Slc5a7 (solute carrier family 5 member 7) - Rat Genome Database

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Gene: Slc5a7 (solute carrier family 5 member 7) Rattus norvegicus
Analyze
Symbol: Slc5a7
Name: solute carrier family 5 member 7
RGD ID: 69270
Description: Enables choline transmembrane transporter activity. Involved in acetylcholine biosynthetic process. Located in several cellular components, including cytoplasmic vesicle; perikaryon; and plasma membrane raft. Biomarker of asthma. Human ortholog(s) of this gene implicated in congenital myasthenic syndrome 20; distal hereditary motor neuronopathy type 7A; and mental depression. Orthologous to human SLC5A7 (solute carrier family 5 member 7); PARTICIPATES IN acetylcholine signaling pathway via muscarinic acetylcholine receptor; acetylcholine signaling pathway via nicotinic acetylcholine receptor; INTERACTS WITH (S)-nicotine; 2,3,7,8-Tetrachlorodibenzofuran; 6-propyl-2-thiouracil.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: CHT; Cht1; hemicholinium-3-sensitive choline transporter; high affinity choline transporter 1; solute carrier family 5 (choline transporter) member 7; solute carrier family 5 (choline transporter), member 7; solute carrier family 5 (sodium/choline cotransporter), member 7; solute carrier family 5, member 7
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
mRatBN7.297,595,440 - 7,626,258 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl97,595,444 - 7,626,258 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx910,642,717 - 10,673,490 (-)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.0914,881,214 - 14,911,984 (-)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.0913,632,603 - 13,663,363 (-)NCBIRnor_WKY
Rnor_6.095,294,377 - 5,330,822 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl95,294,381 - 5,330,815 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.094,342,128 - 4,379,724 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.49133,838 - 165,943 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.19133,837 - 165,939 (+)NCBI
Celera93,418,007 - 3,448,801 (-)NCBICelera
Cytogenetic Map9q11NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. Regulation of the high-affinity choline transporter activity and trafficking by its association with cholesterol-rich lipid rafts. Cuddy LK, etal., J Neurochem. 2014 Mar;128(5):725-40. doi: 10.1111/jnc.12490. Epub 2013 Nov 4.
2. 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.
3. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
4. Expression of the high-affinity choline transporter, CHT1, in the neuronal and non-neuronal cholinergic system of human and rat skin. Haberberger RV, etal., J Invest Dermatol 2002 Oct;119(4):943-8.
5. Down-regulation of cholinergic signaling in the habenula induces anhedonia-like behavior. Han S, etal., Sci Rep. 2017 Apr 18;7(1):900. doi: 10.1038/s41598-017-01088-6.
6. Pivotal Advance: Up-regulation of acetylcholine synthesis and paracrine cholinergic signaling in intravascular transplant leukocytes during rejection of rat renal allografts. Hecker A, etal., J Leukoc Biol. 2009 Jul;86(1):13-22. doi: 10.1189/jlb.1107722. Epub 2009 Apr 30.
7. Ultrastructural localization of high-affinity choline transporter in the rat anteroventral thalamus and ventral tegmental area: differences in axon morphology and transporter distribution. Holmstrand EC, etal., J Comp Neurol. 2010 Jun 1;518(11):1908-24. doi: 10.1002/cne.22310.
8. Localisation of the high-affinity choline transporter-1 in the rat skeletal motor unit. Lips KS, etal., Cell Tissue Res 2002 Mar;307(3):275-80. Epub 2002 Feb 14.
9. Down-regulation of the non-neuronal acetylcholine synthesis and release machinery in acute allergic airway inflammation of rat and mouse. Lips KS, etal., Life Sci. 2007 May 30;80(24-25):2263-9. Epub 2007 Jan 23.
10. Expression of acetylcholine receptors by experimental rat renal allografts. Meixner M, etal., Biomed Res Int. 2014;2014:289656. doi: 10.1155/2014/289656. Epub 2014 Jul 9.
11. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
12. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
13. Identification and characterization of the high-affinity choline transporter. Okuda T, etal., Nat Neurosci 2000 Feb;3(2):120-5.
14. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
15. Expression of the high-affinity choline transporter CHT1 in epithelia. Pfeil U, etal., Life Sci. 2003 Mar 28;72(18-19):2087-90.
16. GOA pipeline RGD automated data pipeline
17. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
18. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
19. Comprehensive gene review and curation RGD comprehensive gene curation
20. Constitutive high-affinity choline transporter endocytosis is determined by a carboxyl-terminal tail dileucine motif. Ribeiro FM, etal., J Neurochem. 2005 Jul;94(1):86-96.
21. SEC14-like protein 1 interacts with cholinergic transporters. Ribeiro FM, etal., Neurochem Int. 2007 Jan;50(2):356-64. Epub 2006 Nov 7.
22. Acetyl-CoA the key factor for survival or death of cholinergic neurons in course of neurodegenerative diseases. Szutowicz A, etal., Neurochem Res. 2013 Aug;38(8):1523-42. doi: 10.1007/s11064-013-1060-x. Epub 2013 May 16.
Additional References at PubMed
PMID:11027560   PMID:11068039   PMID:12237312   PMID:12654636   PMID:15173594   PMID:16162937   PMID:17196556   PMID:17548533   PMID:18088276   PMID:19405101   PMID:20510655   PMID:25041985  
PMID:27569547   PMID:27996060  


