F13b (coagulation factor XIII B chain) - Rat Genome Database

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Gene: F13b (coagulation factor XIII B chain) Rattus norvegicus
Analyze
Symbol: F13b
Name: coagulation factor XIII B chain
RGD ID: 1311668
Description: Predicted to be involved in blood coagulation, fibrin clot formation. Orthologous to human F13B (coagulation factor XIII B chain); PARTICIPATES IN acenocoumarol pharmacodynamics pathway; alteplase pharmacodynamics pathway; aminocaproic acid pharmacodynamics pathway; INTERACTS WITH (+)-schisandrin B; 17beta-estradiol; 2,3,7,8-tetrachlorodibenzodioxine.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: coagulation factor XIII, B polypeptide; coagulation factor XIII, beta subunit; LOC289055
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81353,681,639 - 53,707,114 (+)NCBIGRCr8
mRatBN7.21351,130,908 - 51,156,383 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1351,130,920 - 51,156,381 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1353,730,358 - 53,753,759 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01355,018,290 - 55,041,691 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01352,293,853 - 52,323,690 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01356,598,891 - 56,623,132 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1356,598,957 - 56,623,124 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01361,616,993 - 61,641,168 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41352,867,851 - 52,889,426 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11352,881,574 - 52,902,300 (+)NCBI
Celera1351,393,593 - 51,416,193 (+)NCBICelera
Cytogenetic Map13q13NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
2. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
3. Mutations affecting disulphide bonds contribute to a fairly common prevalence of F13B gene defects: results of a genetic study in 14 families with factor XIII B deficiency. Ivaskevicius V, etal., Haemophilia. 2010 Jul 1;16(4):675-82. doi: 10.1111/j.1365-2516.2010.02207.x. Epub 2010 Mar 10.
4. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
5. Fibrinogen and fibrin structure and functions. Mosesson MW J Thromb Haemost. 2005 Aug;3(8):1894-904.
6. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
7. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
8. SMPDB Annotation Import Pipeline Pipeline to import SMPDB annotations from SMPDB into RGD
9. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
10. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
11. Comprehensive gene review and curation RGD comprehensive gene curation
Additional References at PubMed
PMID:12477932   PMID:18224415  


Genomics

Comparative Map Data
F13b
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81353,681,639 - 53,707,114 (+)NCBIGRCr8
mRatBN7.21351,130,908 - 51,156,383 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1351,130,920 - 51,156,381 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1353,730,358 - 53,753,759 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01355,018,290 - 55,041,691 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01352,293,853 - 52,323,690 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01356,598,891 - 56,623,132 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1356,598,957 - 56,623,124 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01361,616,993 - 61,641,168 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41352,867,851 - 52,889,426 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11352,881,574 - 52,902,300 (+)NCBI
Celera1351,393,593 - 51,416,193 (+)NCBICelera
Cytogenetic Map13q13NCBI
F13B
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381197,038,741 - 197,067,260 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1197,038,741 - 197,067,260 (-)EnsemblGRCh38hg38GRCh38
GRCh371197,007,871 - 197,036,390 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361195,274,944 - 195,303,020 (-)NCBINCBI36Build 36hg18NCBI36
Build 341193,739,977 - 193,768,021NCBI
Celera1170,133,795 - 170,161,866 (-)NCBICelera
Cytogenetic Map1q31.3NCBI
HuRef1168,165,553 - 168,193,910 (-)NCBIHuRef
CHM1_11198,430,602 - 198,458,850 (-)NCBICHM1_1
T2T-CHM13v2.01196,300,565 - 196,329,084 (-)NCBIT2T-CHM13v2.0
F13b
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391139,429,285 - 139,451,496 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1139,429,440 - 139,451,490 (+)EnsemblGRCm39 Ensembl
GRCm381139,501,547 - 139,523,758 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1139,501,702 - 139,523,752 (+)EnsemblGRCm38mm10GRCm38
MGSCv371141,398,284 - 141,420,333 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361141,318,138 - 141,340,167 (+)NCBIMGSCv36mm8
Celera1142,138,905 - 142,161,049 (+)NCBICelera
Cytogenetic Map1FNCBI
cM Map161.57NCBI
F13b
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495540633,632,144 - 33,660,535 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495540633,633,911 - 33,660,506 (-)NCBIChiLan1.0ChiLan1.0
F13B
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2152,319,904 - 52,348,993 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1152,289,056 - 52,318,146 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01172,623,336 - 172,651,945 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11176,938,155 - 176,965,609 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1176,937,158 - 176,965,773 (-)Ensemblpanpan1.1panPan2
F13B
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.175,674,458 - 5,700,928 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl75,674,416 - 5,700,905 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha75,303,651 - 5,331,440 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.075,370,630 - 5,398,422 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl75,370,530 - 5,396,990 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.175,305,382 - 5,333,161 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.075,406,384 - 5,434,127 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.075,439,496 - 5,467,295 (+)NCBIUU_Cfam_GSD_1.0
F13b
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440934477,477,966 - 77,500,748 (+)NCBIHiC_Itri_2
SpeTri2.0NW_0049365676,712,666 - 6,735,539 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
F13B
(Sus scrofa - pig)		 No map positions available.
F13B
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12532,357,540 - 32,390,349 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl2532,357,993 - 32,389,973 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366605533,265,712 - 33,296,197 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
F13b
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247983,231,462 - 3,274,186 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046247983,231,592 - 3,261,500 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in F13b
276 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:172
Count of miRNA genes:126
Interacting mature miRNAs:133
Transcripts:ENSRNOT00000016944
Prediction methods:Microtar, Miranda, Rnahybrid
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.


