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Aliases for F9 Gene

Aliases for F9 Gene

  • Coagulation Factor IX 2 3
  • Plasma Thromboplastic Component 2 3
  • Plasma Thromboplastin Component 3 4
  • Christmas Factor 3 4
  • EC 4 63
  • THPH8 3 6
  • HEMB 3 6
  • PTC 3 4
  • Christmas Disease 2
  • Hemophilia B 2
  • Factor IX F9 3
  • Factor IX 2
  • EC 3.4.21 63
  • Factor 9 3
  • F9 P22 3
  • FIX F9 3
  • P19 3
  • FIX 3

External Ids for F9 Gene

Previous GeneCards Identifiers for F9 Gene

  • GC0XP133196
  • GC0XP135470
  • GC0XP136557
  • GC0XP137318
  • GC0XP138338
  • GC0XP138440
  • GC0XP138612
  • GC0XP127880

Summaries for F9 Gene

Entrez Gene Summary for F9 Gene

  • This gene encodes vitamin K-dependent coagulation factor IX that circulates in the blood as an inactive zymogen. This factor is converted to an active form by factor XIa, which excises the activation peptide and thus generates a heavy chain and a light chain held together by one or more disulfide bonds. The role of this activated factor IX in the blood coagulation cascade is to activate factor X to its active form through interactions with Ca+2 ions, membrane phospholipids, and factor VIII. Alterations of this gene, including point mutations, insertions and deletions, cause factor IX deficiency, which is a recessive X-linked disorder, also called hemophilia B or Christmas disease. [provided by RefSeq, Jul 2008]

GeneCards Summary for F9 Gene

F9 (Coagulation Factor IX) is a Protein Coding gene. Diseases associated with F9 include hemophilia b and thrombophilia, x-linked, due to factor ix defect. Among its related pathways are Hemostasis and Formation of Fibrin Clot (Clotting Cascade). GO annotations related to this gene include calcium ion binding and serine-type endopeptidase activity. An important paralog of this gene is HP.

UniProtKB/Swiss-Prot for F9 Gene

  • Factor IX is a vitamin K-dependent plasma protein that participates in the intrinsic pathway of blood coagulation by converting factor X to its active form in the presence of Ca(2+) ions, phospholipids, and factor VIIIa

Gene Wiki entry for F9 Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for F9 Gene

Genomics for F9 Gene

Regulatory Elements for F9 Gene

Genomic Location for F9 Gene

139,530,733 bp from pter
139,565,697 bp from pter
34,965 bases
Plus strand

Genomic View for F9 Gene

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
Genomic Location for F9 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for F9 Gene

Proteins for F9 Gene

  • Protein details for F9 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Coagulation factor IX
    Protein Accession:
    Secondary Accessions:
    • A8K9N4
    • F2RM36
    • Q5FBE1
    • Q5JYJ8

    Protein attributes for F9 Gene

    461 amino acids
    Molecular mass:
    51778 Da
    Quaternary structure:
    • Heterodimer of a light chain and a heavy chain; disulfide-linked
    • In 1952, one of the earliest researchers of the disease, Dr. R.G. Macfarlane used the patients surname, Christmas, to refer to the disease and also to refer to the clotting factor which he called the Christmas Factor At the time Stephen Christmas was a 5-year-old boy. He died in 1993 at the age of 46 from acquired immunodeficiency syndrome contracted through treatment with blood products

    Three dimensional structures from OCA and Proteopedia for F9 Gene

    Alternative splice isoforms for F9 Gene


neXtProt entry for F9 Gene

Proteomics data for F9 Gene at MOPED

Post-translational modifications for F9 Gene

  • Activated by factor XIa, which excises the activation peptide
  • Predominantly O-glucosylated at Ser-99 by POGLUT1 in vitro. Xylosylation at this site is minor
  • The iron and 2-oxoglutarate dependent 3-hydroxylation of aspartate and asparagine is (R) stereospecific within EGF domains.
  • Glycosylation at Ser99, Ser107, Asn203, Thr205, Asn213, and Thr215
  • Modification sites at PhosphoSitePlus

Other Protein References for F9 Gene

ENSEMBL proteins:
Reactome Protein details:
REFSEQ proteins:

