This gene is a member of the regulatory factor X gene family, which encodes transcription factors that contain a highly-conserved winged helix DNA binding domain. The protein encoded by this gene is structurally related to regulatory factors X1, X3, X4, and X5. It is a transcriptional activator that can bind DNA as a monomer or as a heterodimer with other RFX family members. Th... See more...

Aliases for RFX2 Gene

Aliases for RFX2 Gene

  • Regulatory Factor X2 2 3 5
  • Regulatory Factor X, 2 (Influences HLA Class II Expression) 2 3
  • HLA Class II Regulatory Factor RFX2 2 3
  • Trans-Acting Regulatory Factor 2 2 3
  • DNA-Binding Protein RFX2 3 4
  • Regulatory Factor X 2 3 4
  • DNA Binding Protein RFX2 2
  • FLJ14226 2
  • RFX2 5

External Ids for RFX2 Gene

Previous GeneCards Identifiers for RFX2 Gene

  • GC19M006085
  • GC19M005933
  • GC19M005944
  • GC19M005752

Summaries for RFX2 Gene

Entrez Gene Summary for RFX2 Gene

  • This gene is a member of the regulatory factor X gene family, which encodes transcription factors that contain a highly-conserved winged helix DNA binding domain. The protein encoded by this gene is structurally related to regulatory factors X1, X3, X4, and X5. It is a transcriptional activator that can bind DNA as a monomer or as a heterodimer with other RFX family members. This protein can bind to cis elements in the promoter of the IL-5 receptor alpha gene. Two transcript variants encoding different isoforms have been described for this gene, and both variants utilize alternative polyadenylation sites. [provided by RefSeq, Jul 2008]

GeneCards Summary for RFX2 Gene

RFX2 (Regulatory Factor X2) is a Protein Coding gene. Diseases associated with RFX2 include Amyotrophic Lateral Sclerosis 3 and Cellular Ependymoma. Gene Ontology (GO) annotations related to this gene include DNA-binding transcription factor activity and RNA polymerase II proximal promoter sequence-specific DNA binding. An important paralog of this gene is RFX3.

UniProtKB/Swiss-Prot Summary for RFX2 Gene

  • Transcription factor that acts as a key regulator of spermatogenesis. Acts by regulating expression of genes required for the haploid phase during spermiogenesis, such as genes required for cilium assembly and function (By similarity). Recognizes and binds the X-box, a regulatory motif with DNA sequence 5'-GTNRCC(0-3N)RGYAAC-3' present on promoters (PubMed:10330134). Probably activates transcription of the testis-specific histone gene H1-6 (By similarity).

Gene Wiki entry for RFX2 Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for RFX2 Gene

Genomics for RFX2 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for RFX2 Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around RFX2 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for RFX2

Top Transcription factor binding sites by QIAGEN in the RFX2 gene promoter:
  • AhR
  • Arnt
  • E2F
  • E2F-1
  • MIF-1
  • p300

Genomic Locations for RFX2 Gene

Genomic Locations for RFX2 Gene
chr19:5,993,164-6,199,572
(GRCh38/hg38)
Size:
206,409 bases
Orientation:
Minus strand
chr19:5,993,175-6,199,583
(GRCh37/hg19)
Size:
206,409 bases
Orientation:
Minus strand

Genomic View for RFX2 Gene

Genes around RFX2 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
RFX2 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for RFX2 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for RFX2 Gene

Proteins for RFX2 Gene

  • Protein details for RFX2 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    P48378-RFX2_HUMAN
    Recommended name:
    DNA-binding protein RFX2
    Protein Accession:
    P48378
    Secondary Accessions:
    • A8K581
    • B3KNC4
    • Q6IQ44
    • Q8SNA2

