Slc10a6 (solute carrier family 10 member 6) - Rat Genome Database

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Gene: Slc10a6 (solute carrier family 10 member 6) Rattus norvegicus
Analyze
Symbol: Slc10a6
Name: solute carrier family 10 member 6
RGD ID: 727800
Description: Enables sodium-dependent organic anion transmembrane transporter activity. Involved in sodium-dependent organic anion transport. Predicted to be located in membrane. Orthologous to human SLC10A6 (solute carrier family 10 member 6); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; amphetamine; bisphenol A.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: Soat; sodium-dependent organic anion transporter; solute carrier family 10 (sodium/bile acid cotransporter family), member 6; solute carrier family 10 (sodium/bile acid cotransporter), member 6
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2146,080,716 - 6,102,037 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl146,080,717 - 6,103,037 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx146,048,649 - 6,069,672 (+)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.0147,348,900 - 7,369,923 (+)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.0146,048,316 - 6,069,396 (+)NCBIRnor_WKY
Rnor_6.0147,618,022 - 7,682,377 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl147,618,022 - 7,682,377 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0147,592,605 - 7,656,400 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4147,270,695 - 7,292,036 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1147,270,694 - 7,292,036 (+)NCBI
Celera146,219,788 - 6,240,844 (+)NCBICelera
Cytogenetic Map14p22NCBI
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
membrane  (IEA)

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. Identification of a sodium-dependent organic anion transporter from rat adrenal gland. Geyer J, etal., Biochem Biophys Res Commun 2004 Apr 2;316(2):300-6.
3. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
4. NCBI rat LocusLink and RefSeq merged data October 15, 2003 NCBI rat LocusLink and RefSeq merged data October 15, 2003
5. GOA pipeline RGD automated data pipeline
6. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions

Genomics

Comparative Map Data
Slc10a6
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2146,080,716 - 6,102,037 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl146,080,717 - 6,103,037 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx146,048,649 - 6,069,672 (+)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.0147,348,900 - 7,369,923 (+)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.0146,048,316 - 6,069,396 (+)NCBIRnor_WKY
Rnor_6.0147,618,022 - 7,682,377 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl147,618,022 - 7,682,377 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0147,592,605 - 7,656,400 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4147,270,695 - 7,292,036 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1147,270,694 - 7,292,036 (+)NCBI
Celera146,219,788 - 6,240,844 (+)NCBICelera
Cytogenetic Map14p22NCBI
SLC10A6
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38486,823,468 - 86,849,384 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl486,823,468 - 86,849,384 (-)EnsemblGRCh38hg38GRCh38
GRCh37487,744,621 - 87,770,537 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36487,963,865 - 87,989,292 (-)NCBINCBI36Build 36hg18NCBI36
Celera485,034,180 - 85,059,864 (-)NCBICelera
Cytogenetic Map4q21.3NCBI
HuRef483,489,562 - 83,515,298 (-)NCBIHuRef
CHM1_1487,721,091 - 87,746,835 (-)NCBICHM1_1
T2T-CHM13v2.0490,152,961 - 90,178,806 (-)NCBIT2T-CHM13v2.0
Slc10a6
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm395103,753,577 - 103,777,269 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl5103,753,577 - 103,777,269 (-)EnsemblGRCm39 Ensembl
GRCm385103,605,711 - 103,629,403 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl5103,605,711 - 103,629,403 (-)EnsemblGRCm38mm10GRCm38
MGSCv375104,034,730 - 104,058,422 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv365103,846,013 - 103,869,705 (-)NCBIMGSCv36mm8
Celera5100,917,865 - 100,940,762 (-)NCBICelera
Cytogenetic Map5E5NCBI
Slc10a6
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554742,951,052 - 2,980,980 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554742,949,773 - 2,982,458 (+)NCBIChiLan1.0ChiLan1.0
SLC10A6
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1489,855,914 - 89,881,523 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl489,855,914 - 89,881,523 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0479,126,941 - 79,152,786 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
SLC10A6
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.13210,334,148 - 10,362,302 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl3210,279,831 - 10,386,298 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha3231,591,788 - 31,619,733 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.03210,357,252 - 10,385,414 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl3210,357,112 - 10,385,275 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.13210,468,259 - 10,496,648 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.03210,295,452 - 10,323,394 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.03229,631,508 - 29,659,716 (+)NCBIUU_Cfam_GSD_1.0
Slc10a6
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405285267,434 - 295,595 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_004936920285,185 - 309,494 (+)EnsemblSpeTri2.0
SpeTri2.0NW_004936920285,185 - 310,395 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SLC10A6
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl8131,997,314 - 132,021,981 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.18131,997,359 - 132,023,739 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.28141,308,101 - 141,336,069 (+)NCBISscrofa10.2Sscrofa10.2susScr3
SLC10A6
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1735,203,853 - 35,230,698 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl735,203,853 - 35,229,199 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366603713,899,317 - 13,925,334 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Slc10a6
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248723,411,622 - 3,453,627 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046248723,411,860 - 3,438,525 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Slc10a6
147 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:105
Count of miRNA genes:95
Interacting mature miRNAs:97
Transcripts:ENSRNOT00000002819
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
2300159Bmd61Bone mineral density QTL 615.30.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)14126541967Rat
2300183Bmd60Bone mineral density QTL 605.70.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)14126541967Rat
619619Rf4Renal disease susceptibility QTL 44.10.002urine total protein amount (VT:0000032)urine protein excretion rate to body weight ratio (CMO:0001099)14132754612Rat
634352Apr6Acute phase response QTL 63.7blood interleukin-6 amount (VT:0008595)plasma interleukin-6 level (CMO:0001927)14141131407Rat
71115Niddm15Non-insulin dependent diabetes mellitus QTL 154.8blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)14121760611030812Rat
70204Niddm20Non-insulin dependent diabetes mellitus QTL 205.10.000008blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)14121760616960180Rat
724541Niddm53Non-insulin dependent diabetes mellitus QTL 530.001blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)1438130749088978Rat
2293089Iddm31Insulin dependent diabetes mellitus QTL 314.7blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)14381307418274691Rat
2293089Iddm31Insulin dependent diabetes mellitus QTL 314.7blood glucose amount (VT:0000188)age at onset/diagnosis of type 1 diabetes mellitus (CMO:0001140)14381307418274691Rat
1300114Srn2Serum renin concentration QTL 23.27blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)14381307421217635Rat
70195Mcs8Mammary carcinoma susceptibility QTL 84.28mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)14381307424531477Rat
1331740Bw26Body weight QTL 263.028body mass (VT:0001259)body weight (CMO:0000012)14381307430767156Rat

