Human Gene CSF2RA (ENST00000381529.9_12) from GENCODE V47lift37
  Description: colony stimulating factor 2 receptor subunit alpha, transcript variant 2 (from RefSeq NM_172245.4)
Gencode Transcript: ENST00000381529.9_12
Gencode Gene: ENSG00000198223.19_15
Transcript (Including UTRs)
   Position: hg19 chrX:1,387,707-1,428,828 Size: 41,122 Total Exon Count: 13 Strand: +
Coding Region
   Position: hg19 chrX:1,401,597-1,428,372 Size: 26,776 Coding Exon Count: 11 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chrX:1,387,707-1,428,828)mRNA (may differ from genome)Protein (400 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGeneCardsHGNC
MalacardsMGIOMIMPubMedReactomeUniProtKB
WikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: CSF2R_HUMAN
DESCRIPTION: RecName: Full=Granulocyte-macrophage colony-stimulating factor receptor subunit alpha; Short=GM-CSF-R-alpha; Short=GMCSFR-alpha; Short=GMR-alpha; AltName: Full=CDw116; AltName: CD_antigen=CD116; Flags: Precursor;
FUNCTION: Low affinity receptor for granulocyte-macrophage colony- stimulating factor. Transduces a signal that results in the proliferation, differentiation, and functional activation of hematopoietic cells.
SUBUNIT: Heterodimer of an alpha and a beta subunit. The beta subunit is common to the IL3, IL5 and GM-CSF receptors. The signaling GM-CSF receptor complex is a dodecamer of two head-to- head hexamers of two alpha, two beta, and two ligand subunits.
SUBCELLULAR LOCATION: Cell membrane; Single-pass type I membrane protein.
SUBCELLULAR LOCATION: Isoform 3: Secreted (Probable).
SUBCELLULAR LOCATION: Isoform 4: Secreted (Probable).
SUBCELLULAR LOCATION: Isoform 6: Secreted (Probable).
DOMAIN: The WSXWS motif appears to be necessary for proper protein folding and thereby efficient intracellular transport and cell- surface receptor binding.
DOMAIN: The box 1 motif is required for JAK interaction and/or activation.
DISEASE: Defects in CSF2RA are the cause of pulmonary surfactant metabolism dysfunction type 4 (SMDP4) [MIM:300770]. A rare lung disorder due to impaired surfactant homeostasis. It is characterized by alveolar filling with floccular material that stains positive using the periodic acid-Schiff method and is derived from surfactant phospholipids and protein components. Excessive lipoproteins accumulation in the alveoli results in severe respiratory distress.
MISCELLANEOUS: The gene encoding for this protein is located in the pseudoautosomal region 1 (PAR1) of X and Y chromosomes.
SIMILARITY: Belongs to the type I cytokine receptor family. Type 5 subfamily.

-  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


-  MalaCards Disease Associations
  MalaCards Gene Search: CSF2RA
Diseases sorted by gene-association score: surfactant metabolism dysfunction, pulmonary, 4* (1200), csf2ra-related pulmonary surfactant metabolism dysfunction* (500), hereditary pulmonary alveolar proteinosis* (247), pulmonary surfactant metabolism dysfunction* (63), acute basophilic leukemia (10), pulmonary alveolar proteinosis (9), intrinsic asthma (6)
* = Manually curated disease association

-  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: 23.76 RPKM in Whole Blood
Total median expression: 73.36 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 -45.50156-0.292 Picture PostScript Text
3' UTR -146.20456-0.321 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
IPR003961 - Fibronectin_type3
IPR013783 - Ig-like_fold
IPR015321 - IL6_recept-bd
IPR003532 - Short_hematopoietin_rcpt_2_CS

Pfam Domains:
PF09240 - Interleukin-6 receptor alpha chain, binding
PF18611 - IL-3 receptor alpha chain N-terminal domain

SCOP Domains:
49265 - Fibronectin type III

Protein Data Bank (PDB) 3-D Structure
MuPIT help
3CXE - X-ray


ModBase Predicted Comparative 3D Structure on P15509
FrontTopSide
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 orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
      
      
      
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0004713 protein tyrosine kinase activity
GO:0004896 cytokine receptor activity
GO:0005088 Ras guanyl-nucleotide exchange factor activity
GO:0005515 protein binding
GO:0038023 signaling receptor activity

