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SYN3 synapsin III [ Homo sapiens (human) ]

Gene ID: 8224, updated on 2-Nov-2024

Summary

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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
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Genomic context

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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

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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

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Related articles in PubMed

  1. Molecular and in silico analyses of SYN III gene variants in autism spectrum disorder. Baris RO, et al. Ir J Med Sci, 2023 Dec. PMID 37166614
  2. Characterization of transcripts from the synapsin III gene locus. Porton B, et al. J Neurochem, 1999 Dec. PMID 10582583
  3. Mutation analysis of synapsin III gene in schizophrenia. Tsai MT, et al. Am J Med Genet, 2002 Jan 8. PMID 11840510
  4. A rare polymorphism affects a mitogen-activated protein kinase site in synapsin III: possible relationship to schizophrenia. Porton B, et al. Biol Psychiatry, 2004 Jan 15. PMID 14732590
  5. Synapsin III is a key component of α-synuclein fibrils in Lewy bodies of PD brains. Longhena F, et al. Brain Pathol, 2018 Nov. PMID 29330884, Free PMC Article

See all (42) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Molecular and in silico analyses of SYN III gene variants in autism spectrum disorder.
    Title: Molecular and in silico analyses of SYN III gene variants in autism spectrum disorder.
  2. Investigation of possible associations of the BDNF, SNAP-25 and SYN III genes with the neurocognitive measures: BDNF and SNAP-25 genes might be involved in attention domain, SYN III gene in executive function.
    Title: Investigation of possible associations of the BDNF, SNAP-25 and SYN III genes with the neurocognitive measures: BDNF and SNAP-25 genes might be involved in attention domain, SYN III gene in executive function.
  3. Synapsin III is a crucial alpha-synuclein interactant and a key component of Lewy bodies fibrils in the brain of patients affected by Parkinson's disease.
    Title: Synapsin III is a key component of α-synuclein fibrils in Lewy bodies of PD brains.
  4. These findings contribute to previous work showing dysregulation of Synapsins, particularly SYN2, in mood disorders and improve our understanding of the regulatory mechanisms that precipitate these changes likely leading to the BD or MDD phenotype.
    Title: DNA hypomethylation of Synapsin II CpG islands associates with increased gene expression in bipolar disorder and major depression.
  5. Syn-3 may mimic Syn-1A in the ability to bind and modulate Cavs, but preferring Cav2.3 to perhaps participate in triggering fusion of newcomer insulin SGs during second-phase GSIS.
    Title: Syntaxin-3 Binds and Regulates Both R- and L-Type Calcium Channels in Insulin-Secreting INS-1 832/13 Cells.
  6. These findings support a reciprocal modulatory interaction of alpha-syn and synapsin III in the regulation of dopamine neuron synaptic function.
    Title: α-synuclein and synapsin III cooperatively regulate synaptic function in dopamine neurons.
  7. The variations of MnSOD (rs4880) and SYN III (rs3788470, rs3827336, rs5998557) were not major risk factors for PD among Chinese, at least in our study populations
    Title: No association of four candidate genetic variants in MnSOD and SYNIII with Parkinson's disease in two Chinese populations.
  8. A significant difference was determined between attention deficit hyperactivity disorder and synapsin III gene -631 C>G polymorphism compared to the control group.
    Title: Association of synapsin III gene with adult attention deficit hyperactivity disorder.
  9. A protein encoded by this locus was found to be differentially expressed in postmortem brains from patients with atypical frontotemporal lobar degeneration.
    Title: Proteomic analysis identifies dysfunction in cellular transport, energy, and protein metabolism in different brain regions of atypical frontotemporal lobar degeneration.
  10. This protein has been found differentially expressed in thalami from patients with schizophrenia.
    Title: Proteome analysis of the thalamus and cerebrospinal fluid reveals glycolysis dysfunction and potential biomarkers candidates for schizophrenia.
Submit: New GeneRIF Correction See all GeneRIFs (21)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

