see Annotation Detail View

Mammalian Phenotype
References

References - curated
# Reference Title Reference Citation
1. Functional annotation of a full-length mouse cDNA collection. Kawai J, etal., Nature. 2001 Feb 8;409(6821):685-90.
2. MGDs mouse GO annotations MGD data from the GO Consortium
3. Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs. Okazaki Y, etal., Nature. 2002 Dec 5;420(6915):563-73.
4. Mouse MP Annotation Import Pipeline RGD automated import pipeline
5. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
6. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:10349636   PMID:10706709   PMID:10978518   PMID:11042159   PMID:11076861   PMID:12477932   PMID:14681479   PMID:16141072   PMID:16141073   PMID:18684012   PMID:21267068   PMID:21873635  
PMID:23178972   PMID:26013383   PMID:37116499  


Genomics

Comparative Map Data
Slc46a2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39459,905,899 - 59,915,056 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl459,905,126 - 59,915,056 (-)EnsemblGRCm39 Ensembl
GRCm38459,905,899 - 59,915,056 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl459,905,126 - 59,915,056 (-)EnsemblGRCm38mm10GRCm38
MGSCv37459,918,771 - 59,927,928 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36459,999,180 - 60,009,110 (-)NCBIMGSCv36mm8
Celera459,822,589 - 59,831,770 (-)NCBICelera
Cytogenetic Map4B3NCBI
cM Map432.81NCBI
SLC46A2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh389112,878,920 - 112,890,876 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl9112,878,920 - 112,890,876 (-)EnsemblGRCh38hg38GRCh38
GRCh379115,641,200 - 115,653,156 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 369114,681,021 - 114,692,866 (-)NCBINCBI36Build 36hg18NCBI36
Build 349112,720,755 - 112,732,600NCBI
Celera986,314,093 - 86,326,088 (+)NCBICelera
Cytogenetic Map9q32NCBI
HuRef985,239,036 - 85,251,012 (-)NCBIHuRef
CHM1_19115,788,488 - 115,800,474 (-)NCBICHM1_1
T2T-CHM13v2.09125,050,362 - 125,072,489 (-)NCBIT2T-CHM13v2.0
Slc46a2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8579,594,003 - 79,603,074 (-)NCBIGRCr8
mRatBN7.2574,800,226 - 74,808,128 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl574,800,226 - 74,808,128 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx576,700,364 - 76,708,304 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0578,521,999 - 78,529,935 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0578,494,162 - 78,502,102 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0577,165,463 - 77,174,177 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl577,165,598 - 77,173,502 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0581,300,022 - 81,307,920 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4578,044,714 - 78,052,612 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1578,043,262 - 78,057,672 (-)NCBI
Celera573,609,789 - 73,617,699 (-)NCBICelera
Cytogenetic Map5q24NCBI
Slc46a2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495541914,547,103 - 14,557,531 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495541914,547,393 - 14,557,447 (+)NCBIChiLan1.0ChiLan1.0
SLC46A2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21126,549,345 - 26,561,525 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1926,551,704 - 26,563,884 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0984,001,056 - 84,013,231 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.19112,154,001 - 112,165,906 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl9112,154,001 - 112,165,906 (-)Ensemblpanpan1.1panPan2
SLC46A2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11167,297,596 - 67,305,893 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1167,297,597 - 67,305,893 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1165,704,288 - 65,712,588 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.01168,423,487 - 68,431,777 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1168,423,488 - 68,431,777 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.11166,939,761 - 66,948,049 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01166,962,952 - 66,971,235 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01167,707,572 - 67,715,860 (-)NCBIUU_Cfam_GSD_1.0
