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, X2, X3, and X5. It has been shown to interact with itself as well as with regulatory factors X2 and X3, but it does not interact with ... See more...

Aliases for RFX4 Gene

Aliases for RFX4 Gene

  • Regulatory Factor X4 2 3 5
  • Regulatory Factor X, 4 (Influences HLA Class II Expression) 2 3
  • Testis Development Protein NYD-SP10 3 4
  • Transcription Factor RFX4 3 4
  • Winged-Helix Transcription Factor RFX4 3
  • Regulatory Factor X 4 4
  • NYD-SP10 3

External Ids for RFX4 Gene

Previous GeneCards Identifiers for RFX4 Gene

  • GC12P106105
  • GC12P106875
  • GC12P105497
  • GC12P105479
  • GC12P106976
  • GC12P104037

Summaries for RFX4 Gene

Entrez Gene Summary for RFX4 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, X2, X3, and X5. It has been shown to interact with itself as well as with regulatory factors X2 and X3, but it does not interact with regulatory factor X1. Alternative splicing results in multiple transcript variants. [provided by RefSeq, May 2011]

GeneCards Summary for RFX4 Gene

RFX4 (Regulatory Factor X4) is a Protein Coding gene. Diseases associated with RFX4 include Joubert Syndrome 16 and Joubert Syndrome 2. Among its related pathways are Transcriptional Regulatory Network in Embryonic Stem Cell. 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 RFX6.

UniProtKB/Swiss-Prot Summary for RFX4 Gene

  • Transcription factor that plays a role in early brain development. May activate transcription by interacting directly with the X-box. May activate transcription from CX3CL1 promoter through the X-box during brain development.

Gene Wiki entry for RFX4 Gene

Additional gene information for RFX4 Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for RFX4 Gene

Genomics for RFX4 Gene

GeneHancer (GH) Regulatory Elements for RFX4 Gene

Promoters and enhancers for RFX4 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH12J106581 Promoter/Enhancer 1.6 EPDnew FANTOM5 Ensembl ENCODE 523.3 +0.2 193 3.4 REST ZBTB26 EZH2 HDAC2 KLF9 YY1 SAFB ZNF335 CBX8 SCRT1 RFX4 RIC8B MTERF2 piR-36575-025 ENSG00000257545 LOC100287944
GH12J106684 Promoter 0.3 EPDnew 500.1 +101.8 101803 0.1 ENSG00000257711 LOC100505978 RFX4 ENSG00000257918 ENSG00000257545 LOC100287944
GH12J106586 Promoter/Enhancer 0.9 FANTOM5 Ensembl 19.6 +3.3 3294 0.8 GABPA EZH2 SIN3A CHD1 SUZ12 RBBP5 HNRNPLL SCRT2 RFX4 CRY1 RIC8B piR-36575-025 ENSG00000257545 LOC100287944
GH12J106417 Enhancer 1.1 UCNEbase Ensembl ENCODE 9.3 -164.4 -164407 2.6 JUND TEAD1 MAFF FOS MAFK CEBPB JUN FOSL2 BCL6 HMG20A TCP11L2 POLR3B RFX4 RF00017-1242 lnc-CKAP4-3
GH12J106672 Enhancer 0.9 UCNEbase ENCODE CraniofacialAtlas 10.7 +90.0 90016 1.8 SPI1 IKZF1 EZH2 RFX4 POLR3B ENSG00000260329 TMEM263 piR-57056 piR-55705-015 ENSG00000257545 LOC100287944
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around RFX4 on UCSC Golden Path with GeneCards custom track

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for RFX4

Top Transcription factor binding sites by QIAGEN in the RFX4 gene promoter:
  • Arnt
  • ITF-2
  • NF-1
  • Sox5
  • Spz1
  • Tal-1beta
  • USF-1
  • USF1

Genomic Locations for RFX4 Gene

Genomic Locations for RFX4 Gene
chr12:106,582,907-106,762,804
(GRCh38/hg38)
Size:
179,898 bases
Orientation:
Plus strand
chr12:106,976,685-107,156,582
(GRCh37/hg19)
Size:
179,898 bases
Orientation:
Plus strand

Genomic View for RFX4 Gene

Genes around RFX4 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
RFX4 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for RFX4 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for RFX4 Gene

Proteins for RFX4 Gene

  • Protein details for RFX4 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q33E94-RFX4_HUMAN
    Recommended name:
    Transcription factor RFX4
    Protein Accession:
    Q33E94
    Secondary Accessions:
    • A8K5Y0
    • B2RDW4
    • Q33DW6
    • Q33DW7
    • Q33E95
    • Q6YM53
    • Q8MHQ1
    • Q8NC78
    • Q8NDF9
    • Q8SNA1
    • Q96S80
    • Q9BXI0

    Protein attributes for RFX4 Gene

    Size:
    735 amino acids
    Molecular mass:
    83368 Da
    Quaternary structure:
    • Homodimer. Heterodimer with RFX2 and RFX3 (PubMed:11682486). Interacts with GPS2 (By similarity).
    SequenceCaution:
    • Sequence=BAB59001.1; Type=Miscellaneous discrepancy; Note=Probable intron retention.; Evidence={ECO:0000305}; Sequence=BAC11288.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305}; Sequence=BAE48237.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305}; Sequence=BAE48238.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305};

