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SLC5A7 solute carrier family 5 member 7 [ Homo sapiens (human) ]

Gene ID: 60482, updated on 3-Jun-2018
Official Symbol
SLC5A7provided by HGNC
Official Full Name
solute carrier family 5 member 7provided by HGNC
Primary source
HGNC:HGNC:14025
See related
Ensembl:ENSG00000115665 MIM:608761; Vega:OTTHUMG00000130959
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
CHT; CHT1; CMS20; HMN7A
Summary
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]
Expression
Low expression observed in reference dataset See more
Orthologs
See SLC5A7 in Genome Data Viewer
Location:
2q12.3
Exon count:
10
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 2 NC_000002.12 (107986514..108014497)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (108602979..108630663)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene serine/arginine-rich splicing factor 3 pseudogene Neighboring gene 2q12.3 proximal recombination region Neighboring gene long intergenic non-protein coding RNA 1593 Neighboring gene actin family pseudogene 1

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Jun 15 11:32:44 2016

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

  • Acetylcholine Neurotransmitter Release Cycle, organism-specific biosystem (from REACTOME)
    Acetylcholine Neurotransmitter Release Cycle, organism-specific biosystemAcetylcholine neurotransmitter release cycle involves syntheis of choline, loading of clathrin scultpted synaptic vesicles, docking and priming of the acetyl choline loaded synaptic vesicles and then...
  • Choline metabolism in cancer, organism-specific biosystem (from KEGG)
    Choline metabolism in cancer, organism-specific biosystemAbnormal choline metabolism is emerging as a metabolic hallmark that is associated with oncogenesis and tumour progression. Following transformation, oncogenic signalling via pathways such as the RAS...
  • Choline metabolism in cancer, conserved biosystem (from KEGG)
    Choline metabolism in cancer, conserved biosystemAbnormal choline metabolism is emerging as a metabolic hallmark that is associated with oncogenesis and tumour progression. Following transformation, oncogenic signalling via pathways such as the RAS...
  • Cholinergic synapse, organism-specific biosystem (from KEGG)
    Cholinergic synapse, organism-specific biosystemAcetylcholine (ACh) is a neurotransmitter widely distributed in the central (and also peripheral, autonomic and enteric) nervous system (CNS). In the CNS, ACh facilitates many functions, such as lear...
  • Monoamine Transport, organism-specific biosystem (from WikiPathways)
    Monoamine Transport, organism-specific biosystem
    Monoamine Transport
  • NRF2 pathway, organism-specific biosystem (from WikiPathways)
    NRF2 pathway, organism-specific biosystemNRF2 is part of a group of transcription factors called nuclear receptors. It is activated under oxidative stress conditions and subsequently activates several antioxidative genes and proteins.
  • Neuronal System, organism-specific biosystem (from REACTOME)
    Neuronal System, organism-specific biosystemThe human brain contains at least 100 billion neurons, each with the ability to influence many other cells. Clearly, highly sophisticated and efficient mechanisms are needed to enable communication a...
  • Neurotransmitter Release Cycle, organism-specific biosystem (from REACTOME)
    Neurotransmitter Release Cycle, organism-specific biosystemNeurotransmitter is stored in the synaptic vesicle in the pre-synaptic terminal prior to its release in the synaptic cleft upon depolarization of the pre-synaptic membrane. The release of the neurotr...
  • SLC-mediated transmembrane transport, organism-specific biosystem (from REACTOME)
    SLC-mediated transmembrane transport, organism-specific biosystemProteins with transporting functions can be roughly classified into 3 categories: ATP-powered pumps, ion channels, and transporters. Pumps utilize the energy released by ATP hydrolysis to power the m...
  • Transmembrane transport of small molecules, organism-specific biosystem (from REACTOME)
    Transmembrane transport of small molecules, organism-specific biosystem
    Transmembrane transport of small molecules
  • Transmission across Chemical Synapses, organism-specific biosystem (from REACTOME)
    Transmission across Chemical Synapses, organism-specific biosystemChemical synapses are specialized junctions that are used for communication between neurons, neurons and muscle or gland cells. The synapse involves a pre-synaptic neuron and a post-synaptic neuron,...
  • Transport of glucose and other sugars, bile salts and organic acids, metal ions and amine compounds, organism-specific biosystem (from REACTOME)
    Transport of glucose and other sugars, bile salts and organic acids, metal ions and amine compounds, organism-specific biosystemHexoses like glucose, galactose and fructose serve as basic fuel molecules for eukaryotic cells. Indeed, glucose is the main energy source for mammalian cells. These sugars are unable to diffuse acro...
Products Interactant Other Gene Complex Source Pubs Description