Slc46a2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024404947182,586,765 - 182,596,316 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_004936559670,231 - 679,766 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_004936559670,239 - 674,061 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SLC46A2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1253,559,546 - 253,570,113 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11253,559,545 - 253,571,015 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21284,368,646 - 284,379,213 (-)NCBISscrofa10.2Sscrofa10.2susScr3
SLC46A2
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11226,631,295 - 26,646,112 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1226,633,493 - 26,646,038 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366603516,145,372 - 16,158,151 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Slc46a2
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462476022,124,321 - 22,134,906 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462476022,124,321 - 22,134,601 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Slc46a2
505 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:400
Count of miRNA genes:321
Interacting mature miRNAs:349
Transcripts:ENSMUST00000030081
Prediction methods: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 (GRCm39)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1301586Stheal3_msoft tissue heal 3 (mouse)Not determined42865844262658566Mouse
11532714Sluc43_msusceptibility to lung cancer 43 (mouse)446642108123127211Mouse
39128211Lwq22_mliver weight QTL 22 (mouse)41789261688982216Mouse
25314308Mlh1fc1_mMLH1 foci count 1 (mouse)44850000076918237Mouse
26884434Zlq1_mzygomatic length QTL 1, 5 week (mouse)453700000103257197Mouse
1301786Bpq3_mblood pressure QTL 3 (mouse)Not determined44240224076402381Mouse
10412178Habiir2_mhyperoxic acute lung injury imprinted region 2 (mouse)Not determined43945212663283678Mouse
1300574Im2_mimmunoregulatory 2 (mouse)Not determined42807768262077816Mouse
1301213Lgth3_mbody length 3 (mouse)Not determined45010026284100408Mouse
26884437Sklq13_mskull length QTL 13, 16 week (mouse)457700000155684457Mouse
4142318Lyr2_mlymphoma resistance 2 (mouse)Not determined1401045763283678Mouse
1357895Ctrcts_mcataract severity (mouse)Not determined445709925138342753Mouse
1357453Kidq4_mkidney weight QTL 4 (mouse)Not determined41789261688982216Mouse
13207572Spir2_mStreptococcus pneumoniae infection resistance 2 (mouse)45068279588510637Mouse
4142047Mvwf3_mmodifier of von Willebrand factor 3 (mouse)Not determined14010457117072206Mouse
11567249Elorr3_methanol induced loss of righting response 3 (mouse)43722677156268235Mouse
1357877Synch1_msynechia 1 (mouse)Not determined42870992562710107Mouse
10449022Aanq1_maristolochic acid nephrotoxicity QTL 1 (mouse)44660382680603826Mouse
1300977Mopkd1_mmodifier of polycystic kidney disease progression 1 (mouse)Not determined43655083970550967Mouse
27095934Ulnl2_mulna length 2, 5 week (mouse)45770000094788237Mouse
10043964Obq26_mobesity QTL 26 (mouse)Not determined45904725193047251Mouse
1301941Mmtg1_mmodifier of mammary tumor growth 1 (mouse)Not determined44565844283099157Mouse
13524841Hbasrq1_mhabituation of the acoustic startle response QTL 1 (mouse)45447158988471589Mouse
4141911W6q15_mweight 6 weeks QTL 15 (mouse)Not determined1789261688982216Mouse
13524838Hbasrq1a_mhabituation of the acoustic startle response QTL 1a (mouse)45447158988471589Mouse
12879977Bod2_mbone length and organs 2 (mouse)44628353180283678Mouse
10043880Adip23_madiposity 23 (mouse)Not determined44628353180283678Mouse
1301792Hdlq10_mHDL QTL 10 (mouse)Not determined43585970769859853Mouse
1558948Ath8_matherosclerosis 8 (mouse)Not determined445658442105156995Mouse
4141900Skts-fp1_mskin tumor susceptibility in FVB and PWK 1 (mouse)Not determined453550839124055180Mouse
1301990Arvm1_mautoimmune renal vasculitis 1 (mouse)Not determined42933264663332776Mouse
1300966Pabr2_mplasma apolipoprotein B (human) regulator 2 (mouse)Not determined446332646105801860Mouse
1302116Bbaa1_mB.burgdorferi-associated arthritis 1 (mouse)Not determined43825093072251078Mouse
1301995Lprm1_mlymphoproliferation modifier 1 (mouse)Not determined45010026284100408Mouse
1301033Abbp2_mA/J and C57BL/6 blood pressure 2 (mouse)Not determined45355083993763305Mouse
26884449Sklq2_mskull length QTL 2, 5 week (mouse)436700000128993793Mouse
27226724Tibw2_mtibia width 2, proximal, 10 week (mouse)443000000108357197Mouse
27095905Scvln3_msacral vertebrae length 2, 5 week (mouse)455600000128993793Mouse
11532688Mh_mmodifier of hemostasis (mouse)44830477582304775Mouse

