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

Gene ID: 317, updated on 16-Feb-2020

Summary

Official Symbol
APAF1provided by HGNC
Official Full Name
apoptotic peptidase activating factor 1provided by HGNC
Primary source
HGNC:HGNC:576
See related
Ensembl:ENSG00000120868 MIM:602233
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]
Expression
Ubiquitous expression in bone marrow (RPKM 6.1), appendix (RPKM 5.1) and 25 other tissues See more
Orthologs

Genomic context

See APAF1 in Genome Data Viewer
Location:
12q23.1
Exon count:
28
Annotation release Status Assembly Chr Location
109.20191205 current GRCh38.p13 (GCF_000001405.39) 12 NC_000012.12 (98645141..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 member 3 Neighboring gene small nucleolar RNA, H/ACA box 53 Neighboring gene IKBKB interacting protein Neighboring gene probable ribosome biogenesis protein RLP24 pseudogene Neighboring gene ankyrin repeat and sterile alpha motif domain containing 1B Neighboring gene RNA, 5S ribosomal pseudogene 366

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?

HIV-1 interactions

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

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

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 IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cysteine-type endopeptidase activator activity involved in apoptotic process NAS
Non-traceable Author Statement
more info
PubMed 
heat shock protein binding IEA
Inferred from Electronic Annotation
more info
 
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 
Process Evidence Code Pubs
activation of cysteine-type endopeptidase activity involved in apoptotic process IDA
Inferred from Direct Assay
more info
PubMed 
activation of cysteine-type endopeptidase activity involved in apoptotic process by cytochrome c IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
activation of cysteine-type endopeptidase activity involved in apoptotic process by cytochrome c IDA
Inferred from Direct Assay
more info
PubMed 
activation of cysteine-type endopeptidase activity involved in apoptotic process by cytochrome c TAS
Traceable Author Statement
more info
 
aging IEA
Inferred from Electronic Annotation
more info
 
apoptotic process TAS
Traceable Author Statement
more info
PubMed 
cardiac muscle cell apoptotic process IEA
Inferred from Electronic Annotation
more info
 
cell differentiation IEA
Inferred from Electronic Annotation
more info
 
cellular response to transforming growth factor beta stimulus IEA
Inferred from Electronic Annotation
more info
 
forebrain development IEA
Inferred from Electronic Annotation
more info
 
intrinsic apoptotic signaling pathway TAS
Traceable Author Statement
more info
PubMed 
intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress IEA
Inferred from Electronic Annotation
more info
 
kidney development IEA
Inferred from Electronic Annotation
more info
 
negative regulation of G0 to G1 transition TAS
Traceable Author Statement
more info
 
nervous system development TAS
Traceable Author Statement
more info
PubMed 
neural tube closure IEA
Inferred from Electronic Annotation
more info
 
neuron apoptotic process IEA
Inferred from Electronic Annotation
more info
 
neutrophil degranulation TAS
Traceable Author Statement
more info
 
positive regulation of apoptotic process TAS
Traceable Author Statement
more info
PubMed 
positive regulation of apoptotic signaling pathway IEA
Inferred from Electronic Annotation
more info
 
protein homooligomerization IEA
Inferred from Electronic Annotation
more info
 
regulation of apoptotic DNA fragmentation IEA
Inferred from Electronic Annotation
more info
 
regulation of apoptotic process TAS
Traceable Author Statement
more info
PubMed 
response to G1 DNA damage checkpoint signaling TAS
Traceable Author Statement
more info
PubMed 
response to hypoxia IEA
Inferred from Electronic Annotation
more info
 
response to nutrient IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
apoptosome IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
apoptosome IDA
Inferred from Direct Assay
more info
PubMed 
apoptosome TAS
Traceable Author Statement
more info
PubMed 
cytosol IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cytosol TAS
Traceable Author Statement
more info
 
extracellular exosome HDA PubMed 
extracellular region TAS
Traceable Author Statement
more info
 
ficolin-1-rich granule lumen TAS
Traceable Author Statement
more info
 
nucleus IEA
Inferred from Electronic Annotation
more info
 
protein-containing complex IDA
Inferred from Direct Assay
more info
PubMed 
secretory granule lumen TAS
Traceable Author Statement
more info
 

