Human Gene CSF1 (uc001dyw.4)
  Description: Homo sapiens colony stimulating factor 1 (macrophage) (CSF1), transcript variant 1, mRNA.
RefSeq Summary (NM_000757): The protein encoded by this gene is a cytokine that controls the production, differentiation, and function of macrophages. The active form of the protein is found extracellularly as a disulfide-linked homodimer, and is thought to be produced by proteolytic cleavage of membrane-bound precursors. The encoded protein may be involved in development of the placenta. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Sep 2011].
Transcript (Including UTRs)
   Position: hg19 chr1:110,453,233-110,473,616 Size: 20,384 Total Exon Count: 9 Strand: +
Coding Region
   Position: hg19 chr1:110,453,646-110,467,811 Size: 14,166 Coding Exon Count: 8 

Page IndexSequence and LinksUniProtKB CommentsPrimersGenetic AssociationsMalaCards
CTDGene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein Structure
Other SpeciesGO AnnotationsmRNA DescriptionsPathwaysOther NamesModel Information
Methods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr1:110,453,233-110,473,616)mRNA (may differ from genome)Protein (554 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGeneCardsGeneNetwork
H-INVHGNCHPRDLynxMalacardsMGI
neXtProtOMIMPubMedReactomeTreefamUniProtKB
WikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: CSF1_HUMAN
DESCRIPTION: RecName: Full=Macrophage colony-stimulating factor 1; Short=CSF-1; Short=M-CSF; Short=MCSF; AltName: Full=Lanimostim; Contains: RecName: Full=Processed macrophage colony-stimulating factor 1; Flags: Precursor;
FUNCTION: Cytokine that plays an essential role in the regulation of survival, proliferation and differentiation of hematopoietic precursor cells, especially mononuclear phagocytes, such as macrophages and monocytes. Promotes the release of proinflammatory chemokines, and thereby plays an important role in innate immunity and in inflammatory processes. Plays an important role in the regulation of osteoclast proliferation and differentiation, the regulation of bone resorption, and is required for normal bone development. Required for normal male and female fertility. Promotes reorganization of the actin cytoskeleton, regulates formation of membrane ruffles, cell adhesion and cell migration. Plays a role in lipoprotein clearance.
SUBUNIT: Homodimer or heterodimer; disulfide-linked. Interacts with CSF1R.
SUBCELLULAR LOCATION: Cell membrane; Single-pass membrane protein.
SUBCELLULAR LOCATION: Processed macrophage colony-stimulating factor 1: Secreted, extracellular space.
PTM: N- and O-glycosylated. Glycosylation and proteolytic cleavage yield different soluble forms. One high molecular weight soluble form is a proteoglycan containing chondroitin sulfate. O- glycosylated with core 1 or possibly core 8 glycans. Isoform 1 is N- and O-glycosylated. Isoform 3 is only N-glycosylated.
DISEASE: Note=Aberrant expression of CSF1 or CSF1R can promote cancer cell proliferation, invasion and formation of metastases. Overexpression of CSF1 or CSF1R is observed in a significant percentage of breast, ovarian, prostate, and endometrial cancers.
DISEASE: Note=Aberrant expression of CSF1 or CSF1R may play a role in inflammatory diseases, such as rheumatoid arthritis, glomerulonephritis, atherosclerosis, and allograft rejection.

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): CSF1
CDC HuGE Published Literature: CSF1

-  MalaCards Disease Associations
  MalaCards Gene Search: CSF1
Diseases sorted by gene-association score: pigmented villonodular synovitis (30), tenosynovial giant cell tumor (25), pulmonary alveolar proteinosis (19), giant cell tumor (16), rheumatoid arthritis (13), acute non lymphoblastic leukemia (13), malignant histiocytosis (11), arthritis (11), monocytic leukemia (10), dermatophytosis (10), osteopetrosis (10), pancytopenia (9), multicentric reticulohistiocytosis (9), mandibular cancer (8), cherubism (8), ocular cicatricial pemphigoid (8), adult-onset still's disease (8), letterer-siwe disease (8), glomerulonephritis (7), jaw cancer (7), stachybotrys chartarum (7), paget's disease of bone (6), hyperostosis, endosteal (5), histiocytic sarcoma (5), joint disorders (5), acute myeloid leukemia with abnormal bone marrow eosinophils inv(16)(p13q22) or t(16;16)(p13;q22) (4), aplastic anemia (3), myelodysplastic syndrome (2), ovarian cancer, somatic (2), osteoporosis (2), leukemia, acute myeloid (0)