Markers in Region
Slc46a2  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm38459,906,107 - 59,906,340UniSTSGRCm38
MGSCv37459,918,979 - 59,919,212UniSTSGRCm37
Celera459,822,797 - 59,823,030UniSTS
Cytogenetic Map4B3UniSTS
cM Map432.0UniSTS
Slc46a2  
Mouse AssemblyChrPosition (strand)SourceJBrowse
Cytogenetic Map4B3UniSTS


Expression

RNA-SEQ Expression


Sequence


Ensembl Acc Id: ENSMUST00000030081   ⟹   ENSMUSP00000030081
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl459,905,126 - 59,915,056 (-)Ensembl
GRCm38.p6 Ensembl459,905,126 - 59,915,056 (-)Ensembl
RefSeq Acc Id: NM_021053   ⟹   NP_066395
RefSeq Status: VALIDATED
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39459,905,899 - 59,915,056 (-)NCBI
GRCm38459,905,899 - 59,915,056 (-)ENTREZGENE
MGSCv37459,918,771 - 59,927,928 (-)RGD
Celera459,822,589 - 59,831,770 (-)RGD
cM Map4 ENTREZGENE
Sequence:
RefSeq Acc Id: NP_066395   ⟸   NM_021053
- UniProtKB: Q9D3J2 (UniProtKB/Swiss-Prot),   A2ANT4 (UniProtKB/Swiss-Prot),   Q9JLQ3 (UniProtKB/Swiss-Prot),   Q8CA03 (UniProtKB/Swiss-Prot),   A9R9W2 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSMUSP00000030081   ⟸   ENSMUST00000030081

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q8CA03-F1-model_v2 AlphaFold Q8CA03 1-479 view protein structure

Promoters
RGD ID:6883548
Promoter ID:EPDNEW_M5225
Type:multiple initiation site
Name:Slc46a2_1
Description:Mus musculus solute carrier family 46, member 2 , mRNA.
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm38459,915,056 - 59,915,116EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene MGI:1353616 AgrOrtholog
Ensembl Genes ENSMUSG00000028386 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSMUST00000030081 ENTREZGENE
  ENSMUST00000030081.2 UniProtKB/Swiss-Prot
Gene3D-CATH 1.20.1250.20 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro MFS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  MFS_trans_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Tet-R_TetA/multi-R_MdtG UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report mmu:30936 UniProtKB/Swiss-Prot
MGD MGI:1353616 ENTREZGENE
NCBI Gene 30936 ENTREZGENE
PANTHER THYMIC STROMAL COTRANSPORTER HOMOLOG UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ZGC:174356 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam MFS_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Slc46a2 PhenoGen
PRINTS TCRTETA UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF103473 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A2ANT4 ENTREZGENE
  A9R9W2 ENTREZGENE, UniProtKB/TrEMBL
  Q8CA03 ENTREZGENE
  Q9D3J2 ENTREZGENE
  Q9JLQ3 ENTREZGENE
  TSCOT_MOUSE UniProtKB/Swiss-Prot
UniProt Secondary A2ANT4 UniProtKB/Swiss-Prot
  Q9D3J2 UniProtKB/Swiss-Prot
  Q9JLQ3 UniProtKB/Swiss-Prot