Fcnb (ficolin B) - Rat Genome Database

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Gene: Fcnb (ficolin B) Rattus norvegicus
Analyze
Symbol: Fcnb
Name: ficolin B
RGD ID: 621222
Description: Predicted to enable several functions, including antigen binding activity; lipoteichoic acid immune receptor activity; and sialic acid binding activity. Predicted to be involved in several processes, including activation of immune response; positive regulation of interleukin-8 production; and positive regulation of opsonization. Predicted to act upstream of or within several processes, including activation of membrane attack complex; opsonization; and zymogen activation. Predicted to be located in plasma membrane. Predicted to be part of serine-type endopeptidase complex. Predicted to be active in extracellular matrix; extracellular space; and symbiont cell surface. Orthologous to several human genes including FCN1 (ficolin 1); INTERACTS WITH 17alpha-ethynylestradiol; 17beta-estradiol; 17beta-estradiol 3-benzoate.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: collagen/fibrinogen domain-containing protein 2; Fcn2; ficolin-2; ficolin-B; ficolin-beta; L-ficolin
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8331,791,750 - 31,800,188 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl331,791,750 - 31,800,188 (-)EnsemblGRCr8
mRatBN7.2311,393,713 - 11,402,198 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl311,393,739 - 11,402,151 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx314,461,657 - 14,470,038 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0323,046,811 - 23,055,192 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0321,301,038 - 21,309,419 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.036,617,816 - 6,626,193 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl36,617,751 - 6,626,284 (-)Ensemblrn6Rnor6.0
Rnor_5.0311,974,691 - 11,983,068 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.437,010,989 - 7,019,366 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera36,185,644 - 6,194,021 (-)NCBICelera
RGSC_v3.137,011,288 - 7,019,666 (-)NCBI
Cytogenetic Map3p12NCBI
JBrowse:




Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

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. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
3. GOA pipeline RGD automated data pipeline
4. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
5. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:12477932   PMID:15489334   PMID:15804047   PMID:16328467   PMID:20400674   PMID:21037097   PMID:21182092   PMID:22851708  


Genomics

Comparative Map Data
Fcnb
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8331,791,750 - 31,800,188 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl331,791,750 - 31,800,188 (-)EnsemblGRCr8
mRatBN7.2311,393,713 - 11,402,198 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl311,393,739 - 11,402,151 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx314,461,657 - 14,470,038 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0323,046,811 - 23,055,192 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0321,301,038 - 21,309,419 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.036,617,816 - 6,626,193 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl36,617,751 - 6,626,284 (-)Ensemblrn6Rnor6.0
Rnor_5.0311,974,691 - 11,983,068 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.437,010,989 - 7,019,366 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera36,185,644 - 6,194,021 (-)NCBICelera
RGSC_v3.137,011,288 - 7,019,666 (-)NCBI
Cytogenetic Map3p12NCBI
FCN1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh389134,903,232 - 134,917,912 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl9134,903,232 - 134,917,954 (-)Ensemblhg38GRCh38
GRCh379137,795,078 - 137,809,758 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 369136,941,253 - 136,949,630 (-)NCBIBuild 36Build 36hg18NCBI36
Build 349135,027,380 - 135,035,754NCBI
Celera9108,315,253 - 108,323,628 (-)NCBICelera
Cytogenetic Map9q34.3NCBI
HuRef9107,265,062 - 107,273,437 (-)NCBIHuRef
CHM1_19137,950,267 - 137,958,642 (-)NCBICHM1_1
T2T-CHM13v2.09147,124,901 - 147,139,590 (-)NCBIT2T-CHM13v2.0
Fcnb
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39227,966,491 - 27,974,921 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl227,966,390 - 27,974,897 (-)EnsemblGRCm39 EnsemblGRCm39
GRCm38228,076,479 - 28,084,910 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl228,076,378 - 28,084,885 (-)Ensemblmm10GRCm38
MGSCv37227,931,999 - 27,940,398 (-)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv36227,898,488 - 27,906,887 (-)NCBIMGSCv36mm8
Celera227,779,281 - 27,787,680 (-)NCBICelera
Cytogenetic Map2A3NCBI
cM Map219.38NCBI
Fcn1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555133,687,232 - 3,698,673 (-)Ensembl
ChiLan1.0NW_0049555133,690,550 - 3,697,785 (-)NCBIChiLan1.0ChiLan1.0
LOC100994951
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2114,413,958 - 4,422,270 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan194,416,291 - 4,424,603 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v09106,039,315 - 106,047,648 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.19135,040,722 - 135,049,105 (-)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl9135,040,310 - 135,049,111 (-)EnsemblpanPan2panpan1.1
FCN2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1950,868,942 - 50,876,001 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl950,868,973 - 50,875,792 (+)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha950,152,289 - 50,159,350 (+)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.0951,746,147 - 51,753,208 (+)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl951,746,180 - 51,752,999 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1950,506,401 - 50,513,474 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0950,850,289 - 50,857,359 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0950,927,946 - 50,935,059 (+)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
FCN2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1274,103,877 - 274,111,970 (+)EnsemblsusScr11Sscrofa11.1
Sscrofa11.11274,106,276 - 274,111,970 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21308,195,158 - 308,203,079 (+)NCBISscrofa10.2Sscrofa10.2susScr3
FCN1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1123,227,790 - 3,236,161 (+)NCBIChlSab1.1ChlSab1.1chlSab2
Vero_WHO_p1.0NW_0236660581,894,000 - 1,902,427 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Fcn1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247602,743,996 - 2,751,110 (-)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_0046247602,743,996 - 2,751,116 (-)NCBIHetGla 1.0HetGla 1.0hetGla2

