U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

Rfx3 regulatory factor X, 3 (influences HLA class II expression) [ Mus musculus (house mouse) ]

Gene ID: 19726, updated on 5-Mar-2024

Summary

Go to the top of the page Help
Official Symbol
Rfx3provided by MGI
Official Full Name
regulatory factor X, 3 (influences HLA class II expression)provided by MGI
Primary source
MGI:MGI:106582
See related
Ensembl:ENSMUSG00000040929 AllianceGenome:MGI:106582
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Mus musculus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as
MRFX3; C230093O12Rik
Summary
Enables DNA-binding transcription factor activity and transcription cis-regulatory region binding activity. Involved in several processes, including epithelial cilium movement involved in determination of left/right asymmetry; positive regulation of type B pancreatic cell development; and type B pancreatic cell maturation. Acts upstream of or within determination of left/right symmetry. Located in chromatin. Part of transcription regulator complex. Is expressed in several structures, including central nervous system; genitourinary system; inner cell mass; pancreas; and sensory organ. Used to study visceral heterotaxy. Orthologous to human RFX3 (regulatory factor X3). [provided by Alliance of Genome Resources, Apr 2022]
Expression
Broad expression in CNS E18 (RPKM 4.6), whole brain E14.5 (RPKM 4.4) and 22 other tissues See more
Orthologs
human all
NEW
Try the new Gene table
Try the new Transcript table

Genomic context

Go to the top of the page Help
Location:
19 C1; 19 22.36 cM
Exon count:
21
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCm39 (GCF_000001635.27) 19 NC_000085.7 (27739121..27995287, complement)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 19 NC_000085.6 (27761721..28014669, complement)

Chromosome 19 - NC_000085.7Genomic Context describing neighboring genes Neighboring gene STARR-seq mESC enhancer starr_45849 Neighboring gene predicted gene, 35697 Neighboring gene predicted gene, 24782 Neighboring gene STARR-seq mESC enhancer starr_45851 Neighboring gene STARR-seq mESC enhancer starr_45852 Neighboring gene THO complex 3 pseudogene Neighboring gene STARR-positive B cell enhancer ABC_E3248 Neighboring gene peptidylprolyl isomerase A pseudogene chr19_428.1 Neighboring gene STARR-seq mESC enhancer starr_45853 Neighboring gene UPF0729 protein C18orf32 homolog pseudogene

Genomic regions, transcripts, and products

Go to the top of the page Help

Go to nucleotide: Graphics FASTA GenBank

Expression

Go to the top of the page Help
  • Project title: Mouse ENCODE transcriptome data
  • Description: RNA profiling data sets generated by the Mouse ENCODE project.
  • BioProject: PRJNA66167
  • Publication: PMID 25409824
  • Analysis date: n/a

Bibliography

Go to the top of the pageHelp

Related articles in PubMed

  1. Two rotating cilia in the node cavity are sufficient to break left-right symmetry in the mouse embryo. Shinohara K, et al. Nat Commun, 2012 Jan 10. PMID 22233632
  2. A deficiency in RFX3 causes hydrocephalus associated with abnormal differentiation of ependymal cells. Baas D, et al. Eur J Neurosci, 2006 Aug. PMID 16930429
  3. Downregulation of microRNA-342-3p Eases Insulin Resistance and Liver Gluconeogenesis via Regulating Rfx3 in Gestational Diabetes Mellitus. Sun Y, et al. Crit Rev Eukaryot Gene Expr, 2022. PMID 35997120
  4. Novel function of the ciliogenic transcription factor RFX3 in development of the endocrine pancreas. Ait-Lounis A, et al. Diabetes, 2007 Apr. PMID 17229940
  5. Interplay of RFX transcription factors 1, 2 and 3 in motile ciliogenesis. Lemeille S, et al. Nucleic Acids Res, 2020 Sep 18. PMID 32725242, Free PMC Article

