F9 (coagulation factor IX) - Rat Genome Database

Name: F9
Creator: Rat Genome Database
License: Creative Commons CC BY 4.0
Keywords: Rat Gene RGD Genome

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Gene: F9 (coagulation factor IX) Rattus norvegicus

Analyze

Symbol:

Name:

coagulation factor IX

RGD ID:

2589

Description:

Predicted to have calcium ion binding activity and endopeptidase activity. Involved in blood coagulation. Predicted to localize to 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); PARTICIPATES IN coagulation cascade pathway; acenocoumarol pharmacodynamics pathway; alteplase pharmacodynamics pathway; INTERACTS WITH 2,4-dinitrotoluene; 2,6-dinitrotoluene; acenocoumarol.

Type:

protein-coding

RefSeq Status:

VALIDATED

Also known as:

christmas factor; coagulation factor 9; Coagulation factor IX (plasma thromboplastic component Christmas disease hemophilia B); Coagulation factor IX (plasma thromboplastic component, Christmas disease, hemophilia B)

RGD Orthologs

Human

Mouse

Chinchilla

Bonobo

Dog

Squirrel

Pig

Green Monkey

Naked Mole-Rat

Alliance Genes

More Info

more info ...

More Info

Species	Gene symbol and name	Data Source	Assertion derived from	less info ...
Orthologs ¹				less info ...
Homo sapiens (human):	F9 (coagulation factor IX)	HGNC	EggNOG, Ensembl, HomoloGene, Inparanoid, NCBI, OMA, OrthoDB, OrthoMCL, Panther, Treefam
Mus musculus (house mouse):	F9 (coagulation factor IX)	HGNC	Treefam, EggNOG, OrthoMCL, NCBI, OMA, HomoloGene, Inparanoid, Panther, OrthoDB, Ensembl
Chinchilla lanigera (long-tailed chinchilla):	F9 (coagulation factor IX)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	F9 (coagulation factor IX)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	F9 (coagulation factor IX)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	F9 (coagulation factor IX)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	F9 (coagulation factor IX)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (African green monkey):	F9 (coagulation factor IX)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	F9 (coagulation factor IX)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Other homologs ²
Homo sapiens (human):	F10 (coagulation factor X)	HGNC	OrthoDB
Alliance orthologs ³
Mus musculus (house mouse):	F9 (coagulation factor IX)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|TreeFam)
Homo sapiens (human):	F9 (coagulation factor IX)	Alliance	DIOPT (Ensembl Compara\|HGNC\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|TreeFam)
Danio rerio (zebrafish):	f9b (coagulation factor IXb)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|TreeFam)
Danio rerio (zebrafish):	f9a (coagulation factor IXa)	Alliance	DIOPT (Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|TreeFam)
Drosophila melanogaster (fruit fly):	CG30371	Alliance	DIOPT (Hieranoid\|PhylomeDB)
Drosophila melanogaster (fruit fly):	CG14760	Alliance	DIOPT (Hieranoid\|PhylomeDB)

Latest Assembly:

Rnor_6.0 - RGSC Genome Assembly v6.0

Position:

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
mRatBN7.2	X	138,352,334 - 138,396,835 (+)	NCBI
Rnor_6.0 Ensembl	X	143,097,525 - 143,141,794 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_6.0	X	143,097,507 - 143,141,791 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_5.0	X	143,127,239 - 143,171,465 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	X	145,527,978 - 145,575,966 (+)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	X	145,647,657 - 145,648,632 (+)	NCBI
Celera	X	134,429,774 - 134,473,582 (+)	NCBI		Celera
Cytogenetic Map	X	q36	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

autistic disorder (ISO)

blood coagulation disease (ISO)

factor VIII deficiency (ISO)

genetic disease (ISO)

hemophilia B (ISO)

Sepsis (IEP)

syndromic X-linked intellectual disability Lubs type (ISO)

thrombosis (ISO)

type 2 diabetes mellitus (ISO)

X-linked thrombophilia due to factor IX defect (ISO)

X-linked warfarin sensitivity (ISO)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

1,2-dimethylhydrazine (ISO)

2,4-dinitrotoluene (EXP)

2,6-dinitrotoluene (EXP)

acenocoumarol (EXP)

acetamide (EXP)

aflatoxin B1 (ISO)

ammonium chloride (EXP)

benzo[a]pyrene (ISO)

bisphenol A (EXP,ISO)

buta-1,3-diene (ISO)

calcium dichloride (ISO)

chlorohydrocarbon (EXP)

coumarin (ISO)

cyclosporin A (ISO)

Ethyl icosapentate (EXP)

folic acid (ISO)

furan (EXP)

gentamycin (ISO)

glycine betaine (ISO)

medroxyprogesterone acetate (ISO)

methylmercury chloride (EXP)

methyltestosterone (ISO)

N-Nitrosopyrrolidine (ISO)

O-methyleugenol (ISO)

paracetamol (ISO)

perfluorononanoic acid (ISO)

perfluorooctane-1-sulfonic acid (ISO)

phenobarbital (EXP)

phenprocoumon (EXP)

phylloquinone (ISO)

sodium arsenite (ISO)

tamoxifen (ISO)

tetrachloromethane (ISO)

trichloroethene (EXP)

Triptolide (EXP)

valproic acid (ISO)

vitamin K epoxide (ISO)

warfarin (EXP,ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

blood coagulation (IBA,IDA,ISO)

proteolysis (ISO,ISS)

zymogen activation (IBA,ISO,ISS)

