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    SNCB synuclein beta [ Homo sapiens (human) ]

    Gene ID: 6620, updated on 10-Dec-2024

    Summary

    Official Symbol
    SNCBprovided by HGNC
    Official Full Name
    synuclein betaprovided by HGNC
    Primary source
    HGNC:HGNC:11140
    See related
    Ensembl:ENSG00000074317 MIM:602569; AllianceGenome:HGNC:11140
    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 a member of a small family of proteins that inhibit phospholipase D2 and may function in neuronal plasticity. The encoded protein is abundant in lesions of patients with Alzheimer disease. A mutation in this gene was found in individuals with dementia with Lewy bodies. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2015]
    Expression
    Restricted expression toward brain (RPKM 60.7) See more
    Orthologs
    NEW
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    Try the new Transcript table

    Genomic context

    See SNCB in Genome Data Viewer
    Location:
    5q35.2
    Exon count:
    7
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (176620082..176630534, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (177166665..177177114, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (176047083..176057535, complement)

    Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:175976615-175977548 Neighboring gene RNA, 7SL, cytoplasmic 684, pseudogene Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:175979197-175979830 Neighboring gene cadherin related family member 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:175993117-175994082 Neighboring gene Sharpr-MPRA regulatory region 7457 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16658 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16659 Neighboring gene G protein regulated inducer of neurite outgrowth 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16660 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16661 Neighboring gene Sharpr-MPRA regulatory region 11151 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16662 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16663 Neighboring gene microRNA 4281 Neighboring gene eukaryotic translation initiation factor 4E family member 1B Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:176070445-176071086 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:176071087-176071726 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:176072308-176072818 Neighboring gene Sharpr-MPRA regulatory region 4950 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16664 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:176075745-176076614 Neighboring gene VISTA enhancer hs2007 Neighboring gene tetraspanin 17

    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?

    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 calcium ion binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables cuprous ion binding IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables cuprous ion binding IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    enables phospholipase inhibitor activity TAS
    Traceable Author Statement
    more info
    PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables transition metal ion binding IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    Process Evidence Code Pubs
    involved_in chemical synaptic transmission IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in dopamine metabolic process IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in negative regulation of neuron apoptotic process IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in neuron apoptotic process IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in synapse organization IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in synaptic vesicle endocytosis IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    Component Evidence Code Pubs
    is_active_in axon terminus IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    is_active_in cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in cytosol TAS
    Traceable Author Statement
    more info
     
    located_in inclusion body IDA
    Inferred from Direct Assay
    more info
    PubMed 
    is_active_in neuronal cell body IBA
    Inferred from Biological aspect of Ancestor
    more info
     

    General protein information

    Preferred Names
    beta-synuclein
    Names
    I(2)-synuclein

    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_012131.1 RefSeqGene

      Range
      5023..15475
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001001502.3NP_001001502.1  beta-synuclein isoform 1

      See identical proteins and their annotated locations for NP_001001502.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1). Variants 1, 2 and 7 encode the same protein (isoform 1).
      Source sequence(s)
      AC091934, BC002902, BM543516, BQ184193, S69965
      Consensus CDS
      CCDS4406.1
      UniProtKB/Swiss-Prot
      Q16143, Q6IAX7
      Related
      ENSP00000308057.3, ENST00000310112.7
      Conserved Domains (1) summary
      pfam01387
      Location:1121
      Synuclein
    2. NM_001318034.2NP_001304963.1  beta-synuclein isoform 2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) lacks an alternate in-frame exon compared to variant 1. The encoded isoform (2) is shorter than isoform 1. Variants 3 and 5 encode the same protein (isoform 2).
      Source sequence(s)
      AC091934, BQ184193, JF960950
      Consensus CDS
      CCDS83048.1
      UniProtKB/TrEMBL
      G4Y816
      Related
      ENSP00000479489.1, ENST00000614675.4
      Conserved Domains (1) summary
      pfam01387
      Location:176
      Synuclein; Synuclein
    3. NM_001318035.2NP_001304964.1  beta-synuclein isoform 3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) lacks an alternate in-frame exon compared to variant 1. The encoded isoform (3) is shorter than isoform 1. Both variants 4 and 6 encode the same protein (isoform 3).
      Source sequence(s)
      AC091934, BQ184193, JF960951
      UniProtKB/TrEMBL
      G4Y815
      Conserved Domains (1) summary
      pfam01387
      Location:197
      Synuclein
    4. NM_001318036.2NP_001304965.1  beta-synuclein isoform 2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (5) lacks exons in the 5' UTR and coding region compared to variant 1. The encoded isoform (2) is shorter than isoform 1. Variants 3 and 5 encode the same isoform (2).
      Source sequence(s)
      AC091934, BQ184193, JF960952
      Consensus CDS
      CCDS83048.1
      UniProtKB/TrEMBL
      G4Y816
      Conserved Domains (1) summary
      pfam01387
      Location:176
      Synuclein; Synuclein
    5. NM_001318037.2NP_001304966.1  beta-synuclein isoform 3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (6) lacks exons in the 5' UTR and coding region compared to variant 1. The encoded isoform (3) is shorter than isoform 1. Variants 4 and 6 encode the same isoform (3).
      Source sequence(s)
      AC091934, BQ184193, JF960953
      UniProtKB/TrEMBL
      G4Y815
      Conserved Domains (1) summary
      pfam01387
      Location:197
      Synuclein
    6. NM_001363140.2NP_001350069.1  beta-synuclein isoform 1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (7) lacks a segment in the 5' UTR compared to variant 1. Variants 1, 2 and 7 encode the same protein (isoform 1).
      Source sequence(s)
      AC091934
      Consensus CDS
      CCDS4406.1
      UniProtKB/Swiss-Prot
      Q16143, Q6IAX7
      Conserved Domains (1) summary
      pfam01387
      Location:1121
      Synuclein
    7. NM_003085.5NP_003076.1  beta-synuclein isoform 1

      See identical proteins and their annotated locations for NP_003076.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks an exon in the 5' UTR compared to variant 1. Variants 1, 2 and 7 encode the same protein (isoform 1).
      Source sequence(s)
      AC091934, BC002902, BM543516, BQ184193, S69965
      Consensus CDS
      CCDS4406.1
      UniProtKB/Swiss-Prot
      Q16143, Q6IAX7
      Related
      ENSP00000377296.2, ENST00000393693.7
      Conserved Domains (1) summary
      pfam01387
      Location:1121
      Synuclein

    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_000005.10 Reference GRCh38.p14 Primary Assembly

      Range
      176620082..176630534 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011534640.3XP_011532942.1  beta-synuclein isoform X1

      See identical proteins and their annotated locations for XP_011532942.1

      Conserved Domains (1) summary
      pfam01387
      Location:1125
      Synuclein
    2. XM_006714915.4XP_006714978.1  beta-synuclein isoform X1

      See identical proteins and their annotated locations for XP_006714978.1

      Conserved Domains (1) summary
      pfam01387
      Location:1125
      Synuclein
    3. XM_006714914.4XP_006714977.1  beta-synuclein isoform X1

      See identical proteins and their annotated locations for XP_006714977.1

      Conserved Domains (1) summary
      pfam01387
      Location:1125
      Synuclein

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060929.1 Alternate T2T-CHM13v2.0

      Range
      177166665..177177114 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054353307.1XP_054209282.1  beta-synuclein isoform X1

    2. XM_054353308.1XP_054209283.1  beta-synuclein isoform X1

    3. XM_054353306.1XP_054209281.1  beta-synuclein isoform X1