Human Gene RBFOX2 (ENST00000405409.6) from GENCODE V44
  Description: Homo sapiens RNA binding fox-1 homolog 2 (RBFOX2), transcript variant 2, mRNA. (from RefSeq NM_014309)
RefSeq Summary (NM_014309): This gene is one of several human genes similar to the C. elegans gene Fox-1. This gene encodes an RNA binding protein that is thought to be a key regulator of alternative exon splicing in the nervous system and other cell types. The protein binds to a conserved UGCAUG element found downstream of many alternatively spliced exons and promotes inclusion of the alternative exon in mature transcripts. The protein also interacts with the estrogen receptor 1 transcription factor and regulates estrogen receptor 1 transcriptional activity. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008].
Gencode Transcript: ENST00000405409.6
Gencode Gene: ENSG00000100320.24
Transcript (Including UTRs)
   Position: hg38 chr22:35,738,736-35,840,587 Size: 101,852 Total Exon Count: 12 Strand: -
Coding Region
   Position: hg38 chr22:35,744,195-35,840,218 Size: 96,024 Coding Exon Count: 12 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesMethods
Data last updated at UCSC: 2023-08-18 00:09:47

-  Sequence and Links to Tools and Databases
Genomic Sequence (chr22:35,738,736-35,840,587)mRNA (may differ from genome)Protein (367 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGencodeGeneCards

-  Comments and Description Text from UniProtKB
DESCRIPTION: RecName: Full=RNA binding protein fox-1 homolog 2; AltName: Full=Fox-1 homolog B; AltName: Full=Hexaribonucleotide-binding protein 2; AltName: Full=RNA-binding motif protein 9; AltName: Full=RNA-binding protein 9; AltName: Full=Repressor of tamoxifen transcriptional activity;
FUNCTION: RNA-binding protein that regulates alternative splicing events by binding to 5'-UGCAUGU-3' elements. Prevents binding of U2AF2 to the 3'-splice site. Regulates alternative splicing of tissue-specific exons and of differentially spliced exons during erythropoiesis (By similarity). RNA-binding protein that seems to act as a coregulatory factor of ER-alpha.
SUBUNIT: Interacts with ER-alpha N-terminal activation domain.
INTERACTION: P54253:ATXN1; NbExp=6; IntAct=EBI-746056, EBI-930964; P03372:ESR1; NbExp=4; IntAct=EBI-746056, EBI-78473; Q96PU8:QKI; NbExp=2; IntAct=EBI-746056, EBI-945792; Q9NWB1:RBFOX1; NbExp=2; IntAct=EBI-746056, EBI-945906;
SUBCELLULAR LOCATION: Nucleus. Cytoplasm (By similarity).
SIMILARITY: Contains 1 RRM (RNA recognition motif) 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: RBFOX2
Diseases sorted by gene-association score: sarcocystosis (8), human herpesvirus 8 (7), rhizomelic chondrodysplasia punctata, type 1 (5)

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

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 75.46 RPKM in Brain - Cerebellar Hemisphere
Total median expression: 1077.79 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 -109.00369-0.295 Picture PostScript Text
3' UTR -1677.405459-0.307 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
IPR025670 - Fox-1_C_dom
IPR012677 - Nucleotide-bd_a/b_plait
IPR017325 - RNA-bd_Fox-1
IPR000504 - RRM_dom

Pfam Domains:
PF12414 - Calcitonin gene-related peptide regulator C terminal
PF00076 - RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain)

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

ModBase Predicted Comparative 3D Structure on O43251
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
Genome BrowserGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
Protein SequenceProtein Sequence    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003676 nucleic acid binding
GO:0003714 transcription corepressor activity
GO:0003723 RNA binding
GO:0003729 mRNA binding
GO:0005515 protein binding
GO:0008134 transcription factor binding