    Protein attributes for RFX2 Gene

    Size:
    723 amino acids
    Molecular mass:
    79987 Da
    Quaternary structure:
    • Homodimer; probably only forms homodimers in testis (By similarity). Heterodimer; heterodimerizes with RFX1 and RFX3 (PubMed:10330134).
    SequenceCaution:
    • Sequence=BAG51286.1; Type=Erroneous initiation; Evidence={ECO:0000305};

    Alternative splice isoforms for RFX2 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for RFX2 Gene

Post-translational modifications for RFX2 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for RFX2 Gene

Domains & Families for RFX2 Gene

Gene Families for RFX2 Gene

HGNC:
Human Protein Atlas (HPA):
  • Predicted intracellular proteins
  • Transcription factors

Protein Domains for RFX2 Gene

InterPro:
Blocks:
  • DNA-binding RFX
  • RFX1 transcription activation region
ProtoNet:

Suggested Antigen Peptide Sequences for RFX2 Gene

GenScript: Design optimal peptide antigens:
  • RFX2_HUMAN, [AA 620-723] (Q75MR3_HUMAN)
  • Regulatory factor X 2 (RFX2_HUMAN)

Graphical View of Domain Structure for InterPro Entry

P48378

UniProtKB/Swiss-Prot:

RFX2_HUMAN :
  • Belongs to the RFX family.
Family:
  • Belongs to the RFX family.
genes like me logo Genes that share domains with RFX2: view

Function for RFX2 Gene

Molecular function for RFX2 Gene

UniProtKB/Swiss-Prot Function:
Transcription factor that acts as a key regulator of spermatogenesis. Acts by regulating expression of genes required for the haploid phase during spermiogenesis, such as genes required for cilium assembly and function (By similarity). Recognizes and binds the X-box, a regulatory motif with DNA sequence 5'-GTNRCC(0-3N)RGYAAC-3' present on promoters (PubMed:10330134). Probably activates transcription of the testis-specific histone gene H1-6 (By similarity).
GENATLAS Biochemistry:
transactivating DNA binding regulator 2,involved in MHC class II expression,binding the MHC promoter box X

Phenotypes From GWAS Catalog for RFX2 Gene

Gene Ontology (GO) - Molecular Function for RFX2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000977 RNA polymerase II regulatory region sequence-specific DNA binding IEA --
GO:0000978 RNA polymerase II proximal promoter sequence-specific DNA binding ISS --
GO:0000981 DNA-binding transcription factor activity, RNA polymerase II-specific ISM 19274049
GO:0001228 DNA-binding transcription activator activity, RNA polymerase II-specific IEA --
GO:0003677 DNA binding IEA,TAS 8289803
genes like me logo Genes that share ontologies with RFX2: view
genes like me logo Genes that share phenotypes with RFX2: view

Animal Model Products

CRISPR Products

Targeted motifs for RFX2 Gene
HOMER Transcription Factor Regulatory Elements motif RFX2
  • Consensus sequence: GTTGCCATGGCAACM Submotif: canonical Cell Type: LoVo GEO ID: GSE49402

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for RFX2

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models and Transcription Factor Targets for RFX2 Gene

Localization for RFX2 Gene

Subcellular locations from UniProtKB/Swiss-Prot for RFX2 Gene

Nucleus. Cytoplasm. Note=Mainly expressed in the nucleus and at lower level in cytoplasm. {ECO:0000250 UniProtKB:B2GV50}.

Subcellular locations from

COMPARTMENTS
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 RFX2 gene
Compartment Confidence
nucleus 5
cytoskeleton 2
cytosol 2
plasma membrane 1
extracellular 1
mitochondrion 1
endoplasmic reticulum 1
peroxisome 0

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (2)
  • Golgi apparatus (2)
  • Nucleoplasm (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for RFX2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000790 nuclear chromatin ISA --
GO:0005634 nucleus IEA,ISS --
GO:0005737 cytoplasm ISS --
genes like me logo Genes that share ontologies with RFX2: view

