Human Gene RBFOX2 (ENST00000359369.8) Description and Page Index
  Description: Homo sapiens RNA binding fox-1 homolog 2 (RBFOX2), transcript variant 11, mRNA. (from RefSeq NM_001349991)
RefSeq Summary (NM_001349982): 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: ENST00000359369.8
Gencode Gene: ENSG00000100320.23
Transcript (Including UTRs)
   Position: hg38 chr22:35,743,983-35,938,897 Size: 194,915 Total Exon Count: 14 Strand: -
Coding Region
   Position: hg38 chr22:35,744,195-35,809,971 Size: 65,777 Coding Exon Count: 13 

Page IndexSequence and LinksUniProtKB CommentsMalaCardsCTDRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA Descriptions
Other NamesMethods
Data last updated: 2019-09-04

-  Sequence and Links to Tools and Databases
Genomic Sequence (chr22:35,743,983-35,938,897)mRNA (may differ from genome)Protein (370 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaBioGPS
CGAPEnsemblEntrez GeneExonPrimerGeneCardsHGNC

-  Comments and Description Text from UniProtKB
DESCRIPTION: RecName: Full=RNA binding protein fox-1 homolog;
FUNCTION: RNA-binding protein that regulates alternative splicing events (By similarity).
SUBCELLULAR LOCATION: Nucleus (By similarity).

-  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 -24.9084-0.296 Picture PostScript Text
3' UTR -35.20212-0.166 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)

ModBase Predicted Comparative 3D Structure on B0QYY4
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:0003723 RNA binding

Biological Process:
GO:0006397 mRNA processing
GO:0008380 RNA splicing
GO:0043484 regulation of RNA splicing

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm
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.
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.

-  Other Names for This Gene
  Alternate Gene Symbols: B0QYY4, B0QYY4_HUMAN, NM_001349991, RBM9, RP1-41P2.9-006, uc010gwu.1, uc010gwu.2, uc010gwu.3, uc010gwu.4
UCSC ID: uc010gwu.4
RefSeq Accession: NM_001349982
Protein: B0QYY4

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