Markers

Homology

Clone Names

  • MGC126299, MGC126300

Gene Ontology Provided by GOA

Function Evidence Code Pubs
choline binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
choline transmembrane transporter activity IMP
Inferred from Mutant Phenotype
more info
PubMed 
choline transmembrane transporter activity TAS
Traceable Author Statement
more info
 
choline:sodium symporter activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
choline:sodium symporter activity IMP
Inferred from Mutant Phenotype
more info
PubMed 
Process Evidence Code Pubs
acetylcholine biosynthetic process IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
acetylcholine biosynthetic process IMP
Inferred from Mutant Phenotype
more info
PubMed 
choline transport IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
choline transport IEA
Inferred from Electronic Annotation
more info
 
neuromuscular synaptic transmission IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
neurotransmitter secretion TAS
Traceable Author Statement
more info
 
sodium ion transport IEA
Inferred from Electronic Annotation
more info
 
synaptic transmission, cholinergic IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
transmembrane transport TAS
Traceable Author Statement
more info
 
Component Evidence Code Pubs
axon IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cell junction IEA
Inferred from Electronic Annotation
more info
 
dendrite IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
integral component of membrane IDA
Inferred from Direct Assay
more info
PubMed 
neuromuscular junction IDA
Inferred from Direct Assay
more info
PubMed 
perikaryon IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
plasma membrane IDA
Inferred from Direct Assay
more info
PubMed 
plasma membrane TAS
Traceable Author Statement
more info
 
presynapse IEA
Inferred from Electronic Annotation
more info
 
synapse IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Preferred Names
high affinity choline transporter 1
Names
high affinity choline transporter; hemicholinium-3-sensitive choline transporter
solute carrier family 5 (sodium/choline cotransporter), member 7

RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_042267.1 RefSeqGene

    Range
    5001..32475
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001305005.2NP_001291934.1  high affinity choline transporter 1 isoform a

    See identical proteins and their annotated locations for NP_001291934.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Variants 1 and 2 encode the same isoform (a).
    Source sequence(s)
    AC009963, AK315280, DA714970
    Consensus CDS
    CCDS2074.1
    UniProtKB/Swiss-Prot
    Q9GZV3
    UniProtKB/TrEMBL
    B2RCU2
    Related
    ENSP00000387346.1, OTTHUMP00000203760, ENST00000409059.5, OTTHUMT00000330879
    Conserved Domains (1) summary
    cd11474
    Location:8495
    SLC5sbd_CHT; Na(+)- and Cl(-)-dependent choline cotransporter CHT and related proteins; solute-binding domain
  2. NM_001305006.2NP_001291935.1  high affinity choline transporter 1 isoform b

    See identical proteins and their annotated locations for NP_001291935.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) lacks an alternate exon in the 5' end compared to variant 1. This difference causes translation initiation at a downstream AUG and results in an isoform (b) with a shorter N-terminus compared to isoform a.
    Source sequence(s)
    AC009963, AK300801, DA714970
    UniProtKB/TrEMBL
    B4DUU7
    Conserved Domains (1) summary
    cd11474
    Location:1390
    SLC5sbd_CHT; Na(+)- and Cl(-)-dependent choline cotransporter CHT and related proteins; solute-binding domain
  3. NM_001305007.2NP_001291936.1  high affinity choline transporter 1 isoform c

    See identical proteins and their annotated locations for NP_001291936.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) uses an alternate internal splice junction compared to variant 1. This difference causes translation initiation at a downstream AUG and results in an isoform (c) with a shorter N-terminus compared to isoform 1.
    Source sequence(s)
    AC009963, BC111524, DA714970
    UniProtKB/TrEMBL
    Q2T9H3
    Conserved Domains (1) summary
    cd11474
    Location:1248
    SLC5sbd_CHT; Na(+)- and Cl(-)-dependent choline cotransporter CHT and related proteins; solute-binding domain
  4. NM_021815.4NP_068587.1  high affinity choline transporter 1 isoform a

    See identical proteins and their annotated locations for NP_068587.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (a). Variants 1 and 2 both encode the same isoform (a).
    Source sequence(s)
    AC009963, BC111525, DA714970
    Consensus CDS
    CCDS2074.1
    UniProtKB/Swiss-Prot
    Q9GZV3
    Related
    ENSP00000264047.2, OTTHUMP00000161574, ENST00000264047.2, OTTHUMT00000253562
    Conserved Domains (1) summary
    cd11474
    Location:8495
    SLC5sbd_CHT; Na(+)- and Cl(-)-dependent choline cotransporter CHT and related proteins; solute-binding domain

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000002.12 Reference GRCh38.p12 Primary Assembly

    Range
    107986514..108014497
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017004628.1XP_016860117.1  high affinity choline transporter 1 isoform X1

    Conserved Domains (1) summary
    cd11474
    Location:8457
    SLC5sbd_CHT; Na(+)- and Cl(-)-dependent choline cotransporter CHT and related proteins; solute-binding domain
  2. XM_017004629.2XP_016860118.1  high affinity choline transporter 1 isoform X3

    Conserved Domains (1) summary
    cd11474
    Location:1390
    SLC5sbd_CHT; Na(+)- and Cl(-)-dependent choline cotransporter CHT and related proteins; solute-binding domain
  3. XM_011511580.2XP_011509882.1  high affinity choline transporter 1 isoform X2

    Conserved Domains (1) summary
    cd11474
    Location:14411
    SLC5sbd_CHT; Na(+)- and Cl(-)-dependent choline cotransporter CHT and related proteins; solute-binding domain
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