Csf2ra (colony stimulating factor 2 receptor subunit alpha) - Rat Genome Database

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Gene: Csf2ra (colony stimulating factor 2 receptor subunit alpha) Rattus norvegicus
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Symbol: Csf2ra
Name: colony stimulating factor 2 receptor subunit alpha
RGD ID: 1594330
Description: Predicted to enable granulocyte colony-stimulating factor binding activity and granulocyte colony-stimulating factor receptor activity. Involved in response to ethanol. Predicted to be located in plasma membrane. Predicted to be part of granulocyte macrophage colony-stimulating factor receptor complex. Predicted to be active in external side of plasma membrane. Human ortholog(s) of this gene implicated in pulmonary alveolar proteinosis. Orthologous to human CSF2RA (colony stimulating factor 2 receptor subunit alpha); PARTICIPATES IN granulocyte-macrophage colony-stimulating factor signaling pathway; cytokine mediated signaling pathway; Jak-Stat signaling pathway; INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2,3,7,8-Tetrachlorodibenzofuran; acetamide.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: colony stimulating factor 2 receptor alpha subunit; colony stimulating factor 2 receptor, alpha, low-affinity (granulocyte-macrophage); granulocyte-macrophage colony stimulating receptor alpha; granulocyte-macrophage colony-stimulating factor receptor subunit alpha
RGD Orthologs
Human
Mouse
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21498,089 - 103,261 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1489,172 - 103,128 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx14116,168 - 121,062 (-)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.0141,417,943 - 1,422,837 (-)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.014114,615 - 119,509 (-)NCBIRnor_WKY
Rnor_6.0141,462,292 - 1,467,264 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl141,462,358 - 1,467,264 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0141,465,139 - 1,469,667 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Celera14661,818 - 666,688 (+)NCBICelera
Cytogenetic Map14p22NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. Cloning of rat interleukin-3 receptor beta-subunit from cultured microglia and its mRNA expression in vivo. Appel K, etal., J Neurosci 1995 Aug;15(8):5800-9.
2. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
3. GM-CSF receptor expression and signaling is decreased in lungs of ethanol-fed rats. Joshi PC, etal., Am J Physiol Lung Cell Mol Physiol. 2006 Dec;291(6):L1150-8. Epub 2006 Jul 28.
4. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
5. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
6. GOA pipeline RGD automated data pipeline
7. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
8. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
9. Comprehensive gene review and curation RGD comprehensive gene curation
Additional References at PubMed
PMID:17694571  


