Human Gene RFX1 (ENST00000254325.9_7) from GENCODE V47lift37
  Description: regulatory factor X1 (from RefSeq NM_002918.5)
Gencode Transcript: ENST00000254325.9_7
Gencode Gene: ENSG00000132005.9_9
Transcript (Including UTRs)
   Position: hg19 chr19:14,072,342-14,117,132 Size: 44,791 Total Exon Count: 21 Strand: -
Coding Region
   Position: hg19 chr19:14,073,507-14,104,655 Size: 31,149 Coding Exon Count: 20 

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Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr19:14,072,342-14,117,132)mRNA (may differ from genome)Protein (979 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMalacardsMGIOMIMPubMedUniProtKB
WikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: RFX1_HUMAN
DESCRIPTION: RecName: Full=MHC class II regulatory factor RFX1; AltName: Full=Enhancer factor C; Short=EF-C; AltName: Full=Regulatory factor X 1; Short=RFX; AltName: Full=Transcription factor RFX1;
FUNCTION: Regulatory factor essential for MHC class II genes expression. Binds to the X boxes of MHC class II genes. Also binds to an inverted repeat (ENH1) required for hepatitis B virus genes expression and to the most upstream element (alpha) of the RPL30 promoter.
SUBUNIT: Binds DNA as a homodimer.
SUBCELLULAR LOCATION: Nucleus.
SIMILARITY: Belongs to the RFX family.
SIMILARITY: Contains 1 RFX-type winged-helix DNA-binding domain.

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  MalaCards Disease Associations
  MalaCards Gene Search: RFX1
Diseases sorted by gene-association score: mhc class ii deficiency (6), bare lymphocyte syndrome, type ii, complementation group c (4), combined t cell and b cell immunodeficiency (1)

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 21.73 RPKM in Testis
Total median expression: 263.39 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -85.00270-0.315 Picture PostScript Text
3' UTR -446.701165-0.383 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR003150 - DNA-bd_RFX
IPR007668 - RFX1_trans_act
IPR011991 - WHTH_trsnscrt_rep_DNA-bd

Pfam Domains:
PF02257 - RFX DNA-binding domain
PF04589 - RFX1 transcription activation region

SCOP Domains:
46785 - "Winged helix" DNA-binding domain

Protein Data Bank (PDB) 3-D Structure
MuPIT help
1DP7 - X-ray


ModBase Predicted Comparative 3D Structure on P22670
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
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 RGDEnsembl   
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000978 RNA polymerase II core promoter proximal region sequence-specific DNA binding
GO:0000981 RNA polymerase II transcription factor activity, sequence-specific DNA binding
GO:0003677 DNA binding
GO:0003705 transcription factor activity, RNA polymerase II distal enhancer sequence-specific binding
GO:0005515 protein binding

Biological Process:
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0006357 regulation of transcription from RNA polymerase II promoter
GO:0006955 immune response

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0043231 intracellular membrane-bounded organelle


-  Descriptions from all associated GenBank mRNAs
  BC049826 - Homo sapiens regulatory factor X, 1 (influences HLA class II expression), mRNA (cDNA clone MGC:47525 IMAGE:6043247), complete cds.
JD385005 - Sequence 366029 from Patent EP1572962.
JD226505 - Sequence 207529 from Patent EP1572962.
JD232594 - Sequence 213618 from Patent EP1572962.
JD187154 - Sequence 168178 from Patent EP1572962.
JD203955 - Sequence 184979 from Patent EP1572962.
JD099910 - Sequence 80934 from Patent EP1572962.
JD390183 - Sequence 371207 from Patent EP1572962.
JD107125 - Sequence 88149 from Patent EP1572962.
JD128750 - Sequence 109774 from Patent EP1572962.
JD560615 - Sequence 541639 from Patent EP1572962.
JD302052 - Sequence 283076 from Patent EP1572962.
JD485316 - Sequence 466340 from Patent EP1572962.
JD383740 - Sequence 364764 from Patent EP1572962.
JD367854 - Sequence 348878 from Patent EP1572962.
JD517217 - Sequence 498241 from Patent EP1572962.
JD257814 - Sequence 238838 from Patent EP1572962.
JD289415 - Sequence 270439 from Patent EP1572962.
JD291256 - Sequence 272280 from Patent EP1572962.
JD384401 - Sequence 365425 from Patent EP1572962.
A20498 - RFX gene.
X58964 - H.sapiens gene for MHC class II regulatory factor RFX.
JD415980 - Sequence 397004 from Patent EP1572962.
AB527436 - Synthetic construct DNA, clone: pF1KE1026, Homo sapiens RFX1 gene for regulatory factor X, 1, without stop codon, in Flexi system.
AK309824 - Homo sapiens cDNA, FLJ99865.

-  Other Names for This Gene
  Alternate Gene Symbols: ENST00000254325.1, ENST00000254325.2, ENST00000254325.3, ENST00000254325.4, ENST00000254325.5, ENST00000254325.6, ENST00000254325.7, ENST00000254325.8, NM_002918, P22670, RFX1_HUMAN, uc317fod.1, uc317fod.2
UCSC ID: ENST00000254325.9_7
RefSeq Accession: NM_002918.5
Protein: P22670 (aka RFX1_HUMAN)

-  Gene Model Information
  Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.