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    Apaf1 apoptotic peptidase activating factor 1 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 78963, updated on 18-Apr-2019

    Summary

    Official Symbol
    Apaf1provided by RGD
    Official Full Name
    apoptotic peptidase activating factor 1provided by RGD
    Primary source
    RGD:620575
    See related
    Ensembl:ENSRNOG00000008022
    Gene type
    protein coding
    RefSeq status
    PROVISIONAL
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Summary
    protein involved in the initiation of apoptosis [RGD, Feb 2006]
    Expression
    Biased expression in Spleen (RPKM 132.8), Thymus (RPKM 83.9) and 9 other tissues See more
    Orthologs

    Genomic context

    See Apaf1 in Genome Data Viewer
    Location:
    7q13
    Exon count:
    28
    Annotation release Status Assembly Chr Location
    106 current Rnor_6.0 (GCF_000001895.5) 7 NC_005106.4 (31699309..31784192, complement)
    104 previous assembly Rnor_5.0 (GCF_000001895.4) 7 NC_005106.3 (31791073..31872984, complement)

    Chromosome 7 - NC_005106.4Genomic Context describing neighboring genes Neighboring gene ankyrin repeat and sterile alpha motif domain containing 1B Neighboring gene small nuclear ribonucleoprotein-associated protein N pseudogene Neighboring gene NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2-like Neighboring gene uncharacterized LOC103692819 Neighboring gene solute carrier family 25 member 3 Neighboring gene IKBKB interacting protein

    Genomic regions, transcripts, and products

    Expression

    • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
    • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
    • BioProject: PRJNA238328
    • Publication: PMID 24510058
    • Analysis date: Mon Jun 6 17:44:12 2016

    Bibliography

    GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

    Pathways from BioSystems

    • ATM Signaling Pathway, organism-specific biosystem (from WikiPathways)
      ATM Signaling Pathway, organism-specific biosystem
      ATM Signaling Pathway
    • Activation of caspases through apoptosome-mediated cleavage, organism-specific biosystem (from REACTOME)
      Activation of caspases through apoptosome-mediated cleavage, organism-specific biosystemcomputationally inferred pathway (not manually curated)
    • 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...
    • 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 KEGG)
      Apoptosis, organism-specific biosystemApoptosis is a genetically programmed process for the elimination of damaged or redundant cells by activation of caspases (aspartate-specific cysteine proteases). The onset of apoptosis is controlled...
    • 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, conserved biosystem (from KEGG)
      Apoptosis, conserved biosystemApoptosis is a genetically programmed process for the elimination of damaged or redundant cells by activation of caspases (aspartate-specific cysteine proteases). The onset of apoptosis is controlled...
    • Apoptosis, organism-specific biosystem (from REACTOME)
      Apoptosis, organism-specific biosystemcomputationally inferred pathway (not manually curated)
    • Apoptosis - multiple species, organism-specific biosystem (from KEGG)
      Apoptosis - multiple species, organism-specific biosystemApoptosis is an evolutionarily conserved process used by multicellular organisms to developmentally regulate cell number or to eliminate cells that are potentially detrimental to the organism. The ma...
    • Apoptosis - multiple species, conserved biosystem (from KEGG)
      Apoptosis - multiple species, conserved biosystemApoptosis is an evolutionarily conserved process used by multicellular organisms to developmentally regulate cell number or to eliminate cells that are potentially detrimental to the organism. The ma...
    • 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 biosystemcomputationally inferred pathway (not manually curated)
    • Apoptotic machinery, organism-specific biosystem (from KEGG)
      Apoptotic machinery, organism-specific biosystemFunctional set; Cellular processes; Cell signaling
    • Apoptotic machinery, conserved biosystem (from KEGG)
      Apoptotic machinery, conserved biosystemFunctional set; Cellular processes; Cell signaling
    • Cytochrome c-mediated apoptotic response, organism-specific biosystem (from REACTOME)
      Cytochrome c-mediated apoptotic response, organism-specific biosystemcomputationally inferred pathway (not manually curated)
    • 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 biosystemcomputationally inferred pathway (not manually curated)
    • 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...
    • Immune System, organism-specific biosystem (from REACTOME)
      Immune System, organism-specific biosystemcomputationally inferred pathway (not manually curated)
    • Innate Immune System, organism-specific biosystem (from REACTOME)
      Innate Immune System, organism-specific biosystemcomputationally inferred pathway (not manually curated)
    • Intrinsic Pathway for Apoptosis, organism-specific biosystem (from REACTOME)
      Intrinsic Pathway for Apoptosis, organism-specific biosystemcomputationally inferred pathway (not manually curated)
    • 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...
    • Neutrophil degranulation, organism-specific biosystem (from REACTOME)
      Neutrophil degranulation, organism-specific biosystemcomputationally inferred pathway (not manually curated)
    • 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...
    • Platinum drug resistance, organism-specific biosystem (from KEGG)
      Platinum drug resistance, organism-specific biosystemPlatinum-based drugs cisplatin, carboplatin and oxaliplatin are widely used in the therapy of solid malignancies, including testicular, ovarian, head and neck, colorectal, bladder and lung cancers. T...
    • Platinum drug resistance, conserved biosystem (from KEGG)
      Platinum drug resistance, conserved biosystemPlatinum-based drugs cisplatin, carboplatin and oxaliplatin are widely used in the therapy of solid malignancies, including testicular, ovarian, head and neck, colorectal, bladder and lung cancers. T...
    • Programmed Cell Death, organism-specific biosystem (from REACTOME)
      Programmed Cell Death, organism-specific biosystemcomputationally inferred pathway (not manually curated)
    • 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 pathway, organism-specific biosystem (from WikiPathways)
      p53 pathway, organism-specific biosystemp53 (also known as protein 53 or tumor protein 53), is a transcription factor which in humans is encoded by the TP53 gene. p53 is important in multicellular organisms, where it regulates the cell cyc...
    • p53 signal pathway, organism-specific biosystem (from WikiPathways)
      p53 signal pathway, organism-specific biosystemWe've used the following pathway as a reference: http://www.genome.jp/dbget-bin/show_pathway?rno04115+58918
    • 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...

