Human Gene CSF2RB (uc003aqa.4) Description and Page Index
  Description: Homo sapiens colony stimulating factor 2 receptor, beta, low-affinity (granulocyte-macrophage) (CSF2RB), mRNA.
RefSeq Summary (NM_000395): The protein encoded by this gene is the common beta chain of the high affinity receptor for IL-3, IL-5 and CSF. Defects in this gene have been reported to be associated with protein alveolar proteinosis (PAP). [provided by RefSeq, Jul 2008]. Sequence Note: This RefSeq record was created from transcript and genomic sequence data because no single transcript was available for the full length of the gene. The extent of this transcript is supported by transcript alignments. Publication Note: This RefSeq record includes a subset of the publications that are available for this gene. Please see the Gene record to access additional publications. ##Evidence-Data-START## Transcript exon combination :: BC070085.1 [ECO:0000332] RNAseq introns :: single sample supports all introns SAMEA1965299, SAMEA1966682 [ECO:0000348] ##Evidence-Data-END## ##RefSeq-Attributes-START## MANE Ensembl match :: ENST00000403662.8/ ENSP00000384053.3 RefSeq Select criteria :: based on conservation, expression ##RefSeq-Attributes-END##
Transcript (Including UTRs)
   Position: hg19 chr22:37,309,675-37,336,479 Size: 26,805 Total Exon Count: 14 Strand: +
Coding Region
   Position: hg19 chr22:37,318,250-37,334,544 Size: 16,295 Coding Exon Count: 13 

Page IndexSequence and LinksUniProtKB CommentsGenetic AssociationsMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated: 2013-06-15

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr22:37,309,675-37,336,479)mRNA (may differ from genome)Protein (897 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkHGNCHPRDLynxMGIneXtProt
OMIMPubMedReactomeStanford SOURCEUniProtKB

-  Comments and Description Text from UniProtKB
  ID: IL3RB_HUMAN
DESCRIPTION: RecName: Full=Cytokine receptor common subunit beta; AltName: Full=CDw131; AltName: Full=GM-CSF/IL-3/IL-5 receptor common beta subunit; AltName: CD_antigen=CD131; Flags: Precursor;
FUNCTION: High affinity receptor for interleukin-3, interleukin-5 and granulocyte-macrophage colony-stimulating factor.
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. Interacts with TMEM102; this interaction occurs preferentially in the absence of CSF2. Interacts with LYN (By similarity).
INTERACTION: P04141:CSF2; NbExp=2; IntAct=EBI-1809771, EBI-1809826; P05113:IL5; NbExp=2; IntAct=EBI-1809771, EBI-2435811; P05556:ITGB1; NbExp=5; IntAct=EBI-1809771, EBI-703066; O60674:JAK2; NbExp=3; IntAct=EBI-1809771, EBI-518647;
SUBCELLULAR LOCATION: Membrane; Single-pass type I membrane protein.
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.
PTM: May be phosphorylated by LYN (By similarity).
DISEASE: Defects in CSF2RB are the cause of pulmonary surfactant metabolism dysfunction type 5 (SMDP5) [MIM:614370]. SMDP5 is 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.
SIMILARITY: Belongs to the type I cytokine receptor family. Type 4 subfamily.
SIMILARITY: Contains 2 fibronectin type-III domains.

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): CSF2RB
CDC HuGE Published Literature: CSF2RB
Positive Disease Associations: Spondylitis, Ankylosing
Related Studies:
  1. Spondylitis, Ankylosing
    Zhiming Lin et al. Nature genetics 2012, A genome-wide association study in Han Chinese identifies new susceptibility loci for ankylosing spondylitis., Nature genetics. [PubMed 22138694]

-  MalaCards Disease Associations
  MalaCards Gene Search: CSF2RB
Diseases sorted by gene-association score: surfactant metabolism dysfunction, pulmonary, 5* (900), csf2rb-related pulmonary surfactant metabolism dysfunction* (500), hereditary pulmonary alveolar proteinosis* (368), pulmonary surfactant metabolism dysfunction* (53)
* = 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: 36.58 RPKM in Whole Blood
Total median expression: 141.43 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 -92.30217-0.425 Picture PostScript Text
3' UTR -601.261935-0.311 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
IPR003531 - Hempt_rcpt_S_F1_CS
IPR013783 - Ig-like_fold
IPR011365 - IL3_rcpt_beta
IPR015321 - IL6_recept-bd

Pfam Domains:
PF09240 - Interleukin-6 receptor alpha chain, binding
PF09294 - Interferon-alpha/beta receptor, fibronectin type III

