F13a1 (coagulation factor XIII A1 chain) - Rat Genome Database

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Gene: F13a1 (coagulation factor XIII A1 chain) Rattus norvegicus
Analyze
Symbol: F13a1
Name: coagulation factor XIII A1 chain
RGD ID: 621495
Description: Predicted to enable protein-glutamine gamma-glutamyltransferase activity. Involved in blood coagulation. Predicted to be located in cytoplasm and extracellular region. Biomarker of gastric ulcer. Human ortholog(s) of this gene implicated in artery disease (multiple); factor XIII deficiency; priapism; and thrombophilia (multiple). Orthologous to human F13A1 (coagulation factor XIII A chain); PARTICIPATES IN acenocoumarol pharmacodynamics pathway; alteplase pharmacodynamics pathway; aminocaproic acid pharmacodynamics pathway; INTERACTS WITH 2,2',4,4'-Tetrabromodiphenyl ether; 2,3,7,8-tetrachlorodibenzodioxine; 3,7-dihydropurine-6-thione.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: coagulation factor XIII A chain; coagulation factor XIII, A1 polypeptide; coagulation factor XIII, A1 subunit; coagulation factor XIIIa; F13a; protein-glutamine gamma-glutamyltransferase A chain; transglutaminase A chain
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21727,815,723 - 27,992,494 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl1727,815,702 - 27,992,700 (+)Ensembl
Rnor_6.01728,504,650 - 28,680,015 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1728,504,623 - 28,680,362 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01730,406,396 - 30,581,441 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41734,093,525 - 34,270,498 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11734,096,401 - 34,272,682 (+)NCBI
Celera1727,443,244 - 27,619,724 (+)NCBICelera
Cytogenetic Map17p12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
1-chloro-2,4-dinitrobenzene  (ISO)
1-naphthyl isothiocyanate  (ISO)
17beta-estradiol  (ISO)
2,2',4,4'-Tetrabromodiphenyl ether  (EXP)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
3,4-methylenedioxymethamphetamine  (ISO)
3,7-dihydropurine-6-thione  (EXP)
4,4'-sulfonyldiphenol  (ISO)
4-(ethoxymethylene)-2-phenyloxazol-5-one  (ISO)
4-hydroxyphenyl retinamide  (ISO)
aflatoxin B1  (ISO)
all-trans-retinoic acid  (ISO)
ammonium chloride  (EXP)
amphetamine  (EXP)
antirheumatic drug  (ISO)
arsenous acid  (ISO)
belinostat  (ISO)
benzene  (ISO)
benzo[a]pyrene  (ISO)
benzo[b]fluoranthene  (ISO)
bisphenol A  (EXP)
bisphenol F  (ISO)
calcitriol  (ISO)
carbon nanotube  (ISO)
chloroprene  (EXP)
chrysene  (ISO)
copper atom  (EXP)
copper(0)  (EXP)
decabromodiphenyl ether  (EXP)
dextran sulfate  (ISO)
diarsenic trioxide  (ISO)
diclofenac  (ISO)
dioxygen  (ISO)
diuron  (EXP)
dorsomorphin  (ISO)
doxorubicin  (ISO)
endosulfan  (EXP)
ethanol  (ISO)
eugenol  (ISO)
genistein  (ISO)
graphite  (EXP)
indole-3-methanol  (EXP)
iron atom  (ISO)
iron(0)  (ISO)
isoprenaline  (ISO)
ivermectin  (ISO)
lead diacetate  (ISO)
medroxyprogesterone acetate  (ISO)
mercaptopurine  (EXP)
metacetamol  (ISO)
methotrexate  (ISO)
mifepristone  (ISO)
N,N-diethyl-m-toluamide  (EXP)
N-acetyl-L-cysteine  (EXP)
N-nitrosodiethylamine  (EXP)
nickel sulfate  (ISO)
ozone  (ISO)
paclitaxel  (EXP)
paracetamol  (ISO)
permethrin  (EXP)
phenylmercury acetate  (ISO)
pravastatin  (EXP,ISO)
progesterone  (ISO)
purine-6-thiol  (EXP)
raloxifene  (ISO)
resveratrol  (ISO)
SB 431542  (ISO)
silicon dioxide  (EXP,ISO)
succimer  (ISO)
sulforaphane  (ISO)
tamoxifen  (ISO)
tebuconazole  (ISO)
tetrachloromethane  (ISO)
titanium dioxide  (ISO)
tremolite asbestos  (ISO)
tributylstannane  (EXP)
triptonide  (ISO)
troglitazone  (ISO)
tungsten  (ISO)
valproic acid  (ISO)
vitamin D  (ISO)
vorinostat  (ISO)
zaragozic acid A  (EXP,ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function

