Crlf2 (cytokine receptor-like factor 2) - Rat Genome Database

Send us a Message
Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Search RGD Grant Resources Citing RGD About Us Contact Us
Genes Variants Community Projects QTLs Strains Markers Genome Information Ontologies Cell Lines References Download Submit Data
OntoMate (Literature Search) JBrowse (Genome Browser) Synteny Browser (VCMap) Variant Visualizer Multi-Ontology Enrichment (MOET) Gene-Ortholog Location Finder (GOLF) InterViewer (Protein-Protein Interactions) PhenoMiner (Quatitative Phenotypes) Gene Annotator OLGA (Gene List Generator) AllianceMine GViewer (Genome Viewer)
Aging & Age-Related Disease Cancer & Neoplastic Disease Cardiovascular Disease Coronavirus Disease Developmental Disease Diabetes Hematologic Disease Immune & Inflammatory Disease Infectious Disease Liver Disease Neurological Disease Obesity & Metabolic Syndrome Renal Disease Respiratory Disease Sensory Organ Disease
Find Models   new Genetic Models Autism Models Rat PhenoMiner (Quantitative Phenotypes) Chinchilla PhenoMiner Expected Ranges (Quantitative Phenotype) PhenoMiner Term Comparison Hybrid Rat Diversity Panel Phenotypes Phenotypes in Other Animal Models Animal Husbandry Strain Medical Records Phylogenetics Strain Availability Calendar Rats 101 Submissions Photo Archive
Pathways
Rat Community Forum Directory of Rat Laboratories Video Tutorials News RGD Publications RGD Presentations Archive Nomenclature Guidelines Resource Links Laboratory Resources Employment Resources
Gene: Crlf2 (cytokine receptor-like factor 2) Rattus norvegicus
Analyze
Symbol: Crlf2
Name: cytokine receptor-like factor 2
RGD ID: 621078
Description: Enables cytokine activity. Predicted to be involved in several processes, including positive regulation of interleukin-5 production; positive regulation of mast cell activation; and positive regulation of receptor signaling pathway via STAT. Predicted to act upstream of or within inflammatory response. Predicted to be located in external side of plasma membrane. Orthologous to human CRLF2 (cytokine receptor like factor 2); PARTICIPATES IN cytokine mediated signaling pathway; Jak-Stat signaling pathway; INTERACTS WITH 2,2',4,4'-Tetrabromodiphenyl ether; 2,3,7,8-tetrachlorodibenzodioxine; 4,4'-sulfonyldiphenol.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: Crl2; thymic stromal lymphopoietin protein receptor; thymic stromal-derived lymphopoietin, receptor; Tpte2; transmembrane phosphoinositide 3-phosphatase and tensin homolog 2; TSLP receptor; Tslpr
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
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
GRCr814118,932 - 123,632 (+)NCBIGRCr8
mRatBN7.214103,943 - 108,643 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl14103,939 - 108,642 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx14121,877 - 126,551 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0141,423,652 - 1,428,326 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.014120,324 - 124,998 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0141,456,843 - 1,461,543 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl141,456,844 - 1,461,543 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0141,459,624 - 1,464,324 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Celera14656,303 - 661,003 (-)NCBICelera
Cytogenetic Map14p22NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. Cloning of rat thymic stromal lymphopoietin receptor (TSLPR) and characterization of genomic structure of murine Tslpr gene. Blagoev B, etal., Gene 2002 Feb 6;284(1-2):161-8.
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. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
4. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
5. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
6. GOA pipeline RGD automated data pipeline
7. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
8. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, etal., Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16899-903. Epub 2002 Dec 11.
Additional References at PubMed
PMID:11418668   PMID:15488943   PMID:16142237   PMID:17242164   PMID:29257253   PMID:30676545  