Biological Process:
GO:0000381 regulation of alternative mRNA splicing, via spliceosome
GO:0006397 mRNA processing
GO:0007399 nervous system development
GO:0008380 RNA splicing
GO:0008543 fibroblast growth factor receptor signaling pathway
GO:0010724 regulation of definitive erythrocyte differentiation
GO:0016070 RNA metabolic process
GO:0021942 radial glia guided migration of Purkinje cell
GO:0030520 intracellular estrogen receptor signaling pathway
GO:0042127 regulation of cell proliferation
GO:0043484 regulation of RNA splicing
GO:0045892 negative regulation of transcription, DNA-templated
GO:0048813 dendrite morphogenesis
GO:0050885 neuromuscular process controlling balance

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

-  Descriptions from all associated GenBank mRNAs
  DQ891720 - Synthetic construct clone IMAGE:100004350; FLH179401.01X; RZPDo839G02130D RNA binding motif protein 9 (RBM9) gene, encodes complete protein.
AF229058 - Homo sapiens hexaribonucleotide binding protein 2 (HRNBP2) mRNA, complete cds.
AL009266 - H. sapiens cDNA similar to C. elegans RNA binding protein U14946, Q10572, complete cds.
AK291460 - Homo sapiens cDNA FLJ77497 complete cds, highly similar to Homo sapiens RNA binding motif protein 9 (RBM9), transcript variant 1, mRNA.
BC013115 - Homo sapiens RNA binding motif protein 9, mRNA (cDNA clone MGC:16969 IMAGE:4346741), complete cds.
AM419009 - Homo sapiens partial mRNA for RNA binding motif protein 9 (RBM9 gene), splice variant RBM9*1.
BC025281 - Homo sapiens RNA binding motif protein 9, mRNA (cDNA clone MGC:39192 IMAGE:4555865), complete cds.
AK055213 - Homo sapiens cDNA FLJ30651 fis, clone D3OST2000184, highly similar to RNA binding motif protein 9.
AY072786 - Homo sapiens RNA binding motif protein 9 mRNA, complete cds.
CR456559 - Homo sapiens RBM9 full length open reading frame (ORF) cDNA clone (cDNA clone C22ORF:pGEM.RBM9.V2).
AY960684 - Homo sapiens RNA binding motif protein 9 (RBM9) mRNA, complete cds.
AK314632 - Homo sapiens cDNA, FLJ95475.
AB649123 - Homo sapiens RBFOX2 mRNA, partial cds.
CU013159 - Homo sapiens RBM9, mRNA (cDNA clone IMAGE:100000512), complete cds, with stop codon, in Gateway system.
DQ778625 - Homo sapiens unknown mRNA.
KJ893396 - Synthetic construct Homo sapiens clone ccsbBroadEn_02790 RBFOX2 gene, encodes complete protein.
KJ902351 - Synthetic construct Homo sapiens clone ccsbBroadEn_11745 RBFOX2 gene, encodes complete protein.
DQ894897 - Synthetic construct Homo sapiens clone IMAGE:100009357; FLH263701.01L; RZPDo839G01129D RNA binding motif protein 9 (RBM9) gene, encodes complete protein.
DQ894898 - Synthetic construct Homo sapiens clone IMAGE:100009358; FLH179397.01L; RZPDo839G02129D RNA binding motif protein 9 (RBM9) gene, encodes complete protein.
AB463238 - Synthetic construct DNA, clone: pF1KB8462, Homo sapiens RBM9 gene for RNA binding motif protein 9, without stop codon, in Flexi system.
CU013447 - Homo sapiens RBM9, mRNA (cDNA clone IMAGE:100000416), complete cds, without stop codon, in Gateway system.
CU692956 - Synthetic construct Homo sapiens gateway clone IMAGE:100021964 5' read RBM9 mRNA.
AL832604 - Homo sapiens mRNA; cDNA DKFZp451D1017 (from clone DKFZp451D1017).
AK130730 - Homo sapiens cDNA FLJ27220 fis, clone SYN04331.
AK057055 - Homo sapiens cDNA FLJ32493 fis, clone SKNSH2000051.
AK091398 - Homo sapiens cDNA FLJ34079 fis, clone FCBBF3003800.
JD367806 - Sequence 348830 from Patent EP1572962.
JD205447 - Sequence 186471 from Patent EP1572962.
JD339727 - Sequence 320751 from Patent EP1572962.
JD422566 - Sequence 403590 from Patent EP1572962.
JD325514 - Sequence 306538 from Patent EP1572962.
JD375384 - Sequence 356408 from Patent EP1572962.
JD069104 - Sequence 50128 from Patent EP1572962.
JD019671 - Sequence 695 from Patent EP1572962.
JD032016 - Sequence 13040 from Patent EP1572962.
JD479600 - Sequence 460624 from Patent EP1572962.
JD349183 - Sequence 330207 from Patent EP1572962.
JD133580 - Sequence 114604 from Patent EP1572962.
JD396440 - Sequence 377464 from Patent EP1572962.
JD166300 - Sequence 147324 from Patent EP1572962.
JD483885 - Sequence 464909 from Patent EP1572962.
JD121714 - Sequence 102738 from Patent EP1572962.
JD409554 - Sequence 390578 from Patent EP1572962.
JD186426 - Sequence 167450 from Patent EP1572962.
