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SYN3 synapsin III [ Homo sapiens (human) ]

Gene ID: 8224, updated on 8-Dec-2018

Summary

Official Symbol
SYN3provided by HGNC
Official Full Name
synapsin IIIprovided by HGNC
Primary source
HGNC:HGNC:11496
See related
Ensembl:ENSG00000185666 MIM:602705
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

Genomic context

See SYN3 in Genome Data Viewer
Location:
22q12.3
Exon count:
20
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 22 NC_000022.11 (32507820..33058391, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 22 NC_000022.10 (32908539..33454377, complement)

Chromosome 22 - NC_000022.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LL22NC03-104C7.1 Neighboring gene BPI fold containing family C Neighboring gene uncharacterized LOC105373003 Neighboring gene F-box protein 7 Neighboring gene uncharacterized LOC107985545 Neighboring gene uncharacterized LOC105373002 Neighboring gene RNA, 5S ribosomal pseudogene 497 Neighboring gene TIMP metallopeptidase inhibitor 3 Neighboring gene long intergenic non-protein coding RNA 1640 Neighboring gene LARGE xylosyl- and glucuronyltransferase 1 Neighboring gene microRNA 4764

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 FunctionsWhat's a GeneRIF?

Phenotypes

NHGRI GWAS Catalog

Description
Genetic variants near TIMP3 and high-density lipoprotein-associated loci influence susceptibility to age-related macular degeneration.
NHGRI GWA Catalog
Hundreds of variants clustered in genomic loci and biological pathways affect human height.
NHGRI GWA Catalog
Identification, replication, and fine-mapping of Loci associated with adult height in individuals of african ancestry.
NHGRI GWA Catalog
Meta-analysis of genome-wide association studies of adult height in East Asians identifies 17 novel loci.
NHGRI GWA Catalog

Pathways from BioSystems

  • Dopamine Neurotransmitter Release Cycle, organism-specific biosystem (from REACTOME)
    Dopamine Neurotransmitter Release Cycle, organism-specific biosystemDopamine neurotransmitter cycle occurs in dopaminergic neurons. Dopamine is synthesized and loaded into the clathrin sculpted monoamine transport vesicles. The vesicles are docked, primed and fused w...
  • Neuronal System, organism-specific biosystem (from REACTOME)
    Neuronal System, organism-specific biosystemThe human brain contains at least 100 billion neurons, each with the ability to influence many other cells. Clearly, highly sophisticated and efficient mechanisms are needed to enable communication a...
  • Neurotransmitter Release Cycle, organism-specific biosystem (from REACTOME)
    Neurotransmitter Release Cycle, organism-specific biosystemNeurotransmitter is stored in the synaptic vesicle in the pre-synaptic terminal prior to its release in the synaptic cleft upon depolarization of the pre-synaptic membrane. The release of the neurotr...
  • Serotonin Neurotransmitter Release Cycle, organism-specific biosystem (from REACTOME)
    Serotonin Neurotransmitter Release Cycle, organism-specific biosystemSerotonin is synthesized in the serotonergic neurons in the central nervous system and the enterochrommaffin cells of the gastroinetstinal system. Serotonin is loaded into the clathrin sculpted monoa...
  • Synaptic Vesicle Pathway, organism-specific biosystem (from WikiPathways)
    Synaptic Vesicle Pathway, organism-specific biosystemPathway depicting synaptic transmission of neurotransmitters from the presynaptic nerve terminal to the synaptic cleft upon depolarization. Synaptotagmin mediated transport along the nerve cell cytos...
  • Transmission across Chemical Synapses, organism-specific biosystem (from REACTOME)
    Transmission across Chemical Synapses, organism-specific biosystemChemical synapses are specialized junctions that are used for communication between neurons, neurons and muscle or gland cells. The synapse involves a pre-synaptic neuron and a post-synaptic neuron,...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
ATP binding TAS
Traceable Author Statement
more info
PubMed 
Process Evidence Code Pubs
neurotransmitter secretion IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
regulation of synaptic transmission, GABAergic TAS
Traceable Author Statement
more info
PubMed 
synaptic vesicle clustering IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
cell junction IEA
Inferred from Electronic Annotation
more info
 
glutamatergic synapse IEA
Inferred from Electronic Annotation
more info
 
postsynaptic density IEA
Inferred from Electronic Annotation
more info
 
synaptic vesicle TAS
Traceable Author Statement
more info
PubMed 
synaptic vesicle membrane IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 

General protein information

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

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_029545.1 RefSeqGene

    Range
    5001..550839
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

    See identical proteins and their annotated locations for NP_001129246.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (IIIg) uses an alternate in-frame splice site in the mid coding region, compared to variant IIIa, resulting in an isoform (IIIg) that is 1 aa shorter than isoform IIIa.
    Source sequence(s)
    AB209684, AI095028, DB458758, Z71183
    UniProtKB/TrEMBL
    Q17R54, Q59EX7
    Conserved Domains (4) summary
    pfam02078
    Location:93189
    Synapsin; 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
    cl26386
    Location:393535
    DNA_pol3_gamma3; DNA polymerase III subunits gamma and tau domain III
  2. NM_003490.3NP_003481.3  synapsin-3 isoform IIIa

