RFXAP Gene
protein-coding GIFtS: 53
GCID: GC13P037393
|
|
regulatory factor X-associated protein
| |
Aliases for RFXAP gene
(According to
1HGNC,
2Entrez Gene,
3UniProtKB/Swiss-Prot,
4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc,
7Ensembl,
8DME,
9miRBase,
and/or 10fRNAdb) About This Section
|
| Aliases |
|---|
| Regulatory Factor X-Associated Protein1 2 | | RFX DNA-Binding Complex 36 KDa Subunit2 3 | | RFX-Associated Protein2 3 |
Export aliases for RFXAP gene to outside databasesPrevious GC identifers: GC13P035379 GC13P031379 GC13P036329 GC13P035191 GC13P036291 GC13P018207 |
Summaries for RFXAP gene(According to Entrez Gene,
Tocris Bioscience,
Wikipedia's
Gene Wiki,
PharmGKB,
UniProtKB/Swiss-Prot,
and/or
UniProtKB/TrEMBL)
About This Section
| Entrez Gene summary for RFXAP: Major histocompatibility (MHC) class II molecules are transmembrane proteins that have a central role in developmentand control of the immune system. The protein encoded by this gene, along with regulatory factor X-associatedankyrin-containing protein and regulatory factor-5, forms a complex that binds to the X box motif of certain MHC classII gene promoters and activates their transcription. Once bound to the promoter, this complex associates with thenon-DNA-binding factor MHC class II transactivator, which controls the cell type specificity and inducibility of MHCclass II gene expression. Mutations in this gene have been linked to bare lymphocyte syndrome type II, complementationgroup D. Transcript variants utilizing different polyA signals have been found for this gene. (provided by RefSeq, Jul2008) UniProtKB/Swiss-Prot: RFXAP_HUMAN, O00287Function: Part of the RFX complex that binds to the X-box of MHC II promoters Gene Wiki entry for RFXAP
|
Genomic Views for RFXAP gene
(According to
GeneLoc and/or
HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to
UCSC (hg19) and
Ensembl (release 69),
Regulatory elements and Epigenetics data according to
QIAGEN,
SABiosciences, and/or
SwitchGear Genomics) About This Section
| RefSeq DNA sequence:- NC_000013.10 NC_018924.1 NT_024524.14
Regulatory elements: SABiosciences Regulatory transcription factor binding sites in the RFXAP gene promoter: USF1 ISGF-3 MyoD Tal-1beta HNF-1A E47 Nkx6-1 HNF-1 FOXO1a FOXO1 Other transcription factors
Search SABiosciences Chromatin IP Primers for RFXAP
Epigenetics:
|  | QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat RFXAP |
Genomic Location: Genomic View: UCSC Golden Path with GeneCards custom track
Entrez Gene cytogenetic band: 13q14 Ensembl cytogenetic band: 13q13.3 HGNC cytogenetic band: 13q14RFXAP Gene in genomic location: bands according to Ensembl, locations according to
(and/or Entrez Gene and/or Ensembl if different)

GeneLoc information about chromosome 13 GeneLoc Exon Structure GeneLoc location for GC13P037393: view genomic region
(about GC identifiers)
Start:
|
37,393,339 bp from pter |
End:
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37,403,740 bp from pter |
Size:
|
10,402 bases |
Orientation:
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plus strand |
