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APAF1 apoptotic peptidase activating factor 1 [ Homo sapiens (human) ]

Gene ID: 317, updated on 18-Oct-2014
Official Symbol
APAF1provided by HGNC
Official Full Name
apoptotic peptidase activating factor 1provided by HGNC
Primary source
HGNC:HGNC:576
See related
Ensembl:ENSG00000120868; HPRD:03755; MIM:602233; Vega:OTTHUMG00000170214
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
CED4; APAF-1
Summary
This gene encodes a cytoplasmic protein that initiates apoptosis. This protein contains several copies of the WD-40 domain, a caspase recruitment domain (CARD), and an ATPase domain (NB-ARC). Upon binding cytochrome c and dATP, this protein forms an oligomeric apoptosome. The apoptosome binds and cleaves caspase 9 preproprotein, releasing its mature, activated form. Activated caspase 9 stimulates the subsequent caspase cascade that commits the cell to apoptosis. Alternative splicing results in several transcript variants encoding different isoforms. [provided by RefSeq, Jul 2008]
See APAF1 in Epigenomics, MapViewer
Location:
12q23
Exon count:
27
Annotation release Status Assembly Chr Location
106 current GRCh38 (GCF_000001405.26) 12 NC_000012.12 (98645228..98735433)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (99039078..99129211)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene solute carrier family 25 (mitochondrial carrier; phosphate carrier), member 3 Neighboring gene small nucleolar RNA, H/ACA box 53 Neighboring gene IKBKB interacting protein Neighboring gene probable ribosome biogenesis protein RLP24-like Neighboring gene ankyrin repeat and sterile alpha motif domain containing 1B Neighboring gene RNA, 5S ribosomal pseudogene 366

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Protein interactions

Protein Gene Interaction Pubs
Envelope surface glycoprotein gp120 env The mRNA expression levels for alpha-tubulin, TRADD, IFN-gamma R2, GAS1, MADD, NF-kappaB, I-kappa B, 14-3-3 protein, APaf1, PARP, IGF-1 receptor, RB1, Rb2/p130, ARC, and caspase 6 are upregulated in human neuronal cells after treatment with HIV-1 gp120 PubMed
Tat tat HIV-1 Tat 47-59 peptide upregulates gene expression of apoptotic peptidase activating factor 1 (APAF1) in U-937 macrophages PubMed