General protein information

Preferred Names
apoptotic protease-activating factor 1

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_029094.1 RefSeqGene

    Range
    4991..95134
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001160.3NP_001151.1  apoptotic protease-activating factor 1 isoform b

    See identical proteins and their annotated locations for 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, AC013283, AF013263
    Consensus CDS
    CCDS55863.1
    UniProtKB/Swiss-Prot
    O14727
    Related
    ENSP00000353059.2, ENST00000359972.6
    Conserved Domains (6) summary
    COG2319
    Location:6981180
    WD40; 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 ...
    cd08323
    Location:792
    CARD_APAF1; Caspase activation and recruitment domain similar to that found in Apoptotic Protease-Activating Factor 1
    pfam00931
    Location:118403
    NB-ARC; NB-ARC domain
    pfam13191
    Location:115234
    AAA_16; AAA ATPase domain
    sd00039
    Location:649686
    7WD40; WD40 repeat [structural motif]
  2. NM_013229.3NP_037361.1  apoptotic protease-activating factor 1 isoform a

    See identical proteins and their annotated locations for 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, AC013283, AF013263, AF134397
    Consensus CDS
    CCDS55862.1
    UniProtKB/Swiss-Prot
    O14727
    Related
    ENSP00000448449.1, ENST00000550527.5
    Conserved Domains (6) summary
    COG2319
    Location:6981223
    WD40; 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 ...
    cd08323
    Location:792
    CARD_APAF1; Caspase activation and recruitment domain similar to that found in Apoptotic Protease-Activating Factor 1
    pfam00931
    Location:118403
    NB-ARC; NB-ARC domain
    pfam13191
    Location:115234
    AAA_16; AAA ATPase domain
    sd00039
    Location:649686
    7WD40; WD40 repeat [structural motif]
  3. NM_181861.2NP_863651.1  apoptotic protease-activating factor 1 isoform c

    See identical proteins and their annotated locations for 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, AC013283, AF013263, AF149794
    Consensus CDS
    CCDS9069.1
    UniProtKB/Swiss-Prot
    O14727
    Related
    ENSP00000448165.1, ENST00000551964.5
    Conserved Domains (4) summary
    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 ...
    cd08323
    Location:792
    CARD_APAF1; Caspase activation and recruitment domain similar to that found in Apoptotic Protease-Activating Factor 1
    sd00039
    Location:660697
    7WD40; WD40 repeat [structural motif]
    pfam00931
    Location:129414
    NB-ARC; NB-ARC domain
  4. NM_181868.1NP_863658.1  apoptotic protease-activating factor 1 isoform d

    See identical proteins and their annotated locations for 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
    ENSP00000349862.1, ENST00000357310.5
    Conserved Domains (6) summary
    COG2319
    Location:7091191
    WD40; 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 ...
    cd08323
    Location:792
    CARD_APAF1; Caspase activation and recruitment domain similar to that found in Apoptotic Protease-Activating Factor 1
    pfam00931
    Location:129414
    NB-ARC; NB-ARC domain
    pfam13191
    Location:126245
    AAA_16; AAA ATPase domain
    sd00039
    Location:660697
    7WD40; WD40 repeat [structural motif]
  5. NM_181869.1NP_863659.1  apoptotic protease-activating factor 1 isoform e

    See identical proteins and their annotated locations for 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
    ENSP00000334558.1, ENST00000333991.5
    Conserved Domains (2) summary
    cd08323
    Location:792
    CARD_APAF1; Caspase activation and recruitment domain similar to that found in Apoptotic Protease-Activating Factor 1
    pfam13191
    Location:126245
    AAA_16; AAA ATPase domain

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20191205

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000012.12 Reference GRCh38.p13 Primary Assembly

    Range
    98645141..98735433
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017019250.1XP_016874739.1  apoptotic protease-activating factor 1 isoform X1

RNA

  1. XR_429095.3 RNA Sequence

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