Markers in Region
AU047970  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2146,069,916 - 6,070,059 (+)MAPPERmRatBN7.2
Rnor_6.0147,653,017 - 7,653,159NCBIRnor6.0
Rnor_6.0147,640,891 - 7,641,033NCBIRnor6.0
Rnor_5.0147,615,260 - 7,615,402UniSTSRnor5.0
Rnor_5.0147,627,386 - 7,627,528UniSTSRnor5.0
RGSC_v3.4147,234,364 - 7,234,506UniSTSRGSC3.4
Celera146,209,620 - 6,209,762UniSTS
Cytogenetic Map14p22UniSTS


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 2 3 2
Low 3 31 42 26 17 26 8 11 59 29 30 9 8
Below cutoff 12 11 11 11 11 6 7

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000002819   ⟹   ENSRNOP00000002819
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl147,618,022 - 7,682,377 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000088508   ⟹   ENSRNOP00000072386
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl146,080,717 - 6,103,037 (+)Ensembl
Rnor_6.0 Ensembl147,618,022 - 7,682,374 (+)Ensembl
RefSeq Acc Id: NM_198049   ⟹   NP_932166
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2146,080,999 - 6,102,037 (+)NCBI
Rnor_6.0147,618,022 - 7,682,377 (+)NCBI
Rnor_5.0147,592,605 - 7,656,400 (+)NCBI
RGSC_v3.4147,270,695 - 7,292,036 (+)RGD
Celera146,219,788 - 6,240,844 (+)RGD
Sequence:
RefSeq Acc Id: XM_039091662   ⟹   XP_038947590
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2146,080,716 - 6,096,608 (+)NCBI
Protein Sequences
Protein RefSeqs NP_932166 (Get FASTA)   NCBI Sequence Viewer  
  XP_038947590 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein CAE47478 (Get FASTA)   NCBI Sequence Viewer  
  EDL99520 (Get FASTA)   NCBI Sequence Viewer  
  Q70EX6 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_932166   ⟸   NM_198049
- UniProtKB: Q70EX6 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000002819   ⟸   ENSRNOT00000002819
RefSeq Acc Id: ENSRNOP00000072386   ⟸   ENSRNOT00000088508
RefSeq Acc Id: XP_038947590   ⟸   XM_039091662
- Peptide Label: isoform X1

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q70EX6-F1-model_v2 AlphaFold Q70EX6 1-370 view protein structure

Transcriptome

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

Promoters
RGD ID:13699180
Promoter ID:EPDNEW_R9705
Type:initiation region
Name:Slc10a6_1
Description:solute carrier family 10 member 6
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_6.0147,617,968 - 7,618,028EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:727800 AgrOrtholog
BioCyc Gene G2FUF-16483 BioCyc
Ensembl Genes ENSRNOG00000002057 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000072386 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000088508 ENTREZGENE, UniProtKB/Swiss-Prot
Gene3D-CATH 1.20.1530.20 UniProtKB/Swiss-Prot
InterPro BilAc:Na_symport/Acr3 UniProtKB/Swiss-Prot
  Bilac:Na_transpt UniProtKB/Swiss-Prot
  Na+/solute_symporter_sf UniProtKB/Swiss-Prot
  SLC10A6 UniProtKB/Swiss-Prot
KEGG Report rno:289459 UniProtKB/Swiss-Prot
NCBI Gene 289459 ENTREZGENE
PANTHER PTHR10361 UniProtKB/Swiss-Prot
  PTHR10361:SF55 UniProtKB/Swiss-Prot
Pfam SBF UniProtKB/Swiss-Prot
PhenoGen Slc10a6 PhenoGen
UniProt Q70EX6 ENTREZGENE, UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-02-25 Slc10a6  solute carrier family 10 member 6  Slc10a6  solute carrier family 10 (sodium/bile acid cotransporter), member 6  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2013-08-02 Slc10a6  solute carrier family 10 (sodium/bile acid cotransporter), member 6  Slc10a6  solute carrier family 10 (sodium/bile acid cotransporter family), member 6  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-03-07 Slc10a6  solute carrier family 10 (sodium/bile acid cotransporter family), member 6  Soat  sodium-dependent organic anion transporter  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-07-08 Soat  sodium-dependent organic anion transporter      Symbol and Name status set to approved 1299863 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_domains predicted to have nine transmembrane domains 1302411
gene_expression expressed in rat brain, heart, kidney, lung, muscle, spleen, testis, adrenal gland, small intestine, and colon 1302411
gene_function transports estrone-3-sulfate and DHEAS but not taurocholate, estradiol-17-glucuronide, or ouabain 1302411