References

References - curated
1. Anwar R and Langlois S, Br J Haematol. 2009 Jun;146(1):118-20. doi: 10.1111/j.1365-2141.2009.07700.x. Epub 2009 Apr 27.
2. Board P, etal., Blood 1992 Aug 15;80(4):937-41.
3. Boeri D, etal., Diabetes. 2001 Jun;50(6):1432-9.
4. Butt C, etal., Blood. 2003 Apr 15;101(8):3037-41. Epub 2002 Dec 12.
5. Catto AJ, etal., Blood. 1999 Feb 1;93(3):906-8.
6. Catto AJ, etal., Stroke. 1998 Apr;29(4):813-6.
7. Corral J, etal., Hematol J. 2000;1(4):269-73.
8. D'Argenio G, etal., Digestion 2001;63(4):220-8.
9. Elliott L, etal., Br J Haematol. 2007 May;137(3):262-7.
10. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
11. Gemmati D, etal., Am J Hematol. 2001 Jul;67(3):183-8.
12. GOA data from the GO Consortium
13. Ivaskevicius V, etal., Ann Hematol. 2013 Jul;92(7):975-9. doi: 10.1007/s00277-013-1724-2. Epub 2013 Mar 19.
14. Ivaskevicius V, etal., Haematologica. 2010 Jun;95(6):956-62. doi: 10.3324/haematol.2009.017210. Epub 2010 Feb 23.
15. Katona E, etal., Haemophilia. 2014 Jan;20(1):114-20. doi: 10.1111/hae.12267. Epub 2013 Oct 1.
16. Kiss F, etal., Thromb Haemost. 2006 Aug;96(2):176-82.
17. Koseki-Kuno S, etal., Blood. 2003 Dec 15;102(13):4410-2. Epub 2003 Aug 21.
18. Kucher N, etal., Thromb Haemost. 2003 Sep;90(3):434-8.
19. Lauer P, etal., Thromb Haemost. 2002 Dec;88(6):967-74.
20. Louhichi N, etal., Ann Hematol. 2010 May;89(5):499-504. doi: 10.1007/s00277-009-0863-y. Epub 2009 Nov 24.
21. MGD data from the GO Consortium
22. Mikkola H, etal., Blood. 1994 Jul 15;84(2):517-25.
23. Moja EA, etal., Life Sci 1979 Apr 16;24(16):1467-70.
24. Mosesson MW J Thromb Haemost. 2005 Aug;3(8):1894-904.
25. NCBI rat LocusLink and RefSeq merged data July 26, 2002
26. OMIM Disease Annotation Pipeline
27. Oshitani N, etal., Am J Gastroenterol. 1995 Jul;90(7):1116-8.
28. Pastorova VE, etal., Biull Eksp Biol Med. 1979 Feb;87(2):99-101.
29. Pipeline to import KEGG annotations from KEGG into RGD
30. Pipeline to import SMPDB annotations from SMPDB into RGD
31. Reiner AP, etal., Stroke. 2001 Nov;32(11):2580-6.
32. Renner W, etal., Int Angiol. 2002 Mar;21(1):53-7.
33. RGD automated data pipeline
34. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
35. RGD automated import pipeline for gene-chemical interactions
36. RGD comprehensive gene curation
37. Song JW, etal., Yonsei Med J. 2006 Apr 30;47(2):196-200.
38. Tsujimoto I, etal., Am J Pathol. 2011 Dec;179(6):3011-9. doi: 10.1016/j.ajpath.2011.08.037. Epub 2011 Oct 19.
39. Van Hylckama Vlieg A, etal., Br J Haematol. 2002 Oct;119(1):169-75.
40. Wang W, etal., J Hum Genet. 2011 Jun;56(6):460-3. doi: 10.1038/jhg.2011.41. Epub 2011 Apr 21.
Additional References at PubMed
PMID:8889548   PMID:15507206   PMID:18224415   PMID:22516433   PMID:27363989  


