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RFX3 regulatory factor X3 [ Homo sapiens (human) ]

Gene ID: 5991, updated on 7-Oct-2018

Summary

Official Symbol
RFX3provided by HGNC
Official Full Name
regulatory factor X3provided by HGNC
Primary source
HGNC:HGNC:9984
See related
Ensembl:ENSG00000080298 MIM:601337; Vega:OTTHUMG00000019456
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, X2, X4, and X5. It is a transcriptional activator that can bind DNA as a monomer or as a heterodimer with other RFX family members. Multiple transcript variants encoding different isoforms have been described for this gene. [provided by RefSeq, Aug 2013]
Expression
Broad expression in testis (RPKM 2.7), brain (RPKM 2.6) and 24 other tissues See more
Orthologs

Genomic context

See RFX3 in Genome Data Viewer
Location:
9p24.2
Exon count:
28
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 9 NC_000009.12 (3218297..3526529, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (3218297..3525992, complement)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene coactivator associated arginine methyltransferase 1 pseudogene 1 Neighboring gene uncharacterized LOC105375959 Neighboring gene long intergenic non-protein coding RNA 1231 Neighboring gene VISTA enhancer hs1350 Neighboring gene RFX3 antisense RNA 1 Neighboring gene uncharacterized LOC105375962

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 Jun 15 11:32:44 2016

Bibliography

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Phenotypes

NHGRI GWAS Catalog

Description
Genome-wide meta-analysis of systolic blood pressure in children with sickle cell disease.
NHGRI GWA Catalog

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • MGC87155, bA32F11.1

Gene Ontology Provided by GOA

Process Evidence Code Pubs
cell maturation ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
cilium assembly ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
cilium-dependent cell motility ISS
Inferred from Sequence or Structural Similarity
more info
 
endocrine pancreas development ISS
Inferred from Sequence or Structural Similarity
more info
 
epithelial cilium movement involved in determination of left/right asymmetry ISS
Inferred from Sequence or Structural Similarity
more info
 
negative regulation of transcription, DNA-templated IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of transcription by RNA polymerase II ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
positive regulation of transcription, DNA-templated IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of type B pancreatic cell development ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
regulation of insulin secretion ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
regulation of transcription, DNA-templated ISS
Inferred from Sequence or Structural Similarity
more info
 
transcription, DNA-templated IEA
Inferred from Electronic Annotation
more info
 
type B pancreatic cell maturation IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
nuclear chromatin IDA
Inferred from Direct Assay
more info
PubMed 
nucleus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
nucleus IC
Inferred by Curator
more info
PubMed 
transcription factor complex IC
Inferred by Curator
more info
PubMed 

General protein information

Preferred Names
transcription factor RFX3
Names
DNA binding protein RFX3
regulatory factor X, 3 (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.

mRNA and Protein(s)

  1. NM_001282116.1NP_001269045.1  transcription factor RFX3 isoform b

    See identical proteins and their annotated locations for NP_001269045.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) differs in the 5' UTR compared to variant 2. Both variants 2 and 3 encode the same isoform (b).
    Source sequence(s)
    AK289540, AL133549, BC022191, BM666287, BU170404, DB461398
    Consensus CDS
    CCDS6449.1
    UniProtKB/Swiss-Prot
    P48380
    Related
    ENSP00000482598.1, ENST00000617270.4
    Conserved Domains (2) summary
    pfam02257
    Location:184256
    RFX_DNA_binding; RFX DNA-binding domain
    pfam04589
    Location:51133
    RFX1_trans_act; RFX1 transcription activation region
  2. NM_001282117.1NP_001269046.1  transcription factor RFX3 isoform c

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) differs in the 5' UTR and its 3' terminal exon extends past a splice site that is used in variant 2. This results in a novel 3' coding region and 3' UTR, compared to variant 2. It encodes isoform c which is shorter and has a distinct C-terminus, compared to isoform b.
    Source sequence(s)
    BC022191, BC067778, DB036180
    Consensus CDS
    CCDS75809.1
    UniProtKB/Swiss-Prot
    P48380
    Related
    ENSP00000303847.2, ENST00000302303.5
    Conserved Domains (2) summary
    pfam02257
    Location:184256
    RFX_DNA_binding; RFX DNA-binding domain
    pfam04589
    Location:51133
    RFX1_trans_act; RFX1 transcription activation region
  3. NM_002919.3NP_002910.1  transcription factor RFX3 isoform a

    See identical proteins and their annotated locations for NP_002910.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) differs in the 5' UTR and its 3' terminal exon extends past a splice site that is used in variant 2. This results in a novel 3' coding region and 3' UTR, compared to variant 2. It encodes isoform a which is shorter and has a distinct C-terminus, compared to isoform b.
    Source sequence(s)
    AI811824, AL133549, X76092
    Consensus CDS
    CCDS6450.1
    UniProtKB/Swiss-Prot
    P48380
    Related
    ENSP00000351574.2, OTTHUMP00000020993, ENST00000358730.6, OTTHUMT00000051544
    Conserved Domains (2) summary
    pfam02257
    Location:184256
    RFX_DNA_binding; RFX DNA-binding domain
    pfam04589
    Location:51137
    RFX1_trans_act; RFX1 transcription activation region
  4. NM_134428.2NP_602304.1  transcription factor RFX3 isoform b