Go to the HIV-1, Human Interaction Database

  • Activation of caspases through apoptosome-mediated cleavage, organism-specific biosystem (from REACTOME)
    Activation of caspases through apoptosome-mediated cleavage, organism-specific biosystemProcaspase-3 and 7 are cleaved by the apoptosome.
  • Alzheimer's disease, organism-specific biosystem (from KEGG)
    Alzheimer's disease, organism-specific biosystemAlzheimer's disease (AD) is a chronic disorder that slowly destroys neurons and causes serious cognitive disability. AD is associated with senile plaques and neurofibrillary tangles (NFTs). Amyloid-b...
  • Alzheimer's disease, conserved biosystem (from KEGG)
    Alzheimer's disease, conserved biosystemAlzheimer's disease (AD) is a chronic disorder that slowly destroys neurons and causes serious cognitive disability. AD is associated with senile plaques and neurofibrillary tangles (NFTs). Amyloid-b...
  • Alzheimers Disease, organism-specific biosystem (from WikiPathways)
    Alzheimers Disease, organism-specific biosystemThis pathway displays current genes, proteolytic events and other processes associated with the progression of Alzheimer's disease. This pathway was adapted from KEGG on 10/7/2011. Note: mitochondria...
  • Amyotrophic lateral sclerosis (ALS), organism-specific biosystem (from WikiPathways)
    Amyotrophic lateral sclerosis (ALS), organism-specific biosystemAmyotrophic lateral sclerosis (ALS) is a progressive, lethal, degenerative disorder of motor neurons. The hallmark of this disease is the selective death of motor neurons in the brain and spinal cord...
  • Amyotrophic lateral sclerosis (ALS), organism-specific biosystem (from KEGG)
    Amyotrophic lateral sclerosis (ALS), organism-specific biosystemAmyotrophic lateral sclerosis (ALS) is a progressive, lethal, degenerative disorder of motor neurons. The hallmark of this disease is the selective death of motor neurons in the brain and spinal cord...
  • Amyotrophic lateral sclerosis (ALS), conserved biosystem (from KEGG)
    Amyotrophic lateral sclerosis (ALS), conserved biosystemAmyotrophic lateral sclerosis (ALS) is a progressive, lethal, degenerative disorder of motor neurons. The hallmark of this disease is the selective death of motor neurons in the brain and spinal cord...
  • Apoptosis, organism-specific biosystem (from WikiPathways)
    Apoptosis, organism-specific biosystemApoptosis is a distinct form of cell death that is functionally and morphologically different from necrosis. Nuclear chromatin condensation, cytoplasmic shrinking, dilated endoplasmic reticulum, and ...
  • Apoptosis, organism-specific biosystem (from KEGG)
    Apoptosis, organism-specific biosystemApoptosis is a genetically controlled mechanisms of cell death involved in the regulation of tissue homeostasis. The 2 major pathways of apoptosis are the extrinsic (Fas and other TNFR superfamily me...
  • Apoptosis, conserved biosystem (from KEGG)
    Apoptosis, conserved biosystemApoptosis is a genetically controlled mechanisms of cell death involved in the regulation of tissue homeostasis. The 2 major pathways of apoptosis are the extrinsic (Fas and other TNFR superfamily me...
  • Apoptosis, organism-specific biosystem (from REACTOME)
    Apoptosis, organism-specific biosystemApoptosis is a distinct form of cell death that is functionally and morphologically different from necrosis. Nuclear chromatin condensation, cytoplasmic shrinking, dilated endoplasmic reticulum, and ...
  • Apoptosis Modulation and Signaling, organism-specific biosystem (from WikiPathways)
    Apoptosis Modulation and Signaling, organism-specific biosystemApoptosis, or cell death program, can be activated by various mechanisms within the extrinsic and the intrinsic pathway. While activation of cell death receptors leads to the engagement of the extrin...
  • Apoptosis Modulation by HSP70, organism-specific biosystem (from WikiPathways)
    Apoptosis Modulation by HSP70, organism-specific biosystem
    Apoptosis Modulation by HSP70
  • Apoptotic factor-mediated response, organism-specific biosystem (from REACTOME)
    Apoptotic factor-mediated response, organism-specific biosystemIn response to apoptotic signals, mitochondrial proteins are released into the cytosol and activate both caspase-dependent and -independent cell death pathways. Cytochrome c induces apoptosome form...
  • Caspase cascade in apoptosis, organism-specific biosystem (from Pathway Interaction Database)
    Caspase cascade in apoptosis, organism-specific biosystem
    Caspase cascade in apoptosis
  • Cytochrome c-mediated apoptotic response, organism-specific biosystem (from REACTOME)
    Cytochrome c-mediated apoptotic response, organism-specific biosystemUpon its release from the mitochondrial intermembrane space, Cytochrome c binds to and causes a conformational change in the cytoplasmic protein Apaf1. This conformational change allows the Cytochrom...
  • DNA damage response, organism-specific biosystem (from WikiPathways)
    DNA damage response, organism-specific biosystemThis is the first pathway out of two pathways which deals with DNA damage response. It has two central gene products (ATM and ATR) which are connected to the sources of DNA damage (in blue). The two ...
  • Direct p53 effectors, organism-specific biosystem (from Pathway Interaction Database)
    Direct p53 effectors, organism-specific biosystem
    Direct p53 effectors
  • E2F transcription factor network, organism-specific biosystem (from Pathway Interaction Database)
    E2F transcription factor network, organism-specific biosystem
    E2F transcription factor network
  • FAS pathway and Stress induction of HSP regulation, organism-specific biosystem (from WikiPathways)
