Description: Homo sapiens coagulation factor IX (F9), mRNA. RefSeq Summary (NM_000133): 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. Alternative splicing results in multiple transcript variants encoding different isoforms that may undergo similar proteolytic processing. [provided by RefSeq, Sep 2015]. Transcript (Including UTRs) Position: hg19 chrX:138,612,895-138,645,617 Size: 32,723 Total Exon Count: 8 Strand: + Coding Region Position: hg19 chrX:138,612,924-138,644,230 Size: 31,307 Coding Exon Count: 8
ID:FA9_HUMAN DESCRIPTION: RecName: Full=Coagulation factor IX; EC=3.4.21.22; AltName: Full=Christmas factor; AltName: Full=Plasma thromboplastin component; Short=PTC; Contains: RecName: Full=Coagulation factor IXa light chain; Contains: RecName: Full=Coagulation factor IXa heavy chain; Flags: Precursor; 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. CATALYTIC ACTIVITY: Selective cleavage of Arg-|-Ile bond in factor X to form factor Xa. SUBUNIT: Heterodimer of a light chain and a heavy chain; disulfide-linked. SUBCELLULAR LOCATION: Secreted. TISSUE SPECIFICITY: Synthesized primarily in the liver and secreted in plasma. DOMAIN: Calcium binds to the gamma-carboxyglutamic acid (Gla) residues and, with stronger affinity, to another site, beyond the Gla domain. PTM: Activated by factor XIa, which excises the activation peptide. PTM: The iron and 2-oxoglutarate dependent 3-hydroxylation of aspartate and asparagine is (R) stereospecific within EGF domains. DISEASE: Defects in F9 are the cause of recessive X-linked hemophilia B (HEMB) [MIM:306900]; also known as Christmas disease. DISEASE: 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. DISEASE: Defects in F9 are the cause of thrombophilia due to factor IX defect (THPH8) [MIM:300807]. A hemostatic disorder characterized by a tendency to thrombosis. PHARMACEUTICAL: Available under the name BeneFix (Baxter and American Home Products). Used to treat hemophilia B. MISCELLANEOUS: In 1952, one of the earliest researchers of the disease, Dr. R.G. Macfarlane used the patient's 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. SIMILARITY: Belongs to the peptidase S1 family. SIMILARITY: Contains 2 EGF-like domains. SIMILARITY: Contains 1 Gla (gamma-carboxy-glutamate) domain. SIMILARITY: Contains 1 peptidase S1 domain. WEB RESOURCE: Name=Wikipedia; Note=Factor IX entry; URL="http://en.wikipedia.org/wiki/Factor_IX"; WEB RESOURCE: Name=HAEMB; Note=Hemophilia B mutation database; URL="http://www.kcl.ac.uk/ip/petergreen/haemBdatabase.html"; WEB RESOURCE: Name=GeneReviews; URL="http://www.ncbi.nlm.nih.gov/sites/GeneTests/lab/gene/F9"; WEB RESOURCE: Name=SeattleSNPs; URL="http://pga.gs.washington.edu/data/f9/"; WEB RESOURCE: Name=BeneFix; Note=Clinical information on BeneFix; URL="http://www.wyeth.com/products/benefix.asp"; WEB RESOURCE: Name=Protein Spotlight; Note=The Christmas Factor - Issue 41 of December 2003; URL="http://web.expasy.org/spotlight/back_issues/sptlt041.shtml";
Mahajan, A. et al. 2007, Allelic heterogeneity of molecular events in human coagulation factor IX in Asian Indians, Hum Mutat 2007 28(5) 526.
[PubMed 17397055]
that universal, presumably endogenous factors are predominant in the causation of the spontaneous mutations in F9.
factor VIII and factor IX genes Goodeve AC et al. 1994, A comparison of the allelic frequencies of ten DNA polymorphisms associated with factor VIII and factor IX genes in Thai and Western European populations., Blood coagulation & fibrinolysis. 1994 Feb;5(1):29-35.
[PubMed 7910050]
factor VIII and factor IX genes Goodeve AC et al. 1994, A comparison of the allelic frequencies of ten DNA polymorphisms associated with factor VIII and factor IX genes in Thai and Western European populations., Blood coagulation & fibrinolysis. 1994 Feb;5(1):29-35.
[PubMed 7910050]
The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.