Pathways & Interactions for RFX2 Gene

PathCards logo

SuperPathways for RFX2 Gene

No Data Available

Gene Ontology (GO) - Biological Process for RFX2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001675 acrosome assembly ISS --
GO:0006355 regulation of transcription, DNA-templated IEA --
GO:0006357 regulation of transcription by RNA polymerase II ISS --
GO:0007283 spermatogenesis IEA --
GO:0007286 spermatid development ISS --
genes like me logo Genes that share ontologies with RFX2: view

No data available for Pathways by source and SIGNOR curated interactions for RFX2 Gene

Drugs & Compounds for RFX2 Gene

No Compound Related Data Available

Transcripts for RFX2 Gene

mRNA/cDNA for RFX2 Gene

2 REFSEQ mRNAs :
14 NCBI additional mRNA sequence :
24 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for RFX2

Alternative Splicing Database (ASD) splice patterns (SP) for RFX2 Gene

ExUns: 1a · 1b · 1c ^ 2 ^ 3 ^ 4 ^ 5a · 5b ^ 6 ^ 7 ^ 8 ^ 9a · 9b · 9c ^ 10a · 10b · 10c ^ 11 ^ 12 ^ 13a · 13b ^ 14 ^ 15 ^ 16 ^ 17 ^ 18 ^
SP1: - - - - -
SP2: - - -
SP3: - - - - -
SP4: - - - -
SP5: - -
SP6: - - - - -
SP7: - - - - - - - - -
SP8: - - - - -
SP9: - - - - - - -
SP10: - - - - - -
SP11:
SP12:
SP13: - - - - -
SP14: - - - - - - - - - - -
SP15:

ExUns: 19 ^ 20 ^ 21a · 21b · 21c
SP1:
SP2:
SP3:
SP4:
SP5:
SP6:
SP7:
SP8:
SP9:
SP10:
SP11:
SP12:
SP13:
SP14:
SP15:

Relevant External Links for RFX2 Gene

GeneLoc Exon Structure for
RFX2

Expression for RFX2 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for RFX2 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for RFX2 Gene

This gene is overexpressed in Testis (x6.9) and Whole Blood (x4.5).

Protein differential expression in normal tissues from HIPED for RFX2 Gene

This gene is overexpressed in Testis (68.6).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for RFX2 Gene



Protein tissue co-expression partners for RFX2 Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for RFX2

SOURCE GeneReport for Unigene cluster for RFX2 Gene:

Hs.465709

Evidence on tissue expression from TISSUES for RFX2 Gene

  • Nervous system(4.8)
  • Lung(2.2)
genes like me logo Genes that share expression patterns with RFX2: view

No data available for mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for RFX2 Gene

Orthologs for RFX2 Gene

This gene was present in the common ancestor of animals and fungi.

Orthologs for RFX2 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia RFX2 30 31
  • 99.27 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia RFX2 30 31
  • 90.07 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia RFX2 30 31
  • 89.47 (n)
OneToOne
Oppossum
(Monodelphis domestica)
Mammalia RFX2 31
  • 87 (a)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Rfx2 30
  • 83.77 (n)
Mouse
(Mus musculus)
Mammalia Rfx2 30 17 31
  • 83.59 (n)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia RFX2 31
  • 76 (a)
OneToOne
Chicken
(Gallus gallus)
Aves RFX2 30 31
  • 79.83 (n)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia rfx2 30
  • 72.21 (n)
Str.11047 30
African clawed frog
(Xenopus laevis)
Amphibia Xl.1771 30
Zebrafish
(Danio rerio)
Actinopterygii rfx2 30 31
  • 71.27 (n)
OneToOne
-- 30
Fruit Fly
(Drosophila melanogaster)
Insecta Rfx 31 32
  • 27 (a)
OneToMany
Worm
(Caenorhabditis elegans)
Secernentea daf-19 32
  • 33 (a)
Baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes RFX1 33
Sea Squirt
(Ciona savignyi)
Ascidiacea -- 31
  • 41 (a)
OneToMany
Species where no ortholog for RFX2 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • 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)
  • Green Algae (Chlamydomonas reinhardtii)
  • Honey Bee (Apis mellifera)
  • K. Lactis Yeast (Kluyveromyces lactis)
  • Lizard (Anolis carolinensis)
  • 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 Vase (Ciona intestinalis)
  • 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)