    FAS pathway and Stress induction of HSP regulation, organism-specific biosystemThis pathway describes the Fas induced apoptosis and interplay with Hsp27 in response to stress. More info: [http://www.biocarta.com/pathfiles/h_hsp27Pathway.asp BioCarta].
  • Formation of apoptosome, organism-specific biosystem (from REACTOME)
    Formation of apoptosome, organism-specific biosystemCytoplasmic cytochrome c binds to apoptotic protease activating factor-1 (Apaf-1) promoting the formation of an Apaf-1 oligomer (the apoptosome) which in turn binds and activates caspase-9.
  • HIV-1 Nef: Negative effector of Fas and TNF-alpha, organism-specific biosystem (from Pathway Interaction Database)
    HIV-1 Nef: Negative effector of Fas and TNF-alpha, organism-specific biosystem
    HIV-1 Nef: Negative effector of Fas and TNF-alpha
  • Hepatitis B, organism-specific biosystem (from KEGG)
    Hepatitis B, organism-specific biosystemHepatitis B virus (HBV) is an enveloped virus and contains a partially double-stranded relaxed circular DNA (RC-DNA) genome. After entry into hepatocytes, HBV RC-DNA is transported to the nucleus and...
  • Huntington's disease, organism-specific biosystem (from KEGG)
    Huntington's disease, organism-specific biosystemHuntington disease (HD) is an autosomal-dominant neurodegenerative disorder that primarily affects medium spiny striatal neurons (MSN). The symptoms are choreiform, involuntary movements, personality...
  • Huntington's disease, conserved biosystem (from KEGG)
    Huntington's disease, conserved biosystemHuntington disease (HD) is an autosomal-dominant neurodegenerative disorder that primarily affects medium spiny striatal neurons (MSN). The symptoms are choreiform, involuntary movements, personality...
  • Integrated Pancreatic Cancer Pathway, organism-specific biosystem (from WikiPathways)
    Integrated Pancreatic Cancer Pathway, organism-specific biosystemAn integrated pathway model which displays the protein-protein interactions (PPIs) among the relevant proteins for pancreatic cancer. This pathway is a collection of different mechanistic protein pat...
  • Intrinsic Pathway for Apoptosis, organism-specific biosystem (from REACTOME)
    Intrinsic Pathway for Apoptosis, organism-specific biosystemThe intrinsic (Bcl-2 inhibitable or mitochondrial) pathway of apoptosis functions in response to various types of intracellular stress including growth factor withdrawal, DNA damage, unfolding stress...
  • Legionellosis, organism-specific biosystem (from KEGG)
    Legionellosis, organism-specific biosystemLegionellosis is a potentially fatal infectious disease caused by the bacterium Legionella pneumophila and other legionella species. Two distinct clinical and epidemiological syndromes are associated...
  • Legionellosis, conserved biosystem (from KEGG)
    Legionellosis, conserved biosystemLegionellosis is a potentially fatal infectious disease caused by the bacterium Legionella pneumophila and other legionella species. Two distinct clinical and epidemiological syndromes are associated...
  • Parkinson's disease, organism-specific biosystem (from KEGG)
    Parkinson's disease, organism-specific biosystemParkinson's disease (PD) is a progressive neurodegenerative movement disorder that results primarily from the death of dopaminergic (DA) neurons in the substantia nigra pars compacta (SNc). Mutations...
  • Parkinsons Disease Pathway, organism-specific biosystem (from WikiPathways)
    Parkinsons Disease Pathway, organism-specific biosystemMost people with Parkinson's disease have idiopathic Parkinson's disease (having no specific known cause). A small proportion of cases, however, can be attributed to known genetic factors. Mutations ...
  • Small cell lung cancer, organism-specific biosystem (from KEGG)
    Small cell lung cancer, organism-specific biosystemLung cancer is a leading cause of cancer death among men and women in industrialized countries. Small cell lung carcinoma (SCLC) is a highly aggressive neoplasm, which accounts for approximately 25% ...
  • Small cell lung cancer, conserved biosystem (from KEGG)
    Small cell lung cancer, conserved biosystemLung cancer is a leading cause of cancer death among men and women in industrialized countries. Small cell lung carcinoma (SCLC) is a highly aggressive neoplasm, which accounts for approximately 25% ...
  • Tuberculosis, organism-specific biosystem (from KEGG)
    Tuberculosis, organism-specific biosystemTuberculosis, or TB, is an infectious disease caused by Mycobacterium tuberculosis. One third of the world's population is thought to be infected with TB. About 90% of those infected result in latent...
  • Tuberculosis, conserved biosystem (from KEGG)
    Tuberculosis, conserved biosystemTuberculosis, or TB, is an infectious disease caused by Mycobacterium tuberculosis. One third of the world's population is thought to be infected with TB. About 90% of those infected result in latent...
  • p53 signaling pathway, organism-specific biosystem (from KEGG)
    p53 signaling pathway, organism-specific biosystemp53 activation is induced by a number of stress signals, including DNA damage, oxidative stress and activated oncogenes. The p53 protein is employed as a transcriptional activator of p53-regulated ge...
  • p53 signaling pathway, conserved biosystem (from KEGG)
    p53 signaling pathway, conserved biosystemp53 activation is induced by a number of stress signals, including DNA damage, oxidative stress and activated oncogenes. The p53 protein is employed as a transcriptional activator of p53-regulated ge...
  • p75(NTR)-mediated signaling, organism-specific biosystem (from Pathway Interaction Database)
    p75(NTR)-mediated signaling, organism-specific biosystem
    p75(NTR)-mediated signaling
Products Interactant Other Gene Complex Source Pubs Description

