Human Gene RFXANK (uc002nls.3) Description and Page Index
  Description: Homo sapiens regulatory factor X-associated ankyrin-containing protein (RFXANK), transcript variant 1, mRNA.
RefSeq Summary (NM_003721): Major histocompatibility (MHC) class II molecules are transmembrane proteins that have a central role in development and control of the immune system. The protein encoded by this gene, along with regulatory factor X-associated protein and regulatory factor-5, forms a complex that binds to the X box motif of certain MHC class II gene promoters and activates their transcription. Once bound to the promoter, this complex associates with the non-DNA-binding factor MHC class II transactivator, which controls the cell type specificity and inducibility of MHC class II gene expression. This protein contains ankyrin repeats involved in protein-protein interactions. Mutations in this gene have been linked to bare lymphocyte syndrome type II, complementation group B. Multiple alternatively spliced transcript variants encoding different isoforms have been described for this gene. [provided by RefSeq, Jul 2013].
Transcript (Including UTRs)
   Position: hg19 chr19:19,303,008-19,312,678 Size: 9,671 Total Exon Count: 10 Strand: +
Coding Region
   Position: hg19 chr19:19,304,756-19,312,528 Size: 7,773 Coding Exon Count: 8 

Page IndexSequence and LinksUniProtKB CommentsGenetic AssociationsMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr19:19,303,008-19,312,678)mRNA (may differ from genome)Protein (260 aa)
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-  Comments and Description Text from UniProtKB
  ID: RFXK_HUMAN
DESCRIPTION: RecName: Full=DNA-binding protein RFXANK; AltName: Full=Ankyrin repeat family A protein 1; AltName: Full=Regulatory factor X subunit B; Short=RFX-B; AltName: Full=Regulatory factor X-associated ankyrin-containing protein;
FUNCTION: Activates transcription from class II MHC promoters. Activation requires the activity of the MHC class II transactivator (MHC2TA). May regulate other genes in the cell. RFX binds the X1 box of MHC-II promoters. Isoform RFX-B-delta5 is not involved in the positive regulation of MHC class II genes.
SUBUNIT: The RFX heterotetrameric complex consists of 2 molecules of RFX5 and one each of RFXAP and RFX-B/RFXANK; with each subunit representing a separate complementation group. RFX forms cooperative DNA binding complexes with X2BP and CBF/NF-Y. RFX associates with MHC2TA to form an active transcriptional complex.
SUBCELLULAR LOCATION: Nucleus.
TISSUE SPECIFICITY: Ubiquitous.
DOMAIN: The third ankyrin repeat is required for association with the two other RFX subunits; RFX5 and RFXAP. The three central ANK repeats mediate binding to the PxLPxI/L motif of RFX5.
DISEASE: Defects in RFXANK are a cause of bare lymphocyte syndrome type 2 (BLS2) [MIM:209920]; also known as hereditary MHC class II deficiency or HLA class II-deficient combined immunodeficiency. BLS2 is a severe combined immunodeficiency disease with early onset. It is characterized by a profound defect in constitutive and interferon-gamma induced MHC II expression, absence of cellular and humoral T-cell response to antigen challenge, hypogammaglobulinemia and impaired antibody production. The consequence include extreme susceptibility to viral, bacterial and fungal infections.
SIMILARITY: Contains 5 ANK repeats.
WEB RESOURCE: Name=RFXANKbase; Note=RFXANK mutation db; URL="http://bioinf.uta.fi/RFXANKbase/";

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): RFXANK
CDC HuGE Published Literature: RFXANK
Positive Disease Associations: Potassium
Related Studies:
  1. Potassium
    , , . [PubMed 0]

-  MalaCards Disease Associations
  MalaCards Gene Search: RFXANK
Diseases sorted by gene-association score: bare lymphocyte syndrome, type ii, complementation group c* (1182), mhc class ii deficiency (12), mature b-cell neoplasm (10), acrocallosal syndrome (9), bare lymphocyte syndrome, type i (6), splenic disease (5), sciatic neuropathy (5), primary immunodeficiency disease (3), combined t cell and b cell immunodeficiency (1)
* = Manually curated disease association

-  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: 29.37 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 851.20 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 -224.00505-0.444 Picture PostScript Text
3' UTR -58.10150-0.387 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
IPR002110 - Ankyrin_rpt
IPR020683 - Ankyrin_rpt-contain_dom
IPR017362 - DNA-bd_RFXANK

