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SYNGR1 synaptogyrin 1 [ Homo sapiens (human) ]

Gene ID: 9145, updated on 24-Nov-2020

Summary

Official Symbol
SYNGR1provided by HGNC
Official Full Name
synaptogyrin 1provided by HGNC
Primary source
HGNC:HGNC:11498
See related
Ensembl:ENSG00000100321 MIM:603925
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
Summary
This gene encodes an integral membrane protein associated with presynaptic vesicles in neuronal cells. The exact function of this protein is unclear, but studies of a similar murine protein suggest that it functions in synaptic plasticity without being required for synaptic transmission. The gene product belongs to the synaptogyrin gene family. Three alternatively spliced variants encoding three different isoforms have been identified. [provided by RefSeq, Jul 2008]
Expression
Biased expression in brain (RPKM 53.1), ovary (RPKM 17.1) and 11 other tissues See more
Orthologs

Genomic context

See SYNGR1 in Genome Data Viewer
Location:
22q13.1
Exon count:
6
Annotation release Status Assembly Chr Location
109.20201120 current GRCh38.p13 (GCF_000001405.39) 22 NC_000022.11 (39349991..39385575)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 22 NC_000022.10 (39745954..39781593)

Chromosome 22 - NC_000022.11Genomic Context describing neighboring genes Neighboring gene small nucleolar RNA, C/D box 139 Neighboring gene ribosomal protein L3 Neighboring gene small nucleolar RNA, C/D box 43 Neighboring gene TGF-beta activated kinase 1 (MAP3K7) binding protein 1 Neighboring gene uncharacterized LOC100506472 Neighboring gene CRISPRi-validated cis-regulatory element chr22.2018

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
Genetics of rheumatoid arthritis contributes to biology and drug discovery.
GeneReviews: Not available
Genome-wide data reveal novel genes for methotrexate response in a large cohort of juvenile idiopathic arthritis cases.
GeneReviews: Not available
Loci associated with N-glycosylation of human immunoglobulin G show pleiotropy with autoimmune diseases and haematological cancers.
GeneReviews: Not available

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Potential readthrough

Included gene: TAB1

Homology

Clone Names

  • MGC1939

Gene Ontology Provided by GOA

Function Evidence Code Pubs
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
cellular response to leukemia inhibitory factor IEA
Inferred from Electronic Annotation
more info
 
neutrophil degranulation TAS
Traceable Author Statement
more info
 
protein targeting IEA
Inferred from Electronic Annotation
more info
 
regulated exocytosis ISS
Inferred from Sequence or Structural Similarity
more info
 
regulation of long-term neuronal synaptic plasticity ISS
Inferred from Sequence or Structural Similarity
more info
 
regulation of short-term neuronal synaptic plasticity ISS
Inferred from Sequence or Structural Similarity
more info
 
synaptic vesicle membrane organization ISS
Inferred from Sequence or Structural Similarity
more info
 
Component Evidence Code Pubs
azurophil granule membrane TAS
Traceable Author Statement
more info
 
integral component of synaptic vesicle membrane IEA
Inferred from Electronic Annotation
more info
 
melanosome IEA
Inferred from Electronic Annotation
more info
 
neuromuscular junction IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
plasma membrane TAS
Traceable Author Statement
more info
 
synaptic vesicle membrane IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 

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_047102.1 RefSeqGene

    Range
    5043..40627
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_004711.5NP_004702.2  synaptogyrin-1 isoform 1a

    See identical proteins and their annotated locations for NP_004702.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1a) represents the longest transcript and encodes the longest predominantly expressed isoform.
    Source sequence(s)
    AA412350, AJ002305, BC000731, BI667990, BX501388, DA337769
    Consensus CDS
    CCDS13989.1
    UniProtKB/Swiss-Prot
    O43759
    Related
    ENSP00000332287.5, ENST00000328933.10
    Conserved Domains (1) summary
    pfam01284
    Location:21167
    MARVEL; Membrane-associating domain
  2. NM_145731.4NP_663783.1  synaptogyrin-1 isoform 1b

    See identical proteins and their annotated locations for NP_663783.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1b) has a distinct 3' UTR and contains an alternate 3' coding exon, as compared to variant 1a. The encoded isoform (1b) has a distinct C-terminus, compared to isoform 1a.
    Source sequence(s)
    AJ002304, AW304782, BC000731, BI667990
    Consensus CDS
    CCDS13990.1
    UniProtKB/Swiss-Prot
    O43759
    Related
    ENSP00000318845.4, ENST00000318801.8
    Conserved Domains (1) summary
    pfam01284
    Location:21167
    MARVEL; Membrane-associating domain
  3. NM_145738.3NP_663791.1  synaptogyrin-1 isoform 1c

    See identical proteins and their annotated locations for NP_663791.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1c) encodes the shortest isoform. It contains a distinct 5' UTR and 5' coding region resulting in a frameshift and downstream translation initiation site, when compared to isoform 1a.
    Source sequence(s)
    AJ002303, AJ002304, AL022326, AW304782
    Consensus CDS
    CCDS13991.1
    UniProtKB/Swiss-Prot
    O43759
    Related
    ENSP00000370946.4, ENST00000381535.4
    Conserved Domains (1) summary
    pfam01284
    Location:35168
    MARVEL; Membrane-associating domain

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20201120

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000022.11 Reference GRCh38.p13 Primary Assembly

    Range
    39349991..39385575
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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