    Alternative splice isoforms for RFX4 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for RFX4 Gene

Post-translational modifications for RFX4 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for RFX4 Gene

Domains & Families for RFX4 Gene

Gene Families for RFX4 Gene

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

Protein Domains for RFX4 Gene

Blocks:
  • DNA-binding RFX
InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for RFX4 Gene

GenScript: Design optimal peptide antigens:
  • cDNA FLJ61497, highly similar to Homo sapiens regulatory factor X 4, transcript variant 2, mRNA (B4DZB7_HUMAN)
  • Testis development protein NYD-SP10 (RFX4_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q33E94

UniProtKB/Swiss-Prot:

RFX4_HUMAN :
  • Belongs to the RFX family.
Family:
  • Belongs to the RFX family.
genes like me logo Genes that share domains with RFX4: view

Function for RFX4 Gene

Molecular function for RFX4 Gene

UniProtKB/Swiss-Prot Function:
Transcription factor that plays a role in early brain development. May activate transcription by interacting directly with the X-box. May activate transcription from CX3CL1 promoter through the X-box during brain development.

Phenotypes From GWAS Catalog for RFX4 Gene

Gene Ontology (GO) - Molecular Function for RFX4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000978 RNA polymerase II proximal promoter sequence-specific DNA binding IDA 16893423
GO:0000981 DNA-binding transcription factor activity, RNA polymerase II-specific ISM 19274049
GO:0001228 DNA-binding transcription activator activity, RNA polymerase II-specific IDA 16893423
GO:0003677 DNA binding IEA --
GO:0003700 DNA-binding transcription factor activity IBA 21873635
genes like me logo Genes that share ontologies with RFX4: view
genes like me logo Genes that share phenotypes with RFX4: view

Animal Model Products

CRISPR Products

miRNA for RFX4 Gene

miRTarBase miRNAs that target RFX4

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for RFX4

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for RFX4 Gene

Localization for RFX4 Gene

Subcellular locations from UniProtKB/Swiss-Prot for RFX4 Gene

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 RFX4 gene
Compartment Confidence
nucleus 4
cytosol 2
plasma membrane 1
extracellular 1
cytoskeleton 1
mitochondrion 1
endoplasmic reticulum 1
golgi apparatus 1

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for RFX4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000790 nuclear chromatin ISA --
GO:0005634 nucleus IBA 21873635
genes like me logo Genes that share ontologies with RFX4: view

Pathways & Interactions for RFX4 Gene

PathCards logo

SuperPathways for RFX4 Gene

SuperPathway Contained pathways
1 Transcriptional Regulatory Network in Embryonic Stem Cell
-
genes like me logo Genes that share pathways with RFX4: view

Pathways by source for RFX4 Gene

1 Qiagen pathway for RFX4 Gene
  • Transcriptional Regulatory Network in Embryonic Stem Cell

SIGNOR curated interactions for RFX4 Gene

Activates:

Gene Ontology (GO) - Biological Process for RFX4 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:0021537 telencephalon development IEA --
GO:0021914 negative regulation of smoothened signaling pathway involved in ventral spinal cord patterning IBA 21873635
GO:0045944 positive regulation of transcription by RNA polymerase II IDA 16893423
genes like me logo Genes that share ontologies with RFX4: view

Drugs & Compounds for RFX4 Gene

No Compound Related Data Available

Transcripts for RFX4 Gene

mRNA/cDNA for RFX4 Gene

4 REFSEQ mRNAs :
17 NCBI additional mRNA sequence :
12 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 RFX4

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for RFX4 Gene

No ASD Table

Relevant External Links for RFX4 Gene

GeneLoc Exon Structure for
RFX4

Expression for RFX4 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for RFX4 Gene

mRNA differential expression in normal tissues according to GTEx for RFX4 Gene

This gene is overexpressed in Testis (x10.5), Brain - Caudate (basal ganglia) (x5.0), Brain - Nucleus accumbens (basal ganglia) (x4.7), and Brain - Amygdala (x4.3).

Protein differential expression in normal tissues from HIPED for RFX4 Gene

This gene is overexpressed in Testis (42.0) and Ovary (27.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for RFX4 Gene



Protein tissue co-expression partners for RFX4 Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for RFX4

SOURCE GeneReport for Unigene cluster for RFX4 Gene:

Hs.388827

mRNA Expression by UniProt/SwissProt for RFX4 Gene:

Q33E94-RFX4_HUMAN
Tissue specificity: Isoform 1: Expressed in brain and gliomas (at protein level). Isoform 2: Testis-specific (at protein level). Isoform 3: Testis-specific (at protein level). Isoform 3: Expressed at a higher level in adult testes and ejaculated spematozoa than in fetal testes. Isoform 4: Testis-specific.

