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; pattern recognition 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 be located in plasma membrane. Predicted to be part of serine-type endopeptidase complex. Predicted to be active in collagen-containing extracellular matrix and extracellular space. 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 Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8331,791,750 - 31,800,188 (-)NCBIGRCr8
mRatBN7.2311,393,713 - 11,402,198 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl311,393,739 - 11,402,151 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx314,461,657 - 14,470,038 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0323,046,811 - 23,055,192 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0321,301,038 - 21,309,419 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.036,617,816 - 6,626,193 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl36,617,751 - 6,626,284 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0311,974,691 - 11,983,068 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.437,010,989 - 7,019,366 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.137,011,288 - 7,019,666 (-)NCBI
Celera36,185,644 - 6,194,021 (-)NCBICelera
Cytogenetic Map3p12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

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. 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 (-)NCBIGRCr8
mRatBN7.2311,393,713 - 11,402,198 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl311,393,739 - 11,402,151 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx314,461,657 - 14,470,038 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0323,046,811 - 23,055,192 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0321,301,038 - 21,309,419 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.036,617,816 - 6,626,193 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl36,617,751 - 6,626,284 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0311,974,691 - 11,983,068 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.437,010,989 - 7,019,366 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.137,011,288 - 7,019,666 (-)NCBI
Celera36,185,644 - 6,194,021 (-)NCBICelera
Cytogenetic Map3p12NCBI
FCN1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh389134,903,232 - 134,917,912 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl9134,903,232 - 134,917,912 (-)EnsemblGRCh38hg38GRCh38
GRCh379137,795,078 - 137,809,758 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 369136,941,253 - 136,949,630 (-)NCBINCBI36Build 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 Ensembl
GRCm38228,076,479 - 28,084,910 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl228,076,378 - 28,084,885 (-)EnsemblGRCm38mm10GRCm38
MGSCv37227,931,999 - 27,940,398 (-)NCBIGRCm37MGSCv37mm9NCBIm37
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 (-)EnsemblChiLan1.0
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 (-)Ensemblpanpan1.1panPan2
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 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha950,152,289 - 50,159,350 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0951,746,147 - 51,753,208 (+)NCBIROS_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_1.0
FCN2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1274,103,877 - 274,111,970 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
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_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046247602,743,996 - 2,751,116 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Fcnb
28 total Variants
miRNA Target Status

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 (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
70202Alc19Alcohol consumption QTL 192.5drinking behavior trait (VT:0001422)ethanol intake volume to total fluid intake volume ratio (CMO:0001591)3127494778Rat
631679Cm10Cardiac mass QTL 107.340.0001heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)3131158234Rat
631831Alc8Alcohol consumption QTL 82.7consumption behavior trait (VT:0002069)calculated ethanol drink intake rate (CMO:0001615)3133230976Rat
61468Bp15Blood pressure QTL 154.4blood pressure trait (VT:0000183)diastolic blood pressure (CMO:0000005)3133278763Rat
61468Bp15Blood pressure QTL 154.4blood pressure trait (VT:0000183)systolic blood pressure (CMO:0000004)3133278763Rat
61468Bp15Blood pressure QTL 154.4blood pressure trait (VT:0000183)pulse pressure (CMO:0000292)3133278763Rat
631545Bp85Blood pressure QTL 853.1arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3133278763Rat
4889966Bss95Bone structure and strength QTL 954.4tibia area (VT:1000281)tibia-fibula cross-sectional area (CMO:0001718)3136847613Rat
2312664Scl62Serum cholesterol level QTL 620.05blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)3138710544Rat
631568Bp92Blood pressure QTL 922.20.005arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3139874793Rat
2290452Scl56Serum cholesterol level QTL 562.26blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)3191609953Rat
1298526Arunc3Aerobic running capacity QTL 32.2exercise endurance trait (VT:0002332)maximum distance run on treadmill (CMO:0001406)3822719433703538Rat
10401810Kidm53Kidney mass QTL 53kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)3822719447233430Rat
70203Gcr2Gastric cancer resistance QTL 22.6stomach morphology trait (VT:0000470)stomach tumor susceptibility score (CMO:0002043)3865816227494778Rat
1358357Srcrtb1Stress Responsive Cort Basal QTL 16.360.002blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)3865816227494778Rat
6893355Bw101Body weight QTL 1010.40.38body mass (VT:0001259)body weight (CMO:0000012)31077870430357018Rat
6893363Bw105Body weight QTL 1052.60.0036body mass (VT:0001259)body weight (CMO:0000012)31077870430357018Rat
1558654Bw56Body weight QTL 564.50.0000171body mass (VT:0001259)body weight (CMO:0000012)31077870430357018Rat
70191BpQTLcluster4Blood pressure QTL cluster 43arterial blood pressure trait (VT:2000000)absolute change in mean arterial blood pressure (CMO:0000533)31077870450302886Rat
70191BpQTLcluster4Blood pressure QTL cluster 43arterial blood pressure trait (VT:2000000)absolute change in systolic blood pressure (CMO:0000607)31077870450302886Rat
1558647Cm46Cardiac mass QTL 465.40.0000055heart mass (VT:0007028)heart wet weight (CMO:0000069)31077882330356773Rat
1558650Cm48Cardiac mass QTL 4840.0001heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)31077882330356773Rat
1558657Cm43Cardiac mass QTL 436.60.0000000293heart mass (VT:0007028)heart wet weight (CMO:0000069)31077882330356773Rat
1358905Hrtrt17Heart rate QTL 175.90.000014heart pumping trait (VT:2000009)heart rate (CMO:0000002)31086191289878372Rat