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Proteins for RFXAP gene
(According to
1UniProtKB,
HORDE,
neXtProt,
Ensembl,
and/or Reactome,
Modification sites according to 2PhosphoSitePlus,
Specific Peptides from DME,
Protein expression images according to data from SPIRE MOPED and PaxDb,
RefSeq according to NCBI,
PDB rendering according to OCA and/or Proteopedia,
Recombinant Proteins
from
EMD Millipore,
R&D Systems,
GenScript,
Enzo Life Sciences,
OriGene,
Novus Biologicals,
Sino Biological,
ProSpec, and/or
Uscn,
Biochemical Assays by
EMD Millipore,
R&D Systems,
OriGene,
GenScript,
Cell Signaling Technology,
Enzo Life Sciences, and/or
Uscn,
Ontologies according to Gene
Ontology Consortium 01 Mar 2013 and
Entrez Gene,
Antibodies by
EMD Millipore,
R&D Systems,
GenScript,
Cell Signaling Technology,
OriGene,
Novus Biologicals,
Thermo Fisher Scientific,
Abcam, and/or
Uscn)
About This Section
| UniProtKB/Swiss-Prot: RFXAP_HUMAN, O00287 (See
protein sequence)Recommended Name: Regulatory factor X-associated protein Size: 272 amino acids; 28232 Da
Subunit: The RFX heterotetrameric complex consists of 2 molecules of RFX5 and one each of RFXAP and RFX-B/RFXANK; witheach subunit representing a separate complementation group. RFX forms cooperative DNA binding complexes with X2BP andCBF/NF-Y. RFX associates with CIITA to form an active transcriptional complex
Subcellular location: Nucleus
1 PDB 3D structure from and Proteopedia for RFXAP:2KW3 (3D)
 
Secondary accessions: B2R9T8 Q5VZM6 Q8TC40Explore the universe of human proteins at neXtProt for RFXAP: NX_O00287
Post-translational modifications:
Phosphorylated1
View modification sites using PhosphoSitePlus2View neXtProt modification sites for NX_O00287 RFXAP Protein expression data from MOPED and PaxDb: About this image 
REFSEQ proteins: NP_000529.1 ENSEMBL proteins: ENSP00000255476 Human Recombinant Protein Products:
Gene Ontology (GO): 1 cellular component term (GO ID links to tree view): About this table | GO ID | Qualified GO term | Evidence | PubMed IDs |
|---|
| GO:0005634 | nucleus |
IEA | -- |
RFXAP for ontologies About GeneDecksing
RFXAP Antibody Products: Assay Products for RFXAP: |
Protein
Domains / Families for RFXAP gene(According to InterPro, ProtoNet,
UniProtKB, and/or BLOCKS,
Sets of similar genes according to GeneDecks)
About This Section
| ProtoNet protein and cluster: O00287 UniProtKB/Swiss-Prot: RFXAP_HUMAN, O00287Domain: The C-terminal domain is necessary for the RFX complex formation |
Function for RFXAP gene
(According to 1UniProtKB,
Genatlas,
LifeMap Discovery™,
IUBMB, and/or
2DME,
Human phenotypes from GenomeRNAi,
Animal models from MGI Mar 06 2013,
bound targets from SABiosciences,
miRNA Gene Targets from miRTarBase
shRNA from
OriGene,
RNAi from
EMD Millipore,
siRNAs from
OriGene,
QIAGEN,
microRNA from QIAGEN,
Gene Editing from DNA2.0,
Clones from EMD Millipore,
OriGene,
SwitchGear Genomics,
GenScript,
Sino Biological,
DNA2.0,
and Vector BioLabs,
Cell Lines from GenScript,
LifeMap BioReagents,
In Situ Hybridization Assays from Advanced Cell Diagnostics,
Ontologies according to Gene Ontology Consortium 01 Mar 2013 via
Entrez Gene.)
