RFX1 Gene (Protein Coding)

Regulatory Factor X1

GC19M013961
GIFtS:
38
This gene encodes a member of the regulatory factor X (RFX) family of transcription factors, which are characterized by a winged-helix DNA-binding domain. The encoded transcription factor contains an N-terminal activation domain and a C-terminal repression domain, and may activate or repress target gene expression depending on cellular context. This transcription factor has bee... See more...

Aliases for RFX1 Gene

Aliases for RFX1 Gene

  • Regulatory Factor X1 2 3 5
  • Enhancer Factor C 2 3 4
  • Regulatory Factor X, 1 (Influences HLA Class II Expression) 2 3
  • MHC Class II Regulatory Factor RFX1 3 4
  • MHC Class II Regulatory Factor RFX 2 3
  • Trans-Acting Regulatory Factor 1 2 3
  • Transcription Factor RFX1 3 4
  • RFX 3 4
  • Regulatory Factor X 1 4
  • EF-C 4
  • EFC 3

External Ids for RFX1 Gene

Previous GeneCards Identifiers for RFX1 Gene

  • GC19M014429
  • GC19M013917
  • GC19M013933
  • GC19M014072
  • GC19M013643

Summaries for RFX1 Gene

Entrez Gene Summary for RFX1 Gene

  • This gene encodes a member of the regulatory factor X (RFX) family of transcription factors, which are characterized by a winged-helix DNA-binding domain. The encoded transcription factor contains an N-terminal activation domain and a C-terminal repression domain, and may activate or repress target gene expression depending on cellular context. This transcription factor has been shown to regulate a wide variety of genes involved in immunity and cancer, including the MHC class II genes and genes that may be involved in cancer progression. This gene exhibits altered expression in glioblastoma and the autoimmune disease systemic lupus erythematosis (SLE). [provided by RefSeq, Jul 2016]

GeneCards Summary for RFX1 Gene

RFX1 (Regulatory Factor X1) is a Protein Coding gene. Diseases associated with RFX1 include Bare Lymphocyte Syndrome, Type Ii. Gene Ontology (GO) annotations related to this gene include RNA polymerase II proximal promoter sequence-specific DNA binding and transcription factor activity, RNA polymerase II distal enhancer sequence-specific binding. An important paralog of this gene is RFX3.

UniProtKB/Swiss-Prot Summary for RFX1 Gene

  • Regulatory factor essential for MHC class II genes expression. Binds to the X boxes of MHC class II genes. Also binds to an inverted repeat (ENH1) required for hepatitis B virus genes expression and to the most upstream element (alpha) of the RPL30 promoter.

Gene Wiki entry for RFX1 Gene

Additional gene information for RFX1 Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for RFX1 Gene

Genomics for RFX1 Gene

GeneHancer (GH) Regulatory Elements for RFX1 Gene

Promoters and enhancers for RFX1 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 RFX1 on UCSC Golden Path with GeneCards custom track

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for RFX1

Top Transcription factor binding sites by QIAGEN in the RFX1 gene promoter:
  • CBF-A
  • CBF-C
  • E2F
  • E2F-1
  • E2F-2
  • E2F-3a
  • E2F-4
  • E2F-5
  • HOXA5

Genomic Locations for RFX1 Gene

Genomic Locations for RFX1 Gene
chr19:13,961,530-14,007,514
(GRCh38/hg38)
Size:
45,985 bases
Orientation:
Minus strand
chr19:14,072,342-14,117,851
(GRCh37/hg19)
Size:
45,510 bases
Orientation:
Minus strand

Genomic View for RFX1 Gene

Genes around RFX1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
RFX1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for RFX1 Gene
GeneLoc Logo Genomic Neighborhood • Exon Structure • Gene Density

RefSeq DNA sequence for RFX1 Gene

Proteins for RFX1 Gene

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  3. Assay

  • Protein details for RFX1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    P22670-RFX1_HUMAN
    Recommended name:
    MHC class II regulatory factor RFX1
    Protein Accession:
    P22670

    Protein attributes for RFX1 Gene

    Size:
    979 amino acids
    Molecular mass:
    104758 Da
    Quaternary structure:
    • Homodimer; binds DNA as a homodimer (PubMed:10706293). Heterodimer; heterodimerizes with RFX2 and RFX3 (PubMed:10330134).