    See identical proteins and their annotated locations for NP_602304.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) represents the longest transcript and encodes the longest isoform (b). Both variants 2 and 3 encode the same isoform (b).
    Source sequence(s)
    AL133549, BC022191, BM666287, BU170404, DB461398
    Consensus CDS
    CCDS6449.1
    UniProtKB/Swiss-Prot
    P48380
    Related
    ENSP00000371434.3, OTTHUMP00000020994, ENST00000382004.7, OTTHUMT00000051545
    Conserved Domains (2) summary
    pfam02257
    Location:184256
    RFX_DNA_binding; RFX DNA-binding domain
    pfam04589
    Location:51133
    RFX1_trans_act; RFX1 transcription activation region

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109 details...Open this link in a new tab

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

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000009.12 Reference GRCh38.p12 Primary Assembly

    Range
    3218297..3526529 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011518001.1XP_011516303.1  transcription factor RFX3 isoform X7

    Conserved Domains (1) summary
    pfam02257
    Location:101173
    RFX_DNA_binding; RFX DNA-binding domain
  2. XM_017015001.1XP_016870490.1  transcription factor RFX3 isoform X6

  3. XM_024447633.1XP_024303401.1  transcription factor RFX3 isoform X4

    Conserved Domains (2) summary
    pfam02257
    Location:155231
    RFX_DNA_binding; RFX DNA-binding domain
    pfam04589
    Location:51137
    RFX1_trans_act; RFX1 transcription activation region
  4. XM_006716847.3XP_006716910.1  transcription factor RFX3 isoform X9

  5. XM_017015002.2XP_016870491.1  transcription factor RFX3 isoform X8

  6. XM_024447632.1XP_024303400.1  transcription factor RFX3 isoform X3

    Conserved Domains (2) summary
    pfam02257
    Location:190262
    RFX_DNA_binding; RFX DNA-binding domain
    pfam04589
    Location:57143
    RFX1_trans_act; RFX1 transcription activation region
  7. XM_006716844.2XP_006716907.1  transcription factor RFX3 isoform X5

    See identical proteins and their annotated locations for XP_006716907.1

    Conserved Domains (2) summary
    pfam02257
    Location:184256
    RFX_DNA_binding; RFX DNA-binding domain
    pfam04589
    Location:51137
    RFX1_trans_act; RFX1 transcription activation region
  8. XM_017015000.2XP_016870489.1  transcription factor RFX3 isoform X5

    Conserved Domains (2) summary
    pfam02257
    Location:184256
    RFX_DNA_binding; RFX DNA-binding domain
    pfam04589
    Location:51137
    RFX1_trans_act; RFX1 transcription activation region
  9. XM_024447631.1XP_024303399.1  transcription factor RFX3 isoform X1

    Conserved Domains (2) summary
    pfam02257
    Location:214286
    RFX_DNA_binding; RFX DNA-binding domain
    pfam04589
    Location:81167
    RFX1_trans_act; RFX1 transcription activation region
  10. XM_011517999.2XP_011516301.1  transcription factor RFX3 isoform X5

    See identical proteins and their annotated locations for XP_011516301.1

    Conserved Domains (2) summary
    pfam02257
    Location:184256
    RFX_DNA_binding; RFX DNA-binding domain
    pfam04589
    Location:51137
    RFX1_trans_act; RFX1 transcription activation region
  11. XM_024447630.1XP_024303398.1  transcription factor RFX3 isoform X1

    Conserved Domains (2) summary
    pfam02257
    Location:214286
    RFX_DNA_binding; RFX DNA-binding domain
    pfam04589
    Location:81167
    RFX1_trans_act; RFX1 transcription activation region
  12. XM_006716845.2XP_006716908.1  transcription factor RFX3 isoform X5

    See identical proteins and their annotated locations for XP_006716908.1

    Conserved Domains (2) summary
    pfam02257
    Location:184256
    RFX_DNA_binding; RFX DNA-binding domain
    pfam04589
    Location:51137
    RFX1_trans_act; RFX1 transcription activation region
  13. XM_024447635.1XP_024303403.1  transcription factor RFX3 isoform X5

    Conserved Domains (2) summary
    pfam02257
    Location:184256
    RFX_DNA_binding; RFX DNA-binding domain
    pfam04589
    Location:51137
    RFX1_trans_act; RFX1 transcription activation region
  14. XM_006716840.2XP_006716903.1  transcription factor RFX3 isoform X2

    Conserved Domains (2) summary
    pfam02257
    Location:194266
    RFX_DNA_binding; RFX DNA-binding domain
    pfam04589
    Location:61147
    RFX1_trans_act; RFX1 transcription activation region
  15. XM_024447634.1XP_024303402.1  transcription factor RFX3 isoform X5

    Conserved Domains (2) summary
    pfam02257
    Location:184256
    RFX_DNA_binding; RFX DNA-binding domain
    pfam04589
    Location:51137
    RFX1_trans_act; RFX1 transcription activation region
  16. XM_011517998.2XP_011516300.1  transcription factor RFX3 isoform X5

    See identical proteins and their annotated locations for XP_011516300.1

    Conserved Domains (2) summary
    pfam02257
    Location:184256
    RFX_DNA_binding; RFX DNA-binding domain
    pfam04589
    Location:51137
    RFX1_trans_act; RFX1 transcription activation region
  17. XM_006716843.2XP_006716906.1  transcription factor RFX3 isoform X5

    See identical proteins and their annotated locations for XP_006716906.1

    Conserved Domains (2) summary
    pfam02257
    Location:184256
    RFX_DNA_binding; RFX DNA-binding domain
    pfam04589
    Location:51137
    RFX1_trans_act; RFX1 transcription activation region
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