Human Gene SLC5A7 (uc010ywn.2)
  Description: Homo sapiens solute carrier family 5 (choline transporter), member 7 (SLC5A7), mRNA.
RefSeq Summary (NM_021815): This gene encodes a sodium ion- and chloride ion-dependent high-affinity transporter that mediates choline uptake for acetylcholine synthesis in cholinergic neurons. The protein transports choline from the extracellular space into presynaptic terminals for synthesis into acetylcholine. Increased choline uptake results from increased density of this protein in synaptosomal plasma membranes in response to depolarization of cholinergic terminals. Dysfunction of cholinergic signaling has been implicated in various disorders including depression, attention-deficit disorder, and schizophrenia. An allelic variant of this gene is associated with autosomal dominant distal hereditary motor neuronopathy type VIIA. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2015].
Transcript (Including UTRs)
   Position: hg19 chr2:108,602,995-108,630,443 Size: 27,449 Total Exon Count: 8 Strand: +
Coding Region
   Position: hg19 chr2:108,609,475-108,627,317 Size: 17,843 Coding Exon Count: 6 

Page IndexSequence and LinksUniProtKB CommentsPrimersGenetic AssociationsMalaCards
CTDGene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein Structure
Other SpeciesGO AnnotationsmRNA DescriptionsPathwaysOther NamesGeneReviews
Model InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr2:108,602,995-108,630,443)mRNA (may differ from genome)Protein (467 aa)
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-  Comments and Description Text from UniProtKB
  ID: SC5A7_HUMAN
DESCRIPTION: RecName: Full=High affinity choline transporter 1; AltName: Full=Hemicholinium-3-sensitive choline transporter; Short=CHT; AltName: Full=Solute carrier family 5 member 7;
FUNCTION: Imports choline from the extracellular space to the neuron with high affinity. Choline uptake is the rate-limiting step in acetylcholine synthesis. Sodium ion- and chloride ion- dependent.
SUBCELLULAR LOCATION: Membrane; Multi-pass membrane protein.
TISSUE SPECIFICITY: Expressed in putamen, spinal cord and medulla. Specific for cholinergic neurons.
PTM: Phosphorylated (By similarity).
MISCELLANEOUS: Specifically inhibited by nanomolar concentrations of hemicholinium 3.
SIMILARITY: Belongs to the sodium:solute symporter (SSF) (TC 2.A.21) family.

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): SLC5A7
CDC HuGE Published Literature: SLC5A7
Positive Disease Associations: heart rate , Tunica Media
Related Studies:
  1. heart rate
    Neumann, S. A. et al. 2005, Heart rate variability is associated with polymorphic variation in the choline transporter gene., Psychosomatic medicine. 2005 Mar-Apr;67(2):168-71. [PubMed 15784779]
    These findings show that polymorphic variation in the CHT1 gene is associated significantly with interindividual variability in HRV indices related to parasympathetic (cholinergic) activity.
  2. Tunica Media
    , , . [PubMed 0]

-  MalaCards Disease Associations
  MalaCards Gene Search: SLC5A7
Diseases sorted by gene-association score: myasthenic syndrome, congenital, 20, presynaptic* (1231), neuronopathy, distal hereditary motor, type viia* (1000), distal hereditary motor neuropathy type 7* (350), presynaptic congenital myasthenic syndromes* (350), anal canal adenocarcinoma (15), congenital myasthenic syndrome with episodic apnea (13), anus adenocarcinoma (11), brain germinoma (8), congenital myasthenic syndrome (6), synchronous bilateral breast carcinoma (6), tracheal cancer (6)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 1.35 RPKM in Colon - Sigmoid
Total median expression: 8.68 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -146.90386-0.381 Picture PostScript Text
3' UTR -709.133126-0.227 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR001734 - Na/solute_symporter

Pfam Domains:
PF00474 - Sodium:solute symporter family

ModBase Predicted Comparative 3D Structure on Q9GZV3
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
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 RGD    
 Protein Sequence    
 Alignment    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005307 choline:sodium symporter activity
GO:0015220 choline transmembrane transporter activity
GO:0015293 symporter activity
GO:0022857 transmembrane transporter activity
GO:0033265 choline binding

Biological Process:
GO:0006811 ion transport
GO:0006814 sodium ion transport
GO:0007269 neurotransmitter secretion
GO:0007271 synaptic transmission, cholinergic
GO:0007274 neuromuscular synaptic transmission
GO:0008292 acetylcholine biosynthetic process
GO:0015871 choline transport
GO:0042136 neurotransmitter biosynthetic process
GO:0055085 transmembrane transport

Cellular Component:
GO:0005886 plasma membrane
GO:0005887 integral component of plasma membrane
GO:0016020 membrane
GO:0016021 integral component of membrane
GO:0030054 cell junction
GO:0030424 axon
GO:0030425 dendrite
GO:0031594 neuromuscular junction
GO:0043025 neuronal cell body
GO:0043204 perikaryon
GO:0045202 synapse
GO:0098793 presynapse


