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SLC6A9 solute carrier family 6 member 9 [ Homo sapiens (human) ]

Gene ID: 6536, updated on 22-Jan-2020

Summary

Official Symbol
SLC6A9provided by HGNC
Official Full Name
solute carrier family 6 member 9provided by HGNC
Primary source
HGNC:HGNC:11056
See related
Ensembl:ENSG00000196517 MIM:601019
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
GLYT1; GCENSG
Summary
The amino acid glycine acts as an inhibitory neurotransmitter in the central nervous system. The protein encoded by this gene is one of two transporters that stop glycine signaling by removing it from the synaptic cleft. [provided by RefSeq, Jun 2016]
Expression
Broad expression in skin (RPKM 13.4), adrenal (RPKM 9.7) and 18 other tissues See more
Orthologs

Genomic context

See SLC6A9 in Genome Data Viewer
Location:
1p34.1
Exon count:
18
Annotation release Status Assembly Chr Location
109.20191205 current GRCh38.p13 (GCF_000001405.39) 1 NC_000001.11 (43996483..44031462, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (44462155..44497171, complement)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene beta-1,4-galactosyltransferase 2 Neighboring gene Sharpr-MPRA regulatory region 11322 Neighboring gene coiled-coil domain containing 24 Neighboring gene uncharacterized LOC107984948 Neighboring gene VISTA enhancer hs1857 Neighboring gene Kruppel like factor 17 Neighboring gene keratin 8 pseudogene 47

Genomic regions, transcripts, and products

Expression

  • 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 Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

Associated conditions

Description Tests
Glycine encephalopathy with normal serum glycine
MedGen: C4310943 OMIM: 617301 GeneReviews: GLYT1 Encephalopathy
Compare labs

NHGRI GWAS Catalog

Description
Genome-wide survival analysis of age at onset of alcohol dependence in extended high-risk COGA families.
NHGRI GWA Catalog

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • DKFZp547A1118

Gene Ontology Provided by GOA

Function Evidence Code Pubs
glycine:sodium symporter activity TAS
Traceable Author Statement
more info
PubMed 
Process Evidence Code Pubs
amino acid transmembrane transport IEA
Inferred from Electronic Annotation
more info
 
glycine secretion, neurotransmission IEA
Inferred from Electronic Annotation
more info
 
neurotransmitter uptake IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
hippocampal mossy fiber to CA3 synapse IEA
Inferred from Electronic Annotation
more info
 
integral component of plasma membrane TAS
Traceable Author Statement
more info
PubMed 
integral component of postsynaptic membrane IEA
Inferred from Electronic Annotation
more info
 
integral component of presynaptic membrane IEA
Inferred from Electronic Annotation
more info
 
integral component of synaptic vesicle membrane IEA
Inferred from Electronic Annotation
more info
 
membrane TAS
Traceable Author Statement
more info
PubMed 
parallel fiber to Purkinje cell synapse IEA
Inferred from Electronic Annotation
more info
 
plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
plasma membrane TAS
Traceable Author Statement
more info
 
postsynaptic density IEA
Inferred from Electronic Annotation
more info
 

General protein information

Preferred Names
sodium- and chloride-dependent glycine transporter 1
Names
glyT-1
solute carrier family 6 (neurotransmitter transporter, glycine), member 9

NCBI Reference Sequences (RefSeq)

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_050929.1 RefSeqGene

    Range
    5031..40010
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001024845.3NP_001020016.1  sodium- and chloride-dependent glycine transporter 1 isoform 3

    See identical proteins and their annotated locations for NP_001020016.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) differs in the 5' UTR and coding region compared to variant 2. The resulting isoform (3) is shorter and has a distinct N-terminus compared to isoform 2. Variants 3 and 9 both encode the same isoform (3).
    Source sequence(s)
    AI884725, AL139220, CN354684, S70609
    Consensus CDS
    CCDS30695.1
    UniProtKB/Swiss-Prot
    P48067
    Related
    ENSP00000361384.3, ENST00000372310.7
    Conserved Domains (1) summary
    cd11498
    Location:11594
    SLC6sbd_GlyT1; Na(+)- and Cl(-)-dependent glycine transporter GlyT1; solute-binding domain
  2. NM_001261380.2NP_001248309.1  sodium- and chloride-dependent glycine transporter 1 isoform 4

    See identical proteins and their annotated locations for NP_001248309.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) lacks an alternate in-frame exon and uses an alternate in-frame splice site in the 5' coding region compared to variant 2. The resulting protein (isoform 4) is shorter compared to isoform 2.
    Source sequence(s)
    AK296438, AL139220, DA403430
    UniProtKB/TrEMBL
    B7Z3W8
    Conserved Domains (1) summary
    cd11498
    Location:30598
    SLC6sbd_GlyT1; Na(+)- and Cl(-)-dependent glycine transporter GlyT1; solute-binding domain
  3. NM_001328626.2NP_001315555.1  sodium- and chloride-dependent glycine transporter 1 isoform 5