Evidence on tissue expression from TISSUES for RFX4 Gene

  • Nervous system(4.7)
genes like me logo Genes that share expression patterns with RFX4: view

No data available for Phenotype-based relationships between genes and organs from Gene ORGANizer for RFX4 Gene

Orthologs for RFX4 Gene

This gene was present in the common ancestor of animals.

Orthologs for RFX4 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia RFX4 31 30
  • 99.77 (n)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia RFX4 31
  • 98 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia RFX4 31
  • 96 (a)
OneToOne
dog
(Canis familiaris)
Mammalia RFX4 31 30
  • 93.7 (n)
OneToOne
cow
(Bos Taurus)
Mammalia RFX4 31 30
  • 92.56 (n)
OneToOne
mouse
(Mus musculus)
Mammalia Rfx4 17 31 30
  • 90.39 (n)
chicken
(Gallus gallus)
Aves RFX4 31 30
  • 83.66 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia RFX4 31
  • 93 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia rfx4 30
  • 75.48 (n)
Str.4920 30
zebrafish
(Danio rerio)
Actinopterygii rfx4 31 30
  • 75.26 (n)
OneToOne
Dr.20543 30
worm
(Caenorhabditis elegans)
Secernentea daf-19 31
  • 21 (a)
OneToMany
Species where no ortholog for RFX4 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)
  • 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)
  • rat (Rattus norvegicus)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • 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 RFX4 Gene

ENSEMBL:
Gene Tree for RFX4 (if available)
TreeFam:
Gene Tree for RFX4 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for RFX4: view image

Paralogs for RFX4 Gene

Paralogs for RFX4 Gene

(6) SIMAP similar genes for RFX4 Gene using alignment to 8 proteins:

  • RFX4_HUMAN
  • B4DZB7_HUMAN
  • F8VRD4_HUMAN
  • F8VU87_HUMAN
  • F8VX50_HUMAN
  • F8VZC4_HUMAN
  • F8W1T9_HUMAN
  • R4GMS3_HUMAN
genes like me logo Genes that share paralogs with RFX4: view

Variants for RFX4 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for RFX4 Gene

SNP ID Clinical significance and condition Chr 12 pos Variation AA Info Type
713419 Benign: not provided 106,601,331(+) C/G MISSENSE_VARIANT,INTRON_VARIANT
719284 Benign: not provided 106,601,349(+) A/G INTRON_VARIANT
724359 Likely Benign: not provided 106,750,751(+) T/C SYNONYMOUS_VARIANT
776746 Benign: not provided 106,720,770(+) G/A SYNONYMOUS_VARIANT
776747 Benign: not provided 106,761,353(+) T/G MISSENSE_VARIANT

Additional dbSNP identifiers (rs#s) for RFX4 Gene

Structural Variations from Database of Genomic Variants (DGV) for RFX4 Gene

Variant ID Type Subtype PubMed ID
esv3428589 CNV insertion 20981092
esv3580458 CNV loss 25503493
esv990753 CNV insertion 20482838
nsv522964 CNV loss 19592680
nsv560090 CNV gain 21841781
nsv832511 CNV gain 17160897
nsv9005 CNV gain 18304495
nsv952470 CNV deletion 24416366

Variation tolerance for RFX4 Gene

Residual Variation Intolerance Score: 14.6% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 3.08; 50.80% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for RFX4 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
RFX4

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for RFX4 Gene

Disorders for RFX4 Gene

MalaCards: The human disease database

(4) MalaCards diseases for RFX4 Gene - From: DISEASES

Disorder Aliases PubMed IDs
joubert syndrome 16
  • jbts16
joubert syndrome 2
  • jbts2
cellular ependymoma
  • epithelial ependymoma
joubert syndrome 1
  • jbts1
- elite association - COSMIC cancer census association via MalaCards
Search RFX4 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for RFX4

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with RFX4: view

No data available for UniProtKB/Swiss-Prot and Genatlas for RFX4 Gene

Publications for RFX4 Gene

  1. Human regulatory factor X 4 (RFX4) is a testis-specific dimeric DNA-binding protein that cooperates with other human RFX members. (PMID: 11682486) Morotomi-Yano K … Miki Y (The Journal of biological chemistry 2002) 2 3 4 23 54
  2. Identification of a novel substrate for tyrosine kinase in human testes. (PMID: 16193984) Huang X … Sha J (Journal of nanoscience and nanotechnology 2005) 3 4 23 54
  3. Identification of glioma-specific RFX4-E and -F isoforms and humoral immune response in patients. (PMID: 16271074) Matsushita H … Nakayama E (Cancer science 2005) 3 4 23 54
  4. Case-control association study of 65 candidate genes revealed a possible association of a SNP of HTR5A to be a factor susceptible to bipolar disease in Bulgarian population. (PMID: 19328558) Yosifova A … Nakamura Y (Journal of affective disorders 2009) 3 41 54
  5. Genetic correlates of brain aging on MRI and cognitive test measures: a genome-wide association and linkage analysis in the Framingham Study. (PMID: 17903297) Seshadri S … Wolf PA (BMC medical genetics 2007) 3 41 54

Products for RFX4 Gene

Sources for RFX4 Gene