Genomics

Comparative Map Data
Crlf2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr814118,932 - 123,632 (+)NCBIGRCr8
mRatBN7.214103,943 - 108,643 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl14103,939 - 108,642 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx14121,877 - 126,551 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0141,423,652 - 1,428,326 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.014120,324 - 124,998 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0141,456,843 - 1,461,543 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl141,456,844 - 1,461,543 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0141,459,624 - 1,464,324 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Celera14656,303 - 661,003 (-)NCBICelera
Cytogenetic Map14p22NCBI
CRLF2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38Y1,190,490 - 1,212,649 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38X1,190,490 - 1,212,649 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 EnsemblY1,190,490 - 1,212,723 (-)EnsemblGRCh38hg38GRCh38
GRCh38.p14 EnsemblX1,190,490 - 1,212,723 (-)EnsemblGRCh38hg38GRCh38
GRCh37Y1,264,869 - 1,281,542 (-)NCBIGRCh37GRCh37hg19GRCh37
GRCh37X1,314,869 - 1,331,542 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36Y1,274,894 - 1,291,529 (-)NCBINCBI36Build 36hg18NCBI36
Build 36X1,274,894 - 1,291,529 (-)NCBINCBI36Build 36hg18NCBI36
CeleraX5,605,262 - 5,605,961 (-)NCBICelera
Cytogenetic MapX;YNCBI
CHM1_1X1,345,456 - 1,361,581 (-)NCBICHM1_1
T2T-CHM13v2.0X1,035,684 - 1,058,464 (-)NCBIT2T-CHM13v2.0
T2T-CHM13v2.0Y1,050,430 - 1,072,677 (-)NCBIT2T-CHM13v2.0
Crlf2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm395109,702,575 - 109,707,301 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl5109,702,575 - 109,706,859 (-)EnsemblGRCm39 Ensembl
GRCm385109,554,709 - 109,559,128 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl5109,554,709 - 109,558,993 (-)EnsemblGRCm38mm10GRCm38
MGSCv375109,983,728 - 109,988,012 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv365109,795,011 - 109,799,248 (-)NCBIMGSCv36mm8
Celera5106,655,703 - 106,673,432 (-)NCBICelera
Cytogenetic Map5FNCBI
cM Map553.24NCBI
Crlf2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0NW_004955499940,250 - 955,458 (-)NCBIChiLan1.0ChiLan1.0
LOC100981146
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2Y45,865,325 - 45,891,246 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1-v2X1,030,768 - 1,056,303 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1X1,034,411 - 1,060,265 (-)NCBINHGRI_mPanPan1
NHGRI_mPanPan1Y1,063,595 - 1,089,386 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0X933,459 - 957,950 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
CRLF2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1X780,924 - 801,961 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 EnsemblX780,711 - 802,836 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_TashaX719,633 - 740,407 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0X688,940 - 709,953 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 EnsemblX688,660 - 710,093 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1X682,055 - 702,828 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0X697,563 - 718,580 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0X694,446 - 715,490 (-)NCBIUU_Cfam_GSD_1.0
Crlf2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024404953503,508 - 509,770 (-)NCBIHiC_Itri_2
SpeTri2.0NW_0049366443,866,973 - 3,872,749 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CRLF2
(Sus scrofa - pig)		 No map positions available.
LOC103247474
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Vero_WHO_p1.0NW_023666141213,570 - 241,034 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Crlf2
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_004624834596,067 - 610,333 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Crlf2
13 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:30
Count of miRNA genes:30
Interacting mature miRNAs:30
Transcripts:ENSRNOT00000075656
Prediction methods:Miranda, 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
RH141167  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.214108,385 - 108,603 (-)MAPPERmRatBN7.2
Rnor_6.0141,456,883 - 1,457,100NCBIRnor6.0
Rnor_5.0141,459,664 - 1,459,881UniSTSRnor5.0
Celera14656,343 - 656,560UniSTS
AI177846  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.214106,395 - 106,571 (-)MAPPERmRatBN7.2
Rnor_6.0141,458,915 - 1,459,090NCBIRnor6.0
Rnor_5.0141,461,696 - 1,461,871UniSTSRnor5.0
Celera14658,375 - 658,550UniSTS


