Human Gene BACE1 (uc010rxh.2)
  Description: Homo sapiens beta-site APP-cleaving enzyme 1 (BACE1), transcript variant e, mRNA.
RefSeq Summary (NM_001207048): This gene encodes a member of the peptidase A1 family of aspartic proteases. Alternative splicing results in multiple transcript variants, at least one of which encodes a preproprotein that is proteolytically processed to generate the mature protease. This transmembrane protease catalyzes the first step in the formation of amyloid beta peptide from amyloid precursor protein. Amyloid beta peptides are the main constituent of amyloid beta plaques, which accumulate in the brains of human Alzheimer's disease patients. [provided by RefSeq, Nov 2015].
Transcript (Including UTRs)
   Position: hg19 chr11:117,156,402-117,166,386 Size: 9,985 Total Exon Count: 8 Strand: -
Coding Region
   Position: hg19 chr11:117,160,282-117,166,263 Size: 5,982 Coding Exon Count: 8 

Page IndexSequence and LinksPrimersGenetic AssociationsMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr11:117,156,402-117,166,386)mRNA (may differ from genome)Protein (401 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
H-INVHGNCLynxMalacardsMGIOMIM
PubMedTreefamUniProtKBWikipediaBioGrid CRISPR DB

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): BACE1
CDC HuGE Published Literature: BACE1
Positive Disease Associations: Alzheimer's Disease , Body Weight Changes , Cardiovascular Diseases
Related Studies:
  1. Alzheimer's Disease
    Shi, J. et al. 2004, The 1239G/C polymorphism in exon 5 of BACE1 gene may be associated with sporadic Alzheimer's disease in Chinese Hans., American journal of medical genetics Part B, Neuropsychiatric genetics. 2004 Jan;124(1):54-7. [PubMed 14681914]
    Our findings suggest that the 1239G/C polymorphism in exon 5 of BACE1 gene may be associated with sporadic AD in Chinese Hans.
  2. Alzheimer's Disease
    Kan, R. et al. 2005, Genetic association of BACE1 gene polymorphism C786G with late-onset Alzheimer's disease in Chinese., Journal of molecular neuroscience. 2005 ;25(2):127-31. [PubMed 15784960]
    These results suggest that BACE1 gene polymorphism C786G might act as an APOE e4 allele-dependent risk factor for developing LOAD in Chinese.
  3. Alzheimer's Disease
    Liu HC et al. 2003, The association of beta-site APP cleaving enzyme (BACE) C786G polymorphism with Alzheimer's disease., Brain research. 2003 Jan;961(1):88-91. [PubMed 12535780]
           more ... click here to view the complete list

-  MalaCards Disease Associations
  MalaCards Gene Search: BACE1
Diseases sorted by gene-association score: nervous system disease (27), alzheimer disease (23), central nervous system disease (16), disease of mental health (16), autonomic nervous system neoplasm (14), peripheral nervous system neoplasm (14), chromosomal disease (14), hypotrichosis 1 (13), deafness, autosomal recessive 74 (11), toxic encephalopathy (11), acquired metabolic disease (10), inclusion body myositis (10), amyloidosis (9), myositis (9), cerebral amyloid angiopathy (8), nervous system cancer (7), cystoisosporiasis (6), balanoposthitis (6), tracheitis (6), glucose metabolism disease (5), dementia (5), hair disease (5), peroneal nerve paralysis (5), down syndrome (5), hermansky-pudlak syndrome 5 (5), retinitis pigmentosa 33 (4), dementia, frontotemporal (4), skull base meningioma (4), basal ganglia disease (4), achromatopsia 3 (3), neuroblastoma (2), schizophrenia (1), achromatopsia (1)

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 31.70 RPKM in Brain - Spinal cord (cervical c-1)
Total median expression: 384.03 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -43.52123-0.354 Picture PostScript Text
3' UTR -1208.113880-0.311 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR009119 - Pept_A1_BACE
IPR009120 - Pept_A1_BACE1
IPR001461 - Peptidase_A1
IPR021109 - Peptidase_aspartic
IPR009007 - Peptidase_aspartic_catalytic

Pfam Domains:
PF00026 - Eukaryotic aspartyl protease
PF14541 - Xylanase inhibitor C-terminal