Cellular Component

cellular_component (ND)

extracellular space (IBA,ISO,ISS)

Molecular Function

calcium ion binding (ISO,ISS)

endopeptidase activity (ISO,ISS)

molecular_function (ND)

peptidase activity (ISO)

protein binding (ISO)

serine-type endopeptidase activity (IEA)

Molecular Pathway Annotations Click to see Annotation Detail View

acenocoumarol pharmacodynamics pathway (ISO)

alteplase pharmacodynamics pathway (ISO)

aminocaproic acid pharmacodynamics pathway (ISO)

anistreplase pharmacodynamics pathway (ISO)

aprotinin pharmacodynamics pathway (ISO)

argatroban pharmacodynamics pathway (ISO)

bivalirudin pharmacodynamics pathway (ISO)

coagulation cascade pathway (IDA,IEA,ISO)

complement system pathway (IEA)

dicoumarol pharmacodynamics pathway (ISO)

enoxaparin pharmacodynamics pathway (ISO)

fondaparinux pharmacodynamics pathway (ISO)

heparin pharmacodynamics pathway (ISO)

phenindione pharmacodynamics pathway (ISO)

reteplase pharmacodynamics pathway (ISO)

tranexamic acid pharmacodynamics pathway (ISO)

warfarin pharmacodynamics pathway (ISO)

References

References - curated


1.	Attree O, etal., Genomics. 1989 Apr;4(3):266-72.
2.	Driscoll MC, etal., Blood. 1989 Aug 1;74(2):737-42.
3.	Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
4.	Giannelli F, etal., Nucleic Acids Res. 1991 Apr 25;19 Suppl:2193-219.
5.	GOA data from the GO Consortium
6.	Golino P Thromb Res. 2002 May 1;106(3):V257-65.
7.	Knobl P, etal., Thromb Haemost. 1994 Jun;71(6):692-7.
8.	Laudes IJ, etal., Am J Pathol. 2002 May;160(5):1867-75.
9.	Lin HF, etal., Blood. 1997 Nov 15;90(10):3962-6.
10.	MGD data from the GO Consortium
11.	NCBI rat LocusLink and RefSeq merged data July 26, 2002
12.	Nobukata H, etal., Toxicol Lett. 1999 Jan 11;104(1-2):93-101.
13.	Norris LA, Best Pract Res Clin Obstet Gynaecol. 2003 Jun;17(3):369-83.
14.	OMIM Disease Annotation Pipeline
15.	Pipeline to import KEGG annotations from KEGG into RGD
16.	Pipeline to import SMPDB annotations from SMPDB into RGD
17.	Reijnen MJ, etal., Proc Natl Acad Sci U S A 1992 Jul 15;89(14):6300-3.
18.	RGD automated data pipeline
19.	RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
20.	RGD automated import pipeline for gene-chemical interactions
21.	RGD comprehensive gene curation
22.	Sarkar G, etal., Genomics 1990 Jan;6(1):133-43.
23.	Smith SA, etal., Crit Rev Biochem Mol Biol. 2015;50(4):326-36. doi: 10.3109/10409238.2015.1050550. Epub 2015 May 28.
24.	Verma D, etal., Proc Natl Acad Sci U S A. 2010 Apr 13;107(15):7101-6. doi: 10.1073/pnas.0912181107. Epub 2010 Mar 29.
25.	Wang L, etal., Proc Natl Acad Sci U S A 1997 Oct 14;94(21):11563-6.
26.	Zhang L, etal., Zhonghua Xue Ye Xue Za Zhi. 2010 May;31(5):294-299.

Additional References at PubMed

PMID:2472424	PMID:2592373	PMID:8632006	PMID:9169594	PMID:14722079	PMID:15178576	PMID:20121197	PMID:20838739	PMID:23533145	PMID:25790442

Genomics

Comparative Map Data

F9
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
mRatBN7.2	X	138,352,334 - 138,396,835 (+)	NCBI
Rnor_6.0 Ensembl	X	143,097,525 - 143,141,794 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_6.0	X	143,097,507 - 143,141,791 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_5.0	X	143,127,239 - 143,171,465 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	X	145,527,978 - 145,575,966 (+)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	X	145,647,657 - 145,648,632 (+)	NCBI
Celera	X	134,429,774 - 134,473,582 (+)	NCBI		Celera
Cytogenetic Map	X	q36	NCBI

F9
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38.p13 Ensembl	X	139,530,758 - 139,563,458 (+)	Ensembl	GRCh38		hg38	GRCh38
GRCh38.p13 Ensembl	X	139,530,739 - 139,563,459 (+)	Ensembl	GRCh38		hg38	GRCh38
GRCh38	X	139,530,720 - 139,563,459 (+)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh37	X	138,612,898 - 138,645,618 (+)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	X	138,440,561 - 138,473,283 (+)	NCBI	NCBI36		hg18	NCBI36
Build 34	X	138,338,414 - 138,371,137	NCBI
Celera	X	138,980,334 - 139,013,056 (+)	NCBI
Cytogenetic Map	X	q27.1	NCBI
HuRef	X	127,880,671 - 127,913,025 (+)	NCBI		HuRef
CHM1_1	X	138,523,783 - 138,556,510 (+)	NCBI		CHM1_1

