Human Gene RBFOX3 (ENST00000580155.5) from GENCODE V44
  Description: RNA-binding protein that regulates alternative splicing events (By similarity). (from UniProt A6NFN3)
RefSeq Summary (NM_001082575): This gene encodes a member of the RNA-binding FOX protein family which is involved in the regulation of alternative splicing of pre-mRNA. The protein has an N-terminal proline-rich region, an RNA recognition motif (RRM) domain, and a C-terminal alanine-rich region. This gene produces the neuronal nuclei (NeuN) antigen that has been widely used as a marker for post-mitotic neurons. This gene has its highest expression in the central nervous system and plays a prominent role in neural tissue development and regulation of adult brain function. Mutations in this gene have been associated with numerous neurological disorders. Alternative splicing of this gene results in multiple transcript variants encoding distinct isoforms. [provided by RefSeq, May 2017]. Sequence Note: This RefSeq record was created from transcript and genomic sequence data to make the sequence consistent with the reference genome assembly. The genomic coordinates used for the transcript record were based on transcript alignments.
Gencode Transcript: ENST00000580155.5
Gencode Gene: ENSG00000167281.20
Transcript (Including UTRs)
   Position: hg38 chr17:79,090,816-79,516,148 Size: 425,333 Total Exon Count: 15 Strand: -
Coding Region
   Position: hg38 chr17:79,090,883-79,115,715 Size: 24,833 Coding Exon Count: 11 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
RNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA DescriptionsOther Names
Methods
Data last updated at UCSC: 2023-08-18 00:09:47

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr17:79,090,816-79,516,148)mRNA (may differ from genome)Protein (312 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblExonPrimerGencodeGeneCardsHGNC
LynxMalacardsMGIneXtProtPubMedUniProtKB
Wikipedia

-  Comments and Description Text from UniProtKB
  ID: RFOX3_HUMAN
DESCRIPTION: RecName: Full=RNA binding protein fox-1 homolog 3; AltName: Full=Fox-1 homolog C;
FUNCTION: RNA-binding protein that regulates alternative splicing events (By similarity).
SUBCELLULAR LOCATION: Nucleus (By similarity). 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: RBFOX3
Diseases sorted by gene-association score: sella turcica neoplasm (10), tuberculum sellae meningioma (10), spinocerebellar ataxia 36 (7), gangliocytoma (7), cerebral ventricle cancer (6), cerebellar liponeurocytoma (6), supratentorial cancer (6), cerebrum cancer (6), vertebral artery occlusion (5), spinal cord ependymoma (5), tanycytic ependymoma (5), pineal parenchymal tumor of intermediate differentiation (5), childhood oligodendroglioma (5), papillary ependymoma (5), cauda equina neoplasm (5), brain germinoma (4), nervous system disease (1)

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -180.10513-0.351 Picture PostScript Text
3' UTR -7.3067-0.109 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 A6NFN3
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-  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 BrowserGenome BrowserNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
MGIRGDEnsembl   
Protein SequenceProtein SequenceProtein Sequence   
AlignmentAlignmentAlignment   

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003676 nucleic acid binding
GO:0003677 DNA binding
GO:0003723 RNA binding
GO:0003729 mRNA 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:0043484 regulation of RNA splicing

Cellular Component:
GO:0005622 intracellular
GO:0005634 nucleus
GO:0005737 cytoplasm
GO:0043025 neuronal cell body
GO:0043204 perikaryon


-  Descriptions from all associated GenBank mRNAs
  AK293617 - Homo sapiens cDNA FLJ56884 complete cds.
AK293905 - Homo sapiens cDNA FLJ58356 complete cds.
AK054893 - Homo sapiens cDNA FLJ30331 fis, clone BRACE2007232.
BC093713 - Homo sapiens hexaribonucleotide binding protein 3, mRNA (cDNA clone IMAGE:7939558), complete cds.
AK124644 - Homo sapiens cDNA FLJ42653 fis, clone BRACE3032983.
AK128131 - Homo sapiens cDNA FLJ46252 fis, clone TESTI4021821.
AB528944 - Synthetic construct DNA, clone: pF1KE0793, Homo sapiens FLJ56884 gene for hexaribonucleotide binding protein 3, without stop codon, in Flexi system.

-  Other Names for This Gene
  Alternate Gene Symbols: A6NFN3, B4DEG6, ENST00000580155.1, ENST00000580155.2, ENST00000580155.3, ENST00000580155.4, NM_001385846, RFOX3_HUMAN, uc010dhs.1, uc010dhs.2, uc010dhs.3, uc010dhs.4, uc010dhs.5
UCSC ID: ENST00000580155.5
RefSeq Accession: NM_001082575
Protein: A6NFN3 (aka RFOX3_HUMAN)
CCDS: CCDS45805.1

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