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STX16 syntaxin 16 [ Homo sapiens (human) ]

Gene ID: 8675, updated on 7-Jun-2020

Summary

Official Symbol
STX16provided by HGNC
Official Full Name
syntaxin 16provided by HGNC
Primary source
HGNC:HGNC:11431
See related
Ensembl:ENSG00000124222 MIM:603666
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
SYN16
Summary
This gene encodes a protein that is a member of the syntaxin or t-SNARE (target-SNAP receptor) family. These proteins are found on cell membranes and serve as the targets for V-SNARES (vesicle-SNAP receptors) permitting specific synaptic vesicle docking and fusion. A microdeletion in the region of chromosome 20 where this gene is located has been associated with pseudohypoparathyroidism type Ib. Multiple transcript variants have been found for this gene. Read-through transcription also exists between this gene and the neighboring downstream aminopeptidase-like 1 (NPEPL1) gene. [provided by RefSeq, Mar 2011]
Expression
Ubiquitous expression in spleen (RPKM 25.9), lymph node (RPKM 25.7) and 25 other tissues See more
Orthologs

Genomic context

See STX16 in Genome Data Viewer
Location:
20q13.32
Exon count:
9
Annotation release Status Assembly Chr Location
109.20200522 current GRCh38.p13 (GCF_000001405.39) 20 NC_000020.11 (58651283..58679526)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 20 NC_000020.10 (57226309..57254582)

Chromosome 20 - NC_000020.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC107985410 Neighboring gene long intergenic non-protein coding RNA 1711 Neighboring gene STX16-NPEPL1 readthrough (NMD candidate) Neighboring gene aminopeptidase like 1 Neighboring gene piezo type mechanosensitive ion channel component 1 pseudogene 2

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
Pseudohypoparathyroidism type 1B
MedGen: C1864100 OMIM: 603233 GeneReviews: Disorders of GNAS Inactivation
Compare labs

NHGRI GWAS Catalog

Description
Longitudinal genome-wide association of cardiovascular disease risk factors in the Bogalusa heart study.
NHGRI GWA Catalog

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Readthrough STX16-NPEPL1

Readthrough gene: STX16-NPEPL1, Included gene: NPEPL1

Homology

Clone Names

  • MGC90328

Gene Ontology Provided by GOA

Function Evidence Code Pubs
SNAP receptor activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
SNAP receptor activity IDA
Inferred from Direct Assay
more info
PubMed 
SNARE binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
syntaxin binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
Golgi ribbon formation IMP
Inferred from Mutant Phenotype
more info
PubMed 
intracellular protein transport IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
retrograde transport, endosome to Golgi IDA
Inferred from Direct Assay
more info
PubMed 
retrograde transport, endosome to Golgi IMP
Inferred from Mutant Phenotype
more info
PubMed 
vesicle docking IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
vesicle fusion IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Component Evidence Code Pubs
Golgi apparatus IDA
Inferred from Direct Assay
more info
PubMed 
Golgi cisterna IDA
Inferred from Direct Assay
more info
PubMed 
Golgi membrane TAS
Traceable Author Statement
more info
 
SNARE complex IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
SNARE complex IDA
Inferred from Direct Assay
more info
PubMed 
SNARE complex TAS
Traceable Author Statement
more info
PubMed 
cytoplasm IDA
Inferred from Direct Assay
more info
PubMed 
cytosol IEA
Inferred from Electronic Annotation
more info
 
endomembrane system IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
focal adhesion HDA PubMed 
integral component of membrane IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
integral component of synaptic vesicle membrane IEA
Inferred from Electronic Annotation
more info
 
intracellular membrane-bounded organelle IDA
Inferred from Direct Assay
more info
PubMed 
perinuclear region of cytoplasm IDA
Inferred from Direct Assay
more info
PubMed 
trans-Golgi network IDA
Inferred from Direct Assay
more info
PubMed 
trans-Golgi network membrane TAS
Traceable Author Statement
more info
 

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_011831.2 RefSeqGene

    Range
    4982..33255
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001001433.3NP_001001433.1  syntaxin-16 isoform a

    See identical proteins and their annotated locations for NP_001001433.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (a, also referred to as isoform B).
    Source sequence(s)
    AL050327, AL139349, KF456959
    Consensus CDS
    CCDS13468.1
    UniProtKB/Swiss-Prot
    O14662
    Related
    ENSP00000360183.4, ENST00000371141.8
    Conserved Domains (2) summary
    COG5325
    Location:75301
    COG5325; t-SNARE complex subunit, syntaxin [Intracellular trafficking and secretion]
    cd15845
    Location:233291
    SNARE_syntaxin16; SNARE motif of syntaxin 16
  2. NM_001134772.3NP_001128244.1  syntaxin-16 isoform c