Genomics

Comparative Map Data
F13a1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21727,815,723 - 27,992,494 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl1727,815,702 - 27,992,700 (+)Ensembl
Rnor_6.01728,504,650 - 28,680,015 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1728,504,623 - 28,680,362 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01730,406,396 - 30,581,441 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41734,093,525 - 34,270,498 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11734,096,401 - 34,272,682 (+)NCBI
Celera1727,443,244 - 27,619,724 (+)NCBICelera
Cytogenetic Map17p12NCBI
F13A1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl66,144,084 - 6,321,013 (-)EnsemblGRCh38hg38GRCh38
GRCh3866,144,084 - 6,320,662 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh3766,144,317 - 6,320,895 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 3666,089,310 - 6,265,923 (-)NCBINCBI36hg18NCBI36
Build 3466,089,316 - 6,265,901NCBI
Celera67,372,733 - 7,550,578 (-)NCBI
Cytogenetic Map6p25.1NCBI
HuRef66,020,217 - 6,197,010 (-)NCBIHuRef
CHM1_166,146,854 - 6,323,031 (-)NCBICHM1_1
F13a1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391337,051,150 - 37,234,220 (-)NCBIGRCm39mm39
GRCm39 Ensembl1337,051,152 - 37,234,220 (-)Ensembl
GRCm381336,867,178 - 37,050,244 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1336,867,178 - 37,050,244 (-)EnsemblGRCm38mm10GRCm38
MGSCv371336,959,047 - 37,142,113 (-)NCBIGRCm37mm9NCBIm37
MGSCv361336,874,653 - 37,056,670 (-)NCBImm8
Celera1337,983,710 - 38,163,470 (-)NCBICelera
Cytogenetic Map13A3.3NCBI
F13a1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554657,443,166 - 7,617,436 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554657,444,118 - 7,617,366 (+)NCBIChiLan1.0ChiLan1.0
F13A1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.166,159,012 - 6,337,000 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl66,157,926 - 6,513,961 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v065,978,505 - 6,156,705 (-)NCBIMhudiblu_PPA_v0panPan3
F13A1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1356,186,750 - 6,347,522 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl356,187,235 - 6,349,773 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha356,191,814 - 6,354,808 (-)NCBI
ROS_Cfam_1.0356,267,724 - 6,430,557 (-)NCBI
UMICH_Zoey_3.1356,122,455 - 6,285,137 (-)NCBI
UNSW_CanFamBas_1.0356,148,410 - 6,311,467 (-)NCBI
UU_Cfam_GSD_1.0357,481,872 - 7,644,350 (-)NCBI
F13a1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494617,930,084 - 18,091,733 (+)NCBI
SpeTri2.0NW_0049365346,199,066 - 6,360,374 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
F13A1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl73,751,291 - 3,900,765 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.173,751,290 - 3,900,797 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.273,952,957 - 4,102,446 (-)NCBISscrofa10.2Sscrofa10.2susScr3
F13A1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11765,885,498 - 66,040,026 (+)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl1765,885,658 - 66,040,040 (+)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_0236660446,090,570 - 6,385,150 (-)NCBIVero_WHO_p1.0
F13a1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462475619,103,064 - 19,259,632 (+)NCBIHetGla_female_1.0hetGla2

