Free for academic non-profit institutions. Other users need a Commercial license

Aliases for CRLF3 Gene

Aliases for CRLF3 Gene

  • Cytokine Receptor Like Factor 3 2 3 5
  • Type I Cytokine Receptor-Like Factor P48 3 4
  • Cytokine Receptor-Related Protein 4 3 4
  • Cytokine Receptor-Like Molecule 9 3 4
  • Cytokine Receptor-Like Factor 3 2 3
  • CREME-9 3 4
  • CREME9 3 4
  • CYTOR4 3 4
  • CRLM9 3 4
  • P48.2 3
  • FRWS 3
  • P48 4

External Ids for CRLF3 Gene

Previous GeneCards Identifiers for CRLF3 Gene

  • GC17U990197
  • GC17M031015
  • GC17M028961
  • GC17M029255
  • GC17M026133
  • GC17M029109
  • GC17M025319
  • GC17M029096

Summaries for CRLF3 Gene

Entrez Gene Summary for CRLF3 Gene

  • This gene encodes a cytokine receptor-like factor that may negatively regulate cell cycle progression at the G0/G1 phase. Studies of the related rat protein suggest that it may regulate neuronal morphology and synaptic vesicle biogenesis. This gene is one of several genes located in the neurofibromatosis type I tumor suppressor region on the q arm of chromosome 17, a region that is subject to microdeletions, duplications, chromosomal breaks and rearrangements. Alternative splicing of this gene results in multiple transcript variants. Related pseudogenes have been identified on chromosomes 2 and 5. [provided by RefSeq, Aug 2012]

GeneCards Summary for CRLF3 Gene

CRLF3 (Cytokine Receptor Like Factor 3) is a Protein Coding gene.

UniProtKB/Swiss-Prot for CRLF3 Gene

  • May play a role in the negative regulation of cell cycle progression.

Gene Wiki entry for CRLF3 Gene

Additional gene information for CRLF3 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for CRLF3 Gene

Genomics for CRLF3 Gene

Regulatory Elements for CRLF3 Gene

Enhancers for CRLF3 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH17H030806 1.3 FANTOM5 Ensembl ENCODE 9.6 +15.9 15858 5.4 HDGF CTCF RB1 BATF ZNF121 POLR2A ATF7 ETV6 RUNX3 ZNF687 SUZ12P1 ATAD5 RPS17P3 CRLF3 LOC101927093 LRRC37BP1 ENSG00000276250
GH17H030905 1.2 ENCODE 10.1 -81.7 -81748 2.1 MLX ZFP64 DMAP1 YY1 SLC30A9 ZNF143 SP3 NFYC ZC3H11A SSRP1 UTP6 SUZ12P1 NF1 GOSR1 NSRP1 ENSG00000266490 RNF135 ATAD5 ENSG00000264456 LRRC37BP1
GH17H030727 1.2 Ensembl ENCODE 7 +95.9 95938 2.2 HDGF PKNOX1 ATF1 TCF12 ATF7 RUNX3 SP5 YY2 REST MBD2 SUZ12P1 ENSG00000266490 LOC105371722 CRLF3 LOC101927093 RAB11FIP4 ENSG00000265443 ENSG00000263603
GH17H030715 1.3 Ensembl ENCODE dbSUPER 5.9 +109.5 109476 0.6 BCOR HDGF CTCF TFAP4 FOXA2 BACH1 ARID4B ZMYM3 SIN3A RAD21 LRRC37BP1 ENSG00000266490 CRLF3 GC17P030711 ENSG00000279337
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around CRLF3 on UCSC Golden Path with GeneCards custom track

Promoters for CRLF3 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000093035 876 2601 HDGF PKNOX1 ARNT ARID4B SIN3A FEZF1 ZNF2 ZNF207 ZNF143 SP3

Genomic Locations for CRLF3 Gene

Genomic Locations for CRLF3 Gene
55,389 bases
Minus strand

Genomic View for CRLF3 Gene

Genes around CRLF3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
CRLF3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for CRLF3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for CRLF3 Gene

Proteins for CRLF3 Gene

  • Protein details for CRLF3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Cytokine receptor-like factor 3
    Protein Accession:
    Secondary Accessions:
    • A6NJF3
    • B2R8C3
    • Q2MLY7
    • Q9UNI3
    • Q9Y6M8

