RFXAP regulatory factor X associated protein [Homo sapiens (human)] - Gene

Summary

Official Symbol: RFXAPprovided by HGNC
Official Full Name: regulatory factor X associated proteinprovided by HGNC
Primary source: HGNC:HGNC:9988
See related: Ensembl:ENSG00000133111 MIM:601861; AllianceGenome:HGNC:9988
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
Also known as: MHC2D4
Summary: Major histocompatibility (MHC) class II molecules are transmembrane proteins that have a central role in development and control of the immune system. The protein encoded by this gene, along with regulatory factor X-associated ankyrin-containing protein and regulatory factor-5, forms a complex that binds to the X box motif of certain MHC class II gene promoters and activates their transcription. Once bound to the promoter, this complex associates with the non-DNA-binding factor MHC class II transactivator, which controls the cell type specificity and inducibility of MHC class II gene expression. Mutations in this gene have been linked to bare lymphocyte syndrome type II, complementation group D. Transcript variants utilizing different polyA signals have been found for this gene. [provided by RefSeq, Jul 2008]
Expression: Ubiquitous expression in testis (RPKM 3.9), brain (RPKM 3.7) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 13q13.3

Exon count:: 3

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	13	NC_000013.11 (36819222..36829104)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	13	NC_060937.1 (36038804..36048682)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	13	NC_000013.10 (37393359..37403241)

Chromosome 13 - NC_000013.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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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?

Fisetin inhibits proliferation of pancreatic adenocarcinoma by inducing DNA damage via RFXAP/KDM4A-dependent histone H3K36 demethylation.
Title: Fisetin inhibits proliferation of pancreatic adenocarcinoma by inducing DNA damage via RFXAP/KDM4A-dependent histone H3K36 demethylation.
Data show a negative correlation between microRNA miR-212-3p and regulatory factor X-associated protein (RFXAP) in pancreatic cancer (PC) tissue.
Title: Pancreatic cancer-derived exosomes transfer miRNAs to dendritic cells and inhibit RFXAP expression via miR-212-3p.
RFXAP(C) consists of two alpha-helices that form a V-shaped structure that packs within the RFX5(N)(2) staple.
Title: Solution structure of the heterotrimeric complex between the interaction domains of RFX5 and RFXAP from the RFX gene regulatory complex.
Study demonstrates that coordinate loss of MHCII expression in OCI-Ly2 DLBCL cells is associated with an 11-base deletion in the cDNA encoding RFX-AP, that is required for activating MHCII transcription.
Title: Coordinate loss of MHC class II expression in the diffuse large B cell lymphoma cell line OCI-Ly2 is due to a novel mutation in RFX-AP.
the interaction between RFX5 and RFXAP promote folding of a poorly structured region ofRFXAP, which is required for high affinity binding of RFXB to the RFX5.RFXAP complex
Title: Formation of the RFX gene regulatory complex induces folding of the interaction domain of RFXAP.
RFXAP and RFXB have roles in relieving autoinhibition of RFX5
Title: Assembly of the RFX complex on the MHCII promoter: role of RFXAP and RFXB in relieving autoinhibition of RFX5.
The transcriptional silent state of RFXAP correlated with reduced recruitment of RNA polymerase II to RFXAP chromatin in the MHC-II deficiency patient.
Title: Transcriptional silencing of RFXAP in MHC class II-deficiency.
Only the C-terminal half of the protein is conserved among vertebrates. The C-terminal third of RFXAP, with an extensive glutamine-rich tract, could rescue HLA-DR, but not HLA-DQ or HLA-DP expression in a bare lymphocyte syndrome cell line.
Title: Conserved residues of the bare lymphocyte syndrome transcription factor RFXAP determine coordinate MHC class II expression.
The identification of nuclear import and export sites on RFX molecules provides potential targets to modulate MHC class II expression.
Title: A hierarchy of nuclear localization signals governs the import of the regulatory factor X complex subunits and MHC class II expression.

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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

Associated conditions

Description	Tests
MHC class II deficiency MedGen: C2931418 GeneReviews: Not available	Compare labs

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

WI-16351 (e-PCR)
- UniSTS:64039

G62030 (e-PCR)
- UniSTS:139119

WI-22737 (e-PCR)
- UniSTS:15528

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
contributes_to DNA-binding transcription activator activity, RNA polymerase II-specific	IDA Inferred from Direct Assay more info	PubMed
contributes_to RNA polymerase II transcription regulatory region sequence-specific DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in positive regulation of MHC class II biosynthetic process	NAS Non-traceable Author Statement more info	PubMed
involved_in 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	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

Component	Evidence Code	Pubs
part_of RNA polymerase II transcription regulator complex	IPI Inferred from Physical Interaction more info	PubMed
located_in nuclear speck	IDA Inferred from Direct Assay more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: regulatory factor X-associated protein

Names: RFX DNA-binding complex 36 kDa subunit; RFX-associated protein

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.