Rfx4 regulatory factor X, 4 (influences HLA class II expression) [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Rfx4provided by MGI
Official Full Name: regulatory factor X, 4 (influences HLA class II expression)provided by MGI
Primary source: MGI:MGI:1918387
See related: Ensembl:ENSMUSG00000020037 AllianceGenome:MGI:1918387
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: NYD-sp10; 4933412G19Rik
Summary: Predicted to enable DNA-binding transcription activator activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Acts upstream of or within several processes, including cilium assembly; negative regulation of smoothened signaling pathway; and regulation of gene expression. Located in nucleus. Is expressed in several structures, including central nervous system; eye; future brain; genitourinary system; and liver. Orthologous to human RFX4 (regulatory factor X4). [provided by Alliance of Genome Resources, Nov 2024]
Expression: Biased expression in testis adult (RPKM 21.4), CNS E11.5 (RPKM 8.8) and 7 other tissues See more
Orthologs: human all
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Genomic context

Location:: 10 C1; 10 41.63 cM

Exon count:: 22

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	10	NC_000076.7 (84591895..84742402)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	10	NC_000076.6 (84756036..84906538)

Chromosome 10 - NC_000076.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

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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?

provide a novel conditional KO animal model in which to investigate the downstream genes directly and/or indirectly regulated by RFX4 isoform 1. This model could provide new insights into the pathogenesis of obstructive hydrocephalus and holoprosencephaly in humans, both relatively common and disabling birth defects
Title: Conditional ablation of the RFX4 isoform 1 transcription factor: Allele dosage effects on brain phenotype.
the dominant Rfx4 transcript present begins at a downstream exon and lacks the DNA binding domain
Title: Differential expression of Rfx1-4 during mouse spermatogenesis.
Rfx4 is a regionally specific transcriptional regulator of ciliogenesis and thus is also a regionally specific modulator of Shh signaling during development of the central nervous system.
Title: The Rfx4 transcription factor modulates Shh signaling by regional control of ciliogenesis.
GPS2 interacts with RFX4_v3 to modulate transactivation of genes involved in brain morphogenesis, including Cx3Cl1
Title: G-protein pathway suppressor 2 (GPS2) interacts with the regulatory factor X4 variant 3 (RFX4_v3) and functions as a transcriptional co-activator.
mouse regulatory factor X4 transcript is expressed in the suprachiasmatic nucleus and regulated by light
Title: Restricted expression and photic induction of a novel mouse regulatory factor X4 transcript in the suprachiasmatic nucleus.
Data implicate the RFX4_v3 variant transcript as being crucial for early brain development, as well as for the genesis of the subcommissural organ.
Title: Graded phenotypic response to partial and complete deficiency of a brain-specific transcript variant of the winged helix transcription factor RFX4.

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Variation

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Alleles

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

Chemically induced (ENU) (1) 1 citation
Targeted (2) 1 citation
Transgenic (1) 1 citation

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

Rfx4 (e-PCR), detects polymorphism
- UniSTS:547630

Rfx4 (e-PCR), detects polymorphism
- UniSTS:507951

Rfx4 (e-PCR), detects polymorphism
- UniSTS:547646

Rfx4 (e-PCR), detects polymorphism
- UniSTS:547647

Rfx4 (e-PCR), detects polymorphism
- UniSTS:547648

Rfx4 (e-PCR), detects polymorphism
- UniSTS:547649

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables DNA-binding transcription activator activity, RNA polymerase II-specific	IEA Inferred from Electronic Annotation more info
enables DNA-binding transcription activator activity, RNA polymerase II-specific	ISO Inferred from Sequence Orthology more info
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 RNA polymerase II cis-regulatory region sequence-specific DNA binding	IEA Inferred from Electronic Annotation more info
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding	ISO Inferred from Sequence Orthology more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables sequence-specific double-stranded DNA binding	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
acts_upstream_of_or_within cilium assembly	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within negative regulation of smoothened signaling pathway	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within positive regulation of transcription by RNA polymerase II	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within regulation of protein processing	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
acts_upstream_of_or_within regulation of transcription by RNA polymerase II	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within telencephalon development	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: transcription factor RFX4

Names: regulatory factor X 4 protein; winged-helix transcription factor RFX4

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_001024918.1 → NP_001020089.1 transcription factor RFX4 isoform 1

See identical proteins and their annotated locations for NP_001020089.1

Status: VALIDATED

Description

Transcript Variant: This variant (1) encodes the longer isoform (1).

Source sequence(s)

AB086957, BB595996

Consensus CDS

CCDS24082.1

UniProtKB/Swiss-Prot

B2RS52, Q3V158, Q76KT2, Q7TNK1, Q8HWA6, Q9D453

Related

ENSMUSP00000051107.7, ENSMUST00000060397.13

Conserved Domains (1) summary

pfam02257
Location:59 → 134

RFX_DNA_binding; RFX DNA-binding domain
NM_027689.3 → NP_081965.2 transcription factor RFX4 isoform 2

See identical proteins and their annotated locations for NP_081965.2

Status: VALIDATED

Description

Transcript Variant: This variant (2) differs in the 5' UTR, lacks a portion of the 5' coding region, and initiates translation at an alternate start codon, compared to variant 1. The encoded isoform (2) has a distinct N-terminus and is shorter than isoform 1.

Source sequence(s)

AC122349

Consensus CDS

CCDS24083.1

UniProtKB/Swiss-Prot

Q7TNK1

Related

ENSMUSP00000093035.5, ENSMUST00000095388.5

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_000076.7 Reference GRCm39 C57BL/6J

Range

84591895..84742402

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_030245278.2 → XP_030101138.1 transcription factor RFX4 isoform X3

Conserved Domains (1) summary

pfam02257
Location:59 → 134

RFX_DNA_binding; RFX DNA-binding domain
XM_006514115.5 → XP_006514178.1 transcription factor RFX4 isoform X4

See identical proteins and their annotated locations for XP_006514178.1

Conserved Domains (1) summary

pfam02257
Location:2 → 51

RFX_DNA_binding; RFX DNA-binding domain
XM_030245279.2 → XP_030101139.1 transcription factor RFX4 isoform X4

Conserved Domains (1) summary

pfam02257
Location:2 → 51

RFX_DNA_binding; RFX DNA-binding domain
XM_006514113.5 → XP_006514176.1 transcription factor RFX4 isoform X1

Conserved Domains (1) summary

pfam02257
Location:69 → 144

RFX_DNA_binding; RFX DNA-binding domain
XM_006514114.5 → XP_006514177.1 transcription factor RFX4 isoform X2

Conserved Domains (1) summary

pfam02257
Location:69 → 144

RFX_DNA_binding; RFX DNA-binding domain