    Status: REVIEWED

    Description
    Transcript Variant: This variant (6) differs in the 5' UTR and coding sequence compared to variant 2. The resulting isoform (5) is shorter at the N-terminus compared to isoform 2.
    Source sequence(s)
    AL139220
    Consensus CDS
    CCDS85966.1
    UniProtKB/TrEMBL
    B7Z589
    Related
    ENSP00000434460.1, ENST00000475075.6
    Conserved Domains (1) summary
    cl00456
    Location:1483
    SLC5-6-like_sbd; Solute carrier families 5 and 6-like; solute binding domain
  4. NM_001328627.1NP_001315556.1  sodium- and chloride-dependent glycine transporter 1 isoform 6

    Status: REVIEWED

    Description
    Transcript Variant: This variant (7) lacks an alternate exon in the 5' end compared to variant 2. The resulting isoform (6) has a shorter and distinct N-terminus compared to isoform 2.
    Source sequence(s)
    AL139220
    Conserved Domains (1) summary
    cl00456
    Location:42573
    SLC5-6-like_sbd; Solute carrier families 5 and 6-like; solute binding domain
  5. NM_001328628.1NP_001315557.1  sodium- and chloride-dependent glycine transporter 1 isoform 7

    Status: REVIEWED

    Description
    Transcript Variant: This variant (8) lacks two alternate exons in the 5' end compared to variant 2. The resulting isoform (7) has a shorter and distinct N-terminus compared to isoform 2.
    Source sequence(s)
    AL139220
    Conserved Domains (1) summary
    cl00456
    Location:30529
    SLC5-6-like_sbd; Solute carrier families 5 and 6-like; solute binding domain
  6. NM_001328629.1NP_001315558.1  sodium- and chloride-dependent glycine transporter 1 isoform 3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (9) differs in the 5' UTR and coding sequence compared to variant 2. The resulting isoform (3) has a shorter and distinct N-terminus compared to isoform 2. Variants 3 and 9 both encode the same isoform (3).
    Source sequence(s)
    AL139220
    Consensus CDS
    CCDS30695.1
    UniProtKB/Swiss-Prot
    P48067
    Related
    ENSP00000501314.1, ENST00000673836.1
    Conserved Domains (1) summary
    cd11498
    Location:11594
    SLC6sbd_GlyT1; Na(+)- and Cl(-)-dependent glycine transporter GlyT1; solute-binding domain
  7. NM_001328630.2NP_001315559.1  sodium- and chloride-dependent glycine transporter 1 isoform 8

    Status: REVIEWED

    Description
    Transcript Variant: This variant (10) differs in the 5' UTR and coding sequence and lacks an alternate 3' in-frame exon compared to variant 2. The resulting isoform (8) is shorter at the N-terminus and lacks an alternate C-terminal segment compared to isoform 2.
    Source sequence(s)
    AL139220
  8. NM_006934.4NP_008865.2  sodium- and chloride-dependent glycine transporter 1 isoform 1

    See identical proteins and their annotated locations for NP_008865.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) lacks an alternate in-frame exon compared to variant 2. The resulting isoform (1) has the same N- and C-termini but is shorter compared to isoform 2.
    Source sequence(s)
    AI884725, AL139220, S70612
    Consensus CDS
    CCDS41316.1
    UniProtKB/Swiss-Prot
    P48067
    Related
    ENSP00000350362.2, ENST00000357730.6
    Conserved Domains (1) summary
    cd11498
    Location:30613
    SLC6sbd_GlyT1; Na(+)- and Cl(-)-dependent glycine transporter GlyT1; solute-binding domain
  9. NM_201649.4NP_964012.2  sodium- and chloride-dependent glycine transporter 1 isoform 2

    See identical proteins and their annotated locations for NP_964012.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) represents the longest transcript and encodes the longest isoform (2).
    Source sequence(s)
    AI884725, AL139220, S70609
    Consensus CDS
    CCDS41317.1
    UniProtKB/Swiss-Prot
    P48067
    Related
    ENSP00000353791.2, ENST00000360584.6
    Conserved Domains (1) summary
    cd11498
    Location:84667
    SLC6sbd_GlyT1; Na(+)- and Cl(-)-dependent glycine transporter GlyT1; solute-binding domain

RNA

  1. NR_048548.2 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) lacks an alternate 5' exon compared to variant 2. This variant is represented as non-coding because the use of the 5'-most supported translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AK315233, AL139220

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20191205

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000001.11 Reference GRCh38.p13 Primary Assembly

    Range
    43996483..44031462 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_024449295.1XP_024305063.1  sodium- and chloride-dependent glycine transporter 1 isoform X3

    Conserved Domains (1) summary
    cl00456
    Location:1529
    SLC5-6-like_sbd; Solute carrier families 5 and 6-like; solute binding domain
  2. XM_017002153.2XP_016857642.1  sodium- and chloride-dependent glycine transporter 1 isoform X4

    Conserved Domains (1) summary
    cl00456
    Location:26556
    SLC5-6-like_sbd; Solute carrier families 5 and 6-like; solute binding domain
  3. XM_017002152.2XP_016857641.1  sodium- and chloride-dependent glycine transporter 1 isoform X2

  4. XM_011542017.2XP_011540319.1  sodium- and chloride-dependent glycine transporter 1 isoform X1

    Conserved Domains (1) summary
    cl00456
    Location:84585
    SLC5-6-like_sbd; Solute carrier families 5 and 6-like; solute binding domain
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