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    F9 coagulation factor IX [ Mus musculus (house mouse) ]

    Gene ID: 14071, updated on 2-Nov-2024

    Summary

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    Official Symbol
    F9provided by MGI
    Official Full Name
    coagulation factor IXprovided by MGI
    Primary source
    MGI:MGI:88384
    See related
    Ensembl:ENSMUSG00000031138 AllianceGenome:MGI:88384
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Mus musculus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
    Also known as
    Cf9; Cf-9
    Summary
    This gene encodes a vitamin K-dependent serine protease that plays a critical role in the intrinsic pathway of blood coagulation. The encoded protein is an inactive zymogen that is activated by coagulation factor XIa to generate factor IXa, a heterodimer containing heavy and light chains. In association with factor VIII, membrane phospholipids and calcium ions, factor IXa cleaves the inactive zymogen factor X to generate active factor Xa. Genetic deletion of this gene in mice results in a severe bleeding phenotype. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, Apr 2015]
    Expression
    Biased expression in liver E18 (RPKM 11.7), liver adult (RPKM 11.4) and 2 other tissues See more
    Orthologs
    human all
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    Genomic context

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    Location:
    X A6; X 33.5 cM
    Exon count:
    8
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) X NC_000086.8 (59044675..59076120)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) X NC_000086.7 (59999329..60030760)

    Chromosome X - NC_000086.8Genomic Context describing neighboring genes Neighboring gene predicted gene, 36631 Neighboring gene STARR-seq mESC enhancer starr_47234 Neighboring gene STARR-seq mESC enhancer starr_47235 Neighboring gene STARR-seq mESC enhancer starr_47236 Neighboring gene synaptophysin-like protein pseudogene Neighboring gene predicted pseudogene 5637 Neighboring gene mcf.2 transforming sequence Neighboring gene STARR-seq mESC enhancer starr_47238 Neighboring gene STARR-seq mESC enhancer starr_47239

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Mouse ENCODE transcriptome data Mouse ENCODE transcriptome data
    • Description: RNA profiling data sets generated by the Mouse ENCODE project.
    • BioProject: PRJNA66167
    • Publication: PMID 25409824
    • Analysis date: n/a

    Bibliography

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    Related articles in PubMed

    1. Novel hemophilia B mouse models exhibiting a range of mutations in the Factor IX gene. Sabatino DE, et al. Blood, 2004 Nov 1. PMID 15217833
    2. Correction of hemophilia B in canine and murine models using recombinant adeno-associated viral vectors. Snyder RO, et al. Nat Med, 1999 Jan. PMID 9883841
    3. Hemostatic agents of broad applicability produced by selective tuning of factor Xa zymogenicity. Ivanciu L, et al. Blood, 2015 Jul 2. PMID 25896653, Free PMC Article
    4. Plant-based oral tolerance to hemophilia therapy employs a complex immune regulatory response including LAP+CD4+ T cells. Wang X, et al. Blood, 2015 Apr 9. PMID 25700434, Free PMC Article
    5. Immune responses to human factor IX in haemophilia B mice of different genetic backgrounds are distinct and modified by TLR4. Sack BK, et al. Haemophilia, 2015 Jan. PMID 25417755, Free PMC Article

    See all (102) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Liver-heart cross-talk mediated by coagulation factor XI protects against heart failure.
      Title: Liver-heart cross-talk mediated by coagulation factor XI protects against heart failure.
    2. The Function of extravascular coagulation factor IX in haemostasis.
      Title: The Function of extravascular coagulation factor IX in haemostasis.
    3. Evaluating the potential benefits of the extravascular pool of factor IX.
      Title: Evaluating the potential benefits of the extravascular pool of factor IX.
    4. Protein S is an important in vivo inhibitor of FIXa. Disruption of the interaction between PS and FIXa causes an increased rate of thrombus formation in mice.
      Title: Anticoagulant Protein S Targets the Factor IXa Heparin-Binding Exosite to Prevent Thrombosis.
    5. Authors investigated the interaction of coagulation factor IX in the development of atherosclerosis. Severe deficiency of FIX did not protect the animals from the development of atherosclerotic plaques in the aortic areas.
      Title: The role of clotting factor IX in the development of atherosclerosis.
    6. activation peptide of factor IX regulates endothelial intercellular adhesion and thus could be used in the treatment of vascular hyperpermeability.
      Title: Activation peptide of coagulation factor IX regulates endothelial permeability.
    7. structural features within residues of the 39-loop contribute to the resistance of FIXa to inhibition by plasma inhibitors ZPI and TFPI.
      Title: Residues of the 39-loop restrict the plasma inhibitor specificity of factor IXa.
    8. Data indicate that the hyperactivating factor IX (FIX)-R338L mutation resulted in a robust 15-fold gain in potency and therefore provides a promising strategy to improve the efficacy, feasibility, and safety of hemophilia gene therapy.
      Title: Hyperfunctional coagulation factor IX improves the efficacy of gene therapy in hemophilic mice.
    9. hnRNP A3 is a major liver nuclear protein binding to age related increase element of the factor IX gene.
      Title: Heterogeneous nuclear ribonucleoprotein A3 is the liver nuclear protein binding to age related increase element RNA of the factor IX gene.
    10. functional role of binding of F9 to collagen IV in hemostasis.
      Title: Abnormal hemostasis in a knock-in mouse carrying a variant of factor IX with impaired binding to collagen type IV.
    Submit: New GeneRIF Correction See all GeneRIFs (19)

