csf1ra colony stimulating factor 1 receptor, a [Danio rerio (zebrafish)] - Gene

Summary

Official Symbol: csf1raprovided by ZNC
Official Full Name: colony stimulating factor 1 receptor, aprovided by ZNC
Primary source: ZFIN:ZDB-GENE-001205-1
See related: Ensembl:ENSDARG00000102986 AllianceGenome:ZFIN:ZDB-GENE-001205-1
Gene type: protein coding
RefSeq status: PROVISIONAL
Organism: Danio rerio
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
Also known as: fms; csf1r; CSF-1R; M-CSF-R; panther
Summary: Predicted to enable growth factor binding activity and macrophage colony-stimulating factor receptor activity. Acts upstream of or within several processes, including immune response in brain or nervous system; macrophage chemotaxis; and myeloid cell development. Predicted to be located in membrane. Predicted to be part of CSF1-CSF1R complex and receptor complex. Predicted to be active in plasma membrane. Is expressed in several structures, including hematopoietic cell; hematopoietic system; integument; nervous system; and neural crest cell. Used to study CSF1R-related brain malformation and osteopetrosis. Human ortholog(s) of this gene implicated in adult-onset leukoencephalopathy with axonal spheroids and pigmented glia; diabetes mellitus; gastrointestinal system cancer (multiple); lung cancer (multiple); and renal cell carcinoma. Orthologous to human CSF1R (colony stimulating factor 1 receptor). [provided by Alliance of Genome Resources, Nov 2024]
Orthologs: all
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Genomic context

Location:: chromosome: 14

Exon count:: 22

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCz11 (GCF_000002035.6)	14	NC_007125.7 (3143147..3182282, complement)
105	previous assembly	GRCz10 (GCF_000002035.5)	14	NC_007125.6 (3170823..3202038, complement)

Chromosome 14 - NC_007125.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

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Expression

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See details

Project title: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
Description: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
BioProject: PRJEB1986
Analysis date: Fri Dec 8 19:48:10 2017

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Dominant-acting CSF1R variants cause microglial depletion and altered astrocytic phenotype in zebrafish and adult-onset leukodystrophy.
Title: Dominant-acting CSF1R variants cause microglial depletion and altered astrocytic phenotype in zebrafish and adult-onset leukodystrophy.
A Population of Injury-Responsive Lymphoid Cells Expresses mpeg1.1 in the Adult Zebrafish Heart.
Title: A Population of Injury-Responsive Lymphoid Cells Expresses mpeg1.1 in the Adult Zebrafish Heart.
The synergistic role of Pu.1 and Fms in zebrafish osteoclast-reducing osteopetrosis and possible therapeutic strategies.
Title: The synergistic role of Pu.1 and Fms in zebrafish osteoclast-reducing osteopetrosis and possible therapeutic strategies.
Knockout of zebrafish colony-stimulating factor 1 receptor by CRISPR/Cas9 affects metabolism and locomotion capacity.
Title: Knockout of zebrafish colony-stimulating factor 1 receptor by CRISPR/Cas9 affects metabolism and locomotion capacity.
the overlapping roles of the two paralogues released functional constraints on csf1ra, allowing the signaling capacity of Csf1r to serve a novel function in the evolution of pigment pattern in fishes.
Title: Unique and non-redundant function of csf1r paralogues in regulation and evolution of post-embryonic development of the zebrafish.
Data suggest that fms is not required for establishing a population of precursor cells during embryogenesis but is required for recruiting pigment cell precursors to xanthophore fates, with concomitant effects on melanophore organization.
Title: Temporal and cellular requirements for Fms signaling during zebrafish adult pigment pattern development.