Genomics

Comparative Map Data
Csf2ra
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21498,089 - 103,261 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1489,172 - 103,128 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx14116,168 - 121,062 (-)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.0141,417,943 - 1,422,837 (-)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.014114,615 - 119,509 (-)NCBIRnor_WKY
Rnor_6.0141,462,292 - 1,467,264 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl141,462,358 - 1,467,264 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0141,465,139 - 1,469,667 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Celera14661,818 - 666,688 (+)NCBICelera
Cytogenetic Map14p22NCBI
CSF2RA
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38X1,268,814 - 1,325,218 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38Y1,268,814 - 1,325,218 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 EnsemblX1,268,800 - 1,310,381 (+)EnsemblGRCh38hg38GRCh38
GRCh37X1,387,707 - 1,444,111 (+)NCBIGRCh37GRCh37hg19GRCh37
GRCh37Y1,337,707 - 1,394,111 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36X1,347,701 - 1,388,827 (+)NCBINCBI36Build 36hg18NCBI36
Build 36Y1,347,701 - 1,388,827 (+)NCBINCBI36Build 36hg18NCBI36
Build 34Y1,355,172 - 1,396,299NCBI
CeleraX5,684,057 - 5,726,879 (+)NCBICelera
Cytogenetic MapX;YNCBI
CHM1_1X1,418,017 - 1,458,211 (+)NCBICHM1_1
T2T-CHM13v2.0X1,116,126 - 1,174,802 (+)NCBIT2T-CHM13v2.0
T2T-CHM13v2.0Y1,129,416 - 1,189,240 (+)NCBIT2T-CHM13v2.0
Csf2ra
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391961,205,629 - 61,221,141 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1961,212,395 - 61,216,867 (-)EnsemblGRCm39 Ensembl
GRCm381961,217,191 - 61,228,461 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1961,223,957 - 61,228,429 (-)EnsemblGRCm38mm10GRCm38
MGSCv371961,300,305 - 61,304,321 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361961,279,074 - 61,283,022 (-)NCBIMGSCv36mm8
Celera1963,421,543 - 63,425,590 (-)NCBICelera
Cytogenetic Map19D3NCBI
cM Map1956.89NCBI
CSF2RA
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1X832,170 - 855,548 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 EnsemblX832,046 - 853,876 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_TashaX772,774 - 796,202 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0X742,740 - 766,122 (+)NCBIROS_Cfam_1.0
UMICH_Zoey_3.1X734,899 - 758,240 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0X751,242 - 774,663 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0X748,192 - 771,608 (+)NCBIUU_Cfam_GSD_1.0
LOC101965277
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024404953534,206 - 541,365 (-)NCBIHiC_Itri_2
SpeTri2.0NW_0049366443,835,462 - 3,842,471 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CSF2RA
(Sus scrofa - pig)
No map positions available.
LOC103247514
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Vero_WHO_p1.0NW_023666141112,013 - 168,815 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Csf2ra
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_004624834616,180 - 628,794 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Csf2ra
19 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:59
Count of miRNA genes:51
Interacting mature miRNAs:52
Transcripts:ENSRNOT00000070834
Prediction methods:Microtar, Rnahybrid
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2300159Bmd61Bone mineral density QTL 615.30.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)14126541967Rat
2300183Bmd60Bone mineral density QTL 605.70.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)14126541967Rat
619619Rf4Renal disease susceptibility QTL 44.10.002urine total protein amount (VT:0000032)urine protein excretion rate to body weight ratio (CMO:0001099)14132754612Rat
634352Apr6Acute phase response QTL 63.7blood interleukin-6 amount (VT:0008595)plasma interleukin-6 level (CMO:0001927)14141131407Rat

Markers in Region
RH134866  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21497,901 - 98,102 (-)MAPPERmRatBN7.2
Rnor_6.0141,467,396 - 1,467,596NCBIRnor6.0
Rnor_5.0141,469,799 - 1,469,999UniSTSRnor5.0
Celera14666,820 - 667,020UniSTS
RH140244  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21498,313 - 98,612 (-)MAPPERmRatBN7.2
Rnor_6.0141,466,886 - 1,467,184NCBIRnor6.0
Rnor_5.0141,469,289 - 1,469,587UniSTSRnor5.0
Celera14666,310 - 666,608UniSTS


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 2 14 13 12 13 33 6 27 9
Low 1 43 43 28 7 28 8 11 41 29 14 2 8
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000070834   ⟹   ENSRNOP00000064492
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1498,236 - 103,128 (-)Ensembl
Rnor_6.0 Ensembl141,463,359 - 1,467,054 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000077243   ⟹   ENSRNOP00000075442
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1498,236 - 103,128 (-)Ensembl
Rnor_6.0 Ensembl141,462,358 - 1,467,264 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000106970   ⟹   ENSRNOP00000097127
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1489,172 - 103,128 (-)Ensembl
RefSeq Acc Id: NM_001037660   ⟹   NP_001032749
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21498,234 - 103,128 (-)NCBI
Rnor_6.0141,462,358 - 1,467,264 (+)NCBI
Rnor_5.0141,465,139 - 1,469,667 (+)NCBI
Celera14661,818 - 666,688 (+)RGD
Sequence:
RefSeq Acc Id: XM_017599372   ⟹   XP_017454861
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21498,089 - 103,253 (-)NCBI
Rnor_6.0141,462,292 - 1,466,727 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039092399   ⟹   XP_038948327
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21498,089 - 103,253 (-)NCBI
RefSeq Acc Id: XM_039092400   ⟹   XP_038948328
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21498,089 - 103,261 (-)NCBI
RefSeq Acc Id: XM_039092401   ⟹   XP_038948329
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21498,089 - 103,253 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_001032749   ⟸   NM_001037660
- Peptide Label: precursor
- UniProtKB: Q701L2 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_017454861   ⟸   XM_017599372
- Peptide Label: isoform X1
- UniProtKB: A0A0G2KAL6 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000064492   ⟸   ENSRNOT00000070834
RefSeq Acc Id: ENSRNOP00000075442   ⟸   ENSRNOT00000077243
RefSeq Acc Id: XP_038948328   ⟸   XM_039092400
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038948329   ⟸   XM_039092401
- Peptide Label: isoform X4
RefSeq Acc Id: XP_038948327   ⟸   XM_039092399
- Peptide Label: isoform X2
RefSeq Acc Id: ENSRNOP00000097127   ⟸   ENSRNOT00000106970
Protein Domains
Fibronectin type-III