    Protein attributes for CRLF3 Gene

    442 amino acids
    Molecular mass:
    49766 Da
    Quaternary structure:
    No Data Available

    Alternative splice isoforms for CRLF3 Gene


neXtProt entry for CRLF3 Gene

Post-translational modifications for CRLF3 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for CRLF3 Gene

No data available for DME Specific Peptides for CRLF3 Gene

Domains & Families for CRLF3 Gene

Gene Families for CRLF3 Gene

Human Protein Atlas (HPA):
  • Plasma proteins
  • Predicted intracellular proteins

Protein Domains for CRLF3 Gene


Graphical View of Domain Structure for InterPro Entry



  • Belongs to the cytokine receptor-like factor 3 family.
  • Belongs to the cytokine receptor-like factor 3 family.
genes like me logo Genes that share domains with CRLF3: view

Function for CRLF3 Gene

Molecular function for CRLF3 Gene

UniProtKB/Swiss-Prot Function:
May play a role in the negative regulation of cell cycle progression.

Phenotypes From GWAS Catalog for CRLF3 Gene

Gene Ontology (GO) - Molecular Function for CRLF3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 25416956
GO:0042802 identical protein binding IPI 25416956
genes like me logo Genes that share ontologies with CRLF3: view
genes like me logo Genes that share phenotypes with CRLF3: view

Animal Models for CRLF3 Gene

MGI Knock Outs for CRLF3:

miRNA for CRLF3 Gene

miRTarBase miRNAs that target CRLF3

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for CRLF3 Gene

Localization for CRLF3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for CRLF3 Gene

Cytoplasm. Note=The EGFP- and MYC-tagged protein has been shown to be cytoplasmic. {ECO:0000269 PubMed:19427400}.

Subcellular locations from

Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for CRLF3 gene
Compartment Confidence
plasma membrane 5
cytosol 5
nucleus 2
extracellular 1
cytoskeleton 1
peroxisome 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (3)
  • Plasma membrane (3)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for CRLF3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm IDA,IEA 19427400
GO:0005829 cytosol IDA --
GO:0005886 plasma membrane IDA --
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
genes like me logo Genes that share ontologies with CRLF3: view

Pathways & Interactions for CRLF3 Gene

SuperPathways for CRLF3 Gene

No Data Available

Gene Ontology (GO) - Biological Process for CRLF3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000082 G1/S transition of mitotic cell cycle IMP 19427400
GO:0030308 negative regulation of cell growth IDA 19427400
GO:0045893 positive regulation of transcription, DNA-templated IDA 19427400
GO:0045944 positive regulation of transcription from RNA polymerase II promoter IDA 19427400
GO:0046427 positive regulation of JAK-STAT cascade IDA 19427400
genes like me logo Genes that share ontologies with CRLF3: view

No data available for Pathways by source and SIGNOR curated interactions for CRLF3 Gene

Drugs & Compounds for CRLF3 Gene

No Compound Related Data Available

Transcripts for CRLF3 Gene

Unigene Clusters for CRLF3 Gene

Cytokine receptor-like factor 3:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for CRLF3 Gene

No ASD Table

Relevant External Links for CRLF3 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for CRLF3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for CRLF3 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for CRLF3 Gene

This gene is overexpressed in Whole Blood (x5.7).

Protein differential expression in normal tissues from HIPED for CRLF3 Gene

This gene is overexpressed in Lymph node (16.3), Peripheral blood mononuclear cells (15.4), and Tlymphocyte (6.9).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for CRLF3 Gene

Protein tissue co-expression partners for CRLF3 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of CRLF3 Gene:


SOURCE GeneReport for Unigene cluster for CRLF3 Gene:


mRNA Expression by UniProt/SwissProt for CRLF3 Gene:

Tissue specificity: Expressed in several embryonic and adult tissues, including adult and fetal brain, liver, spleen and pancreas. Expressed in adult, but not fetal kidney. Expressed in skin and squamous cell carcinoma (SCC) and in several other cancer types. Also detected in lesion actinic keratosis (AK).

Evidence on tissue expression from TISSUES for CRLF3 Gene

  • Liver(4.1)
genes like me logo Genes that share expression patterns with CRLF3: view

No data available for Phenotype-based relationships between genes and organs from Gene ORGANizer for CRLF3 Gene

Orthologs for CRLF3 Gene

This gene was present in the common ancestor of chordates.

