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

Summary

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

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_000086.8 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: 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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
The Function of extravascular coagulation factor IX in haemostasis.
Title: The Function of extravascular coagulation factor IX in haemostasis.
Evaluating the potential benefits of the extravascular pool of factor IX.
Title: Evaluating the potential benefits of the extravascular pool of factor IX.
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.
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.
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.
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.
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.
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.
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)

Targeted (7) 1 citation
Endonuclease-mediated (7) 1 citation

General gene information

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Markers

AW111646 (e-PCR)
- UniSTS:181291

F9 (e-PCR), detects polymorphism
- UniSTS:525911

M23109 (e-PCR)
- UniSTS:160882

F9 (e-PCR), detects polymorphism
- UniSTS:143058

GDB:192503 (e-PCR)
- UniSTS:99325

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables calcium ion binding	ISO Inferred from Sequence Orthology more info
enables endopeptidase activity	ISO Inferred from Sequence Orthology more info
enables hydrolase activity	IEA Inferred from Electronic Annotation 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	IEA Inferred from Electronic Annotation more info
enables serine-type peptidase 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
acts_upstream_of_or_within hemostasis	IEA Inferred from Electronic Annotation 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

Component	Evidence Code	Pubs
located_in extracellular region	IEA Inferred from Electronic Annotation more info
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

General protein information

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Preferred Names: coagulation factor IX

Names: christmas factor

NP_001292726.1

EC 3.4.21.22

NP_032005.1

EC 3.4.21.22

XP_030107081.1

EC 3.4.21.22

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)

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
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

NC_000086.8 Reference GRCm39 C57BL/6J

Range

59044675..59076120

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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