Domains for F9 Gene

Graphical View of Domain Structure for InterPro Entry



  • P00740
  • Calcium binds to the gamma-carboxyglutamic acid (Gla) residues and, with stronger affinity, to another site, beyond the Gla domain
  • Contains 2 EGF-like domains.
  • Contains 1 Gla (gamma-carboxy-glutamate) domain.
  • Contains 1 peptidase S1 domain.
  • Belongs to the peptidase S1 family.
genes like me logo Genes that share domains with F9: view

No data available for Gene Families for F9 Gene

Function for F9 Gene

Molecular function for F9 Gene

GENATLAS Biochemistry:
coagulation factor IX,vitamin K-dependent (plasma thromboplastic component)
UniProtKB/Swiss-Prot CatalyticActivity:
Selective cleavage of Arg- -Ile bond in factor X to form factor Xa
UniProtKB/Swiss-Prot Function:
Factor IX is a vitamin K-dependent plasma protein that participates in the intrinsic pathway of blood coagulation by converting factor X to its active form in the presence of Ca(2+) ions, phospholipids, and factor VIIIa

Enzyme Numbers (IUBMB) for F9 Gene

Gene Ontology (GO) - Molecular Function for F9 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003824 catalytic activity --
GO:0004175 endopeptidase activity IDA 20121197
GO:0004252 serine-type endopeptidase activity IEA --
GO:0005509 calcium ion binding IDA 14722079
GO:0005515 protein binding --
genes like me logo Genes that share ontologies with F9: view
genes like me logo Genes that share phenotypes with F9: view

Animal Models for F9 Gene

MGI Knock Outs for F9:
  • F9 tm1Dws
  • F9 tm1Emg
  • F9 tm1Ver

miRNA Products

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for F9

In Situ Assay Products

Flow Cytometry Products

No data available for miRNA , Transcription Factor Targeting and HOMER Transcription for F9 Gene

Localization for F9 Gene

Subcellular locations from UniProtKB/Swiss-Prot for F9 Gene


Subcellular locations from

Jensen Localization Image for F9 Gene COMPARTMENTS Subcellular localization image for F9 gene
Compartment Confidence
extracellular 5
endoplasmic reticulum 4
golgi apparatus 4
plasma membrane 4
nucleus 1

Gene Ontology (GO) - Cellular Components for F9 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005576 extracellular region TAS --
GO:0005615 extracellular space IDA 2592373
GO:0005788 endoplasmic reticulum lumen TAS --
GO:0005796 Golgi lumen TAS --
GO:0005886 plasma membrane TAS --
genes like me logo Genes that share ontologies with F9: view

Pathways for F9 Gene

genes like me logo Genes that share pathways with F9: view

Gene Ontology (GO) - Biological Process for F9 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006508 proteolysis TAS --
GO:0007596 blood coagulation TAS --
GO:0007597 blood coagulation, intrinsic pathway TAS --
GO:0007598 blood coagulation, extrinsic pathway TAS --
GO:0017187 peptidyl-glutamic acid carboxylation TAS --
genes like me logo Genes that share ontologies with F9: view

Compounds for F9 Gene

Compound Products


Pharmaceutical: Available under the name BeneFix (Baxter and American Home Products). Used to treat hemophilia B

(1) ApexBio Compounds for F9 Gene

Compound Action Cas Number
Rivaroxaban Factor Xa inhibitor [366789-02-8]

(2) HMDB Compounds for F9 Gene

Compound Synonyms Cas Number PubMed IDs
  • Ca
  • Vitamin K3: 1,4-Dihydro-1,4-dioxo-2-methylnaphthalene

(1) Drugbank Compounds for F9 Gene

Compound Synonyms Cas Number Type Actions PubMed IDs
Gamma-Carboxy-Glutamic Acid

(108) Novoseek inferred chemical compound relationships for F9 Gene

Compound -log(P) Hits PubMed IDs
mononine 92.2 20
gamma-carboxyglutamic acid 87.5 55
erythro-beta-hydroxyaspartic acid 77.8 1
p-amino benzamidine 75.5 3
fibrinogen 69.2 67
genes like me logo Genes that share compounds with F9: view

Transcripts for F9 Gene

mRNA/cDNA for F9 Gene

Unigene Clusters for F9 Gene

Coagulation factor IX:
Representative Sequences:

miRNA Products

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for F9

Primer Products

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for F9 Gene

No ASD Table

Relevant External Links for F9 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for F9 Gene

mRNA expression in normal human tissues for F9 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for F9 Gene

This gene is overexpressed in Liver (52.8).

