The presence of an anti-sense CSF1R transcript starting within the FIRE region has been reported in mouse macrophages and B cells.

The human CSF1R gene, on the minus strand, spans a region of 60,077 bases (Start: 149,413,051 bp from pter; End: 149,473,128 bp from pter) interrupted by introns ranging from 26kb for intron 1, to a range between 6.3kb to less than 0.1 kb for the other introns. The human CSF1R gene is composed of a total of 22 exons, of which the first exon is non-coding and where the remaining 21 exons (starting with exon 2) encode for the CSF1R protein.
The human CSF1R and mouse Csf1r genomic structures are highly conserved.

The 5 end of the human CSF1R gene has 2 alternative transcription start site regions, preceded by two alternative promoters. The transcription of CSF1R mRNA can be initiated at the two independent start sites in a tissue specific manner. The transcription of exon 1 through exon 22 occurs only in placental trophoblasts, and is driven by a trophoblast-specific promoter approximately 20kb upstream of the first exon. The transcript produced is predicted to be approximately 4kb long. In macrophages and a few other tissues (see expression section) transcription of CSF1R occurs only from exon 2 through exon 22 producing a transcript predicted to be approximately 3.9kb in length, which is translated into the CSF1R protein. The transcription this transcript is under the control of two major regulatory regions, which are highly conserved between human and mouse: the Promoter upstream of exon 2 and the fms-intronic regulatory region (FIRE). Most studies on CSF1R transcriptional regulation have focused on the mouse gene. However, most of the features of mouse Csf1r are highly conserved in human.
The mouse Csf1r promoter is TATA-less, and drives transcription from multiple sites (known as broad class transcription start sites). This promoter is not GC rich and there are no CpG islands in the vicinity. This promoter contains binding sites for various transcription factors including: PU.1, C/EBP, PAX5, and FUS/TLS - TBP. The mouse FIRE region is located in the second intron, approximately 2kb downstream from the transcription start site. It contains binding sites for a number of transcription factors including: Sp1 / Sp3, Ets, Egr-2 / Sp1, Runx1, AP-1 as well as PU.1 and C/EBP. With a few exceptions, the features described for the mouse Csfr1 regulatory regions are highly conserved in human. Specifically, the human CSF1R can be regulated in a hormone dependent fashion via a glucocorticoid response element present in the human CSF1R promoter, but not in the mouse Csf1r promoter.

The first CSF1R intron contains a transcriptionally inactive ribosomal protein L7 processed pseudogene that is oriented in the opposite direction of the CSF1R gene itself. This pseudogene is not functional but its sequence is highly conserved across all mammalian species.

The CSF1R protein consists of 972 amino acids and has a molecular mass of approximately 108 kDa. However due to post-translational modifications, which include phosphorylation, glycosylation, and the acquisition of N-linked oligosaccharides, the proteins molecular size increases. The CSF1R protein also contains a signal peptide and a 512 amino acid N-terminal extracellular segment which contains the ligand binding domain, a hydrophobic 25 amino acid membrane spanning region, and intracellular domain 435 amino acids in length that includes all sequences necessary for tyrosine kinase activity (occurring at tyrosine (Y) Y699 and Y708, as well as Y809). The CSF1R protein contains a glycine-rich signature sequence that is characteristic of kinases, as well as an ATP binding site at lysine (K) K616. The immature intracellular glycoprotein has a molecular mass of 130 kDa after it acquires N-linked oligosaccharides of the high mannose type during co-translational glycosylation. The molecular mass of CSF1R is increased further during intracellular transport to the plasma membrane, where the glycoproteins N-linked carbohydrates undergo modifications in the Golgi complex, resulting in an increase to 150 kDa molecular mass. There are variations in molecular mass of CSF1R across species due to the differential processing of carbohydrate chains in a species specific manner.