Orthologs for CRLF3 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia CRLF3 33 34
  • 99.62 (n)
(Canis familiaris)
Mammalia CRLF3 33 34
  • 92.43 (n)
(Bos Taurus)
Mammalia CRLF3 33 34
  • 91.25 (n)
(Monodelphis domestica)
Mammalia CRLF3 34
  • 91 (a)
(Mus musculus)
Mammalia Crlf3 33 16 34
  • 87.56 (n)
(Rattus norvegicus)
Mammalia Crlf3 33
  • 86.95 (n)
(Ornithorhynchus anatinus)
Mammalia CRLF3 34
  • 86 (a)
(Gallus gallus)
Aves CRLF3 33 34
  • 78.4 (n)
(Anolis carolinensis)
Reptilia -- 34
  • 80 (a)
-- 34
  • 79 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia crlf3 33
  • 67.21 (n)
Str.2975 33
African clawed frog
(Xenopus laevis)
Amphibia crlf3-prov 33
(Danio rerio)
Actinopterygii crlf3 33 34
  • 63.93 (n)
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 29 (a)
Species where no ortholog for CRLF3 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for CRLF3 Gene

Gene Tree for CRLF3 (if available)
Gene Tree for CRLF3 (if available)

Paralogs for CRLF3 Gene Pseudogenes for CRLF3 Gene

genes like me logo Genes that share paralogs with CRLF3: view

No data available for Paralogs for CRLF3 Gene

Variants for CRLF3 Gene

Sequence variations from dbSNP and Humsavar for CRLF3 Gene

SNP ID Clin Chr 17 pos Sequence Context AA Info Type
rs1000000348 -- 30,791,795(+) ACAAG(C/T)GTGAG intron-variant, nc-transcript-variant
rs1000078089 -- 30,810,286(+) TGAGC(A/C)CATTG intron-variant, upstream-variant-2KB
rs1000213657 -- 30,801,651(+) GTCTC(A/G)AACTC intron-variant
rs1000219823 -- 30,791,927(+) CTGCA(A/G)CCTCT intron-variant, nc-transcript-variant
rs1000289677 -- 30,807,929(+) AATTT(A/C/T)TGTAT intron-variant

Structural Variations from Database of Genomic Variants (DGV) for CRLF3 Gene

Variant ID Type Subtype PubMed ID
nsv833412 CNV loss 17160897
nsv833411 CNV loss 17160897
nsv513468 CNV insertion 21212237
nsv457720 CNV loss 19166990
esv3892992 CNV loss 25118596
esv3640356 CNV gain 21293372
esv3363883 CNV duplication 20981092
esv2715813 CNV deletion 23290073
esv2661289 CNV deletion 23128226
esv2596745 CNV insertion 19546169

Variation tolerance for CRLF3 Gene

Residual Variation Intolerance Score: 73.1% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 6.04; 75.10% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for CRLF3 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for CRLF3 Gene

Disorders for CRLF3 Gene

Relevant External Links for CRLF3

Genetic Association Database (GAD)
Human Genome Epidemiology (HuGE) Navigator
Atlas of Genetics and Cytogenetics in Oncology and Haematology:

No disorders were found for CRLF3 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for CRLF3 Gene

Publications for CRLF3 Gene

  1. The role of height-associated loci identified in genome wide association studies in the determination of pediatric stature. (PMID: 20546612) Zhao J … Grant SF (BMC medical genetics 2010) 3 45 60
  2. Evaluation of candidate stromal epithelial cross-talk genes identifies association between risk of serous ovarian cancer and TERT, a cancer susceptibility "hot-spot". (PMID: 20628624) Johnatty SE … Australian Cancer Study (Ovarian Cancer) (PLoS genetics 2010) 3 45 60
  3. RNF135 mutations are not present in patients with Sotos syndrome-like features. (PMID: 19291764) Visser R … Losekoot M (American journal of medical genetics. Part A 2009) 3 45 60
  4. Cloning and characterization of a novel intracellular protein p48.2 that negatively regulates cell cycle progression. (PMID: 19427400) Yang F … Liu L (The international journal of biochemistry & cell biology 2009) 3 4 60
  5. Many sequence variants affecting diversity of adult human height. (PMID: 18391951) Gudbjartsson DF … Stefansson K (Nature genetics 2008) 3 45 60

Products for CRLF3 Gene

Sources for CRLF3 Gene

Loading form....