    See identical proteins and their annotated locations for NP_001128244.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) lacks an alternate in-frame exon in the 5' coding region, compared to variant 1, resulting in a shorter isoform (c), compared to isoform a.
    Source sequence(s)
    AL050327, AL139349, KF456959
    Consensus CDS
    CCDS46619.1
    UniProtKB/Swiss-Prot
    O14662
    Related
    ENSP00000350723.4, ENST00000358029.8
    Conserved Domains (2) summary
    COG5325
    Location:71297
    COG5325; t-SNARE complex subunit, syntaxin [Intracellular trafficking and secretion]
    cd15845
    Location:229287
    SNARE_syntaxin16; SNARE motif of syntaxin 16
  3. NM_001134773.3NP_001128245.1  syntaxin-16 isoform d

    See identical proteins and their annotated locations for NP_001128245.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) uses an alternate in-frame splice site in the 5' coding region, compared to variant 1, resulting in a shorter isoform (d), compared to isoform a.
    Source sequence(s)
    AL050327, AL139349, KF456959
    Consensus CDS
    CCDS46620.1
    UniProtKB/Swiss-Prot
    O14662
    Related
    ENSP00000348229.5, ENST00000355957.9
    Conserved Domains (2) summary
    COG5325
    Location:58284
    COG5325; t-SNARE complex subunit, syntaxin [Intracellular trafficking and secretion]
    cd15845
    Location:216274
    SNARE_syntaxin16; SNARE motif of syntaxin 16
  4. NM_001204868.2NP_001191797.1  syntaxin-16 isoform e

    See identical proteins and their annotated locations for NP_001191797.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) differs in the 5' UTR, lacks a portion of the 5' coding region, and uses a downstream start codon, compared to variant 1. The encoded isoform (e) is shorter at the N-terminus, compared to isoform a.
    Source sequence(s)
    AL050327, AL139349, KF456959
    Consensus CDS
    CCDS56199.1
    UniProtKB/Swiss-Prot
    O14662
    UniProtKB/TrEMBL
    B4DJX9
    Related
    ENSP00000352634.4, ENST00000359617.8
    Conserved Domains (2) summary
    cd15845
    Location:180238
    SNARE_syntaxin16; SNARE motif of syntaxin 16
    cl00143
    Location:29135
    SynN; Syntaxin N-terminus domain; syntaxins are nervous system-specific proteins implicated in the docking of synaptic vesicles with the presynaptic plasma membrane; they are a family of receptors for intracellular transport vesicles; each target membrane may ...
  5. NM_003763.6NP_003754.2  syntaxin-16 isoform b

    See identical proteins and their annotated locations for NP_003754.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) uses an alternate in-frame splice site and lacks an alternate in-frame exon in the 5' coding region, compared to variant 1, resulting in a shorter isoform (b, also referred to as isoform A), compared to isoform a.
    Source sequence(s)
    AL050327, AL139349, KF456959
    Consensus CDS
    CCDS13469.1
    UniProtKB/Swiss-Prot
    O14662
    Related
    ENSP00000360173.4, ENST00000371132.8
    Conserved Domains (2) summary
    COG5325
    Location:54280
    COG5325; t-SNARE complex subunit, syntaxin [Intracellular trafficking and secretion]
    cd15845
    Location:212270
    SNARE_syntaxin16; SNARE motif of syntaxin 16

RNA

  1. NR_037941.2 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (6) uses an alternate splice site in the 5' region and lacks an exon in the central region, compared to variant 1. This variant is represented as non-coding because the use of the supported start codon, as used in variant 1, would render the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AL050327, AL139349, KF456959
  2. NR_037942.2 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (7) has alternate exon structure in the 5' region and lacks an exon in the central region, compared to variant 1. This variant is represented as non-coding because it lacks the supported start codon, as found in variant 1, and the use of the next available in-frame start codon would render the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AL050327, AL139349, KF456959
  3. NR_037943.2 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (8) has alternate exon structure in the 5' region and lacks an exon in the central region, compared to variant 1. This variant is represented as non-coding because it lacks the supported start codon, as found in variant 1, and the use of the next available in-frame start codon would render the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AL050327, AL139349, KF456959

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000020.11 Reference GRCh38.p13 Primary Assembly

    Range
    58651283..58679526
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_001001434.1: Suppressed sequence

    Description
    NM_001001434.1: This RefSeq was permanently suppressed because it is a nonsense-mediated mRNA decay (NMD) candidate.
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