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    SYN3 synapsin III [ Homo sapiens (human) ]

    Gene ID: 8224, updated on 27-Nov-2024

    Summary

    Official Symbol
    SYN3provided by HGNC
    Official Full Name
    synapsin IIIprovided by HGNC
    Primary source
    HGNC:HGNC:11496
    See related
    Ensembl:ENSG00000185666 MIM:602705; AllianceGenome:HGNC:11496
    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 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. The protein encoded by this gene shares the synapsin family domain model, with domains A, C, and E exhibiting the highest degree of conservation. The protein contains a unique domain J, located between domains C and E. Based on this gene's localization to 22q12.3, a possible schizophrenia susceptibility locus, and the established neurobiological roles of the synapsins, this family member may represent a candidate gene for schizophrenia. The TIMP3 gene is located within an intron of this gene and is transcribed in the opposite direction. Alternative splicing of this gene results in multiple splice variants that encode different isoforms. [provided by RefSeq, Oct 2008]
    Expression
    Biased expression in brain (RPKM 2.3), testis (RPKM 0.7) and 6 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See SYN3 in Genome Data Viewer
    Location:
    22q12.3
    Exon count:
    18
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 22 NC_000022.11 (32507820..33058381, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 22 NC_060946.1 (32971715..33522831, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 22 NC_000022.10 (32903807..33454367, complement)

    Chromosome 22 - NC_000022.11Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18877 Neighboring gene H3K27ac hESC enhancer GRCh37_chr22:32870558-32871058 Neighboring gene H3K27ac hESC enhancer GRCh37_chr22:32871059-32871559 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_63238 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_63240 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_63244 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr22:32898207-32898893 Neighboring gene H3K27ac hESC enhancer GRCh37_chr22:32897520-32898206 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:32924873-32925374 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:32925375-32925874 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:32927678-32928315 Neighboring gene uncharacterized LOC124905103 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:32928316-32928952 Neighboring gene BPI fold containing family C Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:33012121-33012620 Neighboring gene uncharacterized LOC107985545 Neighboring gene F-box protein 7 Neighboring gene uncharacterized LOC105373002 Neighboring gene SYN3 antisense RNA 1 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr22:33056914-33058113 Neighboring gene RNA, 5S ribosomal pseudogene 497 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:33148296-33149080 Neighboring gene ReSE screen-validated silencer GRCh37_chr22:33153563-33153744 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:33159884-33160394 Neighboring gene uncharacterized LOC124905104 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:33216313-33216812 Neighboring gene ReSE screen-validated silencer GRCh37_chr22:33271816-33272028 Neighboring gene Sharpr-MPRA regulatory region 12398 Neighboring gene ReSE screen-validated silencer GRCh37_chr22:33283107-33283317 Neighboring gene TIMP metallopeptidase inhibitor 3 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:33347343-33347844 Neighboring gene Sharpr-MPRA regulatory region 592 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:33382939-33383840 Neighboring gene H3K27ac hESC enhancer GRCh37_chr22:33448207-33448890 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr22:33450113-33450805 Neighboring gene ETFRF1 pseudogene 1 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr22:33506225-33507424 Neighboring gene uncharacterized LOC124905107 Neighboring gene long intergenic non-protein coding RNA 1640 Neighboring gene LARGE xylosyl- and glucuronyltransferase 1