SCOP Domains:
50630 - Acid proteases

ModBase Predicted Comparative 3D Structure on B7Z3Z4
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The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGD    
 Protein Sequence    
 Alignment    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0004190 aspartic-type endopeptidase activity

Biological Process:
GO:0006508 proteolysis

Cellular Component:
GO:0016020 membrane
GO:0016021 integral component of membrane


-  Descriptions from all associated GenBank mRNAs
  LF208465 - JP 2014500723-A/15968: Polycomb-Associated Non-Coding RNAs.
CQ824591 - Sequence 18 from Patent WO2004047872.
CQ824592 - Sequence 19 from Patent WO2004047872.
CQ824593 - Sequence 20 from Patent WO2004047872.
CQ824594 - Sequence 21 from Patent WO2004047872.
CS236154 - Sequence 18 from Patent WO2005116212.
CS236155 - Sequence 19 from Patent WO2005116212.
CS236156 - Sequence 20 from Patent WO2005116212.
CS236157 - Sequence 21 from Patent WO2005116212.
DL076407 - TREATMENT OF NEURODEGENERATIVE DISEASE THROUGH INTRACRANIAL DELIVERY OF siRNA.
DL076408 - TREATMENT OF NEURODEGENERATIVE DISEASE THROUGH INTRACRANIAL DELIVERY OF siRNA.
DL076409 - TREATMENT OF NEURODEGENERATIVE DISEASE THROUGH INTRACRANIAL DELIVERY OF siRNA.
DL076410 - TREATMENT OF NEURODEGENERATIVE DISEASE THROUGH INTRACRANIAL DELIVERY OF siRNA.
HV187322 - JP 2006515864-A/18: Treatment of Neurodegenerative Disease Through Intracranial Delivery of siRNA.
HV187323 - JP 2006515864-A/19: Treatment of Neurodegenerative Disease Through Intracranial Delivery of siRNA.
HV187324 - JP 2006515864-A/20: Treatment of Neurodegenerative Disease Through Intracranial Delivery of siRNA.
HV187325 - JP 2006515864-A/21: Treatment of Neurodegenerative Disease Through Intracranial Delivery of siRNA.
HV308702 - JP 2010500357-A/18: Compositions, devices and methods for treatment of huntington's disease through intracranial delivery of sirna.
HV308703 - JP 2010500357-A/19: Compositions, devices and methods for treatment of huntington's disease through intracranial delivery of sirna.
HV308704 - JP 2010500357-A/20: Compositions, devices and methods for treatment of huntington's disease through intracranial delivery of sirna.
HV308705 - JP 2010500357-A/21: Compositions, devices and methods for treatment of huntington's disease through intracranial delivery of sirna.
AF201468 - Homo sapiens APP beta-secretase mRNA, complete cds.
JA482030 - Sequence 13 from Patent WO2011072091.
JA482031 - Sequence 14 from Patent WO2011072091.
JA482032 - Sequence 15 from Patent WO2011072091.
JA482033 - Sequence 16 from Patent WO2011072091.
JE980322 - Sequence 13 from Patent EP2862929.
JE980323 - Sequence 14 from Patent EP2862929.
JE980324 - Sequence 15 from Patent EP2862929.
JE980325 - Sequence 16 from Patent EP2862929.
AB032975 - Homo sapiens mRNA for KIAA1149 protein, partial cds.
BC065492 - Homo sapiens beta-site APP-cleaving enzyme 1, mRNA (cDNA clone MGC:71162 IMAGE:6538154), complete cds.
AF200193 - Homo sapiens memapsin 2 mRNA, partial cds.
AF190725 - Homo sapiens beta-site APP cleaving enzyme (BACE) mRNA, complete cds.
AF200343 - Homo sapiens chromosome 11 aspartyl protease 2 mRNA, complete cds.
AK075049 - Homo sapiens cDNA FLJ90568 fis, clone OVARC1001570, highly similar to Beta-secretase 1 precursor (EC 3.4.23.46).
