Fcna ficolin A [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Fcnaprovided by RGD
Official Full Name: ficolin Aprovided by RGD
Primary source: RGD:621221
See related: Ensembl:ENSRNOG00000017063 AllianceGenome:RGD:621221
Gene type: protein coding
RefSeq status: PROVISIONAL
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Also known as: Fcn1
Summary: Predicted to enable several functions, including antigen binding activity; carbohydrate derivative 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 recognition of apoptotic cell. Predicted to be extrinsic component of external side of 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). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Biased expression in Spleen (RPKM 2074.9), Liver (RPKM 144.7) and 1 other tissue See more
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Genomic context

Location:: 3p13

Exon count:: 11

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	3	NC_086021.1 (28844036..28847441, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	3	NC_051338.1 (8445904..8449128, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	3	NC_005102.4 (2850006..2853230, complement)

Chromosome 3 - NC_086021.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
BioProject: PRJNA238328
Publication: PMID 24510058
Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

ficolin-A binds acapsular C. neoformans via their carbohydrate recognizing fibrinogen-like domains leading to enhanced uptake by lung epithelial cells in vitro.
Title: Opsonizing properties of rat ficolin-A in the defence against Cryptococcus neoformans.
The mannose-binding lectin (MBL)-associated-serine protease (MASP)-2 binding site on rat ficolin-A is located within the collagen-like domain and encompasses a conserved motif that is present in both MBLs and ficolins.
Title: Localization and characterization of the mannose-binding lectin (MBL)-associated-serine protease-2 binding site in rat ficolin-A: equivalent binding sites within the collagenous domains of MBLs and ficolins.

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General gene information

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Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables antigen binding	IBA Inferred from Biological aspect of Ancestor more info
enables carbohydrate binding	IEA Inferred from Electronic Annotation more info
enables carbohydrate derivative binding	IBA Inferred from Biological aspect of Ancestor more info
enables metal ion binding	IEA Inferred from Electronic Annotation more info
enables pattern recognition receptor activity	ISS Inferred from Sequence or Structural Similarity more info
enables signaling receptor binding	IBA Inferred from Biological aspect of Ancestor more info

Process	Evidence Code	Pubs
involved_in G protein-coupled receptor signaling pathway	ISS Inferred from Sequence or Structural Similarity more info
involved_in cell surface pattern recognition receptor signaling pathway	ISS Inferred from Sequence or Structural Similarity more info
involved_in complement activation, lectin pathway	IBA Inferred from Biological aspect of Ancestor more info
involved_in positive regulation of interleukin-8 production	ISS Inferred from Sequence or Structural Similarity more info

Component	Evidence Code	Pubs
part_of collagen trimer	IEA Inferred from Electronic Annotation more info
is_active_in collagen-containing extracellular matrix	IBA Inferred from Biological aspect of Ancestor more info
is_active_in extracellular space	IBA Inferred from Biological aspect of Ancestor more info
located_in plasma membrane	ISS Inferred from Sequence or Structural Similarity more info

General protein information

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Preferred Names: ficolin-1

Names: M-ficolin; collagen/fibrinogen domain-containing protein 1; ficolin (collagen/fibrinogen domain containing) 1; ficolin-alpha

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

NM_031348.2 → NP_112638.2 ficolin-1 precursor

See identical proteins and their annotated locations for NP_112638.2

Status: PROVISIONAL

Source sequence(s)

BC088128

UniProtKB/Swiss-Prot

Q9WTS8

UniProtKB/TrEMBL

F7FL15, Q5M8B4

Related

ENSRNOP00000023022.3, ENSRNOT00000023022.7

Conserved Domains (2) summary

cd00087
Location:123 → 333

FReD; Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular ...

pfam01391
Location:67 → 108

Collagen; Collagen triple helix repeat (20 copies)

RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCr8

Genomic

NC_086021.1 Reference GRCr8

Range

28844036..28847441 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_063284644.1 → XP_063140714.1 ficolin-1 isoform X1

UniProtKB/TrEMBL

F7FL15, Q5M8B4
XM_008761614.1 → XP_008759836.1 ficolin-1 isoform X2

Conserved Domains (2) summary

pfam01391
Location:68 → 111

Collagen; Collagen triple helix repeat (20 copies)

cd00087
Location:123 → 253

FReD; Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular ...