Fcna (ficolin A) - Rat Genome Database

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Gene: Fcna (ficolin A) Rattus norvegicus
Analyze
Symbol: Fcna
Name: ficolin A
RGD ID: 621221
Description: Predicted to enable several functions, including antigen binding activity; identical protein binding activity; and pattern recognition receptor 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 extrinsic component of external side of 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 human FCN3 (ficolin 3); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2,3,7,8-Tetrachlorodibenzofuran; 2,4-dinitrotoluene.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: collagen/fibrinogen domain-containing protein 1; Fcn1; ficolin (collagen/fibrinogen domain containing) 1; ficolin-1; ficolin-A; ficolin-alpha; M-ficolin; MGC108660
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
mRatBN7.238,445,904 - 8,449,128 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl38,445,907 - 8,449,105 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx311,551,092 - 11,554,307 (-)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.0320,137,318 - 20,140,531 (-)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.0318,327,168 - 18,330,381 (-)NCBIRnor_WKY
Rnor_6.032,850,006 - 2,853,230 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl32,849,984 - 2,853,272 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.032,831,419 - 2,834,620 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.433,797,916 - 3,801,117 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.133,797,915 - 3,801,117 (-)NCBI
Celera33,270,846 - 3,274,047 (-)NCBICelera
Cytogenetic Map3p13NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


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 MGI mouse gene data--August 2006 MGD data from the GO Consortium
3. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
4. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
5. GOA pipeline RGD automated data pipeline
6. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
7. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:11907111   PMID:12477932   PMID:15804047   PMID:16328467   PMID:17579066   PMID:22516433   PMID:22789560   PMID:22851708  


Genomics

Comparative Map Data
Fcna
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.238,445,904 - 8,449,128 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl38,445,907 - 8,449,105 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx311,551,092 - 11,554,307 (-)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.0320,137,318 - 20,140,531 (-)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.0318,327,168 - 18,330,381 (-)NCBIRnor_WKY
Rnor_6.032,850,006 - 2,853,230 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl32,849,984 - 2,853,272 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.032,831,419 - 2,834,620 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.433,797,916 - 3,801,117 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.133,797,915 - 3,801,117 (-)NCBI
Celera33,270,846 - 3,274,047 (-)NCBICelera
Cytogenetic Map3p13NCBI
FCN3
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38127,369,110 - 27,374,824 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl127,369,110 - 27,374,824 (-)EnsemblGRCh38hg38GRCh38
GRCh37127,695,601 - 27,701,315 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36127,568,188 - 27,573,902 (-)NCBINCBI36Build 36hg18NCBI36
Build 34127,379,744 - 27,385,457NCBI
Celera126,092,884 - 26,098,611 (-)NCBICelera
Cytogenetic Map1p36.11NCBI
HuRef125,951,741 - 25,957,459 (-)NCBIHuRef
CHM1_1127,810,336 - 27,816,061 (-)NCBICHM1_1
T2T-CHM13v2.0127,210,348 - 27,216,135 (-)NCBIT2T-CHM13v2.0
Fcna
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39225,514,677 - 25,525,448 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl225,514,678 - 25,518,042 (-)EnsemblGRCm39 Ensembl
GRCm38225,624,665 - 25,635,440 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl225,624,666 - 25,628,030 (-)EnsemblGRCm38mm10GRCm38
MGSCv37225,480,187 - 25,483,494 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36225,446,675 - 25,449,923 (-)NCBIMGSCv36mm8
Celera225,353,030 - 25,356,335 (-)NCBICelera
Cytogenetic Map2A3NCBI
Fcn3
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554526,630,505 - 6,635,235 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554526,630,548 - 6,635,334 (-)NCBIChiLan1.0ChiLan1.0
FCN3
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1127,676,740 - 27,683,889 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl127,676,866 - 27,683,861 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0126,620,373 - 26,636,424 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
FCN3
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Dog10K_Boxer_Tasha269,476,250 - 69,480,708 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0273,460,937 - 73,465,399 (+)NCBIROS_Cfam_1.0
UMICH_Zoey_3.1270,286,939 - 70,291,401 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0271,298,410 - 71,302,868 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0272,294,469 - 72,298,931 (+)NCBIUU_Cfam_GSD_1.0
Fcn3
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440505845,855,319 - 45,861,098 (-)NCBIHiC_Itri_2
SpeTri2.0NW_00493647411,680,166 - 11,685,214 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
FCN1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.11274,125,666 - 274,132,917 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21308,216,807 - 308,224,034 (-)NCBISscrofa10.2Sscrofa10.2susScr3
FCN3
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.120105,414,626 - 105,420,684 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl20105,414,650 - 105,420,558 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366603311,038,178 - 11,049,768 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Fcn3
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462476411,265,505 - 11,269,650 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462476411,265,740 - 11,269,588 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Fcna
8 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:149
Count of miRNA genes:130
Interacting mature miRNAs:137
Transcripts:ENSRNOT00000023022
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
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
1358185Ept6Estrogen-induced pituitary tumorigenesis QTL 66.7pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)3653764510778823Rat
2292615Ept17Estrogen-induced pituitary tumorigenesis QTL 176.7pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)3653764510778823Rat
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