    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

    EBI GWAS Catalog

    Description
    Genetic variants near TIMP3 and high-density lipoprotein-associated loci influence susceptibility to age-related macular degeneration.
    EBI GWAS Catalog
    Hundreds of variants clustered in genomic loci and biological pathways affect human height.
    EBI GWAS Catalog
    Identification, replication, and fine-mapping of Loci associated with adult height in individuals of african ancestry.
    EBI GWAS Catalog
    Meta-analysis of genome-wide association studies of adult height in East Asians identifies 17 novel loci.
    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 
    Process Evidence Code Pubs
    involved_in neurotransmitter secretion IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in regulation of synaptic transmission, GABAergic TAS
    Traceable Author Statement
    more info
    PubMed 
    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
    located_in extrinsic component of synaptic vesicle membrane IEA
    Inferred from Electronic Annotation
    more info
     
    located_in glutamatergic synapse IEA
    Inferred from Electronic Annotation
    more info
     
    located_in postsynaptic density IEA
    Inferred from Electronic Annotation
    more info
     
    located_in synaptic vesicle TAS
    Traceable Author Statement
    more info
    PubMed 
    is_active_in synaptic vesicle membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
     

    General protein information

    Preferred Names
    synapsin-3
    Names
    cN28H9.2 (synapsin III)

    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_029545.2 RefSeqGene

      Range
      5000..555561
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001135774.2NP_001129246.1  synapsin-3 isoform IIIg

      See identical proteins and their annotated locations for NP_001129246.1

      Status: REVIEWED

      Source sequence(s)
      Z71183, Z80902, Z82181, Z82246, Z83846, Z98256
      UniProtKB/TrEMBL
      Q17R54, Q59EX7
      Conserved Domains (4) summary
      PRK07764
      Location:393535
      PRK07764; DNA polymerase III subunits gamma and tau; Validated
      pfam02078
      Location:93189
      Synapsin; N-terminal domain
      pfam10581
      Location:129
      Synapsin_N; Synapsin N-terminal
      cl17255
      Location:192394
      CPSase_L_D2; Carbamoyl-phosphate synthase L chain, ATP binding domain
    2. NM_001369907.1NP_001356836.1  synapsin-3 isoform IIIa

      Status: REVIEWED

      Source sequence(s)
      Z71183, Z80902, Z82181, Z82246, Z83846, Z98256
      Consensus CDS
      CCDS13908.1
      UniProtKB/Swiss-Prot
      B1B1F9, O14994
      UniProtKB/TrEMBL
      Q59EX7
      Conserved Domains (4) summary
      PRK07764
      Location:394536
      PRK07764; DNA polymerase III subunits gamma and tau; Validated
      pfam02078
      Location:93190
      Synapsin; N-terminal domain
      pfam10581
      Location:129
      Synapsin_N; Synapsin N-terminal
      cl17255
      Location:193395
      CPSase_L_D2; Carbamoyl-phosphate synthase L chain, ATP binding domain
    3. NM_001369908.1NP_001356837.1  synapsin-3 isoform IIIa

      Status: REVIEWED

      Source sequence(s)
      Z71183, Z80902, Z82181, Z82246, Z83846, Z98256
      Consensus CDS
      CCDS13908.1
      UniProtKB/Swiss-Prot
      B1B1F9, O14994
      UniProtKB/TrEMBL
      Q59EX7
      Conserved Domains (4) summary
      PRK07764
      Location:394536
      PRK07764; DNA polymerase III subunits gamma and tau; Validated
      pfam02078
      Location:93190
      Synapsin; N-terminal domain
      pfam10581
      Location:129
      Synapsin_N; Synapsin N-terminal
      cl17255
      Location:193395
      CPSase_L_D2; Carbamoyl-phosphate synthase L chain, ATP binding domain
    4. NM_001369909.1NP_001356838.1  synapsin-3 isoform IIIg

      Status: REVIEWED

      Source sequence(s)
      Z71183, Z80902, Z82181, Z82246, Z83846, Z98256
      UniProtKB/TrEMBL
      Q17R54, Q59EX7
      Conserved Domains (4) summary
      PRK07764
      Location:393535
      PRK07764; DNA polymerase III subunits gamma and tau; Validated
      pfam02078
      Location:93189
      Synapsin; N-terminal domain
      pfam10581
      Location:129
      Synapsin_N; Synapsin N-terminal
      cl17255
      Location:192394
      CPSase_L_D2; Carbamoyl-phosphate synthase L chain, ATP binding domain
    5. NM_001369910.1NP_001356839.1  synapsin-3 isoform IIIg