    Three dimensional structures from OCA and Proteopedia for RFX1 Gene

neXtProt entry for RFX1 Gene

Protein Expression for RFX1 Gene

See protein expression from ProteomicsDB, MOPED, PaxDb, and MaxQB

Post-translational modifications for RFX1 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for RFX1 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for RFX1 Gene

Domains & Families for RFX1 Gene

Gene Families for RFX1 Gene

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

Protein Domains for RFX1 Gene

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

Suggested Antigen Peptide Sequences for RFX1 Gene

GenScript: Design optimal peptide antigens:
  • Transcription factor RFX1 (RFX1_HUMAN)

Graphical View of Domain Structure for InterPro Entry

P22670

UniProtKB/Swiss-Prot:

RFX1_HUMAN :
  • Belongs to the RFX family.
Family:
  • Belongs to the RFX family.
genes like me logo Genes that share domains with RFX1: view

Function for RFX1 Gene

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  2. CRISPR
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  6. Cell Line

Molecular function for RFX1 Gene

UniProtKB/Swiss-Prot Function:
Regulatory factor essential for MHC class II genes expression. Binds to the X boxes of MHC class II genes. Also binds to an inverted repeat (ENH1) required for hepatitis B virus genes expression and to the most upstream element (alpha) of the RPL30 promoter.
GENATLAS Biochemistry:
transactivating DNA binding regulator 1,involved in MHC class II expression,binding the MHC promoter box X

Phenotypes From GWAS Catalog for RFX1 Gene

Gene Ontology (GO) - Molecular Function for RFX1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000978 RNA polymerase II proximal promoter sequence-specific DNA binding IBA 21873635
GO:0000981 DNA-binding transcription factor activity, RNA polymerase II-specific NAS,TAS 19274049
GO:0003677 DNA binding IEA --
GO:0003700 DNA-binding transcription factor activity IBA 21873635
GO:0005515 protein binding IPI 16289097
genes like me logo Genes that share ontologies with RFX1: view
genes like me logo Genes that share phenotypes with RFX1: view

Animal Model Products

CRISPR Products

Transcription Factor Targets for RFX1 Gene

Selected GeneGlobe predicted Target genes for RFX1
Targeted motifs for RFX1 Gene
HOMER Transcription Factor Regulatory Elements motif RFX1
  • Consensus sequence: GGTTGCCATGGCAA Submotif: canonical Cell Type: NPC GEO ID: GSE16256

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for RFX1

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology and Animal Models for RFX1 Gene

Localization for RFX1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for RFX1 Gene

Nucleus.

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nucleoplasm (4)
  • Vesicles (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for RFX1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000790 nuclear chromatin ISA --
GO:0005634 nucleus IBA 21873635
GO:0005654 nucleoplasm IDA --
GO:0043231 intracellular membrane-bounded organelle IDA --
genes like me logo Genes that share ontologies with RFX1: view

No data available for Subcellular locations from COMPARTMENTS for RFX1 Gene

Pathways & Interactions for RFX1 Gene

PathCards logo

SuperPathways for RFX1 Gene

No Data Available

SIGNOR curated interactions for RFX1 Gene

Activates:
Inactivates:

Gene Ontology (GO) - Biological Process for RFX1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006355 regulation of transcription, DNA-templated IEA --
GO:0006357 regulation of transcription by RNA polymerase II IBA 21873635
GO:0006955 immune response TAS 1505960
genes like me logo Genes that share ontologies with RFX1: view

No data available for Pathways by source for RFX1 Gene

Drugs & Compounds for RFX1 Gene

Products:

  1. Drug

(1) Additional Compounds for RFX1 Gene - From: Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
genes like me logo Genes that share compounds with RFX1: view

Transcripts for RFX1 Gene

Products:

  1. CRISPR
  2. miRNA
  3. Inhibitory RNA
  4. Clone

mRNA/cDNA for RFX1 Gene

1 REFSEQ mRNAs :
7 NCBI additional mRNA sequence :
7 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 RFX1

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for RFX1 Gene

ExUns: 1a · 1b ^ 2 ^ 3 ^ 4 ^ 5 ^ 6 ^ 7 ^ 8a · 8b ^ 9a · 9b ^ 10 ^ 11
SP1:
SP2: -
SP3: - - -
SP4:

Relevant External Links for RFX1 Gene

GeneLoc Exon Structure for
RFX1

Expression for RFX1 Gene

Products:

  1. Primer
  2. Gene Expression Assay

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for RFX1 Gene

mRNA expression in normal human tissues for RFX1 Gene
mRNA expression by BioGPS for RFX1 GenemRNA expression by GTEx for RFX1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for RFX1 Gene

This gene is overexpressed in CD8 Tcells (11.6), Blymphocyte (8.2), and Placenta (6.7).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for RFX1 Gene



Protein tissue co-expression partners for RFX1 Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for RFX1

SOURCE GeneReport for Unigene cluster for RFX1 Gene:

Hs.655215

Evidence on tissue expression from TISSUES for RFX1 Gene

  • Liver(4.4)
  • Blood(2.1)
  • Nervous system(2)
genes like me logo Genes that share expression patterns with RFX1: view

No data available for mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for RFX1 Gene

Orthologs for RFX1 Gene

This gene was present in the common ancestor of animals.