Evolution for RFX2 Gene

ENSEMBL:
Gene Tree for RFX2 (if available)
TreeFam:
Gene Tree for RFX2 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for RFX2: view image

Paralogs for RFX2 Gene

Paralogs for RFX2 Gene

(5) SIMAP similar genes for RFX2 Gene using alignment to 12 proteins:

  • RFX2_HUMAN
  • K7EIN5_HUMAN
  • K7EJD4_HUMAN
  • K7EJE4_HUMAN
  • K7ELD5_HUMAN
  • K7ELQ7_HUMAN
  • K7ENC9_HUMAN
  • K7EQA0_HUMAN
  • K7EQU2_HUMAN
  • K7EQY9_HUMAN
  • K7ES56_HUMAN
  • Q75MR3_HUMAN
genes like me logo Genes that share paralogs with RFX2: view

Variants for RFX2 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for RFX2 Gene

SNP ID Clinical significance and condition Chr 19 pos Variation AA Info Type
773898 Benign: not provided 6,047,440(-) C/T SYNONYMOUS_VARIANT
rs748493309 A breast cancer sample p.Glu110Lys
VAR_036530 A breast cancer sample p.Ala37Gly
rs17852566 - p.Arg610Gln
rs2288846 - p.Ala86Thr

Additional dbSNP identifiers (rs#s) for RFX2 Gene

Structural Variations from Database of Genomic Variants (DGV) for RFX2 Gene

Variant ID Type Subtype PubMed ID
esv2718057 CNV deletion 23290073
esv2718058 CNV deletion 23290073
esv3583213 CNV loss 25503493
nsv1140144 CNV insertion 24896259
nsv1142926 CNV tandem duplication 24896259
nsv978761 CNV duplication 23825009

Variation tolerance for RFX2 Gene

Residual Variation Intolerance Score: 26.5% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 8.08; 84.43% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for RFX2 Gene

Human Gene Mutation Database (HGMD)
RFX2
SNPedia medical, phenotypic, and genealogical associations of SNPs for
RFX2

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for RFX2 Gene

Disorders for RFX2 Gene

MalaCards: The human disease database

(6) MalaCards diseases for RFX2 Gene - From: DISEASES

Disorder Aliases PubMed IDs
amyotrophic lateral sclerosis 3
  • als3
cellular ependymoma
  • epithelial ependymoma
amyotrophic lateral sclerosis 1
  • als1
meckel syndrome, type 1
  • mks1
visceral heterotaxy
  • heterotaxia
- elite association - COSMIC cancer census association via MalaCards
Search RFX2 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for RFX2

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
genes like me logo Genes that share disorders with RFX2: view

No data available for UniProtKB/Swiss-Prot and Genatlas for RFX2 Gene

Publications for RFX2 Gene

  1. The genes for MHC class II regulatory factors RFX1 and RFX2 are located on the short arm of chromosome 19. (PMID: 1505960) Pugliatti L … Mach B (Genomics 1992) 2 3 23
  2. Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study. (PMID: 20628086) Bailey SD … DREAM investigators (Diabetes care 2010) 3 41
  3. A genome-wide meta-analysis identifies novel loci associated with schizophrenia and bipolar disorder. (PMID: 20889312) Wang KS … Aragam N (Schizophrenia research 2010) 3 41
  4. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4
  5. Dimeric RFX proteins contribute to the activity and lineage specificity of the interleukin-5 receptor alpha promoter through activation and repression domains. (PMID: 10330134) Iwama A … Sun Z (Molecular and cellular biology 1999) 3 4

Products for RFX2 Gene

Sources for RFX2 Gene