See all (61) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Downregulation of microRNA-342-3p Eases Insulin Resistance and Liver Gluconeogenesis via Regulating Rfx3 in Gestational Diabetes Mellitus.
    Title: Downregulation of microRNA-342-3p Eases Insulin Resistance and Liver Gluconeogenesis via Regulating Rfx3 in Gestational Diabetes Mellitus.
  2. Interplay of RFX transcription factors 1, 2 and 3 in motile ciliogenesis.
    Title: Interplay of RFX transcription factors 1, 2 and 3 in motile ciliogenesis.
  3. These data suggest that Rnf20 functions at the Rfx3 locus regulating cilia motility and cardiac situs and identify H2Bub1 as an upstream transcriptional regulator controlling tissue-specific expression of cilia genes. Our findings mechanistically link the two functional gene ontologies that have been implicated in human CHD: chromatin remodeling and cilia function.
    Title: Histone H2B monoubiquitination regulates heart development via epigenetic control of cilia motility.
  4. The ciliogenic transcription factor Rfx3 is required for the formation of the thalamocortical tract by regulating the patterning of prethalamus and ventral telencephalon
    Title: The ciliogenic transcription factor Rfx3 is required for the formation of the thalamocortical tract by regulating the patterning of prethalamus and ventral telencephalon.
  5. This study unravels a crucial role of RFX3 during early brain development by indirectly regulating GLI3 activity, which leads to FGF8 upregulation and ultimately to disturbed distribution of guidepost neurons required for CC morphogenesis
    Title: The ciliogenic transcription factor RFX3 regulates early midline distribution of guidepost neurons required for corpus callosum development.
  6. High dosage of resveratrol pretreatment inhibited the injury-induced up-regulation of eIF2alpha-CHOP and IRE1alpha-XBP1 pathways.
    Title: Endoplasmic reticulum stress in retinal vascular degeneration: protective role of resveratrol.
  7. Rfx3 is required for the differentiation and function of mature beta-cells and regulates the beta-cell promoter of the glucokinase gene.
    Title: The transcription factor Rfx3 regulates beta-cell differentiation, function, and glucokinase expression.
  8. RFX3 may play roles in haploid cells during mouse spermatogenesis
    Title: Differential expression of Rfx1-4 during mouse spermatogenesis.
  9. RFX3 is also necessary for biogenesis of motile cilia.
    Title: RFX3 governs growth and beating efficiency of motile cilia in mouse and controls the expression of genes involved in human ciliopathies.
  10. These results demonstrate that regulatory factor X3 is necessary for ciliated ependymal cell differentiation in the mouse.
    Title: A deficiency in RFX3 causes hydrocephalus associated with abnormal differentiation of ependymal cells.
Submit: New GeneRIF Correction See all GeneRIFs (12)

Variation

Go to the top of the page Help

Alleles

Alleles of this type are documented at Mouse Genome Informatics  (MGI)
  • Targeted (4)  1 citation
  • Chemically induced (ENU) (1) 
  • Endonuclease-mediated (3) 

Interactions

Go to the top of the page Help
Products Interactant Other Gene Complex Source Pubs Description

General gene information

Go to the top of the page Help

Markers

Homology

Gene Ontology Provided by MGI

Function Evidence Code Pubs
enables DNA binding IEA
Inferred from Electronic Annotation
more info
  
enables DNA-binding transcription factor activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables DNA-binding transcription factor activity, RNA polymerase II-specific IBA
Inferred from Biological aspect of Ancestor
more info
  
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables sequence-specific DNA binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables sequence-specific double-stranded DNA binding ISO
Inferred from Sequence Orthology
more info
  
enables transcription cis-regulatory region binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables transcription cis-regulatory region binding ISO
Inferred from Sequence Orthology
more info
  
Process Evidence Code Pubs
involved_in DNA-templated transcription IMP
Inferred from Mutant Phenotype
more info
 PubMed 
acts_upstream_of_or_within cell differentiation IEA
Inferred from Electronic Annotation
more info
  
involved_in cell maturation IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in cilium assembly IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in cilium-dependent cell motility IMP
Inferred from Mutant Phenotype
more info
 PubMed 
acts_upstream_of_or_within determination of left/right symmetry IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in endocrine pancreas development IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in epithelial cilium movement involved in determination of left/right asymmetry IMP
Inferred from Mutant Phenotype
more info
 PubMed 
acts_upstream_of_or_within multicellular organism development IEA
Inferred from Electronic Annotation
more info
  
involved_in negative regulation of DNA-templated transcription ISO
Inferred from Sequence Orthology
more info
  
involved_in positive regulation of DNA-templated transcription IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in positive regulation of DNA-templated transcription ISO
Inferred from Sequence Orthology
more info
  
involved_in positive regulation of transcription by RNA polymerase II IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in positive regulation of type B pancreatic cell development IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in regulation of DNA-templated transcription IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in regulation of insulin secretion IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in type B pancreatic cell maturation IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Component Evidence Code Pubs
part_of chromatin IDA
Inferred from Direct Assay
more info
 PubMed 
part_of chromatin ISO
Inferred from Sequence Orthology
more info
  
located_in nucleus IEA
Inferred from Electronic Annotation
more info
  
part_of transcription regulator complex IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

Go to the top of the page Help
Preferred Names
transcription factor RFX3
Names
regulatory factor X 3

NCBI Reference Sequences (RefSeq)

Go to the top of the page Help

NEW Try the new Transcript table

RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

  1. NM_001166414.2 → NP_001159886.1  transcription factor RFX3 isoform 1

    See identical proteins and their annotated locations for NP_001159886.1

    Status: VALIDATED

    Source sequence(s)
    AC118005, AC118628, AK030008
    Consensus CDS
    CCDS29725.1
    UniProtKB/Swiss-Prot
    P48381, Q8BLW2, Q8C0R3, Q8VBY6
    Related
    ENSMUSP00000134141.2, ENSMUST00000172907.8
    Conserved Domains (2) summary
    pfam02257
    Location:184 → 256
    RFX_DNA_binding; RFX DNA-binding domain
    pfam04589
    Location:4 → 133
    RFX1_trans_act; RFX1 transcription activation region