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 10 31 24 11 24 39 25 33 9
Low 1 33 26 17 8 17 8 11 35 10 8 2 8
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000075656   ⟹   ENSRNOP00000066370
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl14103,939 - 108,642 (+)Ensembl
Rnor_6.0 Ensembl141,456,844 - 1,461,543 (-)Ensembl
RefSeq Acc Id: NM_134465   ⟹   NP_604460
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr814118,932 - 123,632 (+)NCBI
mRatBN7.214103,943 - 108,643 (+)NCBI
Rnor_6.0141,456,843 - 1,461,543 (-)NCBI
Rnor_5.0141,459,624 - 1,464,324 (-)NCBI
Celera14656,303 - 661,003 (-)RGD
Sequence:
RefSeq Acc Id: XM_008769915   ⟹   XP_008768137
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr814118,982 - 123,632 (+)NCBI
mRatBN7.214103,993 - 108,643 (+)NCBI
Rnor_6.0141,456,843 - 1,461,456 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039091600   ⟹   XP_038947528
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr814118,982 - 123,632 (+)NCBI
mRatBN7.214103,993 - 108,643 (+)NCBI
RefSeq Acc Id: XM_039091601   ⟹   XP_038947529
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr814118,982 - 123,632 (+)NCBI
mRatBN7.214103,993 - 108,643 (+)NCBI
RefSeq Acc Id: XM_039091602   ⟹   XP_038947530
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr814119,032 - 123,632 (+)NCBI
mRatBN7.214104,019 - 108,643 (+)NCBI
RefSeq Acc Id: XM_039091603   ⟹   XP_038947531
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr814119,030 - 123,632 (+)NCBI
mRatBN7.214104,019 - 108,643 (+)NCBI
Reference Protein Sequences
RefSeq Acc Id: NP_604460   ⟸   NM_134465
- Peptide Label: precursor
- UniProtKB: Q8R4S8 (UniProtKB/Swiss-Prot),   Q6AZ53 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_008768137   ⟸   XM_008769915
- Peptide Label: isoform X1
- UniProtKB: Q8R4S8 (UniProtKB/Swiss-Prot),   M0RA33 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000066370   ⟸   ENSRNOT00000075656
RefSeq Acc Id: XP_038947528   ⟸   XM_039091600
- Peptide Label: isoform X2
- UniProtKB: Q8R4S8 (UniProtKB/Swiss-Prot)
RefSeq Acc Id: XP_038947529   ⟸   XM_039091601
- Peptide Label: isoform X3
- UniProtKB: Q8R4S8 (UniProtKB/Swiss-Prot)
RefSeq Acc Id: XP_038947530   ⟸   XM_039091602
- Peptide Label: isoform X4
RefSeq Acc Id: XP_038947531   ⟸   XM_039091603
- Peptide Label: isoform X4
Protein Domains
Fibronectin type-III

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q8R4S8-F1-model_v2 AlphaFold Q8R4S8 1-360 view protein structure

Transcriptome

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

Promoters
RGD ID:13699135
Promoter ID:EPDNEW_R9660
Type:multiple initiation site
Name:Crlf2_1
Description:cytokine receptor-like factor 2
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_6.0141,461,518 - 1,461,578EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:621078 AgrOrtholog
BioCyc Gene G2FUF-16715 BioCyc
Ensembl Genes ENSRNOG00000049828 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000075656 ENTREZGENE
  ENSRNOT00000075656.2 UniProtKB/TrEMBL
Gene3D-CATH 2.60.40.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7108137 IMAGE-MGC_LOAD
InterPro CRLF2-like_D2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  CRLF2_D1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  FN3_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  FN3_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ig-like_fold UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:171499 UniProtKB/TrEMBL
MGC_CLONE MGC:93197 IMAGE-MGC_LOAD
NCBI Gene 171499 ENTREZGENE
PANTHER CYTOKINE RECEPTOR UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  CYTOKINE RECEPTOR-LIKE FACTOR 2-RELATED UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam CRLF2-like_D2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  CRLF2_D1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Crlf2 PhenoGen
PROSITE FN3 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
RatGTEx ENSRNOG00000049828 RatGTEx
SMART FN3 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF49265 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt CRLF2_RAT UniProtKB/Swiss-Prot
  M0RA33 ENTREZGENE, UniProtKB/TrEMBL
  Q6AZ53 ENTREZGENE, UniProtKB/TrEMBL
  Q8R4S8 ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-05-15 Crlf2  cytokine receptor-like factor 2  Tpte2  transmembrane phosphoinositide 3-phosphatase and tensin homolog 2  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-02-22 Tpte2  transmembrane phosphoinositide 3-phosphatase and tensin homolog 2  Tslpr  thymic stromal-derived lymphopoietin, receptor  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2004-09-10 Tslpr  thymic stromal-derived lymphopoietin, receptor      Symbol and Name status set to approved 1299863 APPROVED
2002-08-07 Tslpr  thymic stromal-derived lymphopoietin, receptor      Symbol and Name status set to provisional 70820 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_expression expressed ubiquitously 70482
gene_physical_interaction receptor subunit, forms heterodimeric complex with IL-7 receptor alpha chain to form thymic stromal derived lymphopoietin receptor 70482
gene_process involved in B-cell and T-cell function 70482