Genomics

Comparative Map Data
Slc5a7
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.297,595,440 - 7,626,258 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl97,595,444 - 7,626,258 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx910,642,717 - 10,673,490 (-)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.0914,881,214 - 14,911,984 (-)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.0913,632,603 - 13,663,363 (-)NCBIRnor_WKY
Rnor_6.095,294,377 - 5,330,822 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl95,294,381 - 5,330,815 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.094,342,128 - 4,379,724 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.49133,838 - 165,943 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.19133,837 - 165,939 (+)NCBI
Celera93,418,007 - 3,448,801 (-)NCBICelera
Cytogenetic Map9q11NCBI
SLC5A7
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh382107,986,524 - 108,013,994 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl2107,986,523 - 108,013,994 (+)EnsemblGRCh38hg38GRCh38
GRCh372108,602,980 - 108,630,450 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 362107,969,427 - 107,996,876 (+)NCBINCBI36Build 36hg18NCBI36
Build 342108,061,512 - 108,088,957NCBI
Celera2102,911,066 - 102,938,509 (+)NCBICelera
Cytogenetic Map2q12.3NCBI
HuRef2102,202,059 - 102,229,471 (+)NCBIHuRef
CHM1_12108,606,867 - 108,634,740 (+)NCBICHM1_1
T2T-CHM13v2.02108,448,101 - 108,475,570 (+)NCBIT2T-CHM13v2.0
Slc5a7
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391754,580,618 - 54,606,071 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1754,580,618 - 54,606,062 (-)EnsemblGRCm39 Ensembl
GRCm381754,273,590 - 54,299,038 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1754,273,590 - 54,299,034 (-)EnsemblGRCm38mm10GRCm38
MGSCv371754,412,915 - 54,438,359 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361753,749,658 - 53,773,230 (-)NCBIMGSCv36mm8
Celera1757,690,527 - 57,715,838 (-)NCBICelera
Cytogenetic Map17CNCBI
Slc5a7
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495547011,673,465 - 11,697,163 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495547011,673,491 - 11,694,404 (+)NCBIChiLan1.0ChiLan1.0
SLC5A7
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.12A109,018,073 - 109,045,292 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2A109,017,805 - 109,046,860 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v02A93,917,086 - 93,944,308 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
SLC5A7
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11035,879,880 - 35,908,203 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1035,883,245 - 35,908,569 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1035,802,105 - 35,829,230 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.01036,734,146 - 36,761,272 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1036,737,513 - 36,762,849 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.11036,467,972 - 36,495,096 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01036,749,953 - 36,777,069 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01036,938,435 - 36,965,586 (-)NCBIUU_Cfam_GSD_1.0
Slc5a7
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440629293,916,550 - 93,940,811 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049367291,511,836 - 1,536,200 (+)EnsemblSpeTri2.0
SpeTri2.0NW_0049367291,511,648 - 1,534,042 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SLC5A7
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl347,996,335 - 48,022,379 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1347,994,116 - 48,020,744 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2350,164,607 - 50,190,998 (-)NCBISscrofa10.2Sscrofa10.2susScr3
SLC5A7
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11411,346,281 - 11,373,754 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1411,347,861 - 11,370,297 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_023666041179,149,064 - 179,175,860 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Slc5a7
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462474911,347,609 - 11,371,330 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462474911,347,602 - 11,371,113 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Slc5a7
158 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:916
Count of miRNA genes:307
Interacting mature miRNAs:400
Transcripts:ENSRNOT00000014548
Prediction methods:Microtar, Miranda
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
10054141Gmadr4Adrenal mass QTL 42.450.0074adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)9114209783Rat
70226Eae4Experimental allergic encephalomyelitis QTL 4nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)9125661317Rat
9589055Scfw5Subcutaneous fat weight QTL 55.550.001subcutaneous adipose mass (VT:1000472)abdominal subcutaneous fat pad weight (CMO:0002069)9137999212Rat
7411592Foco8Food consumption QTL 87.40.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)9137999212Rat
9589158Gluco65Glucose level QTL 656.820.001blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)9137999212Rat
1300124Cm4Cardiac mass QTL 43.55heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)9140594091Rat
1298088Edpm11Estrogen-dependent pituitary mass QTL 112.5pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)9143718459Rat
1641911Alcrsp13Alcohol response QTL 13response to alcohol trait (VT:0010489)brain neurotensin receptor 1 density (CMO:0002068)9143718459Rat
10054125Srcrt7Stress Responsive Cort QTL 73.330.0011blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)9187073594Rat
1331757Cdexp1CD45RC expression in CD8 T cells QTL 14.3CD8-positive T cell quantity (VT:0008077)blood CD45RC(high) CD8 T cell count to CD45RC(low) CD8 T cell count ratio (CMO:0001990)9102453767509080Rat
1354650Despr5Despair related QTL 54.010.0017locomotor behavior trait (VT:0001392)amount of time spent in voluntary immobility (CMO:0001043)9125408446254084Rat
2303559Gluco54Glucose level QTL 542blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)9125408446254084Rat
1578675Bss17Bone structure and strength QTL 173.8femur morphology trait (VT:0000559)femoral neck cortical cross-sectional area (CMO:0001702)9336865213533896Rat
61425Cia15Collagen induced arthritis QTL 154.6joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)9510982642921101Rat
631211Bw4Body weight QTL45.31retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)9510982650109826Rat
11353947Bp392Blood pressure QTL 392arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)9728325252283252Rat