F9
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	X	59,044,675 - 59,076,120 (+)	NCBI	GRCm39		mm39
GRCm39 Ensembl	X	59,044,824 - 59,076,119 (+)	Ensembl
GRCm38	X	59,999,329 - 60,030,760 (+)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	X	59,999,464 - 60,030,759 (+)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	X	57,252,641 - 57,283,935 (+)	NCBI	GRCm37		mm9	NCBIm37
MGSCv36	X	56,346,248 - 56,377,542 (+)	NCBI			mm8
Celera	X	46,438,864 - 46,469,954 (+)	NCBI		Celera
Cytogenetic Map	X	A6	NCBI
cM Map	X	33.5	NCBI

F9
(Chinchilla lanigera - long-tailed chinchilla)

Chinchilla Assembly	Chr	Position (strand)	Source	Genome Browsers
Chinchilla Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChiLan1.0 Ensembl	NW_004955489	5,749,187 - 5,780,866 (-)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955489	5,747,718 - 5,780,899 (-)	NCBI	ChiLan1.0	ChiLan1.0

F9
(Pan paniscus - bonobo/pygmy chimpanzee)

Bonobo Assembly	Chr	Position (strand)	Source	Genome Browsers
Bonobo Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
PanPan1.1	X	138,934,144 - 138,967,180 (+)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	X	138,934,167 - 138,967,087 (+)	Ensembl	panpan1.1		panPan2
Mhudiblu_PPA_v0	X	128,684,709 - 128,719,020 (+)	NCBI	Mhudiblu_PPA_v0		panPan3

F9
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1 Ensembl	X	109,501,341 - 109,533,798 (+)	Ensembl	CanFam3.1		canFam3	CanFam3.1
CanFam3.1	X	109,501,341 - 109,533,798 (+)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1

F9
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)

Squirrel Assembly	Chr	Position (strand)	Source	Genome Browsers
Squirrel Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
SpeTri2.0	NW_004936513	8,052,998 - 8,090,245 (-)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

F9
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	X	114,218,707 - 114,250,436 (+)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	X	114,218,704 - 114,250,436 (+)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	X	130,417,620 - 130,448,319 (+)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

F9
(Chlorocebus sabaeus - African green monkey)

Vervet Assembly	Chr	Position (strand)	Source	Genome Browsers
Vervet Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChlSab1.1	X	114,618,397 - 114,650,827 (+)	NCBI
ChlSab1.1 Ensembl	X	114,618,639 - 114,651,365 (+)	Ensembl

F9
(Heterocephalus glaber - naked mole-rat)

Molerat Assembly	Chr	Position (strand)	Source	Genome Browsers
Molerat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HetGla 1.0	NW_004624808	7,137,482 - 7,175,255 (-)	NCBI

Position Markers

DXWox30

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Rnor_6.0	X	143,145,668 - 143,145,818	NCBI	Rnor6.0
Rnor_5.0	X	143,175,347 - 143,175,497	UniSTS	Rnor5.0
RGSC_v3.4	X	145,580,460 - 145,580,610	UniSTS	RGSC3.4
Celera	X	134,477,464 - 134,477,614	UniSTS
Cytogenetic Map	X	q36	UniSTS

GDB:192503

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Rnor_6.0	X	143,140,153 - 143,140,373	NCBI	Rnor6.0
Rnor_5.0	X	143,169,832 - 143,170,052	UniSTS	Rnor5.0
RGSC_v3.4	X	145,574,945 - 145,575,165	UniSTS	RGSC3.4
Celera	X	134,471,949 - 134,472,169	UniSTS
Cytogenetic Map	X	q36	UniSTS

RH127349

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Rnor_6.0	X	143,141,441 - 143,141,635	NCBI	Rnor6.0
Rnor_5.0	X	143,171,120 - 143,171,314	UniSTS	Rnor5.0
RGSC_v3.4	X	145,576,233 - 145,576,427	UniSTS	RGSC3.4
Celera	X	134,473,237 - 134,473,431	UniSTS
Cytogenetic Map	X	q36	UniSTS

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Rnor_6.0	X	143,139,500 - 143,140,176	NCBI	Rnor6.0
Rnor_5.0	X	143,169,179 - 143,169,855	UniSTS	Rnor5.0
RGSC_v3.4	X	145,574,292 - 145,574,968	UniSTS	RGSC3.4
Celera	X	134,471,296 - 134,471,972	UniSTS
Cytogenetic Map	X	q36	UniSTS

QTLs in Region (Rnor_6.0)

The following QTLs overlap with this region.

RGD ID	Symbol	Name	LOD	P Value	Trait	Sub Trait	Chr	Start	Stop	Species
1598837	Memor13	Memory QTL 13	3.2		exploratory behavior trait (VT:0010471)	difference between time of physical contact/close proximity of test subject and social stimulus during sample phase and test phase (CMO:0002678)	X	44320616	158345622	Rat
1598872	Memor14	Memory QTL 14	4.5		exploratory behavior trait (VT:0010471)	difference between time of physical contact/close proximity of test subject and social stimulus during sample phase and test phase (CMO:0002678)	X	101333032	146333032	Rat
738025	Stresp3	Stress response QTL 3	4.61	0.0066	stress-related behavior trait (VT:0010451)	defensive burying - approach	X	107886746	152409805	Rat
1598809	Memor15	Memory QTL 15	4.4		exploratory behavior trait (VT:0010471)	difference between time of physical contact/close proximity of test subject and social stimulus during sample phase and test phase (CMO:0002678)	X	110957467	155957467	Rat
1598856	Memor1	Memory QTL 1	1.9		exploratory behavior trait (VT:0010471)	total horizontal distance resulting from voluntary locomotion in an experimental apparatus (CMO:0001443)	X	110957467	155957467	Rat
10059603	Bw174	Body weight QTL 174	3.4	0.025	body mass (VT:0001259)	body weight (CMO:0000012)	X	118715462	159970021	Rat
738029	Stresp2	Stress response QTL 2	3.4	0.0004	stress-related behavior trait (VT:0010451)	defensive burying - approach	X	120045041	143145818	Rat
634346	Insul4	Insulin level QTL 4	0		blood insulin amount (VT:0001560)	serum insulin level (CMO:0000358)	X	134627816	159970021	Rat

