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RFX4 regulatory factor X4 [ Homo sapiens (human) ]

Gene ID: 5992, updated on 1-Mar-2024

Summary

Official Symbol
RFX4provided by HGNC
Official Full Name
regulatory factor X4provided by HGNC
Primary source
HGNC:HGNC:9985
See related
Ensembl:ENSG00000111783 MIM:603958; AllianceGenome:HGNC:9985
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
NYD-SP10
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, X2, X3, and X5. It has been shown to interact with itself as well as with regulatory factors X2 and X3, but it does not interact with regulatory factor X1. Alternative splicing results in multiple transcript variants. [provided by RefSeq, May 2011]
Expression
Restricted expression toward testis (RPKM 40.0) See more
Orthologs
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Genomic context

See RFX4 in Genome Data Viewer
Location:
12q23.3
Exon count:
20
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (106583004..106762803)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (106546661..106726445)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (106976782..107156581)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4816 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:106696289-106697174 Neighboring gene NANOG hESC enhancer GRCh37_chr12:106725081-106725582 Neighboring gene t-complex 11 like 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:106791431-106791932 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:106791933-106792432 Neighboring gene RNA polymerase III subunit B Neighboring gene ReSE screen-validated silencer GRCh37_chr12:106838256-106838461 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4817 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:106870783-106871355 Neighboring gene NANOG hESC enhancer GRCh37_chr12:106884667-106885244 Neighboring gene ReSE screen-validated silencer GRCh37_chr12:106887966-106888130 Neighboring gene uncharacterized LOC100287944 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:106929421-106929920 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:106934851-106935440 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:106944957-106945458 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:106974861-106975743 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:106977232-106977816 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:106979571-106980156 Neighboring gene Sharpr-MPRA regulatory region 8958 Neighboring gene Sharpr-MPRA regulatory region 7289 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:107038213-107038714 Neighboring gene uncharacterized LOC100505978 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr12:107104586-107105785 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6948 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:107167609-107168160 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4818 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6949 Neighboring gene RIC8 guanine nucleotide exchange factor B Neighboring gene uncharacterized LOC105369961 Neighboring gene NANOG hESC enhancer GRCh37_chr12:107270199-107270748 Neighboring gene eukaryotic translation elongation factor 1 beta 2 pseudogene 4

Genomic regions, transcripts, and products

Expression

  • Project title: 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

EBI GWAS Catalog

Description
Genetic correlates of brain aging on MRI and cognitive test measures: a genome-wide association and linkage analysis in the Framingham Study.
EBI GWAS Catalog
Genome-wide data reveal novel genes for methotrexate response in a large cohort of juvenile idiopathic arthritis cases.
EBI GWAS Catalog
Identification of heart rate-associated loci and their effects on cardiac conduction and rhythm disorders.
EBI GWAS Catalog

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Gene Ontology Provided by GOA

Process Evidence Code Pubs
involved_in cilium assembly IEA
Inferred from Electronic Annotation
more info
 
involved_in positive regulation of transcription by RNA polymerase II IDA
Inferred from Direct Assay
more info
PubMed 
involved_in regulation of protein processing 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 telencephalon development IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
part_of chromatin ISA
Inferred from Sequence Alignment
more info
 
located_in nucleus IEA
Inferred from Electronic Annotation
more info
 

General protein information

Preferred Names
transcription factor RFX4
Names
regulatory factor X, 4 (influences HLA class II expression)
testis development protein NYD-SP10
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.

Genomic

  1. NG_047074.1 RefSeqGene

    Range
    5098..184897
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001206691.2NP_001193620.1  transcription factor RFX4 isoform d

    See identical proteins and their annotated locations for NP_001193620.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4, also known as RFX4_v4) uses an alternate 5' exon and thus differs in the 5' UTR and 5' coding region, compared to variant 3. The encoded isoform (d, also known as RFX4-C) has a distinct N-terminus and is longer than isoform c.
    Source sequence(s)
    AB095365, AI002078, AK074913, AY102009
    Consensus CDS
    CCDS55880.1
    UniProtKB/Swiss-Prot
    Q33E94
    Related
    ENSP00000350552.4, ENST00000357881.8
    Conserved Domains (1) summary
    pfam02257
    Location:68141
    RFX_DNA_binding; RFX DNA-binding domain
  2. NM_032491.6NP_115880.2  transcription factor RFX4 isoform a

    See identical proteins and their annotated locations for NP_115880.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1, also known as RFX4_v1) differs in the 5' UTR, and lacks several exons in the 5' coding region but includes an alternate 5' coding region, compared to variant 3. The encoded isoform (a, also known as RFX4-A) has a distinct and shorter N-terminus, compared to isoform c.
    Source sequence(s)
    BC028582, BC030644
    Consensus CDS
    CCDS9108.1
    UniProtKB/Swiss-Prot
    Q33E94
    Related
    ENSP00000229387.5, ENST00000229387.6
  3. NM_213594.3NP_998759.1  transcription factor RFX4 isoform c

    See identical proteins and their annotated locations for NP_998759.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3, also known as RFX4_v3) represents the longest transcript and encodes isoform c, also known as RFX4-D.
    Source sequence(s)
    AB095366, AI002078, AY102009
    Consensus CDS
    CCDS9106.1
    UniProtKB/Swiss-Prot
    A8K5Y0, B2RDW4, Q33DW6, Q33DW7, Q33E94, Q33E95, Q6YM53, Q8MHQ1, Q8NC78, Q8NDF9, Q8SNA1, Q96S80, Q9BXI0
    Related
    ENSP00000376585.1, ENST00000392842.6
    Conserved Domains (1) summary
    pfam02257
    Location:59132
    RFX_DNA_binding; RFX DNA-binding domain

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000012.12 Reference GRCh38.p14 Primary Assembly

    Range
    106583004..106762803
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060936.1 Alternate T2T-CHM13v2.0

    Range
    106546661..106726445
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_002920.3: Suppressed sequence

    Description
    NM_002920.3: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript and the protein.