Biological Process:
GO:0000165 MAPK cascade
GO:0018108 peptidyl-tyrosine phosphorylation
GO:0019221 cytokine-mediated signaling pathway
GO:0044267 cellular protein metabolic process

Cellular Component:
GO:0005576 extracellular region
GO:0005622 intracellular
GO:0005886 plasma membrane
GO:0005887 integral component of plasma membrane
GO:0016020 membrane
GO:0016021 integral component of membrane


-  Descriptions from all associated GenBank mRNAs
  AK293086 - Homo sapiens cDNA FLJ75868 complete cds, highly similar to Homo sapiens colony stimulating factor 2 receptor, alpha, low-affinity (granulocyte-macrophage) (CSF2RA), transcript variant 1, mRNA.
AK301395 - Homo sapiens cDNA FLJ60179 complete cds, highly similar to Granulocyte-macrophage colony-stimulating factor receptor alpha chain precursor.
BC071835 - Homo sapiens colony stimulating factor 2 receptor, alpha, low-affinity (granulocyte-macrophage), mRNA (cDNA clone MGC:88495 IMAGE:4650755), complete cds.
JD127704 - Sequence 108728 from Patent EP1572962.
M64445 - Human GM-CSF receptor mRNA, complete cds.
BC002635 - Homo sapiens colony stimulating factor 2 receptor, alpha, low-affinity (granulocyte-macrophage), mRNA (cDNA clone MGC:3848 IMAGE:3606186), complete cds.
AL833597 - Homo sapiens mRNA; cDNA DKFZp686C1967 (from clone DKFZp686C1967).
AK309630 - Homo sapiens cDNA, FLJ99671.
L29348 - Homo sapiens granulocyte-macrophage colony-stimulating factor receptor alpha-subunit soluble isoform 2 (GM-CSF-RAS2) mRNA, complete cds.
L29349 - Homo sapiens granulocyte-macrophage colony-stimulating factor receptor alpha-subunit 3 (GM-CSF-RA3) mRNA, complete cds.
U93096 - Human GM-CSF receptor alpha subunit soluble 3 mRNA, complete cds.
X17648 - Human mRNA for granulocyte-macrophage colony-stimulating factor receptor (hGM-CSF-R).
JD285354 - Sequence 266378 from Patent EP1572962.
JD520819 - Sequence 501843 from Patent EP1572962.
M73832 - Human GM-CSF receptor (GM-CSF receptor) mRNA, complete cds.
JD264241 - Sequence 245265 from Patent EP1572962.
DQ893104 - Synthetic construct clone IMAGE:100005734; FLH193774.01X; RZPDo839B1179D colony stimulating factor 2 receptor, alpha, low-affinity (granulocyte-macrophage) (CSF2RA) gene, encodes complete protein.
DQ896376 - Synthetic construct Homo sapiens clone IMAGE:100010836; FLH193770.01L; RZPDo839B1169D colony stimulating factor 2 receptor, alpha, low-affinity (granulocyte-macrophage) (CSF2RA) gene, encodes complete protein.
JD320394 - Sequence 301418 from Patent EP1572962.
KJ896656 - Synthetic construct Homo sapiens clone ccsbBroadEn_06050 CSF2RA gene, encodes complete protein.
AB590144 - Synthetic construct DNA, clone: pFN21AE1531, Homo sapiens CSF2RA gene for colony stimulating factor 2 receptor, alpha, low-affinity, without stop codon, in Flexi system.
CU687176 - Synthetic construct Homo sapiens gateway clone IMAGE:100023158 5' read CSF2RA mRNA.
X54935 - Human mRNA for GMCSFR receptor.
DQ841258 - Homo sapiens colony stimulating factor 2 receptor alpha subunit splice variant mRNA, complete cds, alternatively spliced.
JD153504 - Sequence 134528 from Patent EP1572962.
JD505013 - Sequence 486037 from Patent EP1572962.
JD348159 - Sequence 329183 from Patent EP1572962.
JD377019 - Sequence 358043 from Patent EP1572962.
JD168451 - Sequence 149475 from Patent EP1572962.
JD305747 - Sequence 286771 from Patent EP1572962.
JD356780 - Sequence 337804 from Patent EP1572962.
JD285926 - Sequence 266950 from Patent EP1572962.
JD340674 - Sequence 321698 from Patent EP1572962.
JD340675 - Sequence 321699 from Patent EP1572962.
JD499636 - Sequence 480660 from Patent EP1572962.
JD286638 - Sequence 267662 from Patent EP1572962.
JD511480 - Sequence 492504 from Patent EP1572962.
JD522293 - Sequence 503317 from Patent EP1572962.
JD564347 - Sequence 545371 from Patent EP1572962.
JD558277 - Sequence 539301 from Patent EP1572962.
JD319360 - Sequence 300384 from Patent EP1572962.
JD092547 - Sequence 73571 from Patent EP1572962.
JD430375 - Sequence 411399 from Patent EP1572962.
JD529525 - Sequence 510549 from Patent EP1572962.
JD169839 - Sequence 150863 from Patent EP1572962.
JD306473 - Sequence 287497 from Patent EP1572962.
JD055372 - Sequence 36396 from Patent EP1572962.
JD126192 - Sequence 107216 from Patent EP1572962.
JD096408 - Sequence 77432 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein P15509 (Reactome details) participates in the following event(s):