miRNA Target Status

Predicted Target Of

	Summary Value
Count of predictions:	370
Count of miRNA genes:	238
Interacting mature miRNAs:	285
Transcripts:	ENSRNOT00000004559
Prediction methods:	Miranda, Pita, Rnahybrid, Targetscan
Result types:	miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.

Expression

RNA-SEQ Expression

High: > 1000 TPM value Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM Below Cutoff: < 0.5 TPM

	alimentary part of gastrointestinal system	circulatory system	endocrine system	exocrine system	hemolymphoid system	hepatobiliary system	integumental system	musculoskeletal system	nervous system	renal system	reproductive system	respiratory system	appendage
High
Medium			31	31		31
Low		2	14	8	1	8	2	2	2	1	3	3	2
Below cutoff	1	6	12	2	15	2	6	8	11	10	19	6	6

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_031540	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	CH474019	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FM036569	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JACYVU010000476	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	M26247	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Reference Sequences

RefSeq Acc Id:

ENSRNOT00000004559 ⟹ ENSRNOP00000004559

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0 Ensembl	X	143,097,525 - 143,141,794 (+)	Ensembl

RefSeq Acc Id:

NM_031540 ⟹ NP_113728

RefSeq Status:

VALIDATED

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	X	138,352,334 - 138,396,835 (+)	NCBI
Rnor_6.0	X	143,097,560 - 143,141,786 (+)	NCBI
Rnor_5.0	X	143,127,239 - 143,171,465 (+)	NCBI
Celera	X	134,429,774 - 134,473,582 (+)	NCBI

Sequence:

show sequence

ATGGCAGACGCTCCGGGTCTCATCCCCATCTTCCTTCTGGGCTATCTACTCAGCACTGAATGTG
CAGTTTTTCTTGATCGCGAAAATGCCACCAAAATTCTTACCCGTCCAAAGAGATATAACTCAGG
GAAACTGGAAGAGTTTGTTCAGGGAAACCTTGAGAGAGAGTGCATAGAAGAAAGATGCAGTTTT
GAAGAAGCACGAGAAGTTTTTGAAAACACTGAAAAAACTACTGAATTTTGGAAGCAGTATGTTG
ATGGAGATCAGTGTGAATCAAATCCTTGCTTAAATGGTGGAATATGCAAGGATGATATTAATTC
CTATGAATGTTGGTGCCAAGCTGGATTTGAAGGAAGGAACTGTGAATTAGATGCAACATGTAGC
ATTAAAAATGGCAGGTGTAAGCAGTTTTGTAAAAACAGCCCTGATAACAAGATAATTTGTTCCT
GCACTGAGGGATACCAACTTGCAGAAGACCAGAAGTCCTGTGAACCAGCAGTTCCATTCCCATG
TGGAAGAGTTTCTGTTGCCTACAATTCTAAAAAGATCACCCGTGCTGAGACTGTTTTTTCTAAT
ACCGACTATGGAAATTCCACTGAATTAATCCTGGATGACATCACCAACAGCACCATTCTTGATA
ACCTCACTGAAAATAGTGAACCAATTAATGACTTCACTCGAGTTGTTGGTGGAGAAAATGCGAA
ACCAGGTCAAATCCCTTGGCAGGTCATTCTAAATGGTGAAATTGAGGCATTCTGTGGAGGCGCC
ATCATTAATGAAAAATGGATTGTAACTGCTGCCCACTGTCTTAAACCTGGTGATAAAATTGAGG
TTGTTGCTGGTGAACATAATATTGATGAGAAGGAAGACACAGAACAAAGGAGAAATGTGATTCG
AACTATCCCTCATCACCAGTACAATGCAACTATTAATAAGTATAGTCATGACATTGCCTTGCTG
GAACTGGATAAACCTTTAATACTAAACAGCTATGTAACACCTATCTGTGTTGCCAATAAGGAAT
ATACAAATATCTTCCTCAAGTTTGGTTCTGGTTATGTGAGTGGCTGGGGGAAAGTCTTCAACAA
AGGGAGACAGGCTTCCATTCTTCAGTACCTTAGAGTTCCACTGGTTGACCGAGCCACATGCCTT
AGGTCCACAAAATTCAGCATCTATAACAACATGTTCTGTGCAGGTTACCGTGAAGGAGGCAAAG
ATTCATGTGAAGGAGATAGTGGGGGACCCCATGTTACTGAAGTAGAAGGGACAAGTTTCTTAAC
TGGCATTATTAGCTGGGGTGAAGAATGTGCAATGAAAGGCAAATATGGAATATATACTAAGGTT
TCCAGGTATGTCAACTGGATTAAGGAAAAAACAAAGCTAACTTAATGAAAAACCTAATTCCAAA
GGCAATTCGCTGGGATTGAACATGGATGATTCCTTTGCAAACTAGTCTTTGCACTGTTTGCTAA
ACTTCAATACATATGCTCTATAAATACTGATTTTTCTCTGTGCAGGGGACAAGCCCATGTAGGA
TCTATATTGTATTAGATTAAGTAGGTTAGCAAATATAATCGCTAAAGAAATACTTTAGTAAGAG
ATTAACCAGTTCTGCAAGCCCAGTCCTTATTAAAATTTTAAAATTAGAAAGTGTAGCTCCCCAT
GTTGCCCATAAGACATGATGGTTCTTGATGTAGAGATGTACCCAATTCTCCCTCCTTGGTATCA
GTTCATATTTTAGATCTTCCTCACCTCTCTCAAATTTATTGGTTTTCTGTCCAGAATCTTTAGC
TCGTTTAAGGCCAGAAGAAAGCAGGAACAACTGATACATTAAAACTCATCAAAAGCATGACTTC
CTCTCTTGATTTTCCCGAATCCTGTATCTTTTTCAACTCCCAATCCACAAATCACTGTCCCGTC
CATCATTCTCACCCTCTAGTTCTCCATCAGCTTTGAAAGAGGAAGAGGTGTGAGTTCCAGGACA
GTCAGGAGTACAGAGAAATCCTGTCTTGAAAGAAAAAAGAAAGAGAGGGGCAGGGAGGAAGGAA
GGAAGGAAGAAGGAAGGAAGGAAGAAGGAAGGAGAGAAAGAATGATTAATTTAGTCATATTGGT
ATATATATATAAACACCACTAATCTTACTTGTAACAACCACTTATTTCTCTGAAGTAAATACCT
TTACCTTGATAGATTTCAGGCTATTAACATAAAGTTACTGGAAAAGGAGTTGGGAAAACATATG
CAAAATTACTTTTAAAACTGTTTCAGCCAGTTTTGAACCTCGAACCAGCTGAGCTTTCTAGAAA
CACTTCAACGGTTTATCTTCGGCTTTCTCCAGTGCCAACCACCCTAAGTCGTCTCTCACAGCAG
GCCCCAGGATGCAAGAGTAAATGGCGAACTGAATTGCCCAGTTCTGGTTTTCTGCTCCCCAGTG
AACTGTGTTATCATAATTAACATTGTTATGCTGAATTTTCTAGAGGGGTGCTGACCACCTGACC
CATTTTTCATCTGTGATTTGATGAACTGGCATTTTAATACTTTTCTGGATCTTTGTATGAACTT
GTTTGGAATTGACCCAGTCACCTCACACTTAATGATGTATAAATCGTTTGAACCCCTTGTCACT
GTCACCTGTCCCCACCATACAATATCCTACTTTATTACTGCTGACTCTATTAATGTTCCACTAC
TTACTGCCTCTTTTGTCTTGCAAAAAGTATCAATAAACATCTATCCAAATTGC

