RFX2 regulatory factor X2 [Homo sapiens (human)] - Gene

Summary

Official Symbol: RFX2provided by HGNC
Official Full Name: regulatory factor X2provided by HGNC
Primary source: HGNC:HGNC:9983
See related: Ensembl:ENSG00000087903 MIM:142765; AllianceGenome:HGNC:9983
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Summary: 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, X3, X4, and X5. It is a transcriptional activator that can bind DNA as a monomer or as a heterodimer with other RFX family members. This protein can bind to cis elements in the promoter of the IL-5 receptor alpha gene. Two transcript variants encoding different isoforms have been described for this gene, and both variants utilize alternative polyadenylation sites. [provided by RefSeq, Jul 2008]
Expression: Biased expression in testis (RPKM 41.1), lung (RPKM 6.6) and 4 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 19p13.3

Exon count:: 19

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	19	NC_000019.10 (5993164..6110500, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	19	NC_060943.1 (5980648..6099250, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	19	NC_000019.9 (5993175..6110511, complement)

Chromosome 19 - NC_000019.10 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: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

RFX2 promotes tumor cell stemness through epigenetic regulation of PAF1 in spinal ependymoma.
Title: RFX2 promotes tumor cell stemness through epigenetic regulation of PAF1 in spinal ependymoma.
Novel variations in spermatogenic transcription regulators RFX2 and TAF7 increase risk of azoospermia.
Title: Novel variations in spermatogenic transcription regulators RFX2 and TAF7 increase risk of azoospermia.
Androglobin gene expression patterns and FOXJ1-dependent regulation indicate its functional association with ciliogenesis.
Title: Androglobin gene expression patterns and FOXJ1-dependent regulation indicate its functional association with ciliogenesis.
Rfx2 coordinates multiple, distinct gene expression programs in multi-ciliated epithelial cells, regulating genes that control cell movement, ciliogenesis, and cilia function.
Title: Coordinated genomic control of ciliogenesis and cell movement by RFX2.
Taken together, this study suggests ciliogenic RFX transcription factors regulate FGF-1B promoter activity and the maintenance of F1BGFP(+) NSPCs and GBM-SCs.
Title: Ciliogenic RFX transcription factors regulate FGF1 gene promoter.
Observational study of gene-disease association, gene-environment interaction, and pharmacogenomic / toxicogenomic. (HuGE Navigator)
Title: Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study.
Observational study of gene-disease association. (HuGE Navigator)
Title: Gene-centric association signals for lipids and apolipoproteins identified via the HumanCVD BeadChip.
We show binding of RFX proteins to an evolutionarily conserved X-box in the ALMS1 proximal promoter and present evidence that these proteins are responsible for ALMS1 transcription during growth arrest
Title: Transcriptional regulation of the Alström syndrome gene ALMS1 by members of the RFX family and Sp1.
novel role for the RFX family of transcription factors as modulators of Ras signalling in epithelial cells.
Title: Involvement of RFX proteins in transcriptional activation from a Ras-responsive enhancer element.

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Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
A genome-wide meta-analysis identifies novel loci associated with schizophrenia and bipolar disorder. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

D11S2921 (e-PCR)
- UniSTS:152074

RH48363 (e-PCR)
- UniSTS:78696

RH41878 (e-PCR)
- UniSTS:35205

SHGC-12012 (e-PCR)
- UniSTS:37553

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables DNA binding	TAS Traceable Author Statement more info	PubMed
enables DNA-binding transcription activator activity, RNA polymerase II-specific	IEA Inferred from Electronic Annotation more info
enables DNA-binding transcription factor activity	ISS Inferred from Sequence or Structural Similarity more info
enables DNA-binding transcription factor activity, RNA polymerase II-specific	IBA Inferred from Biological aspect of Ancestor more info
enables DNA-binding transcription factor activity, RNA polymerase II-specific	ISA Inferred from Sequence Alignment 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	ISS Inferred from Sequence or Structural Similarity more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables sequence-specific double-stranded DNA binding	IDA Inferred from Direct Assay more info	PubMed

Process	Evidence Code	Pubs
involved_in acrosome assembly	ISS Inferred from Sequence or Structural Similarity more info
involved_in cellular response to leukemia inhibitory factor	IEA Inferred from Electronic Annotation more info
involved_in cilium assembly	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of transcription by RNA polymerase II	IEA Inferred from Electronic Annotation more info
involved_in regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info
involved_in regulation of transcription by RNA polymerase II	ISS Inferred from Sequence or Structural Similarity more info
involved_in spermatid development	ISS Inferred from Sequence or Structural Similarity more info

Component	Evidence Code	Pubs
located_in chromatin	ISA Inferred from Sequence Alignment more info
located_in cytoplasm	ISS Inferred from Sequence or Structural Similarity more info
located_in nucleus	ISS Inferred from Sequence or Structural Similarity more info

General protein information

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Preferred Names: DNA-binding protein RFX2

Names: HLA class II regulatory factor RFX2; regulatory factor X 2; regulatory factor X, 2 (influences HLA class II expression); trans-acting regulatory factor 2

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_000635.4 → NP_000626.2 DNA-binding protein RFX2 isoform a

See identical proteins and their annotated locations for NP_000626.2

Status: REVIEWED

Description

Transcript Variant: This variant (1) is the longer transcript and encodes the longer protein (isoform a).

Source sequence(s)

AI149945, BC028579, BC071571

Consensus CDS

CCDS12157.1

UniProtKB/Swiss-Prot

A8K581, B3KNC4, P48378, Q6IQ44, Q8SNA2

Related

ENSP00000306335.4, ENST00000303657.10

Conserved Domains (2) summary

pfam02257
Location:200 → 272

RFX_DNA_binding; RFX DNA-binding domain

pfam04589
Location:30 → 153

RFX1_trans_act; RFX1 transcription activation region
NM_134433.3 → NP_602309.1 DNA-binding protein RFX2 isoform b

See identical proteins and their annotated locations for NP_602309.1

Status: REVIEWED

Description

Transcript Variant: This variant (2) includes an alternate in-frame exon, compared to variant 1, resulting in a shorter protein (isoform b) when it is compared to isoform a.

Source sequence(s)

AI149945, AK024288, BC028579, BI464247, DC400266

Consensus CDS

CCDS12158.1

UniProtKB/Swiss-Prot

P48378

Related

ENSP00000467166.1, ENST00000592546.5

Conserved Domains (2) summary

pfam02257
Location:172 → 247

RFX_DNA_binding; RFX DNA-binding domain

pfam04589
Location:4 → 153

RFX1_trans_act; RFX1 transcription activation region