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    SYN2 synapsin II [ Homo sapiens (human) ]

    Gene ID: 6854, updated on 3-Dec-2024

    Summary

    Official Symbol
    SYN2provided by HGNC
    Official Full Name
    synapsin IIprovided by HGNC
    Primary source
    HGNC:HGNC:11495
    See related
    Ensembl:ENSG00000157152 MIM:600755; AllianceGenome:HGNC:11495
    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
    SYNII
    Summary
    This gene is a member of the synapsin gene family. Synapsins encode neuronal phosphoproteins which associate with the cytoplasmic surface of synaptic vesicles. Family members are characterized by common protein domains, and they are implicated in synaptogenesis and the modulation of neurotransmitter release, suggesting a potential role in several neuropsychiatric diseases. This member of the synapsin family encodes a neuron-specific phosphoprotein that selectively binds to small synaptic vesicles in the presynaptic nerve terminal. Polymorphisms in this gene are associated with abnormal presynaptic function and related neuronal disorders, including autism, epilepsy, bipolar disorder and schizophrenia. Alternative splicing of this gene results in multiple transcript variants. The tissue inhibitor of metalloproteinase 4 gene is located within an intron of this gene and is transcribed in the opposite direction. [provided by RefSeq, Feb 2014]
    Expression
    Biased expression in brain (RPKM 41.0) and fat (RPKM 5.3) See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See SYN2 in Genome Data Viewer
    Location:
    3p25.2
    Exon count:
    16
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (12004388..12192032)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (12002345..12190266)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (12045862..12233532)

    Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene MARK2 pseudogene 14 Neighboring gene ReSE screen-validated silencer GRCh37_chr3:12003099-12003242 Neighboring gene RNA, 7SL, cytoplasmic 147, pseudogene Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:12046587-12047087 Neighboring gene Sharpr-MPRA regulatory region 7614 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:12100621-12101122 Neighboring gene actin gamma 1 pseudogene 12 Neighboring gene Sharpr-MPRA regulatory region 15359 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19435 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14064 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr3:12219651-12220850 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19436 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19437 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19438 Neighboring gene MT-CO1 pseudogene 5 Neighboring gene TIMP metallopeptidase inhibitor 4 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:12265535-12266263 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:12328552-12329130 Neighboring gene glutathione S-transferase mu 5 pseudogene 1 Neighboring gene ReSE screen-validated silencer GRCh37_chr3:12348453-12348660 Neighboring gene peroxisome proliferator activated receptor gamma Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr3:12386163-12387362 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19439 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19440 Neighboring gene PPARG eExon liver enhancer

    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
    Schizophrenia
    MedGen: C0036341 OMIM: 181500 GeneReviews: Not available
    Compare labs

    EBI GWAS Catalog

    Description
    A genome-wide approach accounting for body mass index identifies genetic variants influencing fasting glycemic traits and insulin resistance.
    EBI GWAS Catalog
    Meta-analysis of genome-wide association data and large-scale replication identifies additional susceptibility loci for type 2 diabetes.
    EBI GWAS Catalog
    New gene functions in megakaryopoiesis and platelet formation.
    EBI GWAS Catalog

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables ATP binding TAS
    Traceable Author Statement
    more info
    PubMed 
    enables identical protein binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    Process Evidence Code Pubs
    involved_in calcium-ion regulated exocytosis IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in chemical synaptic transmission TAS
    Traceable Author Statement
    more info
    PubMed 
    involved_in neurotransmitter secretion ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in synapse organization IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in synaptic vesicle clustering IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    Component Evidence Code Pubs
    part_of SNARE complex IEA
    Inferred from Electronic Annotation
    more info
     
    located_in Schaffer collateral - CA1 synapse IEA
    Inferred from Electronic Annotation
    more info
     
    located_in glutamatergic synapse IEA
    Inferred from Electronic Annotation
    more info
     
    located_in plasma membrane IEA
    Inferred from Electronic Annotation
    more info
     
    located_in postsynaptic density IEA
    Inferred from Electronic Annotation
    more info
     
    located_in synapse ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    is_active_in synaptic vesicle membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in synaptic vesicle membrane ISS
    Inferred from Sequence or Structural Similarity
    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_011728.3 RefSeqGene

      Range
      5002..192646
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_003178.6NP_003169.2  synapsin-2 isoform IIb

      See identical proteins and their annotated locations for NP_003169.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (IIb) is alternatively spliced at its 3' end, compared to variant IIa. It encodes isoform IIb, which contains a shorter C-terminus with a distinct domain I, compared to isoform IIa.
      Source sequence(s)
      ABBA01025208, AC022234, AC026166, AC091492
      Consensus CDS
      CCDS74901.1
      UniProtKB/TrEMBL
      Q59GM1
      Related
      ENSP00000484916.1, ENST00000620175.4
      Conserved Domains (3) summary
      pfam02078
      Location:115212
      Synapsin; Synapsin, N-terminal domain
      pfam02750
      Location:214416
      Synapsin_C; Synapsin, ATP binding domain
      pfam10581
      Location:230
      Synapsin_N; Synapsin N-terminal
    2. NM_133625.6NP_598328.1  synapsin-2 isoform IIa

      See identical proteins and their annotated locations for NP_598328.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (IIa) represents the shorter transcript but encodes the longer isoform (IIa), which has an alternate C-terminus with distinct H and E domains, compared to isoform IIb.
      Source sequence(s)
      ABBA01025208, AC022234, AC026166, AC091492
      Consensus CDS
      CCDS74900.1
      UniProtKB/Swiss-Prot
      A0A087WW96, A0A087X2E3, A8MY98, Q92777
      UniProtKB/TrEMBL
      Q86VA8
      Related
      ENSP00000480050.1, ENST00000621198.5
      Conserved Domains (3) summary
      pfam02078
      Location:115212
      Synapsin; Synapsin, N-terminal domain
      pfam02750
      Location:214416
      Synapsin_C; Synapsin, ATP binding domain
      pfam10581
      Location:230
      Synapsin_N; Synapsin N-terminal

    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_000003.12 Reference GRCh38.p14 Primary Assembly

      Range
      12004388..12192032
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006713311.4XP_006713374.1  synapsin-2 isoform X1

      UniProtKB/TrEMBL
      Q59GM1
      Conserved Domains (3) summary
      pfam02078
      Location:115212
      Synapsin; Synapsin, N-terminal domain
      pfam02750
      Location:214416
      Synapsin_C; Synapsin, ATP binding domain
      pfam10581
      Location:230
      Synapsin_N; Synapsin N-terminal
    2. XM_006713312.5XP_006713375.1  synapsin-2 isoform X2

      Conserved Domains (1) summary
      pfam02750
      Location:53255
      Synapsin_C; Synapsin, ATP binding domain
    3. XM_006713313.3XP_006713376.1  synapsin-2 isoform X4

      Conserved Domains (1) summary
      cl17255
      Location:1159
      ATP-grasp_4; ATP-grasp domain
    4. XM_017007087.2XP_016862576.1  synapsin-2 isoform X3

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060927.1 Alternate T2T-CHM13v2.0

      Range
      12002345..12190266
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054347643.1XP_054203618.1  synapsin-2 isoform X1

      UniProtKB/TrEMBL
      Q59GM1
    2. XM_054347647.1XP_054203622.1  synapsin-2 isoform X5

      UniProtKB/TrEMBL
      B3KSV8
    3. XM_054347644.1XP_054203619.1  synapsin-2 isoform X2

    4. XM_054347646.1XP_054203621.1  synapsin-2 isoform X4

    5. XM_054347645.1XP_054203620.1  synapsin-2 isoform X3