hide sequence

RefSeq Acc Id:

XM_017601915 ⟹ XP_017457404

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0	X	143,097,507 - 143,141,791 (+)	NCBI

Sequence:

show sequence

CCTGACACTTGCACAATCTCCTAACAAAGGTCAGGCGGCACCTGAACGCCATCATGGCAGACGC
TCCGGGTCTCATCCCCATCTTCCTTCTGGGCTATCTACTCAGCACTGAATGTGCAGTTTTTCTT
GATCGCGAAAATGCCACCAAAATTCTTACCCGTCCAAAGAGATATAACTCAGGGAAACTGGAAG
AGTTTGTTCAGGGAAACCTTGAGAGAGAGTGCATAGAAGAAAGATGCAGTTTTGAAGAAGCACG
AGAAGTTTTTGAAAACACTGAAAAAACTACTGAATTTTGGAAGCAGTATGTTGATGGAGATCAG
TGTGAATCAAATCCTTGCTTAAATGGTGGAATATGCAAGGATGATATTAATTCCTATGAATGTT
GGTGCCAAGCTGGATTTGAAGGAAGGAACTGTGAATTAGATGCAACATGTAGCATTAAAAATGG
CAGGTGTAAGCAGTTTTGTAAAAACAGCCCTGATAACAAGATAATTTGTTCCTGCACTGAGGGA
TACCAACTTGCAGAAGACCAGAAGTCCTGTGAACCAGCAGTTCCATTCCCATGTGGAAGAGTTT
CTGTTGCCTACAATTCTAAAAAGATCACCCGTGCTGAGACTGTTTTTTCTAATACCGACTATGG
AAATTCCACTGAATTAATCCTGGATGACATCACCAACAGCACCATTCTTGATAACCTCACTGAA
AATAGTGAACCAATTAATGACTTCACTCGAGTTGTTGGTGGAGAAAATGCGAAACCAGGTCAAA
TCCCTTGGCAGGGTGGTCAGCTTTTACAGGAGCCTTGTTTGAGCAAATGTTTTGGTATGATCAA
CTGGCAGAGCTCTTCTGACCCCTGGAGCAGCAGGACTAGCGTGAAAGTCATAGTGTTTATGCAT
CAGGTCATTCTAAATGGTGAAATTGAGGCATTCTGTGGAGGCGCCATCATTAATGAAAAATGGA
TTGTAACTGCTGCCCACTGTCTTAAACCTGGTGATAAAATTGAGGTTGTTGCTGGTGAACATAA
TATTGATGAGAAGGAAGACACAGAACAAAGGAGAAATGTGATTCGAACTATCCCTCATCACCAG
TACAATGCAACTATTAATAAGTATAGTCATGACATTGCCTTGCTGGAACTGGATAAACCTTTAA
TACTAAACAGCTATGTAACACCTATCTGTGTTGCCAATAAGGAATATACAAATATCTTCCTCAA
GTTTGGTTCTGGTTATGTGAGTGGCTGGGGGAAAGTCTTCAACAAAGGGAGACAGGCTTCCATT
CTTCAGTACCTTAGAGTTCCACTGGTTGACCGAGCCACATGCCTTAGGTCCACAAAATTCAGCA
TCTATAACAACATGTTCTGTGCAGGTTACCGTGAAGGAGGCAAAGATTCATGTGAAGGAGATAG
TGGGGGACCCCATGTTACTGAAGTAGAAGGGACAAGTTTCTTAACTGGCATTATTAGCTGGGGT
GAAGAATGTGCAATGAAAGGCAAATATGGAATATATACTAAGGTTTCCAGGTATGTCAACTGGA
TTAAGGAAAAAACAAAGCTAACTTAATGAAAAACCTAATTCCAAAGGCAATTCGCTGGGATTGA
ACATGGATGATTCCTTTGCAAACTAGTCTTTGCACTGTTTGCTAAACTTCAATACATATGCTCT
ATAAATACTGATTTTTCTCTGTGCAGGGGACAAGCCCATGTAGGATCTATATTGTATTAGATTA
AGTAGGTTAGCAAATATAATCGCTAAAGAAATACTTTAGTAAGAGATTAACCAGTTCTGCAAGC
CCAGTCCTTATTAAAATTTTAAAATTAGAAAGTGTAGCTCCCCATGTTGCCCATAAGACATGAT