Markers in Region
RH131611  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.238,446,086 - 8,446,305 (+)MAPPERmRatBN7.2
Rnor_6.032,850,189 - 2,850,407NCBIRnor6.0
Rnor_5.032,831,602 - 2,831,820UniSTSRnor5.0
RGSC_v3.433,798,099 - 3,798,317UniSTSRGSC3.4
Celera33,271,029 - 3,271,247UniSTS
Cytogenetic Map3p13UniSTS


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 2 47 37 19 37 4 4 2 13 6 4
Low 1 37 10 4 4 4 7 70 31 28 5 4
Below cutoff 6 4 2

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000023022   ⟹   ENSRNOP00000023022
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl38,445,907 - 8,449,105 (-)Ensembl
Rnor_6.0 Ensembl32,849,984 - 2,853,272 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000106409   ⟹   ENSRNOP00000091955
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl38,445,907 - 8,449,105 (-)Ensembl
RefSeq Acc Id: NM_031348   ⟹   NP_112638
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.238,445,904 - 8,449,105 (-)NCBI
Rnor_6.032,850,006 - 2,853,207 (-)NCBI
Rnor_5.032,831,419 - 2,834,620 (-)NCBI
RGSC_v3.433,797,916 - 3,801,117 (-)RGD
Celera33,270,846 - 3,274,047 (-)RGD
Sequence:
RefSeq Acc Id: XM_008761614   ⟹   XP_008759836
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.238,445,904 - 8,449,128 (-)NCBI
Rnor_6.032,850,006 - 2,853,230 (-)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_112638   ⟸   NM_031348
- Peptide Label: precursor
- UniProtKB: Q5M8B4 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_008759836   ⟸   XM_008761614
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: ENSRNOP00000023022   ⟸   ENSRNOT00000023022
RefSeq Acc Id: ENSRNOP00000091955   ⟸   ENSRNOT00000106409
Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q9WTS8-F1-model_v2 AlphaFold Q9WTS8 1-335 view protein structure

Transcriptome

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

Promoters
RGD ID:13691888
Promoter ID:EPDNEW_R2412
Type:multiple initiation site
Name:Fcna_1
Description:ficolin A
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_6.032,853,220 - 2,853,280EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:621221 AgrOrtholog
BioCyc Gene G2FUF-50434 BioCyc
Ensembl Genes ENSRNOG00000017063 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000023022 ENTREZGENE
  ENSRNOP00000023022.3 UniProtKB/TrEMBL
  ENSRNOP00000091955.1 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000023022 ENTREZGENE
  ENSRNOT00000023022.7 UniProtKB/TrEMBL
  ENSRNOT00000106409.1 UniProtKB/TrEMBL
Gene3D-CATH 3.90.215.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7376326 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:83517 UniProtKB/TrEMBL
MGC_CLONE MGC:108660 IMAGE-MGC_LOAD
NCBI Gene 83517 ENTREZGENE
Pfam Collagen UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Fibrinogen_C UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Fcna PhenoGen
PROSITE FIBRINOGEN_C_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  FIBRINOGEN_C_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART FBG UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF56496 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A8I6AG88_RAT UniProtKB/TrEMBL
  FCN1_RAT UniProtKB/Swiss-Prot
  Q5M8B4 ENTREZGENE, UniProtKB/TrEMBL
  Q9WTS8 ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2014-07-09 Fcna  ficolin A  Fcn1  ficolin (collagen/fibrinogen domain containing) 1  Name and Symbol changed 629549 APPROVED
2008-09-25 Fcn1  ficolin (collagen/fibrinogen domain containing) 1  Fcna  ficolin A  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-01-20 Fcna  ficolin A      Symbol and Name status set to approved 1299863 APPROVED
2002-08-07 Fcna  ficolin A      Symbol and Name status set to provisional 70820 PROVISIONAL