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RFX5 regulatory factor X5 [ Homo sapiens (human) ]

Gene ID: 5993, updated on 4-Jun-2020

Summary

Official Symbol
RFX5provided by HGNC
Official Full Name
regulatory factor X5provided by HGNC
Primary source
HGNC:HGNC:9986
See related
Ensembl:ENSG00000143390 MIM:601863
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
A lack of MHC-II expression results in a severe immunodeficiency syndrome called MHC-II deficiency, or the bare lymphocyte syndrome (BLS; MIM 209920). At least 4 complementation groups have been identified in B-cell lines established from patients with BLS. The molecular defects in complementation groups B, C, and D all lead to a deficiency in RFX, a nuclear protein complex that binds to the X box of MHC-II promoters. The lack of RFX binding activity in complementation group C results from mutations in the RFX5 gene encoding the 75-kD subunit of RFX (Steimle et al., 1995). RFX5 is the fifth member of the growing family of DNA-binding proteins sharing a novel and highly characteristic DNA-binding domain called the RFX motif. Multiple alternatively spliced transcript variants have been found but the full-length natures of only two have been determined. [provided by RefSeq, Jul 2008]
Expression
Ubiquitous expression in lymph node (RPKM 26.5), spleen (RPKM 21.2) and 24 other tissues See more
Orthologs

Genomic context

See RFX5 in Genome Data Viewer
Location:
1q21.3
Exon count:
13
Annotation release Status Assembly Chr Location
109.20200522 current GRCh38.p13 (GCF_000001405.39) 1 NC_000001.11 (151340640..151347319, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (151313116..151319785, complement)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene phosphatidylinositol 4-kinase beta Neighboring gene RNA, 7SL, cytoplasmic 444, pseudogene Neighboring gene Sharpr-MPRA regulatory region 1421 Neighboring gene RFX5 antisense RNA 1 Neighboring gene selenium binding protein 1 Neighboring gene proteasome 20S subunit beta 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?

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Process Evidence Code Pubs
negative regulation of transcription by RNA polymerase II IEA
Inferred from Electronic Annotation
more info
 
positive regulation of transcription by RNA polymerase II IDA
Inferred from Direct Assay
more info
PubMed 
regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Component Evidence Code Pubs
nuclear chromatin ISA
Inferred from Sequence Alignment
more info
 
nucleus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
transcription factor complex IPI
Inferred from Physical Interaction
more info
PubMed 

General protein information

Preferred Names
DNA-binding protein RFX5
Names
regulatory factor X 5
regulatory factor X, 5 (influences HLA class II expression)

NCBI Reference Sequences (RefSeq)

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_007576.1 RefSeqGene

    Range
    5001..11654
    Download
    GenBank, FASTA, Sequence Viewer (Graphics), LRG_101

mRNA and Protein(s)

  1. NM_000449.4NP_000440.1  DNA-binding protein RFX5 isoform 1

    See identical proteins and their annotated locations for NP_000440.1

    Status: REVIEWED

    Source sequence(s)
    AL391069
    Consensus CDS
    CCDS994.1
    UniProtKB/Swiss-Prot
    P48382
    Related
    ENSP00000290524.4, ENST00000290524.8
    Conserved Domains (2) summary
    pfam02257
    Location:90166
    RFX_DNA_binding; RFX DNA-binding domain
    pfam14621
    Location:407614
    RFX5_DNA_bdg; RFX5 DNA-binding domain
  2. NM_001025603.2NP_001020774.1  DNA-binding protein RFX5 isoform 1

    See identical proteins and their annotated locations for NP_001020774.1

    Status: REVIEWED

    Source sequence(s)
    AL391069
    Consensus CDS
    CCDS994.1
    UniProtKB/Swiss-Prot
    P48382
    Related
    ENSP00000389130.2, ENST00000452671.6
    Conserved Domains (2) summary
    pfam02257
    Location:90166
    RFX_DNA_binding; RFX DNA-binding domain
    pfam14621
    Location:407614
    RFX5_DNA_bdg; RFX5 DNA-binding domain
  3. NM_001379412.1NP_001366341.1  DNA-binding protein RFX5 isoform 1

    Status: REVIEWED

    Source sequence(s)
    AL391069
  4. NM_001379413.1NP_001366342.1  DNA-binding protein RFX5 isoform 1

    Status: REVIEWED

    Source sequence(s)
    AL391069
  5. NM_001379414.1NP_001366343.1  DNA-binding protein RFX5 isoform 1

    Status: REVIEWED

    Source sequence(s)
    AL391069
  6. NM_001379415.1NP_001366344.1  DNA-binding protein RFX5 isoform 1

    Status: REVIEWED

    Source sequence(s)
    AL391069
  7. NM_001379416.1NP_001366345.1  DNA-binding protein RFX5 isoform 1

    Status: REVIEWED

    Source sequence(s)
    AL391069
  8. NM_001379417.1NP_001366346.1  DNA-binding protein RFX5 isoform 1

    Status: REVIEWED

    Source sequence(s)
    AL391069
  9. NM_001379418.1NP_001366347.1  DNA-binding protein RFX5 isoform 1

    Status: REVIEWED

    Source sequence(s)
    AL391069
  10. NM_001379419.1NP_001366348.1  DNA-binding protein RFX5 isoform 2

    Status: REVIEWED

    Source sequence(s)
    AL391069
  11. NM_001379420.1NP_001366349.1  DNA-binding protein RFX5 isoform 2

    Status: REVIEWED

    Source sequence(s)
    AL391069

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000001.11 Reference GRCh38.p13 Primary Assembly

    Range
    151340640..151347319 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_024448791.1XP_024304559.1  DNA-binding protein RFX5 isoform X2

    Conserved Domains (1) summary
    pfam14621
    Location:236443
    RFX5_DNA_bdg; RFX5 DNA-binding domain
  2. XM_017002000.1XP_016857489.1  DNA-binding protein RFX5 isoform X2

    Conserved Domains (1) summary
    pfam14621
    Location:236443
    RFX5_DNA_bdg; RFX5 DNA-binding domain
  3. XM_017001999.1XP_016857488.1  DNA-binding protein RFX5 isoform X2

    Conserved Domains (1) summary
    pfam14621
    Location:236443
    RFX5_DNA_bdg; RFX5 DNA-binding domain
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