GGTTCTTGATGTAGAGATGTACCCAATTCTCCCTCCTTGGTATCAGTTCATATTTTAGATCTTC
CTCACCTCTCTCAAATTTATTGGTTTTCTGTCCAGAATCTTTAGCTCGTTTAAGGCCAGAAGAA
AGCAGGAACAACTGATACATTAAAACTCATCAAAAGCATGACTTCCTCTCTTGATTTTCCCGAA
TCCTGTATCTTTTTCAACTCCCAATCCACAAATCACTGTCCCGTCCATCATTCTCACCCTCTAG
TTCTCCATCAGCTTTGAAAGAGGAAGAGGTGTGAGTTCCAGGACAGTCAGGAGTACAGAGAAAT
CCTGTCTTGAAAGAAAAAAGAAAGAGAGGGGCAGGGAGGAAGGAAGGAAGGAAGAAGGAAGGAA
GGAAGAAGGAAGGAGAGAAAGAATGATTAATTTAGTCATATTGGTATATATATATAAACACCAC
TAATCTTACTTGTAACAACCACTTATTTCTCTGAAGTAAATACCTTTACCTTGATAGATTTCAG
GCTATTAACATAAAGTTACTGGAAAAGGAGTTGGGAAAACATATGCAAAATTACTTTTAAAACT
GTTTCAGCCAGTTTTGAACCTCGAACCAGCTGAGCTTTCTAGAAACACTTCAACGGTTTATCTT
CGGCTTTCTCCAGTGCCAACCACCCTAAGTCGTCTCTCACAGCAGGCCCCAGGATGCAAGAGTA
AATGGCGAACTGAATTGCCCAGTTCTGGTTTTCTGCTCCCCAGTGAACTGTGTTATCATAATTA
ACATTGTTATGCTGAATTTTCTAGAGGGGTGCTGACCACCTGACCCATTTTTCATCTGTGATTT
GATGAACTGGCATTTTAATACTTTTCTGGATCTTTGTATGAACTTGTTTGGAATTGACCCAGTC
ACCTCACACTTAATGATGTATAAATCGTTTGAACCCCTTGTCACTGTCACCTGTCCCCACCATA
CAATATCCTACTTTATTACTGCTGACTCTATTAATGTTCCACTACTTACTGCCTCTTTTGTCTT
GCAAAAAGTATCAATAAACATCTATCCAAATTGCTCCAA

hide sequence

Protein Sequences


Protein RefSeqs	NP_113728	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	AAA41162	(Get FASTA)	NCBI Sequence Viewer
	EDL86171	(Get FASTA)	NCBI Sequence Viewer
	EDL86172	(Get FASTA)	NCBI Sequence Viewer
	P16296	(Get FASTA)	NCBI Sequence Viewer

Reference Sequences

RefSeq Acc Id:	NP_113728 ⟸ NM_031540
- Peptide Label:	precursor
- UniProtKB:	P16296 (UniProtKB/Swiss-Prot)
- Sequence:	show sequence MADAPGLIPIFLLGYLLSTECAVFLDRENATKILTRPKRYNSGKLEEFVQGNLERECIEERCSF EEAREVFENTEKTTEFWKQYVDGDQCESNPCLNGGICKDDINSYECWCQAGFEGRNCELDATCS IKNGRCKQFCKNSPDNKIICSCTEGYQLAEDQKSCEPAVPFPCGRVSVAYNSKKITRAETVFSN TDYGNSTELILDDITNSTILDNLTENSEPINDFTRVVGGENAKPGQIPWQVILNGEIEAFCGGA IINEKWIVTAAHCLKPGDKIEVVAGEHNIDEKEDTEQRRNVIRTIPHHQYNATINKYSHDIALL ELDKPLILNSYVTPICVANKEYTNIFLKFGSGYVSGWGKVFNKGRQASILQYLRVPLVDRATCL RSTKFSIYNNMFCAGYREGGKDSCEGDSGGPHVTEVEGTSFLTGIISWGEECAMKGKYGIYTKV SRYVNWIKEKTKLT hide sequence