About This Section
| Function Summary: UniProtKB/Swiss-Prot: RFXAP_HUMAN, O00287Function: Part of the RFX complex that binds to the X-box of MHC II promoters Genatlas biochemistry entry for RFXAP:transactivating DNA binding regulatory factor,component AP,36kDa,involved in MHC class II expression,subunit of the RFXcomplex,interacting with RFX5
Clone Products: |  | Browse Clones for the Expression of Recombinant Proteins Available from EMD Millipore | |  | OriGene Myc/DDK tagged cDNA clones in CMV expression vector in human, mouse, rat for RFXAP (see all 3) OriGene untagged cDNA clones in CMV expression vector in human, mouse, rat for RFXAP (see all 2) OriGene custom cloning services – gene synthesis, subcloning, mutagenesis,
variant library, vector shuttling 
| |  | GenScript: all cDNA clones in your preferred vector: RFXAP (NM_000538) | |  | Browse Sino Biological Human cDNA Clones | |  | DNA2.0 Custom Codon Optimized Gene
Synthesis Service for RFXAP | |  | Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat RFXAP  |
In Situ Assay Products: |
| Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for RFXAP |
Gene Ontology (GO): 3 molecular function terms (GO ID links to tree view): About this table
RFXAP for ontologies About GeneDecksing
1 GenomeRNAi human phenotype for RFXAP:
|
Pathways & Interactions for RFXAP gene
(Pathways according to
EMD Millipore,
R&D Systems,
Cell Signaling Technology,
KEGG,
PharmGKB,
BioSystems,
Reactome,
Tocris Bioscience,
GeneGo (Thomson Reuters),
QIAGEN,
and/or UniProtKB,
Sets of similar genes according to GeneDecks,
Interaction Networks according to
SABiosciences,
and/or STRING,
Interactions according to 1UniProtKB,
2MINT,
3I2D, and/or
4STRING,
with links to IntAct and
Ensembl,
Ontologies according to Gene Ontology Consortium 01 Mar 2013 via
Entrez Gene).
About This Section
| Unified GeneCards pathways  About this table  See pathways by source
| Super-pathway | contained gene-specific pathways |
|---|
| 1 | Tuberculosis | | | 2 | Primary immunodeficiency | | | 3 | Allograft rejection | |
Pathway sources See GeneCards unified pathways Show all pathways
3
Kegg Pathways (Kegg details for RFXAP):
RFXAP for pathways About GeneDecksing
Interactions:
SABiosciences Gene Network CentralTM Interacting Genes and Proteins Network for RFXAP
STRING Interaction
Network Preview (showing 5 interactants - click image to see 7)
 5/9 Interacting proteins for RFXAP (O002873 ENSP000002554764) via UniProtKB, MINT, STRING, and/or I2D (see all 9)About this table
Gene Ontology (GO): 2 biological process terms (GO ID links to tree view): About this table | GO ID | Qualified GO term | Evidence | PubMed IDs |
|---|
| GO:0006355 | regulation of transcription, DNA-dependent |
-- | -- | | GO:0045893 | positive regulation of transcription, DNA-dependent |
IEA | -- |
RFXAP for ontologies About GeneDecksing
|
Drugs & Compounds for RFXAP gene(Chemical Compounds according to UniProtKB, Enzo Life Sciences,
EMD Millipore, Tocris Bioscience
HMDB,
BitterDB, and/or
Novoseek, and Drugs according to
DrugBank,
Enzo Life Sciences, and/or
PharmGKB, with drugs/clinical trials/news
search links to CenterWatch)
About This Section
|
Browse Tocris compounds for RFXAP Search CenterWatch for drugs/clinical trials and news about RFXAP 
|
Transcripts for RFXAP gene(Secondary structures according to
fRNAdb,
GenBank/EMBL/DDBJ Accessions according to
Unigene
(Build 235 Homo sapiens; Mar 10 2013) or GenBank, RefSeq according to Entrez Gene,
DOTS (version 10), and/or
AceView,