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

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

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 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
  
involved_in synaptic vesicle clustering IEA
Inferred from Electronic Annotation
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

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

NCBI Reference Sequences (RefSeq)

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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_001135774.2 → NP_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:393 → 535
    PRK07764; DNA polymerase III subunits gamma and tau; Validated
    pfam02078
    Location:93 → 189
    Synapsin; N-terminal domain
    pfam10581
    Location:1 → 29
    Synapsin_N; Synapsin N-terminal
    cl17255
    Location:192 → 394
    CPSase_L_D2; Carbamoyl-phosphate synthase L chain, ATP binding domain

  2. NM_001369907.1 → NP_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:394 → 536
    PRK07764; DNA polymerase III subunits gamma and tau; Validated
    pfam02078
    Location:93 → 190
    Synapsin; N-terminal domain
    pfam10581
    Location:1 → 29
    Synapsin_N; Synapsin N-terminal
    cl17255
    Location:193 → 395
    CPSase_L_D2; Carbamoyl-phosphate synthase L chain, ATP binding domain

  3. NM_001369908.1 → NP_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:394 → 536
    PRK07764; DNA polymerase III subunits gamma and tau; Validated
    pfam02078
    Location:93 → 190
    Synapsin; N-terminal domain
    pfam10581
    Location:1 → 29
    Synapsin_N; Synapsin N-terminal
    cl17255
    Location:193 → 395
    CPSase_L_D2; Carbamoyl-phosphate synthase L chain, ATP binding domain

  4. NM_001369909.1 → NP_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:393 → 535
    PRK07764; DNA polymerase III subunits gamma and tau; Validated
    pfam02078
    Location:93 → 189
    Synapsin; N-terminal domain
    pfam10581
    Location:1 → 29
    Synapsin_N; Synapsin N-terminal
    cl17255
    Location:192 → 394
    CPSase_L_D2; Carbamoyl-phosphate synthase L chain, ATP binding domain

  5. NM_001369910.1 → NP_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:393 → 535
    PRK07764; DNA polymerase III subunits gamma and tau; Validated
    pfam02078
    Location:93 → 189
    Synapsin; N-terminal domain
    pfam10581
    Location:1 → 29
    Synapsin_N; Synapsin N-terminal
    cl17255
    Location:192 → 394
    CPSase_L_D2; Carbamoyl-phosphate synthase L chain, ATP binding domain

  6. NM_003490.4 → NP_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:394 → 536
    PRK07764; DNA polymerase III subunits gamma and tau; Validated
    pfam02078
    Location:93 → 190
    Synapsin; N-terminal domain
    pfam10581
    Location:1 → 29
    Synapsin_N; Synapsin N-terminal
    cl17255
    Location:193 → 395
    CPSase_L_D2; Carbamoyl-phosphate synthase L chain, ATP binding domain

  7. NM_133633.3 → NP_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:93 → 190
    Synapsin; Synapsin, N-terminal domain
    pfam02750
    Location:193 → 395
    Synapsin_C; Synapsin, ATP binding domain
    pfam10581
    Location:1 → 29
    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_047441527.1 → XP_047297483.1  synapsin-3 isoform X2

    UniProtKB/TrEMBL
    Q17R54

  2. XM_017028961.3 → XP_016884450.1  synapsin-3 isoform X1

    UniProtKB/Swiss-Prot
    B1B1F9, O14994
    UniProtKB/TrEMBL
    Q59EX7
    Conserved Domains (4) summary
    PRK07764
    Location:394 → 536
    PRK07764; DNA polymerase III subunits gamma and tau; Validated
    pfam02078
    Location:93 → 190
    Synapsin; N-terminal domain
    pfam10581
    Location:1 → 29
    Synapsin_N; Synapsin N-terminal
    cl17255
    Location:193 → 395
    CPSase_L_D2; Carbamoyl-phosphate synthase L chain, ATP binding domain