RefSeq Acc Id:

XP_017457404 ⟸ XM_017601915

- Peptide Label:

isoform X1

- Sequence:

show sequence

MADAPGLIPIFLLGYLLSTECAVFLDRENATKILTRPKRYNSGKLEEFVQGNLERECIEERCSF
EEAREVFENTEKTTEFWKQYVDGDQCESNPCLNGGICKDDINSYECWCQAGFEGRNCELDATCS
IKNGRCKQFCKNSPDNKIICSCTEGYQLAEDQKSCEPAVPFPCGRVSVAYNSKKITRAETVFSN
TDYGNSTELILDDITNSTILDNLTENSEPINDFTRVVGGENAKPGQIPWQGGQLLQEPCLSKCF
GMINWQSSSDPWSSRTSVKVIVFMHQVILNGEIEAFCGGAIINEKWIVTAAHCLKPGDKIEVVA
GEHNIDEKEDTEQRRNVIRTIPHHQYNATINKYSHDIALLELDKPLILNSYVTPICVANKEYTN
IFLKFGSGYVSGWGKVFNKGRQASILQYLRVPLVDRATCLRSTKFSIYNNMFCAGYREGGKDSC
EGDSGGPHVTEVEGTSFLTGIISWGEECAMKGKYGIYTKVSRYVNWIKEKTKLT

hide sequence

RefSeq Acc Id:

ENSRNOP00000004559 ⟸ ENSRNOT00000004559

Protein Domains

EGF-like Gla Peptidase S1

Transcriptome

eQTL		View at Phenogen
WGCNA		View at Phenogen
Tissue/Strain Expression		View at Phenogen

Promoters

RGD ID:

13702021

Promoter ID:

EPDNEW_R12545

Type:

initiation region

Name:

F9_1

Description:

coagulation factor IX

SO ACC ID:

SO:0000170

Source:

EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)

Experiment Methods:

Single-end sequencing.

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0	X	143,097,539 - 143,097,599	EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)

ACI/EurMcwi (MCW)

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Medical College of Wisconsin
Description:	Provided by the Medical College of Wisconsin (Dr. Howard Jacob)

ACI/EurMcwi (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

ACI/N (MCW)

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Sequenced By:	Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen) Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform:	SOLiD 4 and 5500
Secondary Analysis:	liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder:	National Institutes of Health
Description:	Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

BBDP/Wor (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

BN/SsN (MCW)

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Sequenced By:	Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen) Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform:	SOLiD 4 and 5500
Secondary Analysis:	liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder:	National Institutes of Health
Description:	Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

Buf/N (MCW)

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Sequenced By:	Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen) Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform:	SOLiD 4 and 5500
Secondary Analysis:	liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder:	National Institutes of Health
Description:	Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

COP/CrCrl (MCW & UW)

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob) University of Wisconsin (Dr. James Shull)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Charles River Laboratories
Description:	Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)

F344/NCrl (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

F344/NRrrc (MCW)

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Sequenced By:	Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen) Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform:	SOLiD 4 and 5500
Secondary Analysis:	liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder:	National Institutes of Health
Description:	Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

FHH/EurMcwi (MCW)

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Medical College of Wisconsin
Description:	Provided by the Medical College of Wisconsin (Dr. Howard Jacob)

FHH/EurMcwi (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

FHL/EurMcwi (MCW)

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Medical College of Wisconsin
Description:	Provided by the Medical College of Wisconsin (Dr. Howard Jacob)

FHL/EurMcwi (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

GH/OmrMcwi (MCW)

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Medical College of Wisconsin
Description:	Provided by the Medical College of Wisconsin (Dr. Howard Jacob)

GK/Ox (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

LE/Stm (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

LEW/Crl (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

LEW/NCrlBR (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

LH/MavRrrc (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

LL/MavRrrc (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

LN/MavRrrc (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

M520/N (MCW)

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Sequenced By:	Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen) Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform:	SOLiD 4 and 5500
Secondary Analysis:	liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder:	National Institutes of Health
Description:	Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

MHS/Gib (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

MNS/Gib (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

MR/N (MCW)

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Sequenced By:	Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen) Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform:	SOLiD 4 and 5500
Secondary Analysis:	liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder:	National Institutes of Health
Description:	Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

SBH/Ygl (MCW)

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Medical College of Wisconsin
Description:	SBH/Ygl sequenced by MCW

SBH/Ygl (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

SBN/Ygl (MCW)

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Medical College of Wisconsin
Description:	SBN/Ygl sequenced by MCW

SBN/Ygl (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

SHR/NHsd (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

SHRSP/Gcrc (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

SR/JrHsd (MCW)

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Harlan Laboratories
Description:	Provided by the Medical College of Wisconsin (Dr. Howard Jacob)

SR/JrHsd (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

SS/Jr (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

SS/JrHsdMcwi (MCW)

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Medical College of Wisconsin
Description:	Provided by the Medical College of Wisconsin (Dr. Howard Jacob)

SS/JrHsdMcwi (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

WAG/Rij (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

WKY/Gcrc (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

WKY/N (MCW)

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Sequenced By:	Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen) Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform:	SOLiD 4 and 5500
Secondary Analysis:	liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder:	National Institutes of Health
Description:	Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