transcript ids from Ensembl
with links to UCSC,
exon structure from GeneLoc,
alternative splicing isoforms according to ASD and/or
ECgene,
RNAi Products from
EMD Millipore,
siRNAs from
OriGene,
QIAGEN,
shRNA from
OriGene,
microRNA from QIAGEN,
Tagged/untagged cDNA clones from
OriGene,
SwitchGear Genomics,
GenScript,
DNA2.0,
Vector BioLabs,
Primers from
OriGene,
SABiosciences, and/or
QIAGEN
) About This Section
| REFSEQ mRNAs for RFXAP gene: NM_000538.3 Unigene Cluster for RFXAP: Regulatory factor X-associated protein Hs.24422 [show with all ESTs]Unigene Representative Sequence: NM_0005382 Ensembl transcripts including schematic representations, and UCSC links where relevant: ENST00000255476(uc001uvu.1) ENST00000472888
Clone Products: |  | OriGene Myc/DDK tagged cDNA clones in CMV expression vector in human, mouse, rat for RFXAP (see all 3) OriGene untagged cDNA clones in CMV expression vector in human, mouse, rat for RFXAP (see all 2) OriGene custom cloning services – gene synthesis, subcloning, mutagenesis,
variant library, vector shuttling 
| |  | GenScript: all cDNA clones in your preferred vector: RFXAP (NM_000538) | |  | DNA2.0 Custom Codon Optimized Gene
Synthesis Service for RFXAP | |  | Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat RFXAP  |
Additional cDNA sequence: AK313912.1 BC026088.1 3 DOTS entries: DT.442706 DT.444375 DT.120779631 24/46 AceView cDNA sequences (see all 46): AW628164 AI360517 CA441149 AI360510 BM856211 BI823132 BF590889 CK825179 W00532 NM_000538 BC026088 BG722888 BM769875 AL079864 BU754029 BG701333 AA253207 AI742868 BE671897 BF059183 BF111841 BX113684 BI560026 H89304 GeneLoc Exon Structure
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Expression for RFXAP gene
(RNA expression data according to
H-InvDB,
NONCODE,
miRBase, and
RNAdb,
Expression images according to data from
BioGPS,
Illumina Human BodyMap, and
CGAP
SAGE,
Sets of similar genes according to GeneDecks,
in vivo and in vitro expression data from LifeMap Discovery™,
plus additional links to
Genevestigator, and/or
SOURCE, and/or
BioGPS, and/or
UniProtKB,
PCR Arrays from
SABiosciences,
Primers from
OriGene,
SABiosciences, and/or
QIAGEN,
In Situ Hybridization Assays from Advanced Cell Diagnostics)
About This Section
| RFXAP expression in normal human tissues (normalized intensities) See probesets specificity/sensitivity at GeneAnnot About this imageBioGPS CGAP TAG: GCTGTTCTAA
About this image See RFXAP Protein Expression from SPIRE MOPED and PaxDB Genevestigator expression for RFXAP
SOURCE GeneReport for Unigene cluster: Hs.24422 UniProtKB/Swiss-Prot: RFXAP_HUMAN, O00287Tissue specificity: Ubiquitous SABiosciences Custom PCR Arrays for RFXAP
Primer Products: |  | OriGene genome-wide validated SYBR primer pairs in human, mouse, rat for RFXAP Browse OriGene validated miRNA SYBR primer pairs
| |  | SABiosciences RT2 qPCR Primer Assay in human, mouse, rat RFXAP | |  | QIAGEN QuantiTect SYBR Green Assays in human, mouse, rat RFXAP | |  | QIAGEN QuantiFast Probe-based Assays in human, mouse, rat RFXAP | In Situ Assay Products: |
| Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for RFXAP |
Orthologs for RFXAP gene
(Orthologs according to
1,2HomoloGene (2older version, for species not in 1newer version),
3euGenes,
4SGD
,
5MGI Mar 06 2013,
with possible further links to
Flybase
and/or
WormBase,
and/or
6Ensembl pan taxonomic compara ,
Gene Trees according to Ensembl and
TreeFam)
About This Section
|
This gene was present in the common ancestor of chordates.
