FIBCD1 fibrinogen C domain containing 1 [Homo sapiens (human)] - Gene

Summary

Official Symbol: FIBCD1provided by HGNC
Official Full Name: fibrinogen C domain containing 1provided by HGNC
Primary source: HGNC:HGNC:25922
See related: Ensembl:ENSG00000130720 MIM:613357; AllianceGenome:HGNC:25922
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Summary: FIBCD1 is a conserved type II transmembrane endocytic receptor that binds chitin and is located primarily in the intestinal brush border (Schlosser et al., 2009 [PubMed 19710473]).[supplied by OMIM, Apr 2010]
Expression: Biased expression in testis (RPKM 2.4), adrenal (RPKM 1.6) and 6 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 9q34.12

Exon count:: 10

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	9	NC_000009.12 (130902440..130940709, complement)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	9	NC_060933.1 (143107312..143145777, complement)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	9	NC_000009.11 (133777827..133814634, complement)

Chromosome 9 - NC_000009.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Crystal structures of human immune protein FIBCD1 suggest an extended binding site compatible with recognition of pathogen-associated carbohydrate motifs.
Title: Crystal structures of human immune protein FIBCD1 suggest an extended binding site compatible with recognition of pathogen-associated carbohydrate motifs.
The role of FIBCD1 in response to Aspergillus fumigatus in lung epithelial cells.
Title: The role of FIBCD1 in response to Aspergillus fumigatus in lung epithelial cells.
FIBCD1 is an endocytic GAG receptor associated with a novel neurodevelopmental disorder.
Title: FIBCD1 is an endocytic GAG receptor associated with a novel neurodevelopmental disorder.
The myokine Fibcd1 is an endogenous determinant of myofiber size and mitigates cancer-induced myofiber atrophy.
Title: The myokine Fibcd1 is an endogenous determinant of myofiber size and mitigates cancer-induced myofiber atrophy.
thses findings support FIBCD1 as a lung epithelial pattern recognition receptor that recognizes the complex Aspergillus fumigatus cell wall polysaccharides and modulates the lung epithelial inflammatory response by suppressing inflammatory mediators and mucins
Title: FIBCD1 Binds Aspergillus fumigatus and Regulates Lung Epithelial Response to Cell Wall Components.
FIBCD1 is expressed in epithelial cells derived from all three germ layers. Endodermal-derived epithelial cells throughout the gastrointestinal tract and the respiratory system showed high expression of FIBCD1 and also mesodermal-derived cells in the genitourinary system and ectodermal-derived epidermis and sebaceous glands cells expressed FIBCD1.
Title: Immunohistochemical Localization of Fibrinogen C Domain Containing 1 on Epithelial and Mucosal Surfaces in Human Tissues.
FIBCD1 may be a novel biomarker to evaluate the prognosis of gastric cancer.
Title: Overexpression of FIBCD1 Is Predictive of Poor Prognosis in Gastric Cancer.
The high affinity ligand N-acetylmannosamine (ManNAc) binds FIBCD1 in the S1 site, predominantly via the acetyl group with the oxygen and acetamide nitrogen hydrogen-bonded to the protein and the methyl group inserted into a hydrophobic pocket.
Title: Crystal structure of the tetrameric fibrinogen-like recognition domain of fibrinogen C domain containing 1 (FIBCD1) protein.
Observational study of gene-disease association. (HuGE Navigator)
Title: New genetic associations detected in a host response study to hepatitis B vaccine.
The recognition unit of FIBCD1 organizes into a noncovalently linked tetrameric structure and uses a hydrophobic funnel (S1) for acetyl group recognition.
Title: The recognition unit of FIBCD1 organizes into a noncovalently linked tetrameric structure and uses a hydrophobic funnel (S1) for acetyl group recognition.

Submit: New GeneRIF Correction See all GeneRIFs (11)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables chitin binding	IDA Inferred from Direct Assay more info	PubMed
enables metal ion binding	IEA Inferred from Electronic Annotation more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Component	Evidence Code	Pubs
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 membrane	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: fibrinogen C domain-containing protein 1

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_001145106.2 → NP_001138578.1 fibrinogen C domain-containing protein 1

See identical proteins and their annotated locations for NP_001138578.1

Status: VALIDATED

Description

Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Both variants 1 and 2 encode the same protein.

Source sequence(s)

AL161733, BC032953, DC404353

Consensus CDS

CCDS6937.1

UniProtKB/Swiss-Prot

A3KFK0, Q6UXK6, Q8N539, Q96SJ7

UniProtKB/TrEMBL

A8K8X4

Related

ENSP00000414501.1, ENST00000448616.5

Conserved Domains (1) summary

cd00087
Location:241 → 457

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 ...
NM_032843.5 → NP_116232.3 fibrinogen C domain-containing protein 1

See identical proteins and their annotated locations for NP_116232.3

Status: VALIDATED

Description

Transcript Variant: This variant (1) represents the longer transcript.

Source sequence(s)

AL161733, BC032953

Consensus CDS

CCDS6937.1

UniProtKB/Swiss-Prot

A3KFK0, Q6UXK6, Q8N539, Q96SJ7

UniProtKB/TrEMBL

A8K8X4

Related

ENSP00000361413.4, ENST00000372338.9

Conserved Domains (1) summary

cd00087
Location:241 → 457

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 ...

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000009.12 Reference GRCh38.p14 Primary Assembly

Range

130902440..130940709 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_047423989.1 → XP_047279945.1 fibrinogen C domain-containing protein 1 isoform X1

UniProtKB/Swiss-Prot

A3KFK0, Q6UXK6, Q8N539, Q96SJ7
XM_047423990.1 → XP_047279946.1 fibrinogen C domain-containing protein 1 isoform X2

UniProtKB/TrEMBL

A3KFJ8

Related

ENSP00000361412.1, ENST00000372337.6

Alternate T2T-CHM13v2.0

Genomic

NC_060933.1 Alternate T2T-CHM13v2.0

Range

143107312..143145777 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054364052.1 → XP_054220027.1 fibrinogen C domain-containing protein 1 isoform X1

UniProtKB/Swiss-Prot

A3KFK0, Q6UXK6, Q8N539, Q96SJ7
XM_054364053.1 → XP_054220028.1 fibrinogen C domain-containing protein 1 isoform X2

UniProtKB/TrEMBL

A3KFJ8