Variants

.
Variants in Fcnb
101 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:95
Count of miRNA genes:72
Interacting mature miRNAs:76
Transcripts:ENSRNOT00000012494
Prediction methods:Microtar, Miranda, 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.


QTLs in Region (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1558647Cm46Cardiac mass QTL 465.40.0000055heart mass (VT:0007028)heart wet weight (CMO:0000069)32267715050766390Rat
1358357Srcrtb1Stress Responsive Cort Basal QTL 16.360.002blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)32905627547904329Rat
6893355Bw101Body weight QTL 1010.40.38body mass (VT:0001259)body weight (CMO:0000012)3576639050766390Rat
10450811Scl73Serum cholesterol level QTL 734.70.001blood LDL cholesterol amount (VT:0000181)blood low density lipoprotein cholesterol level (CMO:0000053)3290432947904329Rat
2292615Ept17Estrogen-induced pituitary tumorigenesis QTL 176.7pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)3655634751556347Rat
10450808Scl72Serum cholesterol level QTL 724.40.001blood LDL cholesterol amount (VT:0000181)blood low density lipoprotein cholesterol level (CMO:0000053)3290432947904329Rat
10450806Scl71Serum cholesterol level QTL 715.80.001blood LDL cholesterol amount (VT:0000181)blood low density lipoprotein cholesterol level (CMO:0000053)3290432947904329Rat
1558654Bw56Body weight QTL 564.50.0000171body mass (VT:0001259)body weight (CMO:0000012)3576639050766390Rat
10401810Kidm53Kidney mass QTL 53kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)32862533967641995Rat
1298526Arunc3Aerobic running capacity QTL 32.2exercise endurance trait (VT:0002332)longest distance run on treadmill (CMO:0001406)3612543751125437Rat
8693641Alc30Alcohol consumption QTL 3020.739drinking behavior trait (VT:0001422)calculated ethanol drink intake rate (CMO:0001615)33083238444921701Rat
631545Bp85Blood pressure QTL 853.1arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3136721849Rat
1358885Bp251Blood pressure QTL 2513.8arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)31141509147Rat
631679Cm10Cardiac mass QTL 107.340.0001heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)3655634751556347Rat
1558657Cm43Cardiac mass QTL 436.63e-08heart mass (VT:0007028)heart wet weight (CMO:0000069)32267715050766390Rat
631568Bp92Blood pressure QTL 922.20.005arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)31527234860272348Rat
6893363Bw105Body weight QTL 1052.60.0036body mass (VT:0001259)body weight (CMO:0000012)3576639050766390Rat
70203Gcr2Gastric cancer resistance QTL 22.6stomach morphology trait (VT:0000470)stomach tumor susceptibility score (CMO:0002043)32905627547904329Rat
1358888Bp264Blood pressure QTL 2644.43arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)35675975141509147Rat
1358185Ept6Estrogen-induced pituitary tumorigenesis QTL 66.7pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)3655634751556347Rat


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
musculoskeletal system
nervous system
renal system
reproductive system
respiratory system
sensory system
visual system
16 11 63 157 91 90 59 92 59 6 351 187 11 133 81 91 31 13 13