Orthologs for RFXAP gene from 5/12 species (see all 12) About this table
| Organism |
Taxonomic classification |
Gene |
Description |
Human Similarity |
Orthology Type |
Details |
mouse (Mus musculus) |
Mammalia |
Rfxap1 , 5 |
regulatory factor X-associated protein1, 5 |
79.97(n)1 80.7(a)1 |
  |
3 (25.69 cM)5 1707671 NM_133231.21 NP_573494.11 548031165 |
chicken (Gallus gallus) |
Aves |
RFXAP1 |
regulatory factor X-associated protein |
67.62(n) 62.6(a) |
  |
418899 XM_417095.3 XP_417095.3 |
lizard (Anolis carolinensis) |
Reptilia |
RFXAP6 |
-- |
76(a) |
1 ↔ 1 |
3(181462708-181464178) |
African clawed frog (Xenopus laevis) |
Amphibia |
Xl.303652 |
Xenopus laevis transcribed sequence with weak similarity more |
77.73(n) |
  |
BJ625098.1 |
zebrafish (Danio rerio) |
Actinopterygii |
Dr.124442 |
Transcribed sequence with weak similarity to protein more |
78.44(n) |
  |
CD760266.1 |
ENSEMBL Gene Tree for RFXAP (if available) TreeFam Gene Tree for RFXAP (if available)  |
Paralogs for RFXAP gene(Paralogs according to
1HomoloGene, 2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68) About This Section
| -- |
Genomic Variants for RFXAP gene(SNPs/Variants according to the
1NCBI SNP Database,
2Ensembl,
3PupaSUITE,
UniProtKB, and
DNA2.0,
Linkage Disequilibrium by HapMap,
Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene
Mutation Database (HGMD) and the Locus Specific Mutation
Databases (LSDB), Blood group antigen gene mutations by BGMUT,
Resequencing Primers from QIAGEN,
Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
About This Section
|
| Genomic Data | Transcription Related Data | Allele Frequencies | | SNP ID | Valid | Clinical significance | Chr 13 pos | Sequence | # | AA Chg | Type | More | # | Allele freq | Pop | Total sample | More |
|---|
HapMap Linkage Disequilibrium report for RFXAP (37393339 - 37403740 bp)
Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions) Database of Genomic Variants (DGV) variations for RFXAP: -- Human Gene Mutation Database (HGMD): RFXAP
Locus Specific Mutation Databases (LSDB): RFXAP
 | SABiosciences Cancer Mutation PCR Assays |
|  | QIAGEN SeqTarget long-range PCR primers in human, mouse, rat for resequencing RFXAP |
|
Disorders
/ Diseases for RFXAP gene
(in which this Gene is Involved, According to MalaCards,
OMIM, UniProtKB,
the University of Copenhagen DISEASES
database, Novoseek,
Genatlas, GeneTests,
GAD,
HuGE Navigator,
and/or TGDB.)
About This Section
|
RFXAP for disorders About GeneDecksing
OMIM gene information: 601861 OMIM disorders: 209920 UniProtKB/Swiss-Prot: RFXAP_HUMAN, O00287
Defects in RFXAP are a cause of bare lymphocyte syndrome type 2 (BLS2) [MIM:209920]; also known as hereditaryMHC class II deficiency or HLA class II-deficient combined immunodeficiency. BLS2 is a severe combinedimmunodeficiency disease with early onset. It is characterized by a profound defect in constitutive andinterferon-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 10 diseases for RFXAP: About MalaCardsbare lymphocyte syndrome, type ii, complementation group d bare lymphocyte syndrome mhc class ii deficiency severe combined immunodeficiency graft versus host disease combined immunodeficiency b-cell lymphomas immunodeficiency tuberculosis acute graft versus host disease 1 disease from the University of Copenhagen DISEASES database for RFXAP:Severe combined immunodeficiency 3 Novoseek disease relationships for RFXAP gene About this table
Export disorders for RFXAP gene to outside databases
|
Publications for RFXAP gene (in
PubMed.