    General gene information

    Homology

    Gene Ontology Provided by RGD

    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 ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    heat shock protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    identical protein binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    identical protein binding ISO
    Inferred from Sequence Orthology
    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 ISO
    Inferred from Sequence Orthology
    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 ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    aging IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    brain development IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    brain development ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    cardiac muscle cell apoptotic process IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    cell differentiation IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    cellular response to transforming growth factor beta stimulus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    forebrain development IEA
    Inferred from Electronic Annotation
    more info
     
    forebrain development ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress IEA
    Inferred from Electronic Annotation
    more info
     
    intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    kidney development IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    multicellular organism development ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    neural tube closure IEA
    Inferred from Electronic Annotation
    more info
     
    neural tube closure ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    neuron apoptotic process IEA
    Inferred from Electronic Annotation
    more info
     
    neuron apoptotic process ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    positive regulation of apoptotic signaling pathway IEA
    Inferred from Electronic Annotation
    more info
     
    positive regulation of apoptotic signaling pathway ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    protein homooligomerization IDA
    Inferred from Direct Assay
    more info
    PubMed 
    regulation of apoptotic DNA fragmentation IEA
    Inferred from Electronic Annotation
    more info
     
    regulation of apoptotic DNA fragmentation ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    response to hypoxia IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    response to nutrient IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    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 ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    cytoplasm IDA
    Inferred from Direct Assay
    more info
    PubMed 
    cytosol IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    cytosol ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    nucleus IEA
    Inferred from Electronic Annotation
    more info
     
    nucleus ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    protein-containing complex ISO
    Inferred from Sequence Orthology
    more info
    PubMed 

    General protein information

    Preferred Names
    apoptotic protease-activating factor 1
    Names
    apaf-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.

    mRNA and Protein(s)

    1. NM_023979.1NP_076469.1  apoptotic protease-activating factor 1

      See identical proteins and their annotated locations for NP_076469.1

      Status: PROVISIONAL

      Source sequence(s)
      AF320222
      UniProtKB/Swiss-Prot
      Q9EPV5
      Related
      ENSRNOP00000010869.6, ENSRNOT00000010869.6
      Conserved Domains (6) summary
      COG2319
      Location:6531038
      WD40; 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 ...
      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:623655
      7WD40; WD40 repeat [structural motif]

    RefSeqs of Annotated Genomes: Rattus norvegicus Annotation Release 106 details...Open this link in a new tab

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

    Reference Rnor_6.0 Primary Assembly

    Genomic

    1. NC_005106.4 Reference Rnor_6.0 Primary Assembly

      Range
      31699309..31784192 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_008765263.2XP_008763485.1  apoptotic protease-activating factor 1 isoform X1

      Conserved Domains (4) summary
      COG2319
      Location:457842
      WD40; WD40 repeat [General function prediction only]
      cd00200
      Location:411714
      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:3218
      NB-ARC; NB-ARC domain
      sd00039
      Location:427459
      7WD40; WD40 repeat [structural motif]

    Alternate Rn_Celera

    Genomic

    1. AC_000075.1 Alternate Rn_Celera

      Range
      22620761..22706298 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
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