    Variation

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    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)

    Pathways from PubChem

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    General gene information

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    Markers

    Homology

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    enables calcium ion binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables calcium ion binding ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    enables endopeptidase activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables endopeptidase activity ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    enables metal ion binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables peptidase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables serine-type endopeptidase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables serine-type endopeptidase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in blood coagulation IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within blood coagulation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in blood coagulation ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in blood coagulation ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in proteolysis ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in zymogen activation IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in zymogen activation ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in zymogen activation ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    Component Evidence Code Pubs
    is_active_in extracellular space IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in extracellular space ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in extracellular space ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  

    General protein information

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    Preferred Names
    coagulation factor IX
    Names
    christmas factor
    NP_001292726.1
    NP_032005.1
    XP_030107081.1

    NCBI Reference Sequences (RefSeq)

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    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_001305797.1 → NP_001292726.1  coagulation factor IX isoform 2 precursor

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks an alternate exon in the coding region but maintains the reading frame, compared to variant 1. This variant encodes isoform 2, which is shorter than isoform 1.
      Source sequence(s)
      AA239875, AK149372
      UniProtKB/TrEMBL
      A0JLY3
      Conserved Domains (4) summary
      smart00020
      Location:198 → 426
      Tryp_SPc; Trypsin-like serine protease
      smart00069
      Location:28 → 92
      GLA; Domain containing Gla (gamma-carboxyglutamate) residues
      cd00190
      Location:199 → 429
      Tryp_SPc; Trypsin-like serine protease; Many of these are synthesized as inactive precursor zymogens that are cleaved during limited proteolysis to generate their active forms. Alignment contains also inactive enzymes that have substitutions of the catalytic triad ...
      pfam14670
      Location:96 → 132
      FXa_inhibition; Coagulation Factor Xa inhibitory site

    2. NM_007979.2 → NP_032005.1  coagulation factor IX isoform 1 preproprotein

      See identical proteins and their annotated locations for NP_032005.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
      Source sequence(s)
      AA239875, AK149372
      Consensus CDS
      CCDS30158.1
      UniProtKB/Swiss-Prot
      P16294, Q3UES1
      UniProtKB/TrEMBL
      A0JLY3
      Related
      ENSMUSP00000033477.5, ENSMUST00000033477.5
      Conserved Domains (5) summary
      smart00020
      Location:236 → 464
      Tryp_SPc; Trypsin-like serine protease
      smart00069
      Location:28 → 92
      GLA; Domain containing Gla (gamma-carboxyglutamate) residues
      cd00054
      Location:93 → 129
      EGF_CA; Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the ...
      cd00190
      Location:237 → 467
      Tryp_SPc; Trypsin-like serine protease; Many of these are synthesized as inactive precursor zymogens that are cleaved during limited proteolysis to generate their active forms. Alignment contains also inactive enzymes that have substitutions of the catalytic triad ...
      pfam14670
      Location:134 → 170
      FXa_inhibition; Coagulation Factor Xa inhibitory site

    RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

    Reference GRCm39 C57BL/6J

    Genomic

    1. NC_000086.8 Reference GRCm39 C57BL/6J

      Range
      59044675..59076120
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_030251221.2 → XP_030107081.1  coagulation factor IX isoform X1

      Conserved Domains (3) summary
      smart00069
      Location:28 → 92
      GLA; Domain containing Gla (gamma-carboxyglutamate) residues
      cd00054
      Location:93 → 129
      EGF_CA; Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the ...
      pfam14670
      Location:134 → 170
      FXa_inhibition; Coagulation Factor Xa inhibitory site
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    P16294.3 GenPept UniProtKB/Swiss-Prot:P16294

    Gene LinkOut

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