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

Gene ID: 14071, updated on 12-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. Characteristics of FXa-storing platelets in hemophilia B mice and the influence of alcohol on the platelets. Han W, et al. Sci Rep, 2023 Oct 1. PMID 37779119, Free PMC Article
  2. 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
  3. 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
  4. 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
  5. Novel, high incidence exercise-induced muscle bleeding model in hemophilia B mice: rationale, development and prophylactic intervention. Tranholm M, et al. J Thromb Haemost, 2015 Jan. PMID 25370152, Free PMC Article

See all (103) 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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