The major site of CSF1R expression is in macrophages. In hematopoiesis, CSF1R is upregulated during monocytic differentiation, but is downregulated during granulopoiesis. CSF1R is expressed predominantly in committed macrophage precursors (CFU-Ms), monocytes, and tissue macrophages. CSF1R mRNA can be detected granulocytes, but is not translated. CSF1R mRNA/protein expression has been reported also in non-hematopoietic cells such as trophoblasts (where is seems to derive from an alternative transcript including the non-coding exon 1), osteoclasts, smooth muscle cells, and neurons, as well as in female mammary gland epithelium during development and lactation. Expression of CSF1R mRNA/protein has also been reported in breast, ovarian, and endometrial tumors, as well as in hepatocellular carcinomas.
CSF1R expression during hematopoiesis is regulated by tissue-specific sets of transcription factors that play a key role in myeloid differentiation. CSF1R is activated in a synergistic manner by the co-expression of the macrophage-specific transcription factor Pu.1 and c-Ets-2. During B-cell lineage restriction and differentiation, the CSF1R gene is repressed by the transcription factor PAX5. It has been shown that PAX5 is required during B-cell differentiation to keep CSF1R in a silent state. It has also been shown that CSF1R can be repressed by Foxp1, a forkhead transcription factor that is in turn regulated by the Beta-2-integrin Mac-1.

CSF1R is located at the cell plasma membrane. Transport of CSF1R from the endoplasmic reticulum (the site of synthesis) to the plasma membrane occurs efficiently with detection of the receptor at the surface within 30 minutes of synthesis.

CSF1R is the receptor for the ligand colony stimulating factor-1 (CSF1). CSF1R is an integral transmembrane glycoprotein that exhibits ligand-induced tyrosine-specific protein kinase activity, which triggers a signaling cascade eventually affecting transcription of CSF1-responsive genes. CSF1R tyrosine phosphorylation is induced upon binding of CSF1, leading to activation of Ras / Erk and class I-A phosphatidylinositol 3-kinase signaling pathways, which in turn activate the signal transducers and activators of transcription (STATs) pathways, specifically STAT1, STAT3, and STAT5. CSF1R activation by CSF1 results in increased growth, proliferation and differentiation.

Like the CSF1R gene, the CSF1R protein sequence appears to be conserved across Euteleostomi (vertebrates) including: Homo sapiens (Human), Canis lupus familiaris (Dog), Mus musculus (Mouse), Rattus norvegicus (Rat), Gallus gallus (Chicken), and Danio rerio (Zebrafish).
CSF1R is a member of the gp140 family of the type I cytokine receptor group and shares a high degree of amino acid sequence homology to platelet-derived growth factor receptor (PDGFRB), specifically in its kinase domain.

None identified as of yet.

Chromosomal abnormalities: A partial deletion of chromosome 5 containing the CSF1R locus has been consistently observed in patients with myelodysplastic syndrome. The CSF1R locus is also affected by the acute megakaryoblastic leukemia-associated translocation t(3;5)(p21;q33) in which the CSF1R gene on chromosome 5 is fused to the RBM6 gene on chromosome 3, resulting in a fusion protein RBM6-CSF1R.
Gene mutations: CSF1R point mutations have been detected mainly in hematopoietic/lymphoid tissue and liver, where they correlate with myelodysplastic syndrome and acute myeloid leukemia (AML) and hepatocellular carcinoma, respectively. Specifically, mutations at codons 301 (exon 7) and 969 (exon 22) seem to occur with a higher frequency in both tissues. According to earlier studies these are activating mutations that would play a role in leukemogenesis. However, later studies have failed to find these mutations in AML patients. Additional mutations were discovered in AML patients at codons 245 (exon 6) and 413 (exon 9). However, their contribution to leukemogenesis is not known.
Epi-mutations: Specific fusion proteins resulting from leukemia-associated chromosomal translocations, including the AML1-MTG fusion proteins, result in transcriptional down-regulation of specific AML1 target genes such as CSF1R. AML1-MTG-induced CSF1R downregulation is epigenetic, as it is marked by specific repressive histone changes as well as DNA hypermethylation at the CSF1R regulatory regions. CSF1R epigenetic down-regulation is associated with block of myeloid differentiation and defects in cell proliferation in vitro.

The only breakpoint known for the CSF1R gene can be inferred by the identification of the novel fusion protein RBM6-CSF1R, in which the N-terminal portion of the RBM6 (a.a. 1-36) is fused to the C-terminal portion of CSF1R (a.a. 574-972). This fusion protein is predicated to be produced by the translocation t(3;5)(p21;q33).