F9 coagulation factor IX [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: F9provided by RGD
Official Full Name: coagulation factor IXprovided by RGD
Primary source: RGD:2589
See related: EnsemblRapid:ENSRNOG00000003430 AllianceGenome:RGD:2589
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Summary: Predicted to enable calcium ion binding activity and serine-type endopeptidase activity. Predicted to be involved in blood coagulation and zymogen activation. Predicted to be active in extracellular space. Human ortholog(s) of this gene implicated in X-linked thrombophilia due to factor IX defect; X-linked warfarin sensitivity; and hemophilia B. Orthologous to human F9 (coagulation factor IX). [provided by Alliance of Genome Resources, Nov 2024]
Expression: Restricted expression toward (RPKM 2185.3) See more
Orthologs: human mouse all
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Genomic context

Location:: Xq36

Exon count:: 8

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	X	NC_086039.1 (143388642..143433143)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	X	NC_051356.1 (138352334..138396835)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	X	NC_005120.4 (143097507..143141791)

Chromosome X - NC_086039.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
BioProject: PRJNA238328
Publication: PMID 24510058
Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Data provide substantial evidence of a participation of fIX in the mechanisms regulating thrombosis prior to those regulating primary haemostasis.
Title: Titrating haemophilia B phenotypes using siRNA strategy: evidence that antithrombotic activity is separated from bleeding liability.
Nitrophorin 2, a factor IX(a)-directed anticoagulant, is a potent and long-lasting inhibitor of arterial thrombosis with minor effects on haemostasis.
Title: Nitrophorin 2, a factor IX(a)-directed anticoagulant, inhibits arterial thrombosis without impairing haemostasis.

Submit: New GeneRIF Correction

General gene information

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Markers

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

DXWox30 (e-PCR)
- UniSTS:517803

RH127349 (e-PCR)
- UniSTS:210659

RH140833 (e-PCR)
- UniSTS:210659

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

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables calcium ion binding	IEA Inferred from Electronic Annotation more info
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	ISO Inferred from Sequence Orthology more info
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
involved_in blood coagulation	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within blood coagulation	ISO Inferred from Sequence Orthology more info
involved_in blood coagulation	ISO Inferred from Sequence Orthology more info
involved_in proteolysis	ISO Inferred from Sequence Orthology more info
involved_in proteolysis	ISS Inferred from Sequence or Structural Similarity more info
involved_in zymogen activation	IBA Inferred from Biological aspect of Ancestor more info
involved_in zymogen activation	IEA Inferred from Electronic Annotation 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	IEA Inferred from Electronic Annotation 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: Coagulation factor IX (plasma thromboplastic component, Christmas disease, hemophilia B); christmas factor; coagulation factor 9

NP_113728.1

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_031540.1 → NP_113728.1 coagulation factor IX precursor

See identical proteins and their annotated locations for NP_113728.1

Status: VALIDATED

Source sequence(s)

FM036569, JAXUCZ010000021, M26247

UniProtKB/Swiss-Prot

F1M1M6, P16296

UniProtKB/TrEMBL

A0A8L2Q0X9

Related

ENSRNOP00000004559.7, ENSRNOT00000004559.9

Conserved Domains (5) summary

smart00020
Location:227 → 455

Tryp_SPc; Trypsin-like serine protease

smart00069
Location:21 → 85

GLA; Domain containing Gla (gamma-carboxyglutamate) residues

cd00054
Location:86 → 122

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:228 → 458

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:127 → 163

FXa_inhibition; Coagulation Factor Xa inhibitory site