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1298066Bp159Blood pressure QTL 1590.004arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)134608804691088046Rat
10755495Bp387Blood pressure QTL 3873.78arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)133466346187525369Rat
9589141Insul28Insulin level QTL 2810.820.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)13931346554313465Rat
6893344Cm79Cardiac mass QTL 791.50.04heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)134372077062022792Rat
70220Bp55Blood pressure QTL 555.75arterial blood pressure trait (VT:2000000)blood pressure measurement (CMO:0000003)133737450982374509Rat
71119Thym2Thymus enlargement QTL 23.8thymus mass (VT:0004954)thymus weight to body weight ratio (CMO:0000612)134619797684753113Rat
61391Bp5Blood pressure QTL 55.6arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)132230187567301875Rat
4889861Pur29Proteinuria QTL 2913.80.005urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)133741558480753406Rat
2317040Aia21Adjuvant induced arthritis QTL 212.75joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)13983154154831541Rat
631645Bp121Blood pressure QTL 1213.3arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)131491565559915655Rat
2317046Aia8Adjuvant induced arthritis QTL 83.9700000286102295joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)13983154154831541Rat
12879441Bp396Blood pressure QTL 396arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)134569998390699983Rat
619615Bp80Blood pressure QTL 800.0354arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)133975454484754544Rat
1581570Eae17Experimental allergic encephalomyelitis QTL 174.1nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)138897350101631289Rat
70170Eae14Experimental allergic encephalomyelitis QTL 140.0024nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)132320344868203448Rat
1331784Bp222Blood pressure QTL 2222.944arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)131769443653050594Rat
61340Bp25Blood pressure QTL 254.20.004arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)133453521879535218Rat
1581573Uae36Urinary albumin excretion QTL 36urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)13599483377046787Rat
1549897Stresp12Stress response QTL 123.35stress-related behavior trait (VT:0010451)number of approaches toward negative stimulus before onset of defensive burying response (CMO:0001960)133843340883433408Rat
7207885Glom27Glomerulus QTL 273.9kidney glomerulus integrity trait (VT:0010546)kidney crescentic glomeruli count to kidney normal glomeruli count ratio (CMO:0002139)1320605871101339738Rat
1558644Cm45Cardiac mass QTL 453.60.002heart mass (VT:0007028)heart wet weight (CMO:0000069)132369296968692969Rat
70181BpQTLcluster11Blood pressure QTL cluster 116.922arterial blood pressure trait (VT:2000000)absolute change in mean arterial blood pressure (CMO:0000533)133124133193395974Rat
61349Bp31Blood pressure QTL 315.75arterial blood pressure trait (VT:2000000)blood pressure measurement (CMO:0000003)133737450982374509Rat
2303563Bw89Body weight QTL 896body mass (VT:0001259)body weight (CMO:0000012)133228447177284471Rat
1354621Rf47Renal function QTL 473.7kidney renin amount (VT:0010559)kidney renin level (CMO:0002166)1330395351101056920Rat
2301962Cm72Cardiac mass QTL 724.12heart left ventricle mass (VT:0007031)heart left ventricle weight (CMO:0000776)133124133158363171Rat
1581554Pur11Proteinuria QTL 11urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)13599483377046787Rat
12879477Bp401Blood pressure QTL 401arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)133726209282262092Rat
1331750Bp220Blood pressure QTL 2202.98arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)133741558482415584Rat
6893338Cm76Cardiac mass QTL 7600.99heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)132369296968692969Rat
1354666Bp244Blood pressure QTL 2444.9arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)131101056920Rat
9589164Gluco66Glucose level QTL 666.670.001blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)131515872260158722Rat
7411662Foco29Food consumption QTL 2920.80.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)13931346554313465Rat


