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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 RFX 2 3
  • Trans-Acting Regulatory Factor 1 2 3
  • Transcription Factor RFX1 3 4
  • Regulatory Factor X 1 3 4
  • RFX 3 4
  • EF-C 4
  • EFC 3

External Ids for RFX1 Gene

Previous GeneCards Identifiers for RFX1 Gene

  • GC19M014429
  • GC19M013917
  • GC19M014072
  • GC19M013643

Summaries for RFX1 Gene

Entrez Gene Summary for RFX1 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 X2, X3, X4, and X5. It is a transcriptional activator that can bind DNA as a monomer or as a heterodimer with RFX family members X2, X3, and X5, but not with X4. This protein binds to the X-boxes of MHC class II genes and is essential for their expression. Also, it can bind to an inverted repeat that is required for expression of hepatitis B virus genes. [provided by RefSeq, Jul 2008]

GeneCards Summary for RFX1 Gene

RFX1 (Regulatory Factor X1) is a Protein Coding gene. Diseases associated with RFX1 include hepatitis b and mhc class ii deficiency. GO annotations related to this gene include RNA polymerase II core promoter proximal region sequence-specific DNA binding and transcription factor activity, RNA polymerase II distal enhancer sequence-specific binding. An important paralog of this gene is RFX5.

UniProtKB/Swiss-Prot 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

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for RFX1 Gene

Genomics for RFX1 Gene

Regulatory Elements for RFX1 Gene

Promoters for RFX1 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters

ENSRs around RFX1 on UCSC Golden Path with GeneCards custom track

Genomic Location for RFX1 Gene

Chromosome:
19
Start:
13,961,530 bp from pter
End:
14,007,514 bp from pter
Size:
45,985 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 StructureGene Density

RefSeq DNA sequence for RFX1 Gene

Proteins for RFX1 Gene

  • 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

Proteomics data for RFX1 Gene at MOPED

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

Protein Domains for RFX1 Gene

Suggested Antigen Peptide Sequences for RFX1 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

P22670

UniProtKB/Swiss-Prot:

RFX1_HUMAN :
  • Contains 1 RFX-type winged-helix DNA-binding domain.
  • Belongs to the RFX family.
Domain:
  • Contains 1 RFX-type winged-helix DNA-binding domain.
Family:
  • Belongs to the RFX family.
genes like me logo Genes that share domains with RFX1: view

Function for RFX1 Gene

Molecular function for RFX1 Gene

GENATLAS Biochemistry:
transactivating DNA binding regulator 1,involved in MHC class II expression,binding the MHC promoter box X
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.
genes like me logo Genes that share phenotypes with RFX1: view

Animal Model Products

  • Taconic Biosciences Mouse Models for RFX1

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

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

Localization for RFX1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for RFX1 Gene

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for RFX1 Gene COMPARTMENTS Subcellular localization image for RFX1 gene
Compartment Confidence
nucleus 5
cytosol 2
cytoskeleton 1

No data available for Gene Ontology (GO) - Cellular Components for RFX1 Gene

Pathways & Interactions for RFX1 Gene

SuperPathways for RFX1 Gene

No Data Available

SIGNOR curated interactions for RFX1 Gene

Activates:

Gene Ontology (GO) - Biological Process for RFX1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006355 regulation of transcription, DNA-templated IEA --
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

(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

Unigene Clusters for RFX1 Gene

Regulatory factor X, 1 (influences HLA class II expression):
Representative Sequences:

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
ECgene alternative splicing isoforms for
RFX1

Expression for RFX1 Gene

mRNA expression in normal human tissues 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, PaxDb, MOPED, and MaxQB for RFX1 Gene