  3. XM_017028962.3 → XP_016884451.1  synapsin-3 isoform X1

    UniProtKB/Swiss-Prot
    B1B1F9, O14994
    UniProtKB/TrEMBL
    Q59EX7
    Conserved Domains (4) summary
    PRK07764
    Location:394 → 536
    PRK07764; DNA polymerase III subunits gamma and tau; Validated
    pfam02078
    Location:93 → 190
    Synapsin; N-terminal domain
    pfam10581
    Location:1 → 29
    Synapsin_N; Synapsin N-terminal
    cl17255
    Location:193 → 395
    CPSase_L_D2; Carbamoyl-phosphate synthase L chain, ATP binding domain

  4. XM_047441525.1 → XP_047297481.1  synapsin-3 isoform X2

    UniProtKB/TrEMBL
    Q17R54

  5. XM_017028963.3 → XP_016884452.1  synapsin-3 isoform X1

    UniProtKB/Swiss-Prot
    B1B1F9, O14994
    UniProtKB/TrEMBL
    Q59EX7
    Conserved Domains (4) summary
    PRK07764
    Location:394 → 536
    PRK07764; DNA polymerase III subunits gamma and tau; Validated
    pfam02078
    Location:93 → 190
    Synapsin; N-terminal domain
    pfam10581
    Location:1 → 29
    Synapsin_N; Synapsin N-terminal
    cl17255
    Location:193 → 395
    CPSase_L_D2; Carbamoyl-phosphate synthase L chain, ATP binding domain

  6. XM_047441526.1 → XP_047297482.1  synapsin-3 isoform X2

    UniProtKB/TrEMBL
    Q17R54

  7. XM_011530405.4 → XP_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:394 → 536
    PRK07764; DNA polymerase III subunits gamma and tau; Validated
    pfam02078
    Location:93 → 190
    Synapsin; N-terminal domain
    pfam10581
    Location:1 → 29
    Synapsin_N; Synapsin N-terminal
    cl17255
    Location:193 → 395
    CPSase_L_D2; Carbamoyl-phosphate synthase L chain, ATP binding domain

  8. XM_011530410.4 → XP_011528712.1  synapsin-3 isoform X3

    Conserved Domains (3) summary
    pfam02078
    Location:5 → 72
    Synapsin; Synapsin, N-terminal domain
    pfam02750
    Location:75 → 277
    Synapsin_C; Synapsin, ATP binding domain
    pfam16620
    Location:330 → 441
    23ISL; Unstructured linker between I-set domains 2 and 3 on MYLCK

  9. XM_047441529.1 → XP_047297485.1  synapsin-3 isoform X4

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

  11. XM_047441530.1 → XP_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_054325984.1 → XP_054181959.1  synapsin-3 isoform X2

    UniProtKB/TrEMBL
    Q17R54

  2. XM_054325981.1 → XP_054181956.1  synapsin-3 isoform X1

    UniProtKB/Swiss-Prot
    B1B1F9, O14994

  3. XM_054325978.1 → XP_054181953.1  synapsin-3 isoform X1

    UniProtKB/Swiss-Prot
    B1B1F9, O14994

  4. XM_054325982.1 → XP_054181957.1  synapsin-3 isoform X2

    UniProtKB/TrEMBL
    Q17R54

  5. XM_054325979.1 → XP_054181954.1  synapsin-3 isoform X1

    UniProtKB/Swiss-Prot
    B1B1F9, O14994

  6. XM_054325983.1 → XP_054181958.1  synapsin-3 isoform X2

    UniProtKB/TrEMBL
    Q17R54

  7. XM_054325980.1 → XP_054181955.1  synapsin-3 isoform X1

    UniProtKB/Swiss-Prot
    B1B1F9, O14994

  8. XM_054325985.1 → XP_054181960.1  synapsin-3 isoform X3

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

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

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

  12. XM_054325989.1 → XP_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.
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
O14994.2 GenPept UniProtKB/Swiss-Prot:O14994

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