JD037297 - Sequence 18321 from Patent EP1572962.
JD463680 - Sequence 444704 from Patent EP1572962.
JD454294 - Sequence 435318 from Patent EP1572962.
JD305211 - Sequence 286235 from Patent EP1572962.
JD216799 - Sequence 197823 from Patent EP1572962.
JD248769 - Sequence 229793 from Patent EP1572962.
JD555015 - Sequence 536039 from Patent EP1572962.
JD250759 - Sequence 231783 from Patent EP1572962.
JD493134 - Sequence 474158 from Patent EP1572962.
LF210343 - JP 2014500723-A/17846: Polycomb-Associated Non-Coding RNAs.
MA445920 - JP 2018138019-A/17846: Polycomb-Associated Non-Coding RNAs.
JD123579 - Sequence 104603 from Patent EP1572962.
JD520477 - Sequence 501501 from Patent EP1572962.
JD284728 - Sequence 265752 from Patent EP1572962.
JD088690 - Sequence 69714 from Patent EP1572962.
JD488838 - Sequence 469862 from Patent EP1572962.
JD286095 - Sequence 267119 from Patent EP1572962.
JD145553 - Sequence 126577 from Patent EP1572962.
JD563946 - Sequence 544970 from Patent EP1572962.
LF337172 - JP 2014500723-A/144675: Polycomb-Associated Non-Coding RNAs.
MA572749 - JP 2018138019-A/144675: Polycomb-Associated Non-Coding RNAs.
JD385841 - Sequence 366865 from Patent EP1572962.
JD385647 - Sequence 366671 from Patent EP1572962.
LF337173 - JP 2014500723-A/144676: Polycomb-Associated Non-Coding RNAs.
MA572750 - JP 2018138019-A/144676: Polycomb-Associated Non-Coding RNAs.
JD472036 - Sequence 453060 from Patent EP1572962.
JD559893 - Sequence 540917 from Patent EP1572962.
JD166404 - Sequence 147428 from Patent EP1572962.
JD286212 - Sequence 267236 from Patent EP1572962.
JD424543 - Sequence 405567 from Patent EP1572962.
JD325096 - Sequence 306120 from Patent EP1572962.
JD524924 - Sequence 505948 from Patent EP1572962.
JD291556 - Sequence 272580 from Patent EP1572962.
JD284590 - Sequence 265614 from Patent EP1572962.
JD236135 - Sequence 217159 from Patent EP1572962.
JD356180 - Sequence 337204 from Patent EP1572962.
JD500653 - Sequence 481677 from Patent EP1572962.
JD045579 - Sequence 26603 from Patent EP1572962.
JD152755 - Sequence 133779 from Patent EP1572962.
JD490932 - Sequence 471956 from Patent EP1572962.
JD403758 - Sequence 384782 from Patent EP1572962.
JD236499 - Sequence 217523 from Patent EP1572962.
JD299238 - Sequence 280262 from Patent EP1572962.
JD301321 - Sequence 282345 from Patent EP1572962.
JD302161 - Sequence 283185 from Patent EP1572962.
JD502081 - Sequence 483105 from Patent EP1572962.
JD298240 - Sequence 279264 from Patent EP1572962.
JD368842 - Sequence 349866 from Patent EP1572962.
JD451860 - Sequence 432884 from Patent EP1572962.
JD166563 - Sequence 147587 from Patent EP1572962.
JD377113 - Sequence 358137 from Patent EP1572962.
JD483335 - Sequence 464359 from Patent EP1572962.
JD565858 - Sequence 546882 from Patent EP1572962.
JD284142 - Sequence 265166 from Patent EP1572962.
JD113016 - Sequence 94040 from Patent EP1572962.
JD104245 - Sequence 85269 from Patent EP1572962.
JD237058 - Sequence 218082 from Patent EP1572962.
JD313170 - Sequence 294194 from Patent EP1572962.
JD495134 - Sequence 476158 from Patent EP1572962.
JD039677 - Sequence 20701 from Patent EP1572962.
JD263056 - Sequence 244080 from Patent EP1572962.
JD306611 - Sequence 287635 from Patent EP1572962.
JD093800 - Sequence 74824 from Patent EP1572962.
JD290128 - Sequence 271152 from Patent EP1572962.
JD501832 - Sequence 482856 from Patent EP1572962.
JD262875 - Sequence 243899 from Patent EP1572962.
JD244802 - Sequence 225826 from Patent EP1572962.
JD436294 - Sequence 417318 from Patent EP1572962.
JD426292 - Sequence 407316 from Patent EP1572962.
JD436402 - Sequence 417426 from Patent EP1572962.
JD512181 - Sequence 493205 from Patent EP1572962.
AK091695 - Homo sapiens cDNA FLJ34376 fis, clone FEBRA2017780, weakly similar to RNA binding motif protein 9.
AX747134 - Sequence 659 from Patent EP1308459.
JD542482 - Sequence 523506 from Patent EP1572962.
LF210344 - JP 2014500723-A/17847: Polycomb-Associated Non-Coding RNAs.
MA445921 - JP 2018138019-A/17847: Polycomb-Associated Non-Coding RNAs.
JD086312 - Sequence 67336 from Patent EP1572962.
JD123603 - Sequence 104627 from Patent EP1572962.
JD502635 - Sequence 483659 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein O43251 (Reactome details) participates in the following event(s):