SOURCE GeneReport for Unigene cluster for RFX1 Gene Hs.655215

genes like me logo Genes that share expression patterns with RFX1: view

Protein tissue co-expression partners for RFX1 Gene

- Elite partner

Primer Products

In Situ Assay Products

No data available for mRNA differential expression in normal tissues and mRNA Expression by UniProt/SwissProt 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
dog
(Canis familiaris)
Mammalia RFX1 35
  • 91.09 (n)
  • 95.89 (a)
RFX1 36
  • 96 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Rfx1 35
  • 87.66 (n)
  • 93.12 (a)
Rfx1 16
Rfx1 36
  • 93 (a)
OneToOne
chimpanzee
(Pan troglodytes)
Mammalia RFX1 35
  • 99.63 (n)
  • 99.9 (a)
RFX1 36
  • 100 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Rfx1 35
  • 87.13 (n)
  • 93.57 (a)
cow
(Bos Taurus)
Mammalia RFX1 36
  • 66 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia RFX1 36
  • 88 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia RFX1 36
  • 65 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia RFX1 36
  • 80 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia rfx1 35
  • 73.93 (n)
  • 77.21 (a)
zebrafish
(Danio rerio)
Actinopterygii rfx1a 35
  • 70.45 (n)
  • 74.9 (a)
rfx1a 36
  • 66 (a)
OneToMany
rfx1b 36
  • 63 (a)
OneToMany
fruit fly
(Drosophila melanogaster)
Insecta Rfx 37
  • 53 (a)
Rfx 36
  • 33 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea -- 36
  • 44 (a)
OneToMany
Species with no ortholog for RFX1:
  • 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)

Paralogs for RFX1 Gene

Paralogs for RFX1 Gene

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

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

Variants for RFX1 Gene

Sequence variations from dbSNP and Humsavar for RFX1 Gene

SNP ID Clin Chr 19 pos Sequence Context AA Info Type
rs2305780 - 13,972,949(-) GCTCC(A/G)CCAGC intron-variant, reference, missense
rs31602 -- 13,982,786(-) TGGAC(A/G)AAGTA intron-variant
rs31603 -- 13,972,425(-) cctga(A/G)gtcag intron-variant
rs31604 -- 13,969,680(-) TCACA(C/T)GTGAC intron-variant
rs1054762 -- 13,968,599(-) GACAT(C/G/T)AGCGC reference, synonymous-codon

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

Variant ID Type Subtype PubMed ID
dgv3738n71 CNV Loss 21882294
nsv911102 CNV Loss 21882294
dgv3739n71 CNV Loss 21882294
dgv3740n71 CNV Loss 21882294
dgv3741n71 CNV Loss 21882294
nsv828451 CNV Loss 20364138
dgv3742n71 CNV Loss 21882294
nsv820186 CNV Loss 19587683
dgv3743n71 CNV Loss 21882294
nsv833761 CNV Loss 17160897

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)

Relevant External Links for RFX1 Gene

HapMap Linkage Disequilibrium report
RFX1

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

Disorders for RFX1 Gene

MalaCards: The human disease database

(3) MalaCards diseases for RFX1 Gene - From: DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
hepatitis b
  • chronic hepatitis b
mhc class ii deficiency
  • severe combined immunodeficiency
bare lymphocyte syndrome, type ii, complementation group c
  • bare lymphocyte syndrome, type ii, complementation group e
- 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

Relevant External Links for RFX1

Human Genome Epidemiology (HuGE) Navigator
RFX1
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
RFX1
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. 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 Dev. 1990) 3 4 23 67
  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. (Mol. Cell. Biol. 1994) 2 3 23
  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
  4. Regulation of FGF1 gene promoter through transcription factor RFX1. (PMID: 20189986) Hsu Y.C. … Chiu I.M. (J. Biol. Chem. 2010) 3 23
  5. Epigenetics and SLE: RFX1 downregulation causes CD11a and CD70 overexpression by altering epigenetic modifications in lupus CD4+ T cells. (PMID: 20223637) Zhao M. … Lu Q. (J. Autoimmun. 2010) 3 23

Products for RFX1 Gene

Sources for RFX1 Gene

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