WKY/NCrl (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

WKY/NHsd (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

WN/N (MCW)

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Sequenced By:	Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen) Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform:	SOLiD 4 and 5500
Secondary Analysis:	liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder:	National Institutes of Health
Description:	Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:2589	AgrOrtholog
Ensembl Genes	ENSRNOG00000003430	Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein	ENSRNOP00000004559	ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript	ENSRNOT00000004559	ENTREZGENE, UniProtKB/Swiss-Prot
Gene3D-CATH	2.40.10.10	UniProtKB/Swiss-Prot
	4.10.740.10	UniProtKB/Swiss-Prot
InterPro	Coagulation_fac-like_Gla_dom	UniProtKB/Swiss-Prot
	Coagulation_factor_IX	UniProtKB/Swiss-Prot
	EGF-like_Ca-bd_dom	UniProtKB/Swiss-Prot
	EGF-like_dom	UniProtKB/Swiss-Prot
	EGF-type_Asp/Asn_hydroxyl_site	UniProtKB/Swiss-Prot
	EGF_Ca-bd_CS	UniProtKB/Swiss-Prot
	GLA-like_dom_SF	UniProtKB/Swiss-Prot
	GLA_domain	UniProtKB/Swiss-Prot
	Pept_S1A_FX	UniProtKB/Swiss-Prot
	Peptidase_S1_PA	UniProtKB/Swiss-Prot
	Peptidase_S1_PA_chymotrypsin	UniProtKB/Swiss-Prot
	Peptidase_S1A	UniProtKB/Swiss-Prot
	Trypsin_dom	UniProtKB/Swiss-Prot
	TRYPSIN_HIS	UniProtKB/Swiss-Prot
	TRYPSIN_SER	UniProtKB/Swiss-Prot
KEGG Report	rno:24946	UniProtKB/Swiss-Prot
NCBI Gene	24946	ENTREZGENE
PANTHER	PTHR24278:SF31	UniProtKB/Swiss-Prot
Pfam	EGF	UniProtKB/Swiss-Prot
	Gla	UniProtKB/Swiss-Prot
	Trypsin	UniProtKB/Swiss-Prot
PharmGKB	F9	RGD
PhenoGen	F9	PhenoGen
PIRSF	Factor_X	UniProtKB/Swiss-Prot
PRINTS	CHYMOTRYPSIN	UniProtKB/Swiss-Prot
	GLABLOOD	UniProtKB/Swiss-Prot
PROSITE	ASX_HYDROXYL	UniProtKB/Swiss-Prot
	EGF_1	UniProtKB/Swiss-Prot
	EGF_2	UniProtKB/Swiss-Prot
	EGF_3	UniProtKB/Swiss-Prot
	EGF_CA	UniProtKB/Swiss-Prot
	GLA_1	UniProtKB/Swiss-Prot
	GLA_2	UniProtKB/Swiss-Prot
	TRYPSIN_DOM	UniProtKB/Swiss-Prot
	TRYPSIN_HIS	UniProtKB/Swiss-Prot
	TRYPSIN_SER	UniProtKB/Swiss-Prot
SMART	EGF	UniProtKB/Swiss-Prot
	EGF_CA	UniProtKB/Swiss-Prot
	GLA	UniProtKB/Swiss-Prot
	Tryp_SPc	UniProtKB/Swiss-Prot
Superfamily-SCOP	SSF50494	UniProtKB/Swiss-Prot
	SSF57630	UniProtKB/Swiss-Prot
UniProt	FA9_RAT	UniProtKB/Swiss-Prot, ENTREZGENE
UniProt Secondary	F1M1M6	UniProtKB/Swiss-Prot

Nomenclature History

Date	Current Symbol	Current Name	Previous Name	Description	Reference	Status
2006-03-30	F9	coagulation factor IX	coagulation factor 9	Name updated	1299863	APPROVED
2003-04-09	F9	coagulation factor 9	Coagulation factor IX (plasma thromboplastic component, Christmas disease, hemophilia B)	Name updated	629478	APPROVED
2002-06-10	F9	Coagulation factor IX (plasma thromboplastic component, Christmas disease, hemophilia B)		Symbol and Name status set to approved	70586	APPROVED

Gene Annotator (Functional Annotation) unavailable	Gene Annotator (Annotation Distribution) unavailable	Variant Visualizer (Genomic Variants) unavailble Variant Visualizer (Genomic Variants) unavailable
Gene Annotator (Functional Annotation)	Gene Annotator (Annotation Distribution)	Variant Visualizer (Genomic Variants)

InterViewer (Protein-Protein Interactions) unavailable	Gviewer (Genome Viewer) unavailable	Variant Visualizer (Damaging Variants) unavailble Variant Visualizer (Damaging Variants) unavailable
InterViewer (Protein-Protein Interactions)	GViewer (Genome Viewer)	Variant Visualizer (Damaging Variants)

Gene Annotator (Annotation Comparison) unavailable	OLGA (Gene List Generator) unavailable
Gene Annotator (Annotation Comparison)	OLGA (Gene List Generator)	Excel (Download)

MOET (Multi-Ontology Enrichement) unavailable	GOLF (Gene-Ortholog Location Finder) unavailable
MOET (Multi-Ontology Enrichement)	GOLF (Gene-Ortholog Location Finder)

Imported Disease Annotations - ClinVar

Imported Disease Annotations - CTD

Imported Disease Annotations - OMIM

RGD Manual Annotations

Imported Annotations - SMPDB

Imported Annotations - KEGG (archival)