SCOP Domains:
49265 - Fibronectin type III

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

1C8P
- NMR MuPIT

1EGJ
- X-ray MuPIT

1GH7
- X-ray MuPIT
To conserve bandwidth, only the images from the first 3 structures are shown.
2GYS - X-ray MuPIT 3CXE - X-ray


ModBase Predicted Comparative 3D Structure on P32927
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 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: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
GO:0004912 interleukin-3 receptor activity
GO:0004914 interleukin-5 receptor activity

Biological Process:
GO:0000165 MAPK cascade
GO:0007165 signal transduction
GO:0007585 respiratory gaseous exchange
GO:0018108 peptidyl-tyrosine phosphorylation
GO:0019221 cytokine-mediated signaling pathway
GO:0032496 response to lipopolysaccharide
GO:0036016 cellular response to interleukin-3
GO:0038043 interleukin-5-mediated signaling pathway
GO:0038156 interleukin-3-mediated signaling pathway
GO:0044267 cellular protein metabolic process

Cellular Component:
GO:0005622 intracellular
GO:0005886 plasma membrane
GO:0005887 integral component of plasma membrane
GO:0016020 membrane
GO:0016021 integral component of membrane
GO:0030526 granulocyte macrophage colony-stimulating factor receptor complex


-  Descriptions from all associated GenBank mRNAs
  BC070085 - Homo sapiens colony stimulating factor 2 receptor, beta, low-affinity (granulocyte-macrophage), mRNA (cDNA clone MGC:87425 IMAGE:30344148), complete cds.
CR456428 - Homo sapiens CSF2RB full length open reading frame (ORF) cDNA clone (cDNA clone C22ORF:pGEM.CSF2RB.V2).
M59941 - Human GM-CSF receptor beta chain mRNA, complete cds.
JD422929 - Sequence 403953 from Patent EP1572962.
JD343111 - Sequence 324135 from Patent EP1572962.
AB384793 - Synthetic construct DNA, clone: pF1KB3343, Homo sapiens CSF2RB gene for cytokine receptor common beta chain precursor, complete cds, without stop codon, in Flexi system.
CU013277 - Homo sapiens CSF2RB, mRNA (cDNA clone IMAGE:100000054), complete cds, without stop codon, in Gateway system.
CU012989 - Homo sapiens CSF2RB, mRNA (cDNA clone IMAGE:100000150), complete cds, with stop codon, in Gateway system.
AK302993 - Homo sapiens cDNA FLJ51731 complete cds, highly similar to Cytokine receptor common beta chain precursor.
JD075968 - Sequence 56992 from Patent EP1572962.
JD124884 - Sequence 105908 from Patent EP1572962.
JD065836 - Sequence 46860 from Patent EP1572962.
JD173182 - Sequence 154206 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa04060 - Cytokine-cytokine receptor interaction
hsa04210 - Apoptosis
hsa04630 - Jak-STAT signaling pathway

BioCarta from NCI Cancer Genome Anatomy Project
h_il3Pathway - IL 3 signaling pathway
h_badPathway - Regulation of BAD phosphorylation

Reactome (by CSHL, EBI, and GO)

Protein P32927 (Reactome details) participates in the following event(s):

R-NUL-879922 Mouse JAK2 binds human common beta chain
R-HSA-879937 The common beta chain IL3RB binds JAK2
R-HSA-450031 Interleukin-3 receptor alpha: Interleukin-3 binds IL3RB:JAK2
R-HSA-913370 Interleukin-5:Interleukin-5 receptor alpha binds IL3RB:JAK2
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-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-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-912757 p-S585-IL3RB binds 14-3-3 proteins
R-HSA-879909 Activation of STAT5a/b by JAK2
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-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-913424 The SHC1:SHIP1 complex is stabilized by GRB2
R-HSA-508247 Gab2 binds the p85 subunit of Class 1A PI3 kinases
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-5688890 Defective CSF2RA causes pulmonary surfactant metabolism dysfunction 4 (SMDP4)
R-HSA-449147 Signaling by Interleukins
R-HSA-392499 Metabolism of proteins
R-HSA-5687613 Diseases associated with surfactant metabolism
R-HSA-1280215 Cytokine Signaling in Immune system
R-HSA-5688849 Defective CSF2RB causes pulmonary surfactant metabolism dysfunction 5 (SMDP5)
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: IL3RB, IL3RB_HUMAN, IL5RB, NM_000395, NP_000386, P32927, Q5JZI1, Q6ICE0
UCSC ID: uc003aqa.4
RefSeq Accession: NM_000395
Protein: P32927 (aka IL3RB_HUMAN or CYRB_HUMAN)
CCDS: CCDS13936.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_000395.2
exon count: 14CDS single in 3' UTR: no RNA size: 4848
ORF size: 2694CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 5483.00frame shift in genome: no % Coverage: 99.96
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # 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.