BC036084 - Homo sapiens beta-site APP-cleaving enzyme 1, mRNA (cDNA clone MGC:33762 IMAGE:5311572), complete cds.
AB050436 - Homo sapiens BACE mRNA for beta-site APP cleaving enzyme I-476, complete cds.
AB050437 - Homo sapiens BACE mRNA for beta-site APP cleaving enzyme I-457, complete cds.
AB050438 - Homo sapiens BACE mRNA for beta-site APP cleaving enzyme I-432, complete cds.
AF204943 - Homo sapiens transmembrane aspartic proteinase Asp 2 (BACE1) mRNA, complete cds.
AF338816 - Homo sapiens beta-site APP cleaving enzyme type B mRNA, complete cds.
AF338817 - Homo sapiens beta-site APP cleaving enzyme type C mRNA, complete cds.
DQ891509 - Synthetic construct clone IMAGE:100004139; FLH177592.01X; RZPDo839B11126D beta-site APP-cleaving enzyme 1 (BACE1) gene, encodes complete protein.
DQ894700 - Synthetic construct Homo sapiens clone IMAGE:100009160; FLH177588.01L; RZPDo839B11125D beta-site APP-cleaving enzyme 1 (BACE1) gene, encodes complete protein.
AB590539 - Synthetic construct DNA, clone: pFN21AE1947, Homo sapiens BACE1 gene for beta-site APP-cleaving enzyme 1, without stop codon, in Flexi system.
AB089958 - Homo sapiens BACE mRNA for beta-site APP cleaving enzyme isoform I-127, complete cds.
CU688052 - Synthetic construct Homo sapiens gateway clone IMAGE:100022491 5' read BACE1 mRNA.
MA444042 - JP 2018138019-A/15968: Polycomb-Associated Non-Coding RNAs.
AB177847 - Homo sapiens mRNA for KIAA1149 splice variant 1.
JD334155 - Sequence 315179 from Patent EP1572962.
JD073038 - Sequence 54062 from Patent EP1572962.
LF376510 - JP 2014500723-A/184013: Polycomb-Associated Non-Coding RNAs.
JD195212 - Sequence 176236 from Patent EP1572962.
JD158037 - Sequence 139061 from Patent EP1572962.
JD365606 - Sequence 346630 from Patent EP1572962.
JD385223 - Sequence 366247 from Patent EP1572962.
JD103133 - Sequence 84157 from Patent EP1572962.
JD084443 - Sequence 65467 from Patent EP1572962.
JD500422 - Sequence 481446 from Patent EP1572962.
JD297593 - Sequence 278617 from Patent EP1572962.
JD224745 - Sequence 205769 from Patent EP1572962.
JD280473 - Sequence 261497 from Patent EP1572962.
JD434693 - Sequence 415717 from Patent EP1572962.
JD386298 - Sequence 367322 from Patent EP1572962.
JD482833 - Sequence 463857 from Patent EP1572962.
JD493694 - Sequence 474718 from Patent EP1572962.
JD381366 - Sequence 362390 from Patent EP1572962.
JD428049 - Sequence 409073 from Patent EP1572962.
AL833810 - Homo sapiens mRNA; cDNA DKFZp564D083 (from clone DKFZp564D083).
JD429869 - Sequence 410893 from Patent EP1572962.
JD043999 - Sequence 25023 from Patent EP1572962.
JD464302 - Sequence 445326 from Patent EP1572962.
LF376509 - JP 2014500723-A/184012: Polycomb-Associated Non-Coding RNAs.
JD265459 - Sequence 246483 from Patent EP1572962.
JD493745 - Sequence 474769 from Patent EP1572962.
JD160015 - Sequence 141039 from Patent EP1572962.
JD239627 - Sequence 220651 from Patent EP1572962.
JD357923 - Sequence 338947 from Patent EP1572962.
JD113412 - Sequence 94436 from Patent EP1572962.
JD082799 - Sequence 63823 from Patent EP1572962.
JD509398 - Sequence 490422 from Patent EP1572962.
JD130898 - Sequence 111922 from Patent EP1572962.
JD348146 - Sequence 329170 from Patent EP1572962.
JD501032 - Sequence 482056 from Patent EP1572962.
JD200463 - Sequence 181487 from Patent EP1572962.