Position Markers
D17Rat13  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21727,835,154 - 27,835,317 (+)MAPPERmRatBN7.2
Rnor_6.01728,523,806 - 28,523,968NCBIRnor6.0
Rnor_5.01730,425,552 - 30,425,714UniSTSRnor5.0
RGSC_v3.41734,113,132 - 34,113,294UniSTSRGSC3.4
RGSC_v3.41734,113,131 - 34,113,294RGDRGSC3.4
RGSC_v3.11734,115,973 - 34,116,135RGD
Celera1727,462,506 - 27,462,668UniSTS
RH 3.4 Map17353.9RGD
RH 3.4 Map17353.9UniSTS
RH 2.0 Map17236.5RGD
SHRSP x BN Map1721.7599RGD
FHH x ACI Map1728.9299RGD
Cytogenetic Map17p12UniSTS
D17Got41  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21727,921,600 - 27,921,737 (+)MAPPERmRatBN7.2
Rnor_6.01728,609,970 - 28,610,106NCBIRnor6.0
Rnor_5.01730,511,396 - 30,511,532UniSTSRnor5.0
RGSC_v3.41734,199,600 - 34,199,736RGDRGSC3.4
RGSC_v3.41734,199,601 - 34,199,737UniSTSRGSC3.4
RGSC_v3.11734,202,441 - 34,202,577RGD
Celera1727,548,846 - 27,548,982UniSTS
RH 3.4 Map17325.72UniSTS
RH 3.4 Map17325.72RGD
RH 2.0 Map17256.6RGD
Cytogenetic Map17p12UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
10401807Kidm52Kidney mass QTL 52kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)17131701463Rat
70184BpQTLcluster14Blood pressure QTL cluster 143.38arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)17131990913Rat
631207Niddm41Non-insulin dependent diabetes mellitus QTL 41blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)17137830672Rat
1354658Spl8Serum phospholipid level QTL 83.8blood VLDL phospholipid amount (VT:0010507)blood very low density lipoprotein phospholipid level (CMO:0001571)17160781592Rat
1354581Bp247Blood pressure QTL 2474.5arterial blood pressure trait (VT:2000000)pulse pressure (CMO:0000292)17169599340Rat
1354662Rf49Renal function QTL 492.9blood creatinine amount (VT:0005328)plasma creatinine level (CMO:0000537)17169599340Rat
1300123Bp194Blood pressure QTL 1942.82arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)17211514934551001Rat
1354613Kidm14Kidney mass QTL 146.2kidney mass (VT:0002707)left kidney wet weight (CMO:0000083)17429913035837242Rat
1354596Bw32Body weight QTL 324.5body mass (VT:0001259)body weight (CMO:0000012)17429913060781592Rat
1354630Cm34Cardiac mass QTL 348.7heart left ventricle mass (VT:0007031)heart left ventricle wet weight (CMO:0000071)17429913069599340Rat
1354638Insul1Insulin level QTL 14.8blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)17429913069599340Rat
1354651Lmblg2Limb length QTL 26tibia length (VT:0004357)tibia length (CMO:0000450)17429913069599340Rat
2303627Vencon8Ventilatory control QTL 80.001respiration trait (VT:0001943)tidal volume (CMO:0000222)17452803849528038Rat
10054088Scort28Serum corticosterone level QTL 282.040.0102blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)17452803849528038Rat
2303561Bw91Body weight QTL 912body mass (VT:0001259)body weight (CMO:0000012)17886846253868462Rat
2300002Iddm36Insulin dependent diabetes mellitus QTL 361.98blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)17999128640540197Rat
1331765Hrtrt15Heart rate QTL 154.094heart pumping trait (VT:2000009)heart rate (CMO:0000002)171533061355836425Rat
1354640Scl32Serum cholesterol level QTL 325.4blood HDL cholesterol amount (VT:0000184)blood high density lipoprotein cholesterol level (CMO:0000052)171578159260781592Rat
1354659Scl68Serum cholesterol level QTL 683.9blood VLDL cholesterol amount (VT:0005144)blood very low density lipoprotein cholesterol level (CMO:0000648)171578159260781592Rat
7394837Memor18Memory QTL 18exploratory behavior trait (VT:0010471)measurement of voluntary locomotion into, out of or within a discrete space in an experimental apparatus (CMO:0000957)171864018263640182Rat
1354628Stl13Serum triglyceride level QTL 133.8blood triglyceride amount (VT:0002644)blood triglyceride level (CMO:0000118)172129303960781592Rat
70157Niddm32Non-insulin dependent diabetes mellitus QTL 324.34blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)172245492450909196Rat
61394Bp8Blood pressure QTL 82.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)172308056759555013Rat
7488966Bp370Blood pressure QTL 3700.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)172365318457246843Rat
12903978Cm118Cardiac mass QTL 1180.001heart mass (VT:0007028)heart wet weight to body weight ratio (CMO:0002408)172365318468653184Rat
12903979Cm119Cardiac mass QTL 1190.001heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)172365318468653184Rat
12903980Cm120Cardiac mass QTL 1200.002heart right ventricle mass (VT:0007033)heart right ventricle weight to body weight ratio (CMO:0000914)172365318468653184Rat
12903981Am17Aortic mass QTL 170.001aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)172365318468653184Rat
1559055Bp278Blood pressure QTL 2780.04arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)172365318468653184Rat
12903982Kidm70Kidney mass QTL 700.001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)172365318470974005Rat
1354619Bp242Blood pressure QTL 2426.3arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)172459934069599340Rat
4889891Eae32Experimental allergic encephalomyelitis QTL 324.80.0002nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis severity score (CMO:0001419)172702794936146731Rat
1581512Cm55Cardiac mass QTL 552.80.05heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)172702794956836890Rat
4889955Bss93Bone structure and strength QTL 934.4tibia size trait (VT:0100001)tibia cortical bone volume to tibia total bone volume ratio (CMO:0001727)172702794960463643Rat
2302377Scl61Serum cholesterol level QTL 614.36blood HDL cholesterol amount (VT:0000184)serum high density lipoprotein cholesterol level (CMO:0000361)172738994653481766Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:143
Count of miRNA genes:110
Interacting mature miRNAs:133
Transcripts:ENSRNOT00000021568
Prediction methods:Microtar, 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 8 21 20 8 20 5 6 5 6 10 3 5
Low 3 35 24 9 11 9 3 5 67 26 29 8 3
Below cutoff 12 12 12 2 3 2