-  Descriptions from all associated GenBank mRNAs
  KJ894492 - Synthetic construct Homo sapiens clone ccsbBroadEn_03886 SLC5A7 gene, encodes complete protein.
KJ903031 - Synthetic construct Homo sapiens clone ccsbBroadEn_12425 SLC5A7 gene, encodes complete protein.
KR711539 - Synthetic construct Homo sapiens clone CCSBHm_00025881 SLC5A7 (SLC5A7) mRNA, encodes complete protein.
AK315280 - Homo sapiens cDNA, FLJ96292, highly similar to Homo sapiens solute carrier family 5 (choline transporter), member 7 (SLC5A7), mRNA.
AB084377 - Homo sapiens mRNA for high-affinity choline transporter CHT1, 5'UTR.
AK300801 - Homo sapiens cDNA FLJ51317 complete cds, highly similar to High-affinity choline transporter 1.
AB043997 - Homo sapiens mRNA for high-affinity choline transporter CHT1, complete cds.
BC111525 - Homo sapiens solute carrier family 5 (choline transporter), member 7, mRNA (cDNA clone MGC:126300 IMAGE:40034618), complete cds.
JD323224 - Sequence 304248 from Patent EP1572962.
BC111524 - Homo sapiens solute carrier family 5 (choline transporter), member 7, mRNA (cDNA clone MGC:126299 IMAGE:40034612), complete cds.
JD538026 - Sequence 519050 from Patent EP1572962.
JD298539 - Sequence 279563 from Patent EP1572962.
JD121295 - Sequence 102319 from Patent EP1572962.
AJ401466 - Homo sapiens mRNA for high affinity choline transporter (CHT1 gene).
AF276871 - Homo sapiens high affinity choline transporter (SLC5A7) mRNA, complete cds.
JD204031 - Sequence 185055 from Patent EP1572962.
JD375765 - Sequence 356789 from Patent EP1572962.
JD491150 - Sequence 472174 from Patent EP1572962.
JD038552 - Sequence 19576 from Patent EP1572962.
JD515705 - Sequence 496729 from Patent EP1572962.
JD284395 - Sequence 265419 from Patent EP1572962.
JD197394 - Sequence 178418 from Patent EP1572962.
JD110425 - Sequence 91449 from Patent EP1572962.
JD046633 - Sequence 27657 from Patent EP1572962.
JD512040 - Sequence 493064 from Patent EP1572962.
JD491053 - Sequence 472077 from Patent EP1572962.
JD078369 - Sequence 59393 from Patent EP1572962.
JD337143 - Sequence 318167 from Patent EP1572962.
JD302439 - Sequence 283463 from Patent EP1572962.
JD053343 - Sequence 34367 from Patent EP1572962.
JD298656 - Sequence 279680 from Patent EP1572962.
JD378807 - Sequence 359831 from Patent EP1572962.
JD383233 - Sequence 364257 from Patent EP1572962.
JD516551 - Sequence 497575 from Patent EP1572962.
JD512398 - Sequence 493422 from Patent EP1572962.
JD327745 - Sequence 308769 from Patent EP1572962.
JD345414 - Sequence 326438 from Patent EP1572962.
JD224923 - Sequence 205947 from Patent EP1572962.
JD329569 - Sequence 310593 from Patent EP1572962.
JD263439 - Sequence 244463 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein Q9GZV3 (Reactome details) participates in the following event(s):

R-HSA-429594 SLC5A7 cotransports Cho, Cl-, Na+ from extracellular region to cytosol
R-HSA-264642 Acetylcholine Neurotransmitter Release Cycle
R-HSA-425366 Transport of bile salts and organic acids, metal ions and amine compounds
R-HSA-425428 Amine compound SLC transporters
R-HSA-112310 Neurotransmitter release cycle
R-HSA-425407 SLC-mediated transmembrane transport
R-HSA-112315 Transmission across Chemical Synapses
R-HSA-382551 Transport of small molecules
R-HSA-112316 Neuronal System

-  Other Names for This Gene
  Alternate Gene Symbols: AK300801, CHT1, NM_021815, NP_068587, Q53TF2, Q9GZV3, SC5A7_HUMAN
UCSC ID: uc010ywn.2
RefSeq Accession: NM_021815
Protein: Q9GZV3 (aka SC5A7_HUMAN)

-  GeneReviews for This Gene
  GeneReviews article(s) related to gene SLC5A7:
cms (Congenital Myasthenic Syndromes Overview)

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: AK300801.1
exon count: 8CDS single in 3' UTR: no RNA size: 1914
ORF size: 1404CDS single in intron: no Alignment % ID: 99.95
txCdsPredict score: 2951.00frame shift in genome: no % Coverage: 99.22
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.