Fcna (ficolin A) - Rat Genome Database

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Gene: Fcna (ficolin A) Rattus norvegicus
Analyze
No known orthologs.
Symbol: Fcna
Name: ficolin A
RGD ID: 621221
Description: Predicted to enable several functions, including antigen binding activity; carbohydrate derivative binding activity; and pattern recognition receptor activity. Predicted to be involved in G protein-coupled receptor signaling pathway; activation of immune response; and positive regulation of interleukin-8 production. Predicted to be located in plasma membrane. Predicted to be part of collagen trimer. Predicted to be active in collagen-containing extracellular matrix and extracellular space. Orthologous to human FCN3 (ficolin 3).
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
Alliance Orthologs
More Info homologs ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8328,844,036 - 28,847,441 (-)NCBIGRCr8
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_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0320,137,318 - 20,140,531 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0318,327,168 - 18,330,381 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
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


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. 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

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
4889966Bss95Bone structure and strength QTL 954.4tibia area (VT:1000281)tibia-fibula cross-sectional area (CMO:0001718)3136847613Rat
2292615Ept17Estrogen-induced pituitary tumorigenesis QTL 176.7pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)3653764510778823Rat
10401810Kidm53Kidney mass QTL 53kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)3822719447233430Rat
1298526Arunc3Aerobic running capacity QTL 32.2exercise endurance trait (VT:0002332)maximum distance run on treadmill (CMO:0001406)3822719433703538Rat
631545Bp85Blood pressure QTL 853.1arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3133278763Rat
631679Cm10Cardiac mass QTL 107.340.0001heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)3131158234Rat
2290452Scl56Serum cholesterol level QTL 562.26blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)3191609953Rat
631568Bp92Blood pressure QTL 922.20.005arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3139874793Rat
70202Alc19Alcohol consumption QTL 192.5drinking behavior trait (VT:0001422)ethanol intake volume to total fluid intake volume ratio (CMO:0001591)3127494778Rat
2312664Scl62Serum cholesterol level QTL 620.05blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)3138710544Rat
61468Bp15Blood pressure QTL 154.4blood pressure trait (VT:0000183)pulse pressure (CMO:0000292)3133278763Rat
1358185Ept6Estrogen-induced pituitary tumorigenesis QTL 66.7pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)3653764510778823Rat
631831Alc8Alcohol consumption QTL 82.7consumption behavior trait (VT:0002069)calculated ethanol drink intake rate (CMO:0001615)3133230976Rat

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

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
9 11 49 113 91 90 59 25 59 6 218 97 93 45 60 31

Sequence


Ensembl Acc Id: ENSRNOT00000023022   ⟹   ENSRNOP00000023022
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
Ensembl Acc Id: ENSRNOT00000106409   ⟹   ENSRNOP00000091955
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
GRCr8328,844,036 - 28,847,237 (-)NCBI
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
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8328,844,036 - 28,847,260 (-)NCBI
mRatBN7.238,445,904 - 8,449,128 (-)NCBI
Rnor_6.032,850,006 - 2,853,230 (-)NCBI
Sequence:
RefSeq Acc Id: XM_063284644   ⟹   XP_063140714
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8328,844,036 - 28,847,441 (-)NCBI
RefSeq Acc Id: NP_112638   ⟸   NM_031348
- Peptide Label: precursor
- UniProtKB: Q9WTS8 (UniProtKB/Swiss-Prot),   Q5M8B4 (UniProtKB/TrEMBL),   F7FL15 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_008759836   ⟸   XM_008761614
- Peptide Label: isoform X2
- Sequence:
Ensembl Acc Id: ENSRNOP00000023022   ⟸   ENSRNOT00000023022
Ensembl Acc Id: ENSRNOP00000091955   ⟸   ENSRNOT00000106409
RefSeq Acc Id: XP_063140714   ⟸   XM_063284644
- Peptide Label: isoform X1
- UniProtKB: F7FL15 (UniProtKB/TrEMBL),   Q5M8B4 (UniProtKB/TrEMBL)
Protein Domains
Collagen-like   Fibrinogen C-terminal

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, UniProtKB/TrEMBL
Ensembl Transcript 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_C-term_domain 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
PANTHER FIBRINOGEN/TENASCIN/ANGIOPOEITIN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  FICOLIN-1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
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
RatGTEx ENSRNOG00000017063 RatGTEx
SMART FBG UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF56496 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A8I6AG88_RAT UniProtKB/TrEMBL
  A6JT93_RAT UniProtKB/TrEMBL
  F7FL15 ENTREZGENE, 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