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    SYNGR1 synaptogyrin 1 [ Homo sapiens (human) ]

    Gene ID: 9145, updated on 19-Sep-2024

    Summary

    Official Symbol
    SYNGR1provided by HGNC
    Official Full Name
    synaptogyrin 1provided by HGNC
    Primary source
    HGNC:HGNC:11498
    See related
    Ensembl:ENSG00000100321 MIM:603925; AllianceGenome:HGNC:11498
    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
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    Genomic context

    See SYNGR1 in Genome Data Viewer
    Location:
    22q13.1
    Exon count:
    6
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 22 NC_000022.11 (39349991..39385575)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 22 NC_060946.1 (39820668..39856199)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 22 NC_000022.10 (39745996..39781580)

    Chromosome 22 - NC_000022.11Genomic Context describing neighboring genes Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:39712838-39713726 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:39714617-39715506 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:39715507-39716396 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:39716397-39717285 Neighboring gene small nucleolar RNA, C/D box 139 Neighboring gene Sharpr-MPRA regulatory region 3662 Neighboring gene small nucleolar RNA, C/D box 43 Neighboring gene ribosomal protein L3 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13750 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19045 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:39753396-39753924 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:39755840-39756638 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:39757867-39758453 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:39758454-39759039 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:39769919-39770434 Neighboring gene Sharpr-MPRA regulatory region 1576 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19046 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13751 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:39811177-39811678 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:39811679-39812178 Neighboring gene TGF-beta activated kinase 1 (MAP3K7) binding protein 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:39824885-39825527 Neighboring gene uncharacterized LOC100506472 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:39829518-39830236 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:39830237-39830954 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19047 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19048 Neighboring gene ReSE screen-validated silencer GRCh37_chr22:39843664-39843855 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:39844165-39845073 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19050 Neighboring gene CRISPRi-validated cis-regulatory element chr22.2018 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13752 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13753 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13754 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19051 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19052 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19053 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19054 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19055 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:39866163-39867092 Neighboring gene ReSE screen-validated silencer GRCh37_chr22:39869361-39869718 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:39869884-39870813 Neighboring gene beta-1,4-mannosyl-glycoprotein 4-beta-N-acetylglucosaminyltransferase Neighboring gene MGAT3 antisense RNA 1

    Genomic regions, transcripts, and products

    Expression

    • Project title: HPA RNA-seq normal tissues 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

    EBI GWAS Catalog

    Description
    Genetics of rheumatoid arthritis contributes to biology and drug discovery.
    EBI GWAS Catalog
    Genome-wide data reveal novel genes for methotrexate response in a large cohort of juvenile idiopathic arthritis cases.
    EBI GWAS Catalog
    Loci associated with N-glycosylation of human immunoglobulin G show pleiotropy with autoimmune diseases and haematological cancers.
    EBI GWAS Catalog

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Potential readthrough

    Included gene: TAB1

    Clone Names

    • MGC1939

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    Process Evidence Code Pubs
    involved_in cellular response to leukemia inhibitory factor IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in protein targeting IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in regulated exocytosis ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in regulation of long-term neuronal synaptic plasticity ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in regulation of short-term neuronal synaptic plasticity ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in synaptic vesicle membrane organization ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    Component Evidence Code Pubs
    located_in Schaffer collateral - CA1 synapse IEA
    Inferred from Electronic Annotation
    more info
     
    located_in azurophil granule membrane TAS
    Traceable Author Statement
    more info
     
    located_in melanosome IEA
    Inferred from Electronic Annotation
    more info
     
    located_in membrane NAS
    Non-traceable Author Statement
    more info
    PubMed 
    is_active_in neuromuscular junction IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in plasma membrane TAS
    Traceable Author Statement
    more info
     
    is_active_in synaptic vesicle membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
     

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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
      A6NP69, A8K0E2, O43757, O43758, O43759, Q53Y02, Q96J56, Q9UGZ4
      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/TrEMBL
      B5MCD7
      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: GCF_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000022.11 Reference GRCh38.p14 Primary Assembly

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

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060946.1 Alternate T2T-CHM13v2.0

      Range
      39820668..39856199
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)