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 63.04 RPKM in Cells - Cultured fibroblasts
Total median expression: 660.67 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -192.87413-0.467 Picture PostScript Text
3' UTR -884.342156-0.410 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR009079 - 4_helix_cytokine-like_core
IPR008001 - MCSF-1

Pfam Domains:
PF05337 - Macrophage colony stimulating factor-1 (CSF-1)

SCOP Domains:
47266 - 4-helical cytokines

Protein Data Bank (PDB) 3-D Structure
MuPIT help
1HMC - X-ray MuPIT 3UEZ - X-ray MuPIT 3UF2 - X-ray MuPIT 4ADF - X-ray MuPIT 4FA8 - X-ray MuPIT


ModBase Predicted Comparative 3D Structure on P09603
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The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologGenome BrowserGenome BrowserNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGDEnsembl   
 Protein SequenceProtein Sequence   
 AlignmentAlignment   

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005125 cytokine activity
GO:0005157 macrophage colony-stimulating factor receptor binding
GO:0005515 protein binding
GO:0008083 growth factor activity
GO:0042802 identical protein binding
GO:0042803 protein homodimerization activity

Biological Process:
GO:0001954 positive regulation of cell-matrix adhesion
GO:0002158 osteoclast proliferation
GO:0002376 immune system process
GO:0003006 developmental process involved in reproduction
GO:0006954 inflammatory response
GO:0007169 transmembrane receptor protein tyrosine kinase signaling pathway
GO:0008283 cell proliferation
GO:0008284 positive regulation of cell proliferation
GO:0010469 regulation of receptor activity
GO:0010628 positive regulation of gene expression
GO:0010743 regulation of macrophage derived foam cell differentiation
GO:0010744 positive regulation of macrophage derived foam cell differentiation
GO:0010759 positive regulation of macrophage chemotaxis
GO:0019221 cytokine-mediated signaling pathway
GO:0030097 hemopoiesis
GO:0030154 cell differentiation
GO:0030225 macrophage differentiation
GO:0030278 regulation of ossification
GO:0030316 osteoclast differentiation
GO:0030335 positive regulation of cell migration
GO:0032270 positive regulation of cellular protein metabolic process
GO:0032946 positive regulation of mononuclear cell proliferation
GO:0038145 macrophage colony-stimulating factor signaling pathway
GO:0040018 positive regulation of multicellular organism growth
GO:0042117 monocyte activation
GO:0042488 positive regulation of odontogenesis of dentin-containing tooth
GO:0043687 post-translational protein modification
GO:0044267 cellular protein metabolic process
GO:0045087 innate immune response
GO:0045651 positive regulation of macrophage differentiation
GO:0045657 positive regulation of monocyte differentiation
GO:0045672 positive regulation of osteoclast differentiation
GO:0045860 positive regulation of protein kinase activity
GO:0046579 positive regulation of Ras protein signal transduction
GO:0048873 homeostasis of number of cells within a tissue
GO:0060444 branching involved in mammary gland duct morphogenesis
GO:0060611 mammary gland fat development
GO:0060763 mammary duct terminal end bud growth
GO:1902228 positive regulation of macrophage colony-stimulating factor signaling pathway
GO:1904141 positive regulation of microglial cell migration

Cellular Component:
GO:0005576 extracellular region
GO:0005615 extracellular space
GO:0005788 endoplasmic reticulum lumen
GO:0005886 plasma membrane
GO:0016020 membrane
GO:0016021 integral component of membrane
GO:0048471 perinuclear region of cytoplasm
GO:1990682 CSF1-CSF1R complex