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000021568   ⟹   ENSRNOP00000021568
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1727,815,702 - 27,992,700 (+)Ensembl
Rnor_6.0 Ensembl1728,504,623 - 28,680,362 (+)Ensembl
RefSeq Acc Id: NM_021698   ⟹   NP_067730
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21727,815,723 - 27,992,494 (+)NCBI
Rnor_6.01728,504,650 - 28,680,015 (+)NCBI
Rnor_5.01730,406,396 - 30,581,441 (+)NCBI
RGSC_v3.41734,093,525 - 34,270,498 (+)RGD
Celera1727,443,244 - 27,619,724 (+)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_067730 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein CAA73104 (Get FASTA)   NCBI Sequence Viewer  
  EDL98278 (Get FASTA)   NCBI Sequence Viewer  
  EDL98279 (Get FASTA)   NCBI Sequence Viewer  
  O08619 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_067730   ⟸   NM_021698
- UniProtKB: O08619 (UniProtKB/Swiss-Prot),   G3V811 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000021568   ⟸   ENSRNOT00000021568
Protein Domains
TGc

Transcriptome

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

Promoters
RGD ID:13700399
Promoter ID:EPDNEW_R10922
Type:single initiation site
Name:F13a1_1
Description:coagulation factor XIII A1 chain
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_6.01728,504,629 - 28,504,689EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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)
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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 (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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-Lx/CubMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH2/CubMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH3/CubMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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)
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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)
DA/OlaHsd (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/DuCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
F344/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
FXLE16/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE18/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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/FarMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
HXB10/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB2/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB20/IpcvMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB31/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB4/IpcvMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
LEXF10A/StmMcwi (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF11/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1A/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1C/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF2B/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF3/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF4/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
LH/MavRrrcAek (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
LL/MavRrrcAek (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
LN/MavRrrcAek (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
M520/NRrrcMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MR/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
MWF/Hsd (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
PVG/Seac (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SBH/Ygl (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: SBH/Ygl sequenced by MCW
SBH/Ygl (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
SBN/Ygl (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: SBN/Ygl sequenced by MCW
SBN/Ygl (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
SHR/NHsd (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
SHR/OlalpcvMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/A3NCrl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/Gcrc (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
SR/JrHsd (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SR/JrHsd (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: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (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
SS/Jr (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
SS/JrHsdMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SS/JrHsdMcwi (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)
SS/JrHsdMcwi (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
WAG/Rij (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
WAG/RijCrl (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
Damaging Variants


