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    RFX2 regulatory factor X2 [ Homo sapiens (human) ]

    Gene ID: 5990, updated on 27-Nov-2024

    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
    NEW
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    Genomic context

    See RFX2 in Genome Data Viewer
    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_000019.10Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9938 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13818 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:5939785-5939965 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:5944489-5945129 Neighboring gene vimentin type intermediate filament associated coiled-coil protein Neighboring gene RAN binding protein 3 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:5952179-5952738 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr19:5953075-5954274 Neighboring gene calcyphosine Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:5957025-5957534 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:5958162-5958810 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:5959460-5960108 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:5960757-5961406 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13819 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9939 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:5962704-5963351 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:5963485-5964036 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:5964037-5964587 Neighboring gene Sharpr-MPRA regulatory region 310 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9940 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9941 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9942 Neighboring gene RANBP3 divergent transcript Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:6015021-6015520 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:6018397-6018898 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9943 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:6065893-6066394 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:6074378-6075171 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr19:6086791-6087292 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr19:6087293-6087792 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:6092583-6093288 Neighboring gene ribosomal protein L32 pseudogene 37 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:6109025-6109525 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9944 Neighboring gene uncharacterized LOC105372255 Neighboring gene Sharpr-MPRA regulatory region 9390 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr19:6134642-6135545 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr19:6135546-6136448 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9945 Neighboring gene acyl-CoA synthetase bubblegum family member 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:6198732-6199335 Neighboring gene OCT4-H3K4me1 hESC enhancer GRCh37_chr19:6199336-6199938 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13821 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13822 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:6216753-6217667 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:6227079-6227744 Neighboring gene Sharpr-MPRA regulatory region 3427 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:6239861-6240362 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:6243510-6244224 Neighboring gene MLLT1 super elongation complex subunit Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:6263043-6263544 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:6263545-6264044 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:6273107-6273706 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:6276605-6277105 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13823 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9947

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

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • FLJ14226

    Gene Ontology Provided by GOA

    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

    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)

    NEW Try the new Transcript table

    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)

    1. NM_000635.4NP_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:200272
      RFX_DNA_binding; RFX DNA-binding domain
      pfam04589
      Location:30153
      RFX1_trans_act; RFX1 transcription activation region
    2. NM_134433.3NP_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:172247
      RFX_DNA_binding; RFX DNA-binding domain
      pfam04589
      Location:4153
      RFX1_trans_act; RFX1 transcription activation region

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000019.10 Reference GRCh38.p14 Primary Assembly

      Range
      5993164..6110500 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047439198.1XP_047295154.1  DNA-binding protein RFX2 isoform X4

    2. XM_017027107.2XP_016882596.1  DNA-binding protein RFX2 isoform X3

    3. XM_047439197.1XP_047295153.1  DNA-binding protein RFX2 isoform X2

    4. XM_047439196.1XP_047295152.1  DNA-binding protein RFX2 isoform X1

      UniProtKB/Swiss-Prot
      A8K581, B3KNC4, P48378, Q6IQ44, Q8SNA2
    5. XM_047439199.1XP_047295155.1  DNA-binding protein RFX2 isoform X5

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060943.1 Alternate T2T-CHM13v2.0

      Range
      5980648..6099250 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054321684.1XP_054177659.1  DNA-binding protein RFX2 isoform X4

    2. XM_054321683.1XP_054177658.1  DNA-binding protein RFX2 isoform X3

    3. XM_054321682.1XP_054177657.1  DNA-binding protein RFX2 isoform X2

    4. XM_054321681.1XP_054177656.1  DNA-binding protein RFX2 isoform X1

      UniProtKB/Swiss-Prot
      A8K581, B3KNC4, P48378, Q6IQ44, Q8SNA2
    5. XM_054321685.1XP_054177660.1  DNA-binding protein RFX2 isoform X5