R-HSA-913360 GM-CSF receptor alpha subunit binds GM-CSF
R-HSA-913371 GM-CSF receptor alpha:GM-CSF binds Bc
R-HSA-5686335 CSF2RA:CSF2RB binds SFTPs
R-HSA-5686359 SFTPs translocate from extracellular region to clathrin-coated vesicle
R-HSA-879934 Recruitment of SHC1 is mediated by Y593 of the common beta chain
R-HSA-909738 SHP1 and SHP2 bind the common beta chain
R-HSA-879907 Tyrosine kinases phosphorylate the receptor
R-HSA-879910 JAK2 is phosphorylated, activated
R-HSA-913451 IL3RB is phosphorylated on Ser-585
R-HSA-879930 STAT5 is recruited by JAK2
R-HSA-921155 p-STAT5 dissociates from the receptor complex
R-HSA-912757 p-S585-IL3RB binds 14-3-3 proteins
R-HSA-879925 SHC1 bound to the common beta chain becomes tyrosine phosphorylated
R-HSA-914036 SHP1 and SHP2 dephosphorylate Y628 of IL3RB
R-HSA-879909 Activation of STAT5a/b by JAK2
R-HSA-914182 14-3-3 zeta binding allows recruitment of PI3K
R-HSA-453111 Phosphorylated SHC recruits GRB2:SOS1
R-HSA-913374 Phosphorylated SHC1 recruits SHIP
R-HSA-508247 Gab2 binds the p85 subunit of Class 1A PI3 kinases
R-HSA-913424 The SHC1:SHIP1 complex is stabilized by GRB2
R-HSA-5672965 RAS GEFs promote RAS nucleotide exchange
R-HSA-512988 Interleukin-3, 5 and GM-CSF signaling
R-HSA-5683826 Surfactant metabolism
R-HSA-5688849 Defective CSF2RB causes pulmonary surfactant metabolism dysfunction 5 (SMDP5)
R-HSA-449147 Signaling by Interleukins
R-HSA-5688890 Defective CSF2RA causes pulmonary surfactant metabolism dysfunction 4 (SMDP4)
R-HSA-392499 Metabolism of proteins
R-HSA-5687613 Diseases associated with surfactant metabolism
R-HSA-1280215 Cytokine Signaling in Immune system
R-HSA-5668914 Diseases of metabolism
R-HSA-168256 Immune System
R-HSA-1643685 Disease
R-HSA-912526 Interleukin receptor SHC signaling
R-HSA-451927 Interleukin-2 family signaling
R-HSA-5673001 RAF/MAP kinase cascade
R-HSA-5684996 MAPK1/MAPK3 signaling
R-HSA-5683057 MAPK family signaling cascades
R-HSA-162582 Signal Transduction

-  Other Names for This Gene
  Alternate Gene Symbols: A7J003, A8KAM1, B4DW68, CSF2R, CSF2RY, CSF2R_HUMAN, ENST00000381529.1, ENST00000381529.2, ENST00000381529.3, ENST00000381529.4, ENST00000381529.5, ENST00000381529.6, ENST00000381529.7, ENST00000381529.8, J3JS76, J3JS77, NM_172245, O00207, P15509, Q14429, Q14430, Q14431, Q16564, uc318qhr.1, uc318qhr.2
UCSC ID: ENST00000381529.9_12
RefSeq Accession: NM_172245.4
Protein: P15509 (aka CSF2R_HUMAN or GMCR_HUMAN)

-  Gene Model Information
  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.