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
nervous system
renal system
reproductive system
respiratory system
2 8 10 32 82 81 59 17 59 1 143 39 22 35 38 22

Sequence


Ensembl Acc Id: ENSRNOT00000016944   ⟹   ENSRNOP00000016944
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1351,130,922 - 51,156,375 (+)Ensembl
Rnor_6.0 Ensembl1356,598,957 - 56,623,124 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000080335   ⟹   ENSRNOP00000075643
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1356,598,979 - 56,622,782 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000089913   ⟹   ENSRNOP00000075504
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1351,130,920 - 51,156,381 (+)Ensembl
Rnor_6.0 Ensembl1356,598,979 - 56,622,782 (+)Ensembl
RefSeq Acc Id: NM_001401310   ⟹   NP_001388239
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81353,681,639 - 53,707,114 (+)NCBI
mRatBN7.21351,130,908 - 51,156,383 (+)NCBI
Protein Sequences
Protein RefSeqs NP_001388239 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAI60876 (Get FASTA)   NCBI Sequence Viewer  
  EDM09620 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000016944.8
  ENSRNOP00000075504.1
Ensembl Acc Id: ENSRNOP00000075643   ⟸   ENSRNOT00000080335
Ensembl Acc Id: ENSRNOP00000075504   ⟸   ENSRNOT00000089913
Ensembl Acc Id: ENSRNOP00000016944   ⟸   ENSRNOT00000016944
RefSeq Acc Id: NP_001388239   ⟸   NM_001401310
- Peptide Label: precursor
- UniProtKB: F6Q1N1 (UniProtKB/TrEMBL),   B1H260 (UniProtKB/TrEMBL)
Protein Domains
Sushi

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-B1H260-F1-model_v2 AlphaFold B1H260 1-661 view protein structure

Transcriptome

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

Promoters
RGD ID:13698869
Promoter ID:EPDNEW_R9390
Type:initiation region
Name:F13b_1
Description:coagulation factor XIII B 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_6.01356,598,943 - 56,599,003EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1311668 AgrOrtholog
BioCyc Gene G2FUF-18073 BioCyc
Ensembl Genes ENSRNOG00000012613 Ensembl, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000016944.8 UniProtKB/TrEMBL
  ENSRNOT00000089913.2 UniProtKB/TrEMBL
Gene3D-CATH Complement Module, domain 1 UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7369453 IMAGE-MGC_LOAD
InterPro ComplSys_Reg/VirEntry_Med UniProtKB/TrEMBL
  Sushi/SCR/CCP_sf UniProtKB/TrEMBL
  Sushi_SCR_CCP UniProtKB/TrEMBL
MGC_CLONE MGC:188246 IMAGE-MGC_LOAD
NCBI Gene 289055 ENTREZGENE
PANTHER COAGULATION FACTOR XIII B CHAIN UniProtKB/TrEMBL
  COMPLEMENT FACTOR H-RELATED UniProtKB/TrEMBL
Pfam Sushi UniProtKB/TrEMBL
PhenoGen F13b PhenoGen
PROSITE SUSHI UniProtKB/TrEMBL
RatGTEx ENSRNOG00000012613 RatGTEx
SMART CCP UniProtKB/TrEMBL
Superfamily-SCOP Complement_control_module UniProtKB/TrEMBL
UniProt A0A0G2KAS2_RAT UniProtKB/TrEMBL
  A6ICM7_RAT UniProtKB/TrEMBL
  B1H260 ENTREZGENE, UniProtKB/TrEMBL
  F6Q1N1 ENTREZGENE
UniProt Secondary F6Q1N1 UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-01-20 F13b  coagulation factor XIII B chain  F13b  coagulation factor XIII, B polypeptide  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-09-09 F13b  coagulation factor XIII, B polypeptide  F13b  coagulation factor XIII, beta subunit   Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 F13b  coagulation factor XIII, beta subunit   F13b_predicted  coagulation factor XIII, beta subunit (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 F13b_predicted  coagulation factor XIII, beta subunit (predicted)      Symbol and Name status set to approved 70820 APPROVED