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

Summary

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
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Genomic context

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_000085.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
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.
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.
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.
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.
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.
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.
RFX3 may play roles in haploid cells during mouse spermatogenesis
Title: Differential expression of Rfx1-4 during mouse spermatogenesis.
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.
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

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Alleles

Alleles of this type are documented at Mouse Genome Informatics (MGI)

Targeted (4) 1 citation
Chemically induced (ENU) (1)
Endonuclease-mediated (3)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

D19Mit132 (e-PCR), detects polymorphism
- UniSTS:128347

D4Bwg0593e (e-PCR), detects polymorphism
- UniSTS:142444

NoName (e-PCR)
- UniSTS:224906

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

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Preferred Names: transcription factor RFX3

Names: regulatory factor X 3

NCBI Reference Sequences (RefSeq)

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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)

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
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
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
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

NC_000085.7 Reference GRCm39 C57BL/6J

Range

27739121..27995287 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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
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
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
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
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
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
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
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