    See identical proteins and their annotated locations for NP_003481.3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (IIIa) encodes the full-length isoform IIIa.
    Source sequence(s)
    AI095028, BC075066, DB458758, Z71183
    Consensus CDS
    CCDS13908.1
    UniProtKB/Swiss-Prot
    O14994
    UniProtKB/TrEMBL
    A0A024R1I8
    Conserved Domains (4) 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
    pfam16620
    Location:448559
    23ISL; Unstructured linker between I-set domains 2 and 3 on MYLCK
  3. NM_133633.2NP_598344.2  synapsin-3 isoform IIIc

    See identical proteins and their annotated locations for NP_598344.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (IIIc) lacks exon 12, which results in a frameshift and early stop codon compared to variant IIIa. The encoded isoform (IIIc) lacks domains J and E, as compared to the full-length isoform IIIa.
    Source sequence(s)
    AI095028, BC075066, DB458758, Z71183
    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: Homo sapiens Annotation Release 109

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

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000022.11 Reference GRCh38.p12 Primary Assembly

    Range
    32507820..33058391 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017028964.2XP_016884453.1  synapsin-3 isoform X2

    UniProtKB/TrEMBL
    Q17R54
    Conserved Domains (4) summary
    pfam02078
    Location:93189
    Synapsin; 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
    cl26386
    Location:393535
    DNA_pol3_gamma3; DNA polymerase III subunits gamma and tau domain III
  2. XM_011530406.3XP_011528708.1  synapsin-3 isoform X1

    See identical proteins and their annotated locations for XP_011528708.1

    UniProtKB/Swiss-Prot
    O14994
    UniProtKB/TrEMBL
    A0A024R1I8
    Related
    ENSP00000351614.2, ENST00000358763.6
    Conserved Domains (4) 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
    pfam16620
    Location:448559
    23ISL; Unstructured linker between I-set domains 2 and 3 on MYLCK
  3. XM_011530410.3XP_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
  4. XM_017028965.2XP_016884454.1  synapsin-3 isoform X4

    Related
    ENSP00000330219.6, ENST00000332840.9
  5. XM_011530408.2XP_011528710.1  synapsin-3 isoform X1

    See identical proteins and their annotated locations for XP_011528710.1

    UniProtKB/Swiss-Prot
    O14994
    UniProtKB/TrEMBL
    A0A024R1I8
    Conserved Domains (4) 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
    pfam16620
    Location:448559
    23ISL; Unstructured linker between I-set domains 2 and 3 on MYLCK
  6. XM_017028961.2XP_016884450.1  synapsin-3 isoform X1

    UniProtKB/Swiss-Prot
    O14994
    UniProtKB/TrEMBL
    A0A024R1I8
    Conserved Domains (4) 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
    pfam16620
    Location:448559
    23ISL; Unstructured linker between I-set domains 2 and 3 on MYLCK
  7. XM_017028962.2XP_016884451.1  synapsin-3 isoform X1

    UniProtKB/Swiss-Prot
    O14994
    UniProtKB/TrEMBL
    A0A024R1I8
    Conserved Domains (4) 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
    pfam16620
    Location:448559
    23ISL; Unstructured linker between I-set domains 2 and 3 on MYLCK
  8. XM_011530407.3XP_011528709.1  synapsin-3 isoform X1

    See identical proteins and their annotated locations for XP_011528709.1

    UniProtKB/Swiss-Prot
    O14994
    UniProtKB/TrEMBL
    A0A024R1I8
    Conserved Domains (4) 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
    pfam16620
    Location:448559
    23ISL; Unstructured linker between I-set domains 2 and 3 on MYLCK
  9. XM_011530405.3XP_011528707.1  synapsin-3 isoform X1

    See identical proteins and their annotated locations for XP_011528707.1

    UniProtKB/Swiss-Prot
    O14994
    UniProtKB/TrEMBL
    A0A024R1I8
    Conserved Domains (4) 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
    pfam16620
    Location:448559
    23ISL; Unstructured linker between I-set domains 2 and 3 on MYLCK
  10. XM_017028963.2XP_016884452.1  synapsin-3 isoform X1

    UniProtKB/Swiss-Prot
    O14994
    UniProtKB/TrEMBL
    A0A024R1I8
    Conserved Domains (4) 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
    pfam16620
    Location:448559
    23ISL; Unstructured linker between I-set domains 2 and 3 on MYLCK

RNA

  1. XR_001755317.2 RNA Sequence

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.
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