Protein differential expression in normal tissues for F9 Gene

This gene is overexpressed in Serum (26.0) and Plasma (20.1).

Integrated Proteomics: protein expression from ProteomicsDB, PaxDb, and MOPED for F9 Gene

SOURCE GeneReport for Unigene cluster for F9 Gene Hs.522798

mRNA Expression by UniProt/SwissProt for F9 Gene

Tissue specificity: Synthesized primarily in the liver and secreted in plasma
genes like me logo Genes that share expressions with F9: view

Expression partners for F9 Gene

In Situ Assay Products

Orthologs for F9 Gene

This gene was present in the common ancestor of animals.

Orthologs for F9 Gene

Organism Taxonomy Gene Similarity Type Details
(Canis familiaris)
Mammalia F9 35
  • 88.32 (n)
  • 86.25 (a)
F9 36
  • 86 (a)
(Mus musculus)
Mammalia F9 35
  • 85.83 (n)
  • 82 (a)
F9 16
F9 36
  • 80 (a)
(Pan troglodytes)
Mammalia F9 35
  • 99.78 (n)
  • 99.78 (a)
F9 36
  • 100 (a)
(Rattus norvegicus)
Mammalia F9 35
  • 85.83 (n)
  • 83.26 (a)
(Bos Taurus)
Mammalia F9 36
  • 84 (a)
(Monodelphis domestica)
Mammalia F9 36
  • 74 (a)
(Ornithorhynchus anatinus)
Mammalia F9 36
  • 67 (a)
(Gallus gallus)
Aves F9 35
  • 61.37 (n)
  • 57.17 (a)
F9 36
  • 54 (a)
(Anolis carolinensis)
Reptilia F9 36
  • 56 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia f9 35
  • 61.87 (n)
  • 54.87 (a)
(Danio rerio)
Actinopterygii f9 35
f9b 35
  • 55.56 (n)
  • 50 (a)
f9a 36
  • 41 (a)
f9b 36
  • 42 (a)
fruit fly
(Drosophila melanogaster)
Insecta CG4914 37
  • 34 (a)
(Caenorhabditis elegans)
Secernentea C07G1.1 37
  • 40 (a)
sea squirt
(Ciona savignyi)
Ascidiacea -- 36
  • 17 (a)
Species with no ortholog for F9:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for F9 Gene

Gene Tree for F9 (if available)
Gene Tree for F9 (if available)

Paralogs for F9 Gene

Paralogs for F9 Gene

genes like me logo Genes that share paralogs with F9: view

Variants for F9 Gene

Sequence variations from dbSNP and Humsavar for F9 Gene

SNP ID Clin Chr 0X pos Sequence Context AA Info Type MAF
rs6047 -- 139,537,280(+) TGTAT(G/T)TTAAA intron-variant
rs6048 other, - 139,551,121(+) CTGAG(A/G)CTGTT reference, missense
rs6049 -- 139,541,196(+) TAAGT(A/G)ACTAT intron-variant
rs28897 -- 139,547,957(+) ggggt(A/C)ttgat intron-variant
rs110583 -- 139,556,372(+) CACTT(C/T)CCTCA intron-variant

Structural Variations from Database of Genomic Variants (DGV) for F9 Gene

Variant ID Type Subtype PubMed ID
esv2740521 CNV Deletion 23290073
nsv521021 CNV Gain 19592680
nsv528242 CNV Gain 19592680

Relevant External Links for F9 Gene

HapMap Linkage Disequilibrium report
Human Gene Mutation Database (HGMD)
Locus Specific Mutation Databases (LSDB)

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for F9 Gene

Disorders for F9 Gene

(3) OMIM Diseases for F9 Gene (300746)


