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    BACE2 beta-secretase 2 [ Homo sapiens (human) ]

    Gene ID: 25825, updated on 3-Dec-2024

    Summary

    Official Symbol
    BACE2provided by HGNC
    Official Full Name
    beta-secretase 2provided by HGNC
    Primary source
    HGNC:HGNC:934
    See related
    Ensembl:ENSG00000182240 MIM:605668; AllianceGenome:HGNC:934
    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
    Also known as
    ASP1; BAE2; DRAP; AEPLC; ALP56; ASP21; CDA13; CEAP1
    Summary
    This gene encodes an integral membrane glycoprotein that functions as an aspartic protease. The encoded protein cleaves amyloid precursor protein into amyloid beta peptide, which is a critical step in the etiology of Alzheimer's disease and Down syndrome. The protein precursor is further processed into an active mature peptide. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2013]
    Expression
    Ubiquitous expression in stomach (RPKM 12.5), gall bladder (RPKM 11.8) and 23 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See BACE2 in Genome Data Viewer
    Location:
    21q22.2-q22.3
    Exon count:
    11
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 21 NC_000021.9 (41168160..41282530)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 21 NC_060945.1 (39556492..39670904)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 21 NC_000021.8 (42540087..42654457)

    Chromosome 21 - NC_000021.9Genomic Context describing neighboring genes Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr21:42519321-42519905 Neighboring gene long intergenic non-protein coding RNA 323 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13329 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:42551642-42552451 Neighboring gene microRNA 3197 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:42572358-42572858 Neighboring gene placenta enriched 4 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:42572859-42573359 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:42594561-42595060 Neighboring gene ReSE screen-validated silencer GRCh37_chr21:42612073-42612217 Neighboring gene NANOG hESC enhancer GRCh37_chr21:42616252-42616757 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr21:42646500-42647699 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:42651763-42652318 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:42652319-42652873 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:42661864-42662364 Neighboring gene FAM3 metabolism regulating signaling molecule B Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18470 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr21:42731293-42732096 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18471 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18472 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13330 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18473 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:42739613-42740114 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18474 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:42740714-42741402 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:42741403-42742089 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 21:42745414 Neighboring gene melanoma risk locus-associated MPRA allelic enhancers 21:42746568 and 21:42746578 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:42750497-42750998 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:42750999-42751498 Neighboring gene MX dynamin like GTPase 2

    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

    Related articles in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Phenotypes

    EBI GWAS Catalog

    Description
    Common genetic variants associated with cognitive performance identified using the proxy-phenotype method.
    EBI GWAS Catalog
    Identification of HKDC1 and BACE2 as genes influencing glycemic traits during pregnancy through genome-wide association studies.
    EBI GWAS Catalog

    HIV-1 interactions

    Replication interactions

    Interaction Pubs
    Knockdown of beta-site APP-cleaving enzyme 2 (BACE2) by siRNA inhibits HIV-1 replication in HeLa P4/R5 cells PubMed

    Protein interactions

    Protein Gene Interaction Pubs
    Tat tat HIV-1 Tat recruits APP into lipid rafts to facilitate the processing of APP by beta-secretase, which leads to increased levels of ABeta42 in HIV-1 infected U-87 MG cells PubMed

    Go to the HIV-1, Human Interaction Database

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • FLJ13585

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables aspartic-type endopeptidase activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    Component Evidence Code Pubs
    located_in Golgi apparatus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in endoplasmic reticulum IEA
    Inferred from Electronic Annotation
    more info
     
    is_active_in endosome IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in melanosome membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in membrane NAS
    Non-traceable Author Statement
    more info
    PubMed 
    is_active_in plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in plasma membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    is_active_in trans-Golgi network IBA
    Inferred from Biological aspect of Ancestor
    more info
     

    General protein information

    Preferred Names
    beta-secretase 2
    Names
    56 kDa aspartic-like protease
    Down syndrome region aspartic protease
    SLCO3A1/BACE2 fusion
    aspartyl protease 1
    beta-site APP-cleaving enzyme 2
    beta-site amyloid beta A4 precursor protein-cleaving enzyme 2
    memapsin-1
    membrane-associated aspartic protease 1
    theta-secretase
    transmembrane aspartic proteinase Asp1
    NP_036237.2
    NP_620476.1
    NP_620477.1
    XP_016883803.1
    XP_054180398.1
    XP_054180399.1

    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.

    mRNA and Protein(s)

    1. NM_012105.5NP_036237.2  beta-secretase 2 isoform A preproprotein

      See identical proteins and their annotated locations for NP_036237.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (a) represents the longest transcript and encodes the longest isoform (A).
      Source sequence(s)
      AF178532, AF188276, AF200342, AL773578
      Consensus CDS
      CCDS13668.1
      UniProtKB/Swiss-Prot
      A8K7P1, Q5DIH8, Q8N2D4, Q9H2V8, Q9NZL1, Q9NZL2, Q9UJT6, Q9Y5Z0
      Related
      ENSP00000332979.6, ENST00000330333.11
      Conserved Domains (2) summary
      cd05473
      Location:89450
      beta_secretase_like; Beta-secretase, aspartic-acid protease important in the pathogenesis of Alzheimer's disease
      pfam00026
      Location:92430
      Asp; Eukaryotic aspartyl protease
    2. NM_138991.3NP_620476.1  beta-secretase 2 isoform C preproprotein

      See identical proteins and their annotated locations for NP_620476.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (c) lacks an alternate in-frame exon, compared to variant a. The encoded isoform (C) is shorter than isoform A.
      Source sequence(s)
      AF188276, AF200342, AL773578
      Consensus CDS
      CCDS13669.1
      UniProtKB/Swiss-Prot
      Q9Y5Z0
      Related
      ENSP00000327528.4, ENST00000347667.5
      Conserved Domains (2) summary
      pfam00026
      Location:92380
      Asp; Eukaryotic aspartyl protease
      cl11403
      Location:89400
      pepsin_retropepsin_like; Cellular and retroviral pepsin-like aspartate proteases
    3. NM_138992.3NP_620477.1  beta-secretase 2 isoform B preproprotein

      See identical proteins and their annotated locations for NP_620477.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (b) lacks an exon in the 3' coding region, which results in a frameshift, compared to variant a. The encoded isoform (B) is shorter and has a distinct C-terminus, compared to isoform A.
      Source sequence(s)
      AF188276, AF188277, AF200342, AL773578
      Consensus CDS
      CCDS13670.1
      UniProtKB/Swiss-Prot
      Q9Y5Z0
      Related
      ENSP00000333854.6, ENST00000328735.10
      Conserved Domains (1) summary
      cl11403
      Location:89393
      pepsin_retropepsin_like; Cellular and retroviral pepsin-like aspartate proteases

    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_000021.9 Reference GRCh38.p14 Primary Assembly

      Range
      41168160..41282530
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017028314.2XP_016883803.1  beta-secretase 2 isoform X1

      UniProtKB/TrEMBL
      B3KNE8

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060945.1 Alternate T2T-CHM13v2.0

      Range
      39556492..39670904
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054324423.1XP_054180398.1  beta-secretase 2 isoform X1

      UniProtKB/TrEMBL
      B3KNE8
    2. XM_054324424.1XP_054180399.1  beta-secretase 2 isoform X2

      UniProtKB/TrEMBL
      B3KNE8