Sequence


Ensembl Acc Id: ENSRNOT00000012494   ⟹   ENSRNOP00000012494
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl331,791,750 - 31,800,188 (-)Ensembl
mRatBN7.2 Ensembl311,393,739 - 11,402,151 (-)Ensembl
Rnor_6.0 Ensembl36,617,751 - 6,626,284 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000102462   ⟹   ENSRNOP00000091036
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl331,791,750 - 31,800,188 (-)Ensembl
mRatBN7.2 Ensembl311,393,739 - 11,402,151 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000110782   ⟹   ENSRNOP00000093251
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl331,793,427 - 31,800,188 (-)Ensembl
mRatBN7.2 Ensembl311,395,390 - 11,402,151 (-)Ensembl
RefSeq Acc Id: NM_053634   ⟹   NP_446086
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8331,791,750 - 31,800,188 (-)NCBI
mRatBN7.2311,393,713 - 11,402,151 (-)NCBI
Rnor_6.036,617,816 - 6,626,193 (-)NCBI
Rnor_5.0311,974,691 - 11,983,068 (-)NCBI
RGSC_v3.437,010,989 - 7,019,366 (-)RGD
Celera36,185,644 - 6,194,021 (-)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_446086 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAH88123 (Get FASTA)   NCBI Sequence Viewer  
  BAB20440 (Get FASTA)   NCBI Sequence Viewer  
  EDL93425 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000012494
  ENSRNOP00000012494.3
GenBank Protein P57756 (Get FASTA)   NCBI Sequence Viewer  
RefSeq Acc Id: NP_446086   ⟸   NM_053634
- Peptide Label: precursor
- UniProtKB: P57756 (UniProtKB/Swiss-Prot),   A6JTM2 (UniProtKB/TrEMBL),   A0A8I6AEL8 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000012494   ⟸   ENSRNOT00000012494
Ensembl Acc Id: ENSRNOP00000093251   ⟸   ENSRNOT00000110782
Ensembl Acc Id: ENSRNOP00000091036   ⟸   ENSRNOT00000102462
Protein Domains
Collagen-like   Fibrinogen C-terminal

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-P57756-F1-model_v2 AlphaFold P57756 1-319 view protein structure

Transcriptome

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

Promoters
RGD ID:13691930
Promoter ID:EPDNEW_R2454
Type:single initiation site
Name:Fcnb_1
Description:ficolin B
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_6.036,626,196 - 6,626,256EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:621222 AgrOrtholog
BioCyc Gene G2FUF-50286 BioCyc
Ensembl Genes ENSRNOG00000009342 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000012494 ENTREZGENE
  ENSRNOT00000012494.7 UniProtKB/Swiss-Prot
Gene3D-CATH 3.90.215.10 UniProtKB/Swiss-Prot
IMAGE_CLONE IMAGE:7376834 IMAGE-MGC_LOAD
InterPro Collagen UniProtKB/Swiss-Prot
  Fibrinogen-like_C UniProtKB/Swiss-Prot
  Fibrinogen_a/b/g_C_1 UniProtKB/Swiss-Prot
  Fibrinogen_a/b/g_C_dom UniProtKB/Swiss-Prot
  Fibrinogen_C-term_domain UniProtKB/Swiss-Prot
  Fibrinogen_CS UniProtKB/Swiss-Prot
KEGG Report rno:114091 UniProtKB/Swiss-Prot
MGC_CLONE MGC:108632 IMAGE-MGC_LOAD
NCBI Gene 114091 ENTREZGENE
PANTHER FIBRINOGEN/TENASCIN/ANGIOPOEITIN UniProtKB/Swiss-Prot
  FICOLIN-2 UniProtKB/Swiss-Prot
Pfam Collagen UniProtKB/Swiss-Prot
  Fibrinogen_C UniProtKB/Swiss-Prot
PhenoGen Fcnb PhenoGen
PROSITE FIBRINOGEN_C_1 UniProtKB/Swiss-Prot
  FIBRINOGEN_C_2 UniProtKB/Swiss-Prot
RatGTEx ENSRNOG00000009342 RatGTEx
SMART FBG UniProtKB/Swiss-Prot
Superfamily-SCOP SSF56496 UniProtKB/Swiss-Prot
UniProt A0A8I6AEL8 ENTREZGENE, UniProtKB/TrEMBL
  A0A8I6GK74_RAT UniProtKB/TrEMBL
  A6JTM2 ENTREZGENE, UniProtKB/TrEMBL
  FCN2_RAT UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2005-01-20 Fcnb  ficolin B      Symbol and Name status set to approved 1299863 APPROVED
2002-08-07 Fcnb  ficolin B      Symbol and Name status set to provisional 70820 PROVISIONAL