Assembly: Rnor_5.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
17 30545681 30545682 T C snv SR/JrHsd (MCW), SS/JrHsdMcwi (MCW), WN/N (KNAW), LH/MavRrrc (KNAW), LL/MavRrrc (KNAW), LN/MavRrrc (KNAW), MR/N (KNAW), SR/JrHsd (KNAW), SS/Jr (KNAW), SS/JrHsdMcwi (KNAW), BUF/N (KNAW), LEW/Crl (KNAW), LEW/NCrl (KNAW), M520/N (KNAW), Crl:SD (UDEL), BUF/MNa (KyushuU), HTX/Kyo (KyushuU), ZFDM (KyushuU)
17 30558490 30558491 C T snv NIG-III/Hok (KyushuU)


Assembly: mRatBN7.2

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
17 27955985 27955986 T C snv BUF/N (2020), LEW/Crl (2019), LH/MavRrrcAek (2020), LL/MavRrrcAek (2020), WN/N (2020), M520/NRrrcMcwi (2019), M520/N (2020), SR/JrHsd (2020), SS/JrHsdMcwi (2019), LN/MavRrrcAek (2020)


Assembly: Rnor_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
17 28644255 28644256 T C snv SR/JrHsd (MCW), WN/N (2020), Buf/N (MCW), M520/N (MCW), MR/N (MCW), WN/N (MCW), LEW/Crl (RGD), LEW/NCrlBR (RGD), LH/MavRrrc (RGD), LN/MavRrrc (RGD), LL/MavRrrc (RGD), SR/JrHsd (RGD), SS/Jr (RGD), SS/JrHsdMcwi (RGD), BUF/N (2020), LEW/Crl (2019), LH/MavRrrcAek (2020), LL/MavRrrcAek (2020), LN/MavRrrcAek (2020), M520/NRrrcMcwi (2019), M520/N (2020), SR/JrHsd (2020), SS/JrHsdMcwi (2019), SS/JrHsdMcwi (MCW)


Assembly: RGSC_v3.4

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
17 34233991 34233992 T C snv SR/JrHsd (MCW), LCR/2Mco (UMich), SS/JrHsdMcwi (MDC), BUF/N (KNAW), M520/N (KNAW), MR/N (KNAW), WN/N (KNAW), LEW/Crl (ICL), LEW/NCrl (ICL), LH/MavRrrc (ICL), LL/MavRrrc (ICL), LN/MavRrrc (ICL), SR/JrHsd (ICL), SS/Jr (ICL), SS/JrHsdMcwi (ICL), HCR/1Mco (UMich), LCR/1Mco (UMich), HCR/2Mco (UMich), SS/JrHsdMcwi (MCW)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:621495 AgrOrtholog
Ensembl Genes ENSRNOG00000015957 Ensembl, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000021568 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000021568 UniProtKB/TrEMBL
Gene3D-CATH 2.60.40.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  3.90.260.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro Factor_XIII_A UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ig-like_fold UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ig_E-set UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Papain-like_cys_pep_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Transglutaminase-like UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Transglutaminase-like_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Transglutaminase_animal UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Transglutaminase_AS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Transglutaminase_C UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Transglutaminase_C_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Transglutaminase_N UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:60327 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
NCBI Gene 60327 ENTREZGENE
PANTHER PTHR11590:SF42 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam Transglut_C UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Transglut_core UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Transglut_N UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen F13a1 PhenoGen
PIRSF TGM_EBP42 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE TRANSGLUTAMINASES UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART TGc UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF49309 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF54001 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF81296 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt F13A_RAT UniProtKB/Swiss-Prot
  G3V811 ENTREZGENE, UniProtKB/TrEMBL
  O08619 ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-01-27 F13a1  coagulation factor XIII A1 chain  F13a1  coagulation factor XIII, A1 polypeptide  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-09-09 F13a1  coagulation factor XIII, A1 polypeptide  F13a1  coagulation factor XIII, A1 subunit  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-03-30 F13a1  coagulation factor XIII, A1 subunit  F13a    Symbol updated 1299863 APPROVED
2005-01-20 F13a  coagulation factor XIII, A1 subunit    coagulation factor XIIIa  Name updated 1299863 APPROVED
2002-08-07 F13a  coagulation factor XIIIa      Symbol and Name status set to provisional 70820 PROVISIONAL