  2. NM_001360357.1 → NP_001347286.1  transcription factor RFX3 isoform 2

    Status: VALIDATED

    Source sequence(s)
    AC118005, AC118628
    Conserved Domains (2) summary
    pfam02257
    Location:194 → 266
    RFX_DNA_binding; RFX DNA-binding domain
    pfam04589
    Location:61 → 147
    RFX1_trans_act; RFX1 transcription activation region

  3. NM_001360358.1 → NP_001347287.1  transcription factor RFX3 isoform 3

    Status: VALIDATED

    Source sequence(s)
    AC118005, AC118628
    Conserved Domains (2) summary
    pfam02257
    Location:225 → 297
    RFX_DNA_binding; RFX DNA-binding domain
    pfam04589
    Location:45 → 178
    RFX1_trans_act; RFX1 transcription activation region

  4. NM_011265.3 → NP_035395.2  transcription factor RFX3 isoform 1

    See identical proteins and their annotated locations for NP_035395.2

    Status: VALIDATED

    Source sequence(s)
    AC118005, AK030008, AK041120, AK140928
    Consensus CDS
    CCDS29725.1
    UniProtKB/Swiss-Prot
    P48381, Q8BLW2, Q8C0R3, Q8VBY6
    Related
    ENSMUSP00000133461.2, ENSMUST00000174850.8
    Conserved Domains (2) summary
    pfam02257
    Location:184 → 256
    RFX_DNA_binding; RFX DNA-binding domain
    pfam04589
    Location:4 → 133
    RFX1_trans_act; RFX1 transcription activation region

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCm39 C57BL/6J

Genomic

  1. NC_000085.7 Reference GRCm39 C57BL/6J

    Range
    27739121..27995287 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011247167.4 → XP_011245469.2  transcription factor RFX3 isoform X1

    Conserved Domains (2) summary
    pfam02257
    Location:225 → 297
    RFX_DNA_binding; RFX DNA-binding domain
    pfam04589
    Location:45 → 178
    RFX1_trans_act; RFX1 transcription activation region

  2. XM_030250796.2 → XP_030106656.1  transcription factor RFX3 isoform X6

    UniProtKB/TrEMBL
    G5E890
    Related
    ENSMUSP00000038760.10, ENSMUST00000046898.17
    Conserved Domains (2) summary
    pfam02257
    Location:156 → 231
    RFX_DNA_binding; RFX DNA-binding domain
    pfam04589
    Location:4 → 133
    RFX1_trans_act; RFX1 transcription activation region

  3. XM_006526784.5 → XP_006526847.1  transcription factor RFX3 isoform X6

    See identical proteins and their annotated locations for XP_006526847.1

    UniProtKB/TrEMBL
    G5E890
    Conserved Domains (2) summary
    pfam02257
    Location:156 → 231
    RFX_DNA_binding; RFX DNA-binding domain
    pfam04589
    Location:4 → 133
    RFX1_trans_act; RFX1 transcription activation region

  4. XM_011247169.4 → XP_011245471.1  transcription factor RFX3 isoform X5

    See identical proteins and their annotated locations for XP_011245471.1

    UniProtKB/Swiss-Prot
    P48381, Q8BLW2, Q8C0R3, Q8VBY6
    Conserved Domains (2) summary
    pfam02257
    Location:184 → 256
    RFX_DNA_binding; RFX DNA-binding domain
    pfam04589
    Location:4 → 133
    RFX1_trans_act; RFX1 transcription activation region

  5. XM_006526778.5 → XP_006526841.1  transcription factor RFX3 isoform X3

    See identical proteins and their annotated locations for XP_006526841.1

    Conserved Domains (2) summary
    pfam02257
    Location:210 → 282
    RFX_DNA_binding; RFX DNA-binding domain
    pfam04589
    Location:30 → 159
    RFX1_trans_act; RFX1 transcription activation region

  6. XM_017318087.3 → XP_017173576.1  transcription factor RFX3 isoform X2

    Conserved Domains (2) summary
    pfam02257
    Location:215 → 287
    RFX_DNA_binding; RFX DNA-binding domain
    pfam04589
    Location:35 → 164
    RFX1_trans_act; RFX1 transcription activation region

  7. XM_030250795.2 → XP_030106655.1  transcription factor RFX3 isoform X4

    Conserved Domains (2) summary
    pfam02257
    Location:197 → 272
    RFX_DNA_binding; RFX DNA-binding domain
    pfam04589
    Location:45 → 178
    RFX1_trans_act; RFX1 transcription activation region

  8. XM_006526785.5 → XP_006526848.1  transcription factor RFX3 isoform X7

    Conserved Domains (1) summary
    pfam02257
    Location:2 → 23
    RFX_DNA_binding; RFX DNA-binding domain

RNA

  1. XR_004940126.1 RNA Sequence

  2. XR_004940125.1 RNA Sequence

  3. XR_003952761.2 RNA Sequence

  4. XR_003952760.2 RNA Sequence

  5. XR_877668.4 RNA Sequence

Nucleotide Protein Strain
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
P48381.2 GenPept UniProtKB/Swiss-Prot:P48381

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

Chemical Information
Molecular Biology Databases
Research Materials
Tools
Miscellaneous