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-M0R536-F1-model_v2 AlphaFold M0R536 1-382 view protein structure

Transcriptome

eQTL   View at Phenogen
WGCNA   View at Phenogen
Tissue/Strain Expression   View at Phenogen

Promoters
RGD ID:13699139
Promoter ID:EPDNEW_R9661
Type:multiple initiation site
Name:Csf2ra_1
Description:colony stimulating factor 2 receptor alpha subunit
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0141,462,331 - 1,462,391EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1594330 AgrOrtholog
BioCyc Gene G2FUF-16717 BioCyc
Ensembl Genes ENSRNOG00000049782 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000064492 ENTREZGENE
  ENSRNOP00000064492.3 UniProtKB/TrEMBL
  ENSRNOP00000075442 ENTREZGENE
  ENSRNOP00000075442.2 UniProtKB/TrEMBL
  ENSRNOP00000097127.1 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000070834 ENTREZGENE
  ENSRNOT00000070834.3 UniProtKB/TrEMBL
  ENSRNOT00000077243 ENTREZGENE
  ENSRNOT00000077243.2 UniProtKB/TrEMBL
  ENSRNOT00000106970.1 UniProtKB/TrEMBL
Gene3D-CATH 2.60.40.10 UniProtKB/TrEMBL
InterPro Fibronectin_type3 UniProtKB/TrEMBL
  FN3_sf UniProtKB/TrEMBL
  Ig-like_fold UniProtKB/TrEMBL
  IL3Ra_N UniProtKB/TrEMBL
  IL6_recept-bd UniProtKB/TrEMBL
  Short_hematopoietin_rcpt_2_CS UniProtKB/TrEMBL
KEGG Report rno:652957 UniProtKB/TrEMBL
NCBI Gene 652957 ENTREZGENE
Pfam IL3Ra_N UniProtKB/TrEMBL
  IL6Ra-bind UniProtKB/TrEMBL
PhenoGen Csf2ra PhenoGen
PROSITE FN3 UniProtKB/TrEMBL
  HEMATOPO_REC_S_F2 UniProtKB/TrEMBL
Superfamily-SCOP FN_III-like UniProtKB/TrEMBL
UniProt A0A0G2KAL6 ENTREZGENE, UniProtKB/TrEMBL
  A0A8I6B5C9_RAT UniProtKB/TrEMBL
  M0R536_RAT UniProtKB/TrEMBL
  Q701L2 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2019-12-06 Csf2ra  colony stimulating factor 2 receptor subunit alpha  Csf2ra  colony stimulating factor 2 receptor alpha subunit  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2016-01-20 Csf2ra  colony stimulating factor 2 receptor alpha subunit  Csf2ra  colony stimulating factor 2 receptor, alpha, low-affinity (granulocyte-macrophage)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2013-08-01 Csf2ra  colony stimulating factor 2 receptor, alpha, low-affinity (granulocyte-macrophage)  Csf2ra  granulocyte-macrophage colony stimulating receptor alpha  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-11-20 Csf2ra  granulocyte-macrophage colony stimulating receptor alpha      Symbol and Name status set to provisional 70820 PROVISIONAL