Markers

Homology

Clone Names

  • DKFZp781B1145

Gene Ontology Provided by GOA

Function Evidence Code Pubs
ADP binding IEA
Inferred from Electronic Annotation
more info
 
ATP binding IEA
Inferred from Electronic Annotation
more info
 
cysteine-type endopeptidase activator activity involved in apoptotic process NAS
Non-traceable Author Statement
more info
PubMed 
identical protein binding IEA
Inferred from Electronic Annotation
more info
 
nucleotide binding TAS
Traceable Author Statement
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Component Evidence Code Pubs
apoptosome IDA
Inferred from Direct Assay
more info
 
apoptosome TAS
Traceable Author Statement
more info
PubMed 
cytosol TAS
Traceable Author Statement
more info
 
extracellular vesicular exosome IDA
Inferred from Direct Assay
more info
PubMed 
nucleus IEA
Inferred from Electronic Annotation
more info
 
Preferred Names
apoptotic protease-activating factor 1
Names
apoptotic protease-activating factor 1

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_029094.1 

    Range
    5001..95134
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001160.2NP_001151.1  apoptotic protease-activating factor 1 isoform b

    See proteins identical to NP_001151.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) uses an alternate splice site and lacks an exon in the coding region but maintains the reading frame, compared to variant 3. Variant 2 encodes isoform b, which is shorter than isoform c.
    Source sequence(s)
    AC011248, AF013263
    Consensus CDS
    CCDS55863.1
    UniProtKB/Swiss-Prot
    O14727
    Related
    ENSP00000353059, OTTHUMP00000243256, ENST00000359972, OTTHUMT00000408007
    Conserved Domains (4) summary
    COG2319
    Location:6981180
    COG2319; FOG: WD40 repeat [General function prediction only]
    cd00200
    Location:596859
    WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
    pfam00931
    Location:118403
    NB-ARC; NB-ARC domain
    cd08323
    Location:792
    CARD_APAF1; Caspase activation and recruitment domain similar to that found in Apoptotic Protease-Activating Factor 1
  2. NM_013229.2NP_037361.1  apoptotic protease-activating factor 1 isoform a