      Status: REVIEWED

      Source sequence(s)
      Z71183, Z80902, Z82181, Z82246, Z83846, Z98256
      UniProtKB/TrEMBL
      Q17R54, Q59EX7
      Conserved Domains (4) summary
      PRK07764
      Location:393535
      PRK07764; DNA polymerase III subunits gamma and tau; Validated
      pfam02078
      Location:93189
      Synapsin; N-terminal domain
      pfam10581
      Location:129
      Synapsin_N; Synapsin N-terminal
      cl17255
      Location:192394
      CPSase_L_D2; Carbamoyl-phosphate synthase L chain, ATP binding domain
    6. NM_003490.4NP_003481.3  synapsin-3 isoform IIIa

      See identical proteins and their annotated locations for NP_003481.3

      Status: REVIEWED

      Source sequence(s)
      Z71183, Z80902, Z82181, Z82246, Z83846, Z98256
      Consensus CDS
      CCDS13908.1
      UniProtKB/Swiss-Prot
      B1B1F9, O14994
      UniProtKB/TrEMBL
      Q59EX7
      Related
      ENSP00000351614.2, ENST00000358763.7
      Conserved Domains (4) summary
      PRK07764
      Location:394536
      PRK07764; DNA polymerase III subunits gamma and tau; Validated
      pfam02078
      Location:93190
      Synapsin; N-terminal domain
      pfam10581
      Location:129
      Synapsin_N; Synapsin N-terminal
      cl17255
      Location:193395
      CPSase_L_D2; Carbamoyl-phosphate synthase L chain, ATP binding domain
    7. NM_133633.3NP_598344.2  synapsin-3 isoform IIIc

      See identical proteins and their annotated locations for NP_598344.2

      Status: REVIEWED

      Source sequence(s)
      Z71183, Z80902, Z82181, Z82246, Z83846, Z98256
      UniProtKB/Swiss-Prot
      O14994
      Conserved Domains (3) summary
      pfam02078
      Location:93190
      Synapsin; Synapsin, N-terminal domain
      pfam02750
      Location:193395
      Synapsin_C; Synapsin, ATP binding domain
      pfam10581
      Location:129
      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_000022.11 Reference GRCh38.p14 Primary Assembly

      Range
      32507820..33058381 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047441527.1XP_047297483.1  synapsin-3 isoform X2

      UniProtKB/TrEMBL
      Q17R54
    2. XM_017028961.3XP_016884450.1  synapsin-3 isoform X1

      UniProtKB/Swiss-Prot
      B1B1F9, O14994
      UniProtKB/TrEMBL
      Q59EX7
      Conserved Domains (4) summary
      PRK07764
      Location:394536
      PRK07764; DNA polymerase III subunits gamma and tau; Validated
      pfam02078
      Location:93190
      Synapsin; N-terminal domain
      pfam10581
      Location:129
      Synapsin_N; Synapsin N-terminal
      cl17255
      Location:193395
      CPSase_L_D2; Carbamoyl-phosphate synthase L chain, ATP binding domain
    3. XM_017028962.3XP_016884451.1  synapsin-3 isoform X1

      UniProtKB/Swiss-Prot
      B1B1F9, O14994
      UniProtKB/TrEMBL
      Q59EX7
      Conserved Domains (4) summary
      PRK07764
      Location:394536
      PRK07764; DNA polymerase III subunits gamma and tau; Validated
      pfam02078
      Location:93190
      Synapsin; N-terminal domain
      pfam10581
      Location:129
      Synapsin_N; Synapsin N-terminal
      cl17255
      Location:193395
      CPSase_L_D2; Carbamoyl-phosphate synthase L chain, ATP binding domain
    4. XM_047441525.1XP_047297481.1  synapsin-3 isoform X2