  • Hemophilia B (HEMB) [MIM:306900]: An X-linked blood coagulation disorder characterized by a permanent tendency to hemorrhage, due to factor IX deficiency. It is phenotypically similar to hemophilia A, but patients present with fewer symptoms. Many patients are asymptomatic until the hemostatic system is stressed by surgery or trauma. {ECO:0000269 PubMed:10094553, ECO:0000269 PubMed:10698280, ECO:0000269 PubMed:11122099, ECO:0000269 PubMed:12588353, ECO:0000269 PubMed:12604421, ECO:0000269 PubMed:1346975, ECO:0000269 PubMed:1615485, ECO:0000269 PubMed:1902289, ECO:0000269 PubMed:1958666, ECO:0000269 PubMed:2162822, ECO:0000269 PubMed:2339358, ECO:0000269 PubMed:2372509, ECO:0000269 PubMed:2472424, ECO:0000269 PubMed:25470321, ECO:0000269 PubMed:2592373, ECO:0000269 PubMed:2713493, ECO:0000269 PubMed:2714791, ECO:0000269 PubMed:2738071, ECO:0000269 PubMed:2753873, ECO:0000269 PubMed:2773937, ECO:0000269 PubMed:2775660, ECO:0000269 PubMed:3009023, ECO:0000269 PubMed:3243764, ECO:0000269 PubMed:3401602, ECO:0000269 PubMed:3790720, ECO:0000269 PubMed:6603618, ECO:0000269 PubMed:7981722, ECO:0000269 PubMed:8076946, ECO:0000269 PubMed:8199596, ECO:0000269 PubMed:8257988, ECO:0000269 PubMed:8295821, ECO:0000269 PubMed:8680410, ECO:0000269 PubMed:9222764, ECO:0000269 PubMed:9452115, ECO:0000269 PubMed:9590153, ECO:0000269 PubMed:9600455}. Note=The disease is caused by mutations affecting the gene represented in this entry.
  • Note=Mutations in position 43 (Oxford-3, San Dimas) and 46 (Cambridge) prevents cleavage of the propeptide, mutation in position 93 (Alabama) probably fails to bind to cell membranes, mutation in position 191 (Chapel-Hill) or in position 226 (Nagoya OR Hilo) prevent cleavage of the activation peptide.
  • Thrombophilia, X-linked, due to factor IX defect (THPH8) [MIM:300807]: A hemostatic disorder characterized by a tendency to thrombosis. {ECO:0000269 PubMed:19846852}. Note=The disease is caused by mutations affecting the gene represented in this entry.

(93) Novoseek inferred disease relationships for F9 Gene

Disease -log(P) Hits PubMed IDs
hemophilia b 98.4 193
hemophilia a 88.4 59
coagulopathy 84 57
factor xi deficiency 75.6 7
factor vii deficiency 72.1 5

Genatlas disease for F9 Gene

hemophilia B,Christmas disease,with a higher rate of transmitted mutation with increased maternal age

Relevant External Links for F9

Genetic Association Database (GAD)
Human Genome Epidemiology (HuGE) Navigator
genes like me logo Genes that share disorders with F9: view

Publications for F9 Gene

  1. Human factor IX has a tetrasaccharide O-glycosidically linked to serine 61 through the fucose residue. (PMID: 1517205) Nishimura H. … Iwanaga S. (J. Biol. Chem. 1992) 3 4 23
  2. Sequence-specific 1H NMR assignments, secondary structure, and location of the calcium binding site in the first epidermal growth factor like domain of blood coagulation factor IX. (PMID: 1854745) Huang L.H. … Sweeney W.V. (Biochemistry 1991) 3 4 23
  3. Hemophilia B caused by five different nondeletion mutations in the protease domain of factor IX. (PMID: 1346975) Ludwig M. … Bajaj S.P. (Blood 1992) 3 4 23
  4. Mutations in hemophilia Bm occur at the Arg180-Val activation site or in the catalytic domain of factor IX. (PMID: 2162822) Bertina R.M. … Reitsma P.H. (J. Biol. Chem. 1990) 3 4 23
  5. A mutation adjacent to the beta cleavage site of factor IX (valine 182 to leucine) results in mild haemophilia Bm. (PMID: 2372509) Taylor S.A. … Lillicrap D.P. (Br. J. Haematol. 1990) 3 4 23

Products for F9 Gene

Sources for F9 Gene

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