-  Descriptions from all associated GenBank mRNAs
  LF211919 - JP 2014500723-A/19422: Polycomb-Associated Non-Coding RNAs.
LF206295 - JP 2014500723-A/13798: Polycomb-Associated Non-Coding RNAs.
LF353045 - JP 2014500723-A/160548: Polycomb-Associated Non-Coding RNAs.
BC021117 - Homo sapiens colony stimulating factor 1 (macrophage), mRNA (cDNA clone MGC:31930 IMAGE:4586312), complete cds.
E03219 - DNA encoding human M-CSF(macrophage colony stimulating factor).
E03235 - cDNA encoding human M-CSF.
AK291660 - Homo sapiens cDNA FLJ75722 complete cds, highly similar to Homo sapiens colony stimulating factor 1 (CSF1), transcript variant 1, mRNA.
AB208952 - Homo sapiens mRNA for colony stimulating factor 1 isoform a precursor variant protein.
M37435 - Human macrophage-specific colony-stimulating factor (CSF-1) mRNA, complete cds.
M27087 - Homo sapiens macrophage colony-stimulating factor (M-CSF1) cDNA to mRNA, complete cds.
E01949 - cDNA encoding human M-CSF.
E01950 - cDNA encoding human M-CSF.
E02182 - DNA encoding human M-CSF (colony Stimulating factor).
E02183 - DNA encoding human M-CSF (colony Stimulating factor).
E09614 - Human cDNA encoding M-CSF.
E09615 - Human cDNA encoding M-CSF.
JD395963 - Sequence 376987 from Patent EP1572962.
U22386 - Human macrophage-colony stimulating factor gamma precursor mRNA, complete cds.
AB527768 - Synthetic construct DNA, clone: pF1KB9973, Homo sapiens CSF1 gene for colony stimulating factor 1, without stop codon, in Flexi system.
KJ896655 - Synthetic construct Homo sapiens clone ccsbBroadEn_06049 CSF1 gene, encodes complete protein.
KR710585 - Synthetic construct Homo sapiens clone CCSBHm_00014149 CSF1 (CSF1) mRNA, encodes complete protein.
M64592 - Human macrophage colony stimulating factor (M-CSF-1) mRNA, complete cds.
M76453 - Homo sapiens colony stimulating factor 1 (CSF1) mRNA, partial cds.
X05825 - Human mRNA for colony stimulating factor CSF-4.
JF803735 - Homo sapiens macrophage colony-stimulating factor 1 mRNA, partial cds.
E02184 - DNA encoding human M-CSF.
E02185 - DNA encoding human M-CSF.
E02187 - DNA encoding human M-CSF.
E02188 - DNA encoding human M-CSF.
E02186 - DNA encoding human M-CSF.
E02189 - DNA encoding human M-CSF.
AK300401 - Homo sapiens cDNA FLJ60891 complete cds, highly similar to Macrophage colony-stimulating factor 1 precursor.
LF353041 - JP 2014500723-A/160544: Polycomb-Associated Non-Coding RNAs.
AK311440 - Homo sapiens cDNA, FLJ18482.
LF353039 - JP 2014500723-A/160542: Polycomb-Associated Non-Coding RNAs.
LF353038 - JP 2014500723-A/160541: Polycomb-Associated Non-Coding RNAs.
LF353037 - JP 2014500723-A/160540: Polycomb-Associated Non-Coding RNAs.
LF353036 - JP 2014500723-A/160539: Polycomb-Associated Non-Coding RNAs.
LF353035 - JP 2014500723-A/160538: Polycomb-Associated Non-Coding RNAs.
LF353034 - JP 2014500723-A/160537: Polycomb-Associated Non-Coding RNAs.
JD204702 - Sequence 185726 from Patent EP1572962.
JD393180 - Sequence 374204 from Patent EP1572962.
JD464305 - Sequence 445329 from Patent EP1572962.
JD163723 - Sequence 144747 from Patent EP1572962.
JD140743 - Sequence 121767 from Patent EP1572962.
JD193404 - Sequence 174428 from Patent EP1572962.
JD157738 - Sequence 138762 from Patent EP1572962.
JD173073 - Sequence 154097 from Patent EP1572962.
JD493861 - Sequence 474885 from Patent EP1572962.
JD157450 - Sequence 138474 from Patent EP1572962.
JD270994 - Sequence 252018 from Patent EP1572962.
JD372740 - Sequence 353764 from Patent EP1572962.
JD182431 - Sequence 163455 from Patent EP1572962.
JD067909 - Sequence 48933 from Patent EP1572962.
LF353030 - JP 2014500723-A/160533: Polycomb-Associated Non-Coding RNAs.
JD382550 - Sequence 363574 from Patent EP1572962.
JD373260 - Sequence 354284 from Patent EP1572962.
JD208916 - Sequence 189940 from Patent EP1572962.
JD361276 - Sequence 342300 from Patent EP1572962.
JD148154 - Sequence 129178 from Patent EP1572962.
LF353029 - JP 2014500723-A/160532: Polycomb-Associated Non-Coding RNAs.
JD060919 - Sequence 41943 from Patent EP1572962.
JD396541 - Sequence 377565 from Patent EP1572962.
LF353028 - JP 2014500723-A/160531: Polycomb-Associated Non-Coding RNAs.
LF353027 - JP 2014500723-A/160530: Polycomb-Associated Non-Coding RNAs.
LF353026 - JP 2014500723-A/160529: Polycomb-Associated Non-Coding RNAs.
LF353025 - JP 2014500723-A/160528: Polycomb-Associated Non-Coding RNAs.
MA588622 - JP 2018138019-A/160548: Polycomb-Associated Non-Coding RNAs.
MA588618 - JP 2018138019-A/160544: Polycomb-Associated Non-Coding RNAs.
MA588616 - JP 2018138019-A/160542: Polycomb-Associated Non-Coding RNAs.
MA588615 - JP 2018138019-A/160541: Polycomb-Associated Non-Coding RNAs.
MA588614 - JP 2018138019-A/160540: Polycomb-Associated Non-Coding RNAs.
MA588613 - JP 2018138019-A/160539: Polycomb-Associated Non-Coding RNAs.
MA588612 - JP 2018138019-A/160538: Polycomb-Associated Non-Coding RNAs.
MA588611 - JP 2018138019-A/160537: Polycomb-Associated Non-Coding RNAs.
MA588607 - JP 2018138019-A/160533: Polycomb-Associated Non-Coding RNAs.
MA588606 - JP 2018138019-A/160532: Polycomb-Associated Non-Coding RNAs.
MA588605 - JP 2018138019-A/160531: Polycomb-Associated Non-Coding RNAs.
MA588604 - JP 2018138019-A/160530: Polycomb-Associated Non-Coding RNAs.
MA588603 - JP 2018138019-A/160529: Polycomb-Associated Non-Coding RNAs.
MA588602 - JP 2018138019-A/160528: Polycomb-Associated Non-Coding RNAs.
MA447496 - JP 2018138019-A/19422: Polycomb-Associated Non-Coding RNAs.
MA441872 - JP 2018138019-A/13798: Polycomb-Associated Non-Coding RNAs.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa04060 - Cytokine-cytokine receptor interaction
hsa04640 - Hematopoietic cell lineage

