F9 (coagulation factor IX) - Rat Genome Database

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Gene: F9 (coagulation factor IX) Rattus norvegicus
Analyze
Symbol: F9
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 ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2X138,352,334 - 138,396,835 (+)NCBI
Rnor_6.0 EnsemblX143,097,525 - 143,141,794 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0X143,097,507 - 143,141,791 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0X143,127,239 - 143,171,465 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X145,527,978 - 145,575,966 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1X145,647,657 - 145,648,632 (+)NCBI
CeleraX134,429,774 - 134,473,582 (+)NCBICelera
Cytogenetic MapXq36NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


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

Molecular Function

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 AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2X138,352,334 - 138,396,835 (+)NCBI
Rnor_6.0 EnsemblX143,097,525 - 143,141,794 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0X143,097,507 - 143,141,791 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0X143,127,239 - 143,171,465 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X145,527,978 - 145,575,966 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1X145,647,657 - 145,648,632 (+)NCBI
CeleraX134,429,774 - 134,473,582 (+)NCBICelera
Cytogenetic MapXq36NCBI
F9
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 EnsemblX139,530,739 - 139,563,459 (+)EnsemblGRCh38hg38GRCh38
GRCh38X139,530,720 - 139,563,459 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh37X138,612,898 - 138,645,618 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36X138,440,561 - 138,473,283 (+)NCBINCBI36hg18NCBI36
Build 34X138,338,414 - 138,371,137NCBI
CeleraX138,980,334 - 139,013,056 (+)NCBI
Cytogenetic MapXq27.1NCBI
HuRefX127,880,671 - 127,913,025 (+)NCBIHuRef
CHM1_1X138,523,783 - 138,556,510 (+)NCBICHM1_1
F9
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39X59,044,675 - 59,076,120 (+)NCBIGRCm39mm39
GRCm39 EnsemblX59,044,824 - 59,076,119 (+)Ensembl
GRCm38X59,999,329 - 60,030,760 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 EnsemblX59,999,464 - 60,030,759 (+)EnsemblGRCm38mm10GRCm38
MGSCv37X57,252,641 - 57,283,935 (+)NCBIGRCm37mm9NCBIm37
MGSCv36X56,346,248 - 56,377,542 (+)NCBImm8
CeleraX46,438,864 - 46,469,954 (+)NCBICelera
Cytogenetic MapXA6NCBI
cM MapX33.5NCBI
F9
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554895,749,187 - 5,780,866 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554895,747,718 - 5,780,899 (-)NCBIChiLan1.0ChiLan1.0
F9
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1X138,934,144 - 138,967,180 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 EnsemblX138,934,167 - 138,967,087 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0X128,684,709 - 128,719,020 (+)NCBIMhudiblu_PPA_v0panPan3
F9
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1X109,501,341 - 109,533,798 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 EnsemblX109,501,341 - 109,533,798 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_TashaX95,328,677 - 95,361,130 (+)NCBI
ROS_Cfam_1.0X111,487,863 - 111,520,319 (+)NCBI
UMICH_Zoey_3.1X108,621,887 - 108,654,350 (+)NCBI
UNSW_CanFamBas_1.0X110,806,410 - 110,838,864 (+)NCBI
UU_Cfam_GSD_1.0X110,485,875 - 110,518,335 (+)NCBI
F9
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2X107,524,352 - 107,562,278 (+)NCBI
SpeTri2.0NW_0049365138,052,998 - 8,090,245 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
F9
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 EnsemblX114,218,707 - 114,250,436 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1X114,218,704 - 114,250,436 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2X130,417,620 - 130,448,319 (+)NCBISscrofa10.2Sscrofa10.2susScr3
F9
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1X114,618,397 - 114,650,827 (+)NCBI
ChlSab1.1 EnsemblX114,618,639 - 114,651,365 (+)Ensembl
Vero_WHO_p1.0NW_02366606552,325,926 - 52,357,748 (+)NCBI
F9
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248087,137,482 - 7,175,255 (-)NCBI

Position Markers
DXWox30  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2X138,400,716 - 138,400,867 (+)MAPPER
Rnor_6.0X143,145,668 - 143,145,818NCBIRnor6.0
Rnor_5.0X143,175,347 - 143,175,497UniSTSRnor5.0
RGSC_v3.4X145,580,460 - 145,580,610UniSTSRGSC3.4
CeleraX134,477,464 - 134,477,614UniSTS
Cytogenetic MapXq36UniSTS
GDB:192503  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2X138,395,201 - 138,395,422 (+)MAPPER
Rnor_6.0X143,140,153 - 143,140,373NCBIRnor6.0
Rnor_5.0X143,169,832 - 143,170,052UniSTSRnor5.0
RGSC_v3.4X145,574,945 - 145,575,165UniSTSRGSC3.4
CeleraX134,471,949 - 134,472,169UniSTS
Cytogenetic MapXq36UniSTS
RH127349  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2X138,396,489 - 138,396,684 (+)MAPPER
Rnor_6.0X143,141,441 - 143,141,635NCBIRnor6.0
Rnor_5.0X143,171,120 - 143,171,314UniSTSRnor5.0
RGSC_v3.4X145,576,233 - 145,576,427UniSTSRGSC3.4
CeleraX134,473,237 - 134,473,431UniSTS
Cytogenetic MapXq36UniSTS
F9  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2X138,394,548 - 138,395,225 (+)MAPPER
Rnor_6.0X143,139,500 - 143,140,176NCBIRnor6.0
Rnor_5.0X143,169,179 - 143,169,855UniSTSRnor5.0
RGSC_v3.4X145,574,292 - 145,574,968UniSTSRGSC3.4
CeleraX134,471,296 - 134,471,972UniSTS
Cytogenetic MapXq36UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1598837Memor13Memory QTL 133.2exploratory 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)X44320616158345622Rat
1598872Memor14Memory QTL 144.5exploratory 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)X101333032146333032Rat
738025Stresp3Stress response QTL 34.610.0066stress-related behavior trait (VT:0010451)defensive burying - approachX107886746152409805Rat
1598809Memor15Memory QTL 154.4exploratory 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)X110957467155957467Rat
1598856Memor1Memory QTL 11.9exploratory behavior trait (VT:0010471)total horizontal distance resulting from voluntary locomotion in an experimental apparatus (CMO:0001443)X110957467155957467Rat
10059603Bw174Body weight QTL 1743.40.025body mass (VT:0001259)body weight (CMO:0000012)X118715462159970021Rat
738029Stresp2Stress response QTL 23.40.0004stress-related behavior trait (VT:0010451)defensive burying - approachX120045041143145818Rat
634346Insul4Insulin level QTL 40blood insulin amount (VT:0001560)serum insulin level (CMO:0000358)X134627816159970021Rat

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

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000004559   ⟹   ENSRNOP00000004559
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 EnsemblX143,097,525 - 143,141,794 (+)Ensembl
RefSeq Acc Id: NM_031540   ⟹   NP_113728
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X138,352,334 - 138,396,835 (+)NCBI
Rnor_6.0X143,097,560 - 143,141,786 (+)NCBI
Rnor_5.0X143,127,239 - 143,171,465 (+)NCBI
CeleraX134,429,774 - 134,473,582 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017601915   ⟹   XP_017457404
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0X143,097,507 - 143,141,791 (+)NCBI
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:
RefSeq Acc Id: XP_017457404   ⟸   XM_017601915
- Peptide Label: isoform X1
- 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 AssemblyChrPosition (strand)Source
Rnor_6.0X143,097,539 - 143,097,599EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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

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 Symbol 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