Submit: New GeneRIF Correction

General gene information

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Gene Ontology Provided by ZFIN

Function	Evidence Code	Pubs
enables ATP binding	IEA Inferred from Electronic Annotation more info
enables cytokine binding	IEA Inferred from Electronic Annotation more info
enables growth factor binding	IBA Inferred from Biological aspect of Ancestor more info
enables kinase activity	IEA Inferred from Electronic Annotation more info
enables macrophage colony-stimulating factor receptor activity	IBA Inferred from Biological aspect of Ancestor more info
enables metal ion binding	IEA Inferred from Electronic Annotation more info
enables nucleotide binding	IEA Inferred from Electronic Annotation more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein kinase activity	IEA Inferred from Electronic Annotation more info
enables protein tyrosine kinase activity	IEA Inferred from Electronic Annotation more info
enables transferase activity	IEA Inferred from Electronic Annotation more info
enables transmembrane receptor protein tyrosine kinase activity	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in cell surface receptor protein tyrosine kinase signaling pathway	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within cell surface receptor protein tyrosine kinase signaling pathway	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within cytokine-mediated signaling pathway	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within developmental pigmentation	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within developmental pigmentation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within immune response in brain or nervous system	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within immune system process	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within inflammatory response	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within innate immune response	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within lipid metabolic process	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within macrophage chemotaxis	IMP Inferred from Mutant Phenotype more info
acts_upstream_of_or_within melanocyte differentiation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within melanocyte migration	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within microglia development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within microglia differentiation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in multicellular organism development	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within osteoclast development	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within osteoclast development	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in osteoclast differentiation	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within osteoclast maturation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within phosphorylation	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within pigmentation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of cell migration	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within positive regulation of macrophage chemotaxis	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within positive regulation of neural retina development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within protein phosphorylation	IEA Inferred from Electronic Annotation more info
involved_in regulation of MAPK cascade	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within regulation of developmental pigmentation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within regulation of endocytosis	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within regulation of myelination	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within regulation of odontogenesis	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within regulation of osteoclast development	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within regulation of osteoclast development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within regulation of xanthophore differentiation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within swimming behavior	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within xanthophore differentiation	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
part_of CSF1-CSF1R complex	IBA Inferred from Biological aspect of Ancestor more info
located_in membrane	IEA Inferred from Electronic Annotation more info
is_active_in plasma membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in plasma membrane	IEA Inferred from Electronic Annotation more info
part_of receptor complex	IBA Inferred from Biological aspect of Ancestor more info

General protein information

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Preferred Names: macrophage colony-stimulating factor 1 receptor

Names: CSF-1 receptor; CSF-1-R; c-fms; fms proto-oncogene homolog; pfe; pfeffer; proto-oncogene c-Fms homolog; proto-oncogene fms homolog; sal; salz

NP_571747.1

EC 2.7.10.1

XP_021336731.1

EC 2.7.10.1

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_131672.1 → NP_571747.1 macrophage colony-stimulating factor 1 receptor precursor

See identical proteins and their annotated locations for NP_571747.1

Status: PROVISIONAL

Source sequence(s)

AF240639

UniProtKB/Swiss-Prot

Q9I8N6

UniProtKB/TrEMBL

B3DHL0

Related

ENSDARP00000148187.1, ENSDART00000183810.1

Conserved Domains (6) summary

cd05106
Location:545 → 918

PTKc_CSF-1R; Catalytic domain of the Protein Tyrosine Kinase, Colony-Stimulating Factor-1 Receptor

cd00096
Location:427 → 509

Ig; Immunoglobulin domain

smart00410
Location:222 → 306

IG_like; Immunoglobulin like

pfam07714
Location:584 → 913

Pkinase_Tyr; Protein tyrosine kinase

pfam13927
Location:212 → 293

Ig_3; Immunoglobulin domain

cl11960
Location:311 → 410

Ig; Immunoglobulin domain

RefSeqs of Annotated Genomes: GCF_000002035.6-RS_2024_08

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

Reference GRCz11 Primary Assembly

Genomic

NC_007125.7 Reference GRCz11 Primary Assembly

Range

3143147..3182282 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_021481056.2 → XP_021336731.1 macrophage colony-stimulating factor 1 receptor isoform X1

UniProtKB/TrEMBL

A0A8M9QKN6

Conserved Domains (4) summary

cd05106
Location:545 → 918

PTKc_CSF-1R; Catalytic domain of the Protein Tyrosine Kinase, Colony-Stimulating Factor-1 Receptor

smart00409
Location:222 → 306

IG; Immunoglobulin

smart00410
Location:126 → 200

IG_like; Immunoglobulin like

cl11960
Location:311 → 410

Ig; Immunoglobulin domain