BioCarta from NCI Cancer Genome Anatomy Project
h_stemPathway - Regulation of hematopoiesis by cytokines
h_LDLpathway - Low-density lipoprotein (LDL) pathway during atherogenesis
h_inflamPathway - Cytokines and Inflammatory Response
h_etsPathway - METS affect on Macrophage Differentiation
h_mspPathway - Msp/Ron Receptor Signaling Pathway

Reactome (by CSHL, EBI, and GO)

Protein P09603 (Reactome details) participates in the following event(s):

R-HSA-9009488 IL34 binds CSF1
R-HSA-8952289 FAM20C phosphorylates FAM20C substrates
R-HSA-449836 Other interleukin signaling
R-HSA-6783783 Interleukin-10 signaling
R-HSA-449147 Signaling by Interleukins
R-HSA-381426 Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs)
R-HSA-8957275 Post-translational protein phosphorylation
R-HSA-1280215 Cytokine Signaling in Immune system
R-HSA-392499 Metabolism of proteins
R-HSA-597592 Post-translational protein modification
R-HSA-168256 Immune System

-  Other Names for This Gene
  Alternate Gene Symbols: A8K6J5, CSF1_HUMAN, NM_000757, NP_757351, P09603, Q13130, Q14086, Q14806, Q5VVF3, Q5VVF4, Q9UQR8
UCSC ID: uc001dyw.4
RefSeq Accession: NM_000757
Protein: P09603 (aka CSF1_HUMAN)
CCDS: CCDS816.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_000757.5
exon count: 9CDS single in 3' UTR: no RNA size: 4249
ORF size: 1665CDS single in intron: no Alignment % ID: 99.98
txCdsPredict score: 3514.00frame shift in genome: no % Coverage: 99.65
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: yes # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.