ModBase Predicted Comparative 3D Structure on P00740
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Orthologous Genes in Other Species
Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
JD318968 - Sequence 299992 from Patent EP1572962. BC109214 - Homo sapiens coagulation factor IX, mRNA (cDNA clone MGC:129641 IMAGE:40007636), complete cds. BC109215 - Homo sapiens coagulation factor IX, mRNA (cDNA clone MGC:129642 IMAGE:40007637), complete cds. JD488965 - Sequence 469989 from Patent EP1572962. KJ891137 - Synthetic construct Homo sapiens clone ccsbBroadEn_00531 F9 gene, encodes complete protein. KR711501 - Synthetic construct Homo sapiens clone CCSBHm_00024496 F9 (F9) mRNA, encodes complete protein. KR711502 - Synthetic construct Homo sapiens clone CCSBHm_00024671 F9 (F9) mRNA, encodes complete protein. KR711503 - Synthetic construct Homo sapiens clone CCSBHm_00024741 F9 (F9) mRNA, encodes complete protein. KR711504 - Synthetic construct Homo sapiens clone CCSBHm_00024983 F9 (F9) mRNA, encodes complete protein. A13997 - H.sapiens mRNA for factor IX. J00137 - Human factor IX (Christmas factor) mRNA, complete cds. AB186358 - Homo sapiens F9 mRNA for coagulation factor IX, complete cds. FR846238 - Homo sapiens mRNA for serine protease coagulation factor IX (factor IX F9 gene). FR846239 - Homo sapiens mRNA for coagulation factor IX (FIX F9 gene). FR846240 - Homo sapiens mRNA for coagulation factor IX (F9 p22 gene). HW649498 - JP 2014523411-A/6: LIPID NANOPARTICLE COMPOSITIONS AND METHODS FOR MRNA DELIVERY. JB074623 - Sequence 6 from Patent WO2012170930. JC570532 - Sequence 6 from Patent WO2014089486. MA155780 - JP 2017014278-A/6: LIPID NANOPARTICLE COMPOSITIONS AND METHODS FOR MRNA DELIVERY. J00136 - Human factor IX (Christmas factor) mRNA, complete coding sequence. AK292749 - Homo sapiens cDNA FLJ77200 complete cds, highly similar to Homo sapiens coagulation factor IX (plasma thromboplastic component, Christmas disease, hemophilia B) (F9), mRNA. M11309 - Human coagulation factor IX mRNA, complete cds. A22493 - H.sapiens factor IX mRNA. M35672 - Human coagulation factor IX mRNA, partial cds. A22478 - H.sapiens factor IX exon sequence. JD289767 - Sequence 270791 from Patent EP1572962. JD088628 - Sequence 69652 from Patent EP1572962. JD509251 - Sequence 490275 from Patent EP1572962. JD284301 - Sequence 265325 from Patent EP1572962. JD300018 - Sequence 281042 from Patent EP1572962. JD370936 - Sequence 351960 from Patent EP1572962. JD391751 - Sequence 372775 from Patent EP1572962. JD550859 - Sequence 531883 from Patent EP1572962. JD097819 - Sequence 78843 from Patent EP1572962. JD094318 - Sequence 75342 from Patent EP1572962. JD501714 - Sequence 482738 from Patent EP1572962. JD432039 - Sequence 413063 from Patent EP1572962. JD052113 - Sequence 33137 from Patent EP1572962. JD538492 - Sequence 519516 from Patent EP1572962. JD564879 - Sequence 545903 from Patent EP1572962. JD177875 - Sequence 158899 from Patent EP1572962. JD233552 - Sequence 214576 from Patent EP1572962. JD059243 - Sequence 40267 from Patent EP1572962. MA890449 - JP 2017203045-A/6: LIPID NANOPARTICLE COMPOSITIONS AND METHODS FOR MRNA DELIVERY. MP440719 - Sequence 6 from Patent EP3586861. MP559900 - Sequence 6 from Patent EP3628335.
Biochemical and Signaling Pathways
KEGG - Kyoto Encyclopedia of Genes and Genomes hsa04610 - Complement and coagulation cascades
BioCarta from NCI Cancer Genome Anatomy Project h_intrinsicPathway - Intrinsic Prothrombin Activation Pathway h_plateletAppPathway - Platelet Amyloid Precursor Protein Pathway
Reactome (by CSHL, EBI, and GO)
Protein P00740 (Reactome details) participates in the following event(s):
R-HSA-140823 factor IX -> factor IXa + factor IX activation peptide (TF:F7a catalyst) R-HSA-158333 factor IX -> factor IXa + factor IX activation peptide (factor XIa catalyst) R-HSA-159796 Furin cleaves pro-factor IX to factor IX R-HSA-159803 GGCX gamma-carboxylates 3D-F9(29-461) (pro-factor IX) R-HSA-158278 factor VIIIa + factor IXa -> factor VIIIa:factor IXa R-HSA-5607023 factor IXa associates with cell membrane R-HSA-158164 factor X -> factor Xa + factor X activation peptide (VIIIa:IXa catalyst) R-HSA-140834 Extrinsic Pathway of Fibrin Clot Formation R-HSA-140837 Intrinsic Pathway of Fibrin Clot Formation R-HSA-159782 Removal of aminoterminal propeptides from gamma-carboxylated proteins R-HSA-159763 Transport of gamma-carboxylated protein precursors from the endoplasmic reticulum to the Golgi apparatus R-HSA-159740 Gamma-carboxylation of protein precursors R-HSA-140877 Formation of Fibrin Clot (Clotting Cascade) R-HSA-159854 Gamma-carboxylation, transport, and amino-terminal cleavage of proteins R-HSA-109582 Hemostasis R-HSA-163841 Gamma carboxylation, hypusine formation and arylsulfatase activation R-HSA-597592 Post-translational protein modification R-HSA-392499 Metabolism of proteins
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