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 17 12 16 12 1 10
Low 2 26 40 29 3 29 4 35 29 1
Below cutoff 1 13 8 10 70 10 8

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000012494   ⟹   ENSRNOP00000012494
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl311,393,739 - 11,402,151 (-)Ensembl
Rnor_6.0 Ensembl36,617,751 - 6,626,284 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000102462   ⟹   ENSRNOP00000091036
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl311,393,739 - 11,402,151 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000110782   ⟹   ENSRNOP00000093251
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
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:
Reference Protein Sequences
RefSeq Acc Id: NP_446086   ⟸   NM_053634
- Peptide Label: precursor
- UniProtKB: P57756 (UniProtKB/Swiss-Prot),   A6JTM2 (UniProtKB/TrEMBL),   A0A8I6AEL8 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000012494   ⟸   ENSRNOT00000012494
RefSeq Acc Id: ENSRNOP00000093251   ⟸   ENSRNOT00000110782
RefSeq 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, UniProtKB/TrEMBL
  ENSRNOG00055006306 UniProtKB/Swiss-Prot
  ENSRNOG00060027892 UniProtKB/Swiss-Prot
  ENSRNOG00065020913 UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000012494 ENTREZGENE
  ENSRNOT00000012494.7 UniProtKB/Swiss-Prot
  ENSRNOT00000102462.1 UniProtKB/TrEMBL
  ENSRNOT00000110782.1 UniProtKB/TrEMBL
  ENSRNOT00055010239 UniProtKB/Swiss-Prot
  ENSRNOT00060048461 UniProtKB/Swiss-Prot
  ENSRNOT00065035530 UniProtKB/Swiss-Prot
Gene3D-CATH 3.90.215.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7376834 IMAGE-MGC_LOAD
InterPro Collagen UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Fibrinogen-like_C UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Fibrinogen_a/b/g_C_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Fibrinogen_a/b/g_C_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Fibrinogen_CS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:114091 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
MGC_CLONE MGC:108632 IMAGE-MGC_LOAD
NCBI Gene 114091 ENTREZGENE
PANTHER FIBRINOGEN/TENASCIN/ANGIOPOEITIN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  FICOLIN-2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam Collagen UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Fibrinogen_C UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Fcnb PhenoGen
PROSITE FIBRINOGEN_C_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  FIBRINOGEN_C_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
RatGTEx ENSRNOG00000009342 RatGTEx
  ENSRNOG00055006306 RatGTEx
  ENSRNOG00060027892 RatGTEx
  ENSRNOG00065020913 RatGTEx
SMART FBG UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF56496 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
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