JD422979 - Sequence 404003 from Patent EP1572962.
JD279762 - Sequence 260786 from Patent EP1572962.
JD507913 - Sequence 488937 from Patent EP1572962.
LF376508 - JP 2014500723-A/184011: Polycomb-Associated Non-Coding RNAs.
JD379875 - Sequence 360899 from Patent EP1572962.
JD349051 - Sequence 330075 from Patent EP1572962.
JD323931 - Sequence 304955 from Patent EP1572962.
JD176661 - Sequence 157685 from Patent EP1572962.
JD239150 - Sequence 220174 from Patent EP1572962.
JD260050 - Sequence 241074 from Patent EP1572962.
LF376507 - JP 2014500723-A/184010: Polycomb-Associated Non-Coding RNAs.
JD489827 - Sequence 470851 from Patent EP1572962.
JD551285 - Sequence 532309 from Patent EP1572962.
JD102261 - Sequence 83285 from Patent EP1572962.
JD073462 - Sequence 54486 from Patent EP1572962.
JD197288 - Sequence 178312 from Patent EP1572962.
LF376506 - JP 2014500723-A/184009: Polycomb-Associated Non-Coding RNAs.
JD037904 - Sequence 18928 from Patent EP1572962.
JD202863 - Sequence 183887 from Patent EP1572962.
JD465707 - Sequence 446731 from Patent EP1572962.
JD407864 - Sequence 388888 from Patent EP1572962.
JD211319 - Sequence 192343 from Patent EP1572962.
AK296535 - Homo sapiens cDNA FLJ54693 complete cds, highly similar to Beta-secretase 1 precursor (EC 3.4.23.46).
JD043498 - Sequence 24522 from Patent EP1572962.
LF208466 - JP 2014500723-A/15969: Polycomb-Associated Non-Coding RNAs.
JD295853 - Sequence 276877 from Patent EP1572962.
AF161367 - Homo sapiens HSPC104 mRNA, partial cds.
LF376505 - JP 2014500723-A/184008: Polycomb-Associated Non-Coding RNAs.
JD046052 - Sequence 27076 from Patent EP1572962.
JD431364 - Sequence 412388 from Patent EP1572962.
AK296015 - Homo sapiens cDNA FLJ54690 complete cds, highly similar to Beta-secretase 1 precursor (EC 3.4.23.46).
JD267783 - Sequence 248807 from Patent EP1572962.
AF527782 - Homo sapiens beta-site APP-cleaving enzyme (BACE) mRNA, partial cds, alternatively spliced.
LF376504 - JP 2014500723-A/184007: Polycomb-Associated Non-Coding RNAs.
LF376503 - JP 2014500723-A/184006: Polycomb-Associated Non-Coding RNAs.
MA612087 - JP 2018138019-A/184013: Polycomb-Associated Non-Coding RNAs.
MA612086 - JP 2018138019-A/184012: Polycomb-Associated Non-Coding RNAs.
MA612085 - JP 2018138019-A/184011: Polycomb-Associated Non-Coding RNAs.
MA612084 - JP 2018138019-A/184010: Polycomb-Associated Non-Coding RNAs.
MA612083 - JP 2018138019-A/184009: Polycomb-Associated Non-Coding RNAs.
MA444043 - JP 2018138019-A/15969: Polycomb-Associated Non-Coding RNAs.
MA612082 - JP 2018138019-A/184008: Polycomb-Associated Non-Coding RNAs.
MA612081 - JP 2018138019-A/184007: Polycomb-Associated Non-Coding RNAs.
MA612080 - JP 2018138019-A/184006: Polycomb-Associated Non-Coding RNAs.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa05010 - Alzheimer's disease

-  Other Names for This Gene
  Alternate Gene Symbols: B7Z3Z4, B7Z3Z4_HUMAN, hCG_37942, NM_001207048, NP_001193977
UCSC ID: uc010rxh.2
RefSeq Accession: NM_001207048
Protein: B7Z3Z4 CCDS: CCDS55787.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_001207048.1
exon count: 8CDS single in 3' UTR: no RNA size: 5226
ORF size: 1206CDS single in intron: no Alignment % ID: 99.96
txCdsPredict score: 2543.00frame shift in genome: no % Coverage: 99.67
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.