Markers in Region
D9Got10  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.297,608,362 - 7,608,534 (+)MAPPERmRatBN7.2
Rnor_6.095,307,300 - 5,307,471NCBIRnor6.0
Rnor_5.094,356,015 - 4,356,186UniSTSRnor5.0
RGSC_v3.49152,848 - 153,020RGDRGSC3.4
RGSC_v3.49152,849 - 153,020UniSTSRGSC3.4
RGSC_v3.19152,848 - 153,020RGD
Celera93,430,930 - 3,431,101UniSTS
Cytogenetic Map9q11UniSTS


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 nervous system renal system reproductive system respiratory system
High
Medium 4
Low 3 6 70 10 23 4
Below cutoff 23 9 2 4 2 8 16 4

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000014548   ⟹   ENSRNOP00000014548
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl97,595,444 - 7,626,258 (-)Ensembl
Rnor_6.0 Ensembl95,294,381 - 5,330,815 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000078055   ⟹   ENSRNOP00000068755
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl95,297,307 - 5,329,305 (-)Ensembl
RefSeq Acc Id: NM_053521   ⟹   NP_445973
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.297,595,440 - 7,626,258 (-)NCBI
Rnor_6.095,294,377 - 5,330,822 (-)NCBI
Rnor_5.094,342,128 - 4,379,724 (-)NCBI
RGSC_v3.49133,838 - 165,943 (+)RGD
Celera93,418,007 - 3,448,801 (-)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_445973 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein BAA90484 (Get FASTA)   NCBI Sequence Viewer  
  EDL83229 (Get FASTA)   NCBI Sequence Viewer  
  Q9JMD7 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_445973   ⟸   NM_053521
- UniProtKB: G3V7G1 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000014548   ⟸   ENSRNOT00000014548
RefSeq Acc Id: ENSRNOP00000068755   ⟸   ENSRNOT00000078055

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q9JMD7-F1-model_v2 AlphaFold Q9JMD7 1-580 view protein structure

Transcriptome

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


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:69270 AgrOrtholog
BioCyc Gene G2FUF-28381 BioCyc
Ensembl Genes ENSRNOG00000010597 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000014548 ENTREZGENE
  ENSRNOP00000014548.4 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000014548 ENTREZGENE
  ENSRNOT00000014548.6 UniProtKB/TrEMBL
Gene3D-CATH 1.20.1730.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro Na/Glc_symporter_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Na/solute_symporter UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:85426 UniProtKB/Swiss-Prot
NCBI Gene 85426 ENTREZGENE
Pfam SSF UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Slc5a7 PhenoGen
PROSITE NA_SOLUT_SYMP_3 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt G3V7G1 ENTREZGENE, UniProtKB/TrEMBL
  Q9JMD7 ENTREZGENE, UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-03-09 Slc5a7  solute carrier family 5 member 7  Slc5a7  solute carrier family 5 (sodium/choline cotransporter), member 7  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2013-08-02 Slc5a7  solute carrier family 5 (sodium/choline cotransporter), member 7  Slc5a7  solute carrier family 5 (choline transporter), member 7  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2004-09-10 Slc5a7  solute carrier family 5 (choline transporter), member 7    solute carrier family 5, member 7   Name updated 1299863 APPROVED
2002-06-10 Slc5a7  solute carrier family 5, member 7       Name updated 70584 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_expression expressed in the nerve fibres in the rat skin 634187
gene_process involved in the skin's neuronal and non-neuronal cholinergic system 634187
gene_regulation regulation is Na+-dependent and is blocked by hemicholinium-3 634187