Associations of this gene to articles via
1Entrez Gene,
2UniProtKB/Swiss-Prot,
3HGNC,
4GAD,
5PharmGKB,
6HMDB,
7DrugBank,
8UniProtKB/TrEMBL,
9 Novoseek, and/or
10fRNAdb)
About This Section
|
PubMed articles for RFXAP gene, integrated from 9 sources (see all 43): (articles sorted by number of sources associating them with RFXAP) | |  | Utopia: connect your pdf to the dynamic world of online information |
- RFXAP, a novel subunit of the RFX DNA binding complex is mutated in MHC class II deficiency. (PubMed id 9118943)1, 2, 3, 9 Durand B....Reith W. (1997)
- Solution structure of the heterotrimeric complex betw een the interaction domains of RFX5 and RFXAP from the RFX gene regulatory comp lex. (PubMed id 20732328)1, 2 Laird K.M....Garvie C.W. (2010)
- RFX-B is the gene responsible for the most common cause of the bare lymphocyte syndrome, an MHC class II immunodeficiency. (PubMed id 10072068)1, 2 Nagarajan U.M....Boss J.M. (1999)
- Conserved residues of the bare lymphocyte syndrome transcription factor RFXAP determine coordinate MHC class II expression. (PubMed id 16337482)1, 9 Long A.B....Boss J.M. (2006)
- Coordinate loss of MHC class II expression in the dif fuse large B cell lymphoma cell line OCI-Ly2 is due to a novel mutation in RFX- AP. (PubMed id 20024540)1, 9 Bushway M....Murphy S.P. (2010)
- Formation of the RFX gene regulatory complex induces folding of the interaction domain of RFXAP. (PubMed id 19274739)1, 9 Briggs L....Garvie C.W. (2009)
- Assembly of the RFX complex on the MHCII promoter: role of RFXAP and RFXB in relieving autoinhibition of RFX5. (PubMed id 18723135)1, 9 Garvie C.W. and Boss J.M. (2008)
- Transcriptional silencing of RFXAP in MHC class II-deficiency. (PubMed id 18336911)1, 9 van Eggermond M.C....van den Elsen P.J. (2008)
- Multiple interactions between BRG1 and MHC class II promoter binding proteins. (PubMed id 15781111)1, 9 Mudhasani R. and Fontes J.D. (2005)
- Mutation of RFXAP, a regulator of MHC class II genes, in primary MHC class II deficiency. (PubMed id 9287230)1, 9 Villard J....Mach B. (1997)
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External Searches for RFXAP gene
(in PubMed,
OMIM, and NCBI Bookshelf) About This Section
|
|
Genome Databases showing RFXAP gene
(According to
Entrez Gene,
HGNC,
AceView,
euGenes,
Ensembl,
miRBase,
ECgene,
Kegg,
and/or
H-InvDB)
About This Section
|
|
Other Databases showing RFXAP gene
(According to HUGE)
About This Section
| -- |
Specialized Databases showing RFXAP gene(According to PharmGKB,
ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL, Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot) About This Section
|
| Name | Description |
| PharmGKB entry for RFXAP | Pharmacogenomics, SNPs, Pathways | | RFXAPbase | http://bioinf.uta.fi/RFXAPbase/ |
|
| | |
About This Section
| Patent Information for RFXAP gene: Search GeneIP for patents involving RFXAP
GeneCards and IP: Japan Patent Office Licenses GeneCards European Patent Office Licenses GeneCards Improving the IP Search
|
Products for RFXAP gene(Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, SABiosciences, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Uscn, Thermo Fisher Scientific, Gene Editing from DNA2.0, Clones from EMD Millipore, OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Cell lines from GenScript and LifeMap BioReagents, PCR Arrays from SABiosciences, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, and/or
Enzo Life Sciences), In Situ Hybridization Assays from Advanced Cell Diagnostics About This Section
|
 | |
 | |
 |
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| | | | Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for RFXAP |
|  |  |  | | | ThermoFisher Antibodies for RFXAP |
| | Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat RFXAP |
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