      UniProtKB/TrEMBL
      Q17R54
    5. XM_017028963.3XP_016884452.1  synapsin-3 isoform X1

      UniProtKB/Swiss-Prot
      B1B1F9, O14994
      UniProtKB/TrEMBL
      Q59EX7
      Conserved Domains (4) summary
      PRK07764
      Location:394536
      PRK07764; DNA polymerase III subunits gamma and tau; Validated
      pfam02078
      Location:93190
      Synapsin; N-terminal domain
      pfam10581
      Location:129
      Synapsin_N; Synapsin N-terminal
      cl17255
      Location:193395
      CPSase_L_D2; Carbamoyl-phosphate synthase L chain, ATP binding domain
    6. XM_047441526.1XP_047297482.1  synapsin-3 isoform X2

      UniProtKB/TrEMBL
      Q17R54
    7. XM_011530405.4XP_011528707.1  synapsin-3 isoform X1

      See identical proteins and their annotated locations for XP_011528707.1

      UniProtKB/Swiss-Prot
      B1B1F9, O14994
      UniProtKB/TrEMBL
      Q59EX7
      Conserved Domains (4) summary
      PRK07764
      Location:394536
      PRK07764; DNA polymerase III subunits gamma and tau; Validated
      pfam02078
      Location:93190
      Synapsin; N-terminal domain
      pfam10581
      Location:129
      Synapsin_N; Synapsin N-terminal
      cl17255
      Location:193395
      CPSase_L_D2; Carbamoyl-phosphate synthase L chain, ATP binding domain
    8. XM_011530410.4XP_011528712.1  synapsin-3 isoform X3

      Conserved Domains (3) summary
      pfam02078
      Location:572
      Synapsin; Synapsin, N-terminal domain
      pfam02750
      Location:75277
      Synapsin_C; Synapsin, ATP binding domain
      pfam16620
      Location:330441
      23ISL; Unstructured linker between I-set domains 2 and 3 on MYLCK
    9. XM_047441529.1XP_047297485.1  synapsin-3 isoform X4

    10. XM_047441528.1XP_047297484.1  synapsin-3 isoform X4

    11. XM_047441530.1XP_047297486.1  synapsin-3 isoform X5

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060946.1 Alternate T2T-CHM13v2.0

      Range
      32971715..33522831 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054325984.1XP_054181959.1  synapsin-3 isoform X2

      UniProtKB/TrEMBL
      Q17R54
    2. XM_054325981.1XP_054181956.1  synapsin-3 isoform X1

      UniProtKB/Swiss-Prot
      B1B1F9, O14994
    3. XM_054325978.1XP_054181953.1  synapsin-3 isoform X1

      UniProtKB/Swiss-Prot
      B1B1F9, O14994
    4. XM_054325982.1XP_054181957.1  synapsin-3 isoform X2

      UniProtKB/TrEMBL
      Q17R54
    5. XM_054325979.1XP_054181954.1  synapsin-3 isoform X1

      UniProtKB/Swiss-Prot
      B1B1F9, O14994
    6. XM_054325983.1XP_054181958.1  synapsin-3 isoform X2

      UniProtKB/TrEMBL
      Q17R54
    7. XM_054325980.1XP_054181955.1  synapsin-3 isoform X1

      UniProtKB/Swiss-Prot
      B1B1F9, O14994
    8. XM_054325985.1XP_054181960.1  synapsin-3 isoform X3

    9. XM_054325987.1XP_054181962.1  synapsin-3 isoform X4

    10. XM_054325988.1XP_054181963.1  synapsin-3 isoform X4

    11. XM_054325986.1XP_054181961.1  synapsin-3 isoform X4

    12. XM_054325989.1XP_054181964.1  synapsin-3 isoform X5

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_133632.1: Suppressed sequence

      Description
      NM_133632.1: This RefSeq was permanently suppressed because it is a nonsense-mediated mRNA decay (NMD) candidate.