Pfam Domains:
PF00023 - Ankyrin repeat
PF12796 - Ankyrin repeats (3 copies)
PF13606 - Ankyrin repeat
PF13637 - Ankyrin repeats (many copies)
PF13857 - Ankyrin repeats (many copies)

SCOP Domains:
48403 - Ankyrin repeat

Protein Data Bank (PDB) 3-D Structure
MuPIT help

3UXG
- X-ray MuPIT

3V30
- X-ray MuPIT


ModBase Predicted Comparative 3D Structure on O14593
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 orthologGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGD    
 Protein Sequence    
 Alignment    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003677 DNA binding
GO:0003700 transcription factor activity, sequence-specific DNA binding
GO:0003712 transcription cofactor activity
GO:0042826 histone deacetylase 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:0007265 Ras protein signal transduction
GO:0045944 positive regulation of transcription from RNA polymerase II promoter

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0045171 intercellular bridge


-  Descriptions from all associated GenBank mRNAs
  BC114558 - Homo sapiens regulatory factor X-associated ankyrin-containing protein, mRNA (cDNA clone MGC:138627 IMAGE:40032318), complete cds.
BC114563 - Homo sapiens regulatory factor X-associated ankyrin-containing protein, transcript variant 1, mRNA (cDNA clone MGC:138628 IMAGE:40032319), complete cds.
JD485199 - Sequence 466223 from Patent EP1572962.
JD480782 - Sequence 461806 from Patent EP1572962.
AF094760 - Homo sapiens RFXANK (RFXANK) mRNA, complete cds.
JD540628 - Sequence 521652 from Patent EP1572962.
JD137613 - Sequence 118637 from Patent EP1572962.
JD298492 - Sequence 279516 from Patent EP1572962.
JD266265 - Sequence 247289 from Patent EP1572962.
JD310475 - Sequence 291499 from Patent EP1572962.
AF105427 - Homo sapiens transcription factor RFX-B (RFXB) mRNA, complete cds.
AF077196 - Homo sapiens ankyrin-like protein mRNA, complete cds.
AF105428 - Homo sapiens putative protein RFX-Bdelta4 (RFXB) mRNA, complete cds.
JD149786 - Sequence 130810 from Patent EP1572962.
JD216593 - Sequence 197617 from Patent EP1572962.
JD214907 - Sequence 195931 from Patent EP1572962.
JD073210 - Sequence 54234 from Patent EP1572962.
AB464138 - Synthetic construct DNA, clone: pF1KB8237, Homo sapiens RFXANK gene for regulatory factor X-associated ankyrin-containing protein, without stop codon, in Flexi system.
KJ892576 - Synthetic construct Homo sapiens clone ccsbBroadEn_01970 RFXANK gene, encodes complete protein.
KJ901895 - Synthetic construct Homo sapiens clone ccsbBroadEn_11289 RFXANK gene, encodes complete protein.
KR711856 - Synthetic construct Homo sapiens clone CCSBHm_00031393 RFXANK (RFXANK) mRNA, encodes complete protein.
KR711857 - Synthetic construct Homo sapiens clone CCSBHm_00031394 RFXANK (RFXANK) mRNA, encodes complete protein.
CR456981 - Homo sapiens full open reading frame cDNA clone RZPDo834C125D for gene RFXANK, regulatory factor X-associated ankyrin-containing protein; complete cds, incl. stopcodon.
CR542199 - Homo sapiens full open reading frame cDNA clone RZPDo834E1024D for gene RFXANK, regulatory factor X-associated ankyrin-containing protein; complete cds, without stopcodon.
JD248081 - Sequence 229105 from Patent EP1572962.
X75690 - H.sapiens (TL33) mRNA from LNCaP cell line.
JD492515 - Sequence 473539 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa04612 - Antigen processing and presentation
hsa05340 - Primary immunodeficiency

-  Other Names for This Gene
  Alternate Gene Symbols: ANKRA1, NM_003721, NP_003712, O14593, O95839, Q6FGA8, RFXB, RFXK_HUMAN
UCSC ID: uc002nls.3
RefSeq Accession: NM_003721
Protein: O14593 (aka RFXK_HUMAN)
CCDS: CCDS12395.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_003721.2
exon count: 10CDS single in 3' UTR: no RNA size: 1438
ORF size: 783CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 1766.00frame shift in genome: no % Coverage: 100.00
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
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.