    See proteins identical to NP_037361.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) uses an alternate splice site in the coding region but maintains the reading frame, compared to variant 3. Variant 1 encodes isoform a, which is shorter than isoform c.
    Source sequence(s)
    AC011248, AF013263, AF134397
    Consensus CDS
    CCDS55862.1
    UniProtKB/Swiss-Prot
    O14727
    Related
    ENSP00000448449, OTTHUMP00000243259, ENST00000550527, OTTHUMT00000408010
    Conserved Domains (4) summary
    COG2319
    Location:6981223
    COG2319; FOG: WD40 repeat [General function prediction only]
    cd00200
    Location:596899
    WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
    pfam00931
    Location:118403
    NB-ARC; NB-ARC domain
    cd08323
    Location:792
    CARD_APAF1; Caspase activation and recruitment domain similar to that found in Apoptotic Protease-Activating Factor 1
  3. NM_181861.1NP_863651.1  apoptotic protease-activating factor 1 isoform c

    See proteins identical to NP_863651.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3), also known as Apaf-1L, encodes the longest isoform (c) of this protein.
    Source sequence(s)
    AC011248, AF013263, AF149794
    Consensus CDS
    CCDS9069.1
    UniProtKB/Swiss-Prot
    O14727
    Conserved Domains (4) summary
    COG2319
    Location:7091234
    COG2319; FOG: WD40 repeat [General function prediction only]
    cd00200
    Location:607910
    WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
    pfam00931
    Location:129414
    NB-ARC; NB-ARC domain
    cd08323
    Location:792
    CARD_APAF1; Caspase activation and recruitment domain similar to that found in Apoptotic Protease-Activating Factor 1
  4. NM_181868.1NP_863658.1  apoptotic protease-activating factor 1 isoform d

    See proteins identical to NP_863658.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4), also known as Apaf-1M, lacks an in-frame exon in the coding region, compared to variant 3. Variant 4 encodes isoform d, which is shorter than isoform c.
    Source sequence(s)
    AC011248, AF013263, AJ243003
    Consensus CDS
    CCDS9070.1
    UniProtKB/Swiss-Prot
    O14727
    Related
    ENSP00000349862, ENST00000357310
    Conserved Domains (4) summary
    COG2319
    Location:7091191
    COG2319; FOG: WD40 repeat [General function prediction only]
    cd00200
    Location:607870
    WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
    pfam00931
    Location:129414
    NB-ARC; NB-ARC domain
    cd08323
    Location:792
    CARD_APAF1; Caspase activation and recruitment domain similar to that found in Apoptotic Protease-Activating Factor 1
  5. NM_181869.1NP_863659.1  apoptotic protease-activating factor 1 isoform e

    See proteins identical to NP_863659.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5), also known as APAF-1-ALT, lacks several exons in the coding sequence, resulting in a frameshift and an early termination codon compared to variant 3. Variant 5 encodes isoform e, which is shorter and has a distinct C-terminus compared to isoform c.
    Source sequence(s)
    AB103079, AC011248, AF013263
    Consensus CDS
    CCDS9071.1
    UniProtKB/Swiss-Prot
    O14727
    Related
    ENSP00000334558, ENST00000333991
    Conserved Domains (2) summary
    cd08323
    Location:792
    CARD_APAF1; Caspase activation and recruitment domain similar to that found in Apoptotic Protease-Activating Factor 1
    cl18944
    Location:129318
    AAA; The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, ...

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 106

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38 Primary Assembly

Genomic

  1. NC_000012.12 

    Range
    98645228..98735433
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

RNA

  1. XR_429095.1 RNA Sequence

Alternate HuRef

Genomic

  1. AC_000144.1 

    Range
    96100029..96190306
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate CHM1_1.1

Genomic

  1. NC_018923.2 

    Range
    99004024..99094151
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)