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SNCB synuclein beta [ Homo sapiens (human) ]

Gene ID: 6620, updated on 9-Jul-2019

Summary

Official Symbol
SNCBprovided by HGNC
Official Full Name
synuclein betaprovided by HGNC
Primary source
HGNC:HGNC:11140
See related
Ensembl:ENSG00000074317 MIM:602569
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

Genomic context

See SNCB in Genome Data Viewer
Location:
5q35.2
Exon count:
7
Annotation release Status Assembly Chr Location
109.20190607 current GRCh38.p13 (GCF_000001405.39) 5 NC_000005.10 (176620082..176630561, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (176047210..176057557, complement)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene cadherin related family member 2 Neighboring gene G protein regulated inducer of neurite outgrowth 1 Neighboring gene Sharpr-MPRA regulatory region 11151 Neighboring gene microRNA 4281 Neighboring gene eukaryotic translation initiation factor 4E family member 1B 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 FunctionsWhat's a GeneRIF?

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
calcium ion binding IDA
Inferred from Direct Assay
more info
PubMed 
cuprous ion binding IMP
Inferred from Mutant Phenotype
more info
PubMed 
phospholipase inhibitor activity TAS
Traceable Author Statement
more info
PubMed 
transition metal ion binding IMP
Inferred from Mutant Phenotype
more info
PubMed 
Process Evidence Code Pubs
chemical synaptic transmission IEA
Inferred from Electronic Annotation
more info
 
dopamine metabolic process IEA
Inferred from Electronic Annotation
more info
 
negative regulation of catalytic activity IEA
Inferred from Electronic Annotation
more info
 
negative regulation of neuron apoptotic process IEA
Inferred from Electronic Annotation
more info
 
response to metal ion TAS
Traceable Author Statement
more info
 
synapse organization IEA
Inferred from Electronic Annotation
more info
 
synaptic vesicle endocytosis IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
cytosol TAS
Traceable Author Statement
more info
 
inclusion body IDA
Inferred from Direct Assay
more info
PubMed 
presynapse IEA
Inferred from Electronic Annotation
more info
 

General protein information

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

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_012131.1 RefSeqGene

    Range
    4996..15473
    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
    Related
    ENSP00000308057.3, ENST00000310112.7
    Conserved Domains (1) summary
    pfam01387
    Location:190
    Synuclein; Synuclein
  2. NM_001318034.1NP_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)
    BM543516, 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:1103
    Synuclein; 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:1103
    Synuclein; 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
    Conserved Domains (1) summary
    pfam01387
    Location:190
    Synuclein; 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
    Related
    ENSP00000377296.2, ENST00000393693.7
    Conserved Domains (1) summary
    pfam01387
    Location:190
    Synuclein; Synuclein

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.p13 Primary Assembly

Genomic

  1. NC_000005.10 Reference GRCh38.p13 Primary Assembly

    Range
    176620082..176630561 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006714916.3XP_006714979.1  beta-synuclein isoform X2

    See identical proteins and their annotated locations for XP_006714979.1

    UniProtKB/Swiss-Prot
    Q16143
    Related
    ENSP00000424073.1, ENST00000510387.5
    Conserved Domains (1) summary
    pfam01387
    Location:190
    Synuclein; Synuclein
  2. XM_006714914.3XP_006714977.1  beta-synuclein isoform X1

    See identical proteins and their annotated locations for XP_006714977.1

    Conserved Domains (1) summary
    pfam01387
    Location:1121
    Synuclein; Synuclein
  3. XM_011534640.2XP_011532942.1  beta-synuclein isoform X1

    See identical proteins and their annotated locations for XP_011532942.1

    Conserved Domains (1) summary
    pfam01387
    Location:1121
    Synuclein; Synuclein
  4. XM_006714915.3XP_006714978.1  beta-synuclein isoform X1

    See identical proteins and their annotated locations for XP_006714978.1

    Conserved Domains (1) summary
    pfam01387
    Location:1121
    Synuclein; Synuclein
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