Orthologs for RFX1 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
 Mammalia RFX1 31 30
  • 99.63 (n)
 OneToOne
dog
(Canis familiaris)
 Mammalia RFX1 31 30
  • 91.09 (n)
 OneToOne
oppossum
(Monodelphis domestica)
 Mammalia RFX1 31
  • 88 (a)
 OneToOne
mouse
(Mus musculus)
 Mammalia Rfx1 17 31 30
  • 87.66 (n)
rat
(Rattus norvegicus)
 Mammalia Rfx1 30
  • 87.13 (n)
cow
(Bos Taurus)
 Mammalia RFX1 31
  • 66 (a)
 OneToOne
platypus
(Ornithorhynchus anatinus)
 Mammalia RFX1 31
  • 65 (a)
 OneToOne
lizard
(Anolis carolinensis)
 Reptilia RFX1 31
  • 80 (a)
 OneToOne
tropical clawed frog
(Silurana tropicalis)
 Amphibia rfx1 30
  • 73.93 (n)
zebrafish
(Danio rerio)
 Actinopterygii rfx1a 31 30
  • 70.45 (n)
 OneToMany
rfx1b 31
  • 63 (a)
 OneToMany
fruit fly
(Drosophila melanogaster)
 Insecta Rfx 31 32
  • 33 (a)
 OneToMany
sea squirt
(Ciona savignyi)
 Ascidiacea -- 31
  • 44 (a)
 OneToMany
Species where no ortholog for RFX1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • 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)
  • chicken (Gallus gallus)
  • 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)
  • 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 RFX1 Gene

ENSEMBL:
Gene Tree for RFX1 (if available)
TreeFam:
Gene Tree for RFX1 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for RFX1: view image

Paralogs for RFX1 Gene

Paralogs for RFX1 Gene

(2) SIMAP similar genes for RFX1 Gene using alignment to 2 proteins:

  • RFX1_HUMAN
  • K7EIZ8_HUMAN
genes like me logo Genes that share paralogs with RFX1: view

Variants for RFX1 Gene

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  1. SNP Genotyping and Copy Number Assay

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for RFX1 Gene

SNP ID Clinical significance and condition Chr 19 pos Variation AA Info Type
rs766888168 Benign: Abnormality of neuronal migration 13,963,151(-) C/T MISSENSE_VARIANT
rs2305780 - p.Thr370Ala

Additional dbSNP identifiers (rs#s) for RFX1 Gene

Structural Variations from Database of Genomic Variants (DGV) for RFX1 Gene

Variant ID Type Subtype PubMed ID
nsv1134755 CNV deletion 24896259
nsv820186 CNV loss 19587683
nsv828451 CNV loss 20364138
nsv833761 CNV loss 17160897
nsv953979 CNV deletion 24416366

Variation tolerance for RFX1 Gene

Residual Variation Intolerance Score: 23.3% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 4.70; 66.15% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for RFX1 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
RFX1

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for RFX1 Gene

Disorders for RFX1 Gene

MalaCards: The human disease database

(1) MalaCards diseases for RFX1 Gene - From: Novoseek

Disorder Aliases PubMed IDs
bare lymphocyte syndrome, type ii
  • bls, type ii
- elite association - COSMIC cancer census association via MalaCards
Search RFX1 in MalaCards View complete list of genes associated with diseases

Genatlas disease for RFX1 Gene

immunodeficiency,severe combined with defective expression of MHC class II gene

Additional Disease Information for RFX1

Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with RFX1: view

No data available for UniProtKB/Swiss-Prot for RFX1 Gene

Publications for RFX1 Gene

  1. Structure of the winged-helix protein hRFX1 reveals a new mode of DNA binding. (PMID: 10706293) Gajiwala KS … Burley SK (Nature 2000) 3 4 23 54
  2. RFX1, a transactivator of hepatitis B virus enhancer I, belongs to a novel family of homodimeric and heterodimeric DNA-binding proteins. (PMID: 8289803) Reith W … Mach B (Molecular and cellular biology 1994) 2 3 23 54
  3. 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 54
  4. The DNA-binding defect observed in major histocompatibility complex class II regulatory mutants concerns only one member of a family of complexes binding to the X boxes of class II promoters. (PMID: 1508204) Herrero Sanchez C … Mach B (Molecular and cellular biology 1992) 3 4 23 54
  5. MHC class II regulatory factor RFX has a novel DNA-binding domain and a functionally independent dimerization domain. (PMID: 2253877) Reith W … Mach B (Genes & development 1990) 3 4 23 54

ExternalLinks

View latest publications for RFX1 gene in Mastermind

Products for RFX1 Gene

Sources for RFX1 Gene