R-HSA-6803527 ESRP1 and 2 bind FGFR2 pre-mRNA to promote FGFR2b maturation and expression
R-HSA-6803529 FGFR2 alternative splicing
R-HSA-5654738 Signaling by FGFR2
R-HSA-190236 Signaling by FGFR
R-HSA-9006934 Signaling by Receptor Tyrosine Kinases
R-HSA-162582 Signal Transduction

-  Other Names for This Gene
  Alternate Gene Symbols: A4F5G8, A8K5Z5, B0QYY8, B0QYY9, ENST00000405409.1, ENST00000405409.2, ENST00000405409.3, ENST00000405409.4, ENST00000405409.5, FOX2, HRNBP2, NM_014309, O43251, Q0PRL5, Q0VH35, Q5TF71, Q6IC09, Q8TD00, Q8WYB1, Q96DZ6, Q96NL7, Q9UGW4, Q9UH33, RBM9, RFOX2_HUMAN, RTA, uc003aok.1, uc003aok.2, uc003aok.3, uc003aok.4, uc003aok.5
UCSC ID: ENST00000405409.6
RefSeq Accession: NM_014309
Protein: O43251 (aka RFOX2_HUMAN)
CCDS: CCDS46700.1, CCDS46701.1, CCDS13921.1, CCDS46699.1

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