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Protein

RNA binding protein fox-1 homolog 3

Gene

Rbfox3

Organism
Mus musculus (Mouse)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Pre-mRNA alternative splicing regulator. Regulates alternative splicing of RBFOX2 to enhance the production of mRNA species that are targeted for nonsense-mediated decay (NMD).2 Publications

GO - Molecular functioni

  • DNA binding Source: MGI
  • mRNA binding Source: GO_Central
  • nucleotide binding Source: InterPro

GO - Biological processi

Complete GO annotation...

Keywords - Biological processi

mRNA processing, mRNA splicing

Keywords - Ligandi

RNA-binding

Names & Taxonomyi

Protein namesi
Recommended name:
RNA binding protein fox-1 homolog 3
Alternative name(s):
Fox-1 homolog C
Hexaribonucleotide-binding protein 3
Short name:
Fox-3
Neuronal nuclei antigen
Short name:
NeuN antigen
Gene namesi
Name:Rbfox3
Synonyms:D11Bwg0517e, Hrnbp3
OrganismiMus musculus (Mouse)
Taxonomic identifieri10090 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeMusMus
Proteomesi
  • UP000000589 Componenti: Chromosome 11

Organism-specific databases

MGIiMGI:106368. Rbfox3.

Subcellular locationi

GO - Cellular componenti

  • cytoplasm Source: MGI
  • intracellular Source: MGI
  • neuronal cell body Source: MGI
  • nucleus Source: MGI
  • perikaryon Source: MGI
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Nucleus

Pathology & Biotechi

Disruption phenotypei

Knockout mice have significantly reduced brain weight, impaired neurofilament expression and decreased white matter volume, but normal total body mass. They show increased susceptibility to seizures and reduced anxiety-related behaviors compared with wild type littermates, as well as defective hippocampal gene expression and deficits in synaptic transmission and plasticity in the dentate gyrus.1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00003492081 – 374RNA binding protein fox-1 homolog 3Add BLAST374

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei223Asymmetric dimethylarginine; alternateCombined sources1
Modified residuei223Omega-N-methylarginine; alternateCombined sources1
Modified residuei319Asymmetric dimethylarginineCombined sources1
Modified residuei365Omega-N-methylarginineBy similarity1

Post-translational modificationi

Phosphorylated.1 Publication

Keywords - PTMi

Methylation

Proteomic databases

PaxDbiQ8BIF2.
PeptideAtlasiQ8BIF2.
PRIDEiQ8BIF2.

PTM databases

iPTMnetiQ8BIF2.
PhosphoSitePlusiQ8BIF2.

Expressioni

Tissue specificityi

Widely expressed in brain, including in cerebral cortex, hippocampus, thalamus, caudate/putamen, cerebellum, as well as in the spinal cord (at protein level). Not expressed in all neuronal cells within a region, in cerebellum, expression is absent in Purkinje cells (at protein level). Expressed in the retina in the ganglion cells and some cells in the inner nuclear layer, but absent from the photoreceptor cells and most cells in the inner nuclear layer (at protein level).4 Publications

Developmental stagei

In the neural tube, expressed as early as embryonic day 9.5 (E9.5) and expression is confined to the nervous system. By embryonic day 12.5, can be found in the developing ventral horns and is also detected in the developing dorsal horns as well as in the dorsal root ganglion. Not detected in the ventricular zone, roof plate, floor plate or marginal zone (developing white matter). It is expressed from embryonic stage to adulthood.1 Publication

Inductioni

By retinoic acid. Expression is up-regulated in P19 cells during neural differentiation upon retinoic acid treatment (at the protein level).2 Publications

Gene expression databases

BgeeiENSMUSG00000025576.
ExpressionAtlasiQ8BIF2. baseline and differential.
GenevisibleiQ8BIF2. MM.

Interactioni

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sitei100Interaction with RNABy similarity1
Sitei108Interaction with RNABy similarity1
Sitei109Interaction with RNABy similarity1
Sitei133Interaction with RNABy similarity1
Sitei138Interaction with RNABy similarity1
Sitei142Interaction with RNABy similarity1
Sitei166Interaction with RNABy similarity1
Sitei176Interaction with RNABy similarity1

Binary interactionsi

WithEntry#Exp.IntActNotes
HIF1AQ166652EBI-4567146,EBI-447269From a different organism.
Hif1aQ612212EBI-4567146,EBI-298954

Protein-protein interaction databases

IntActiQ8BIF2. 4 interactors.
MINTiMINT-4110740.
STRINGi10090.ENSMUSP00000017576.

Structurei

3D structure databases

ProteinModelPortaliQ8BIF2.
SMRiQ8BIF2.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini99 – 175RRMPROSITE-ProRule annotationAdd BLAST77

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Compositional biasi4 – 58Pro-richAdd BLAST55
Compositional biasi242 – 295Pro-richAdd BLAST54

Sequence similaritiesi

Contains 1 RRM (RNA recognition motif) domain.PROSITE-ProRule annotation

Phylogenomic databases

eggNOGiKOG0125. Eukaryota.
ENOG4111WJT. LUCA.
GeneTreeiENSGT00390000013767.
HOGENOMiHOG000230971.
HOVERGENiHBG000044.
InParanoidiQ8BIF2.
KOiK14946.
OMAiHTIGPTA.
OrthoDBiEOG091G15X5.
PhylomeDBiQ8BIF2.
TreeFamiTF315942.

Family and domain databases

Gene3Di3.30.70.330. 1 hit.
InterProiIPR025670. Fox-1_C_dom.
IPR012677. Nucleotide-bd_a/b_plait.
IPR017325. RNA-bd_Fox-1.
IPR000504. RRM_dom.
[Graphical view]
PfamiPF12414. Fox-1_C. 2 hits.
PF00076. RRM_1. 1 hit.
[Graphical view]
PIRSFiPIRSF037932. Ataxin_2_bd_A2BP. 1 hit.
SMARTiSM00360. RRM. 1 hit.
[Graphical view]
SUPFAMiSSF54928. SSF54928. 1 hit.
PROSITEiPS50102. RRM. 1 hit.
[Graphical view]

Sequences (5)i

Sequence statusi: Complete.

This entry describes 5 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 1 (identifier: Q8BIF2-1) [UniParc]FASTAAdd to basket
Also known as: Fox3v1, Fox-3-L

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

« Hide

        10         20         30         40         50
MAQPYPPAQY PPPPQNGIPA EYAPPPPHPT QDYSGQTPVP PEHGMTLYTP
60 70 80 90 100
AQTHPEQPGT EASTQPIAGT QTVPQADEAA QTDNQQLHPS DPTEKQQPKR
110 120 130 140 150
LHVSNIPFRF RDPDLRQMFG QFGKILDVEI IFNERGSKGF GFVTFETSSD
160 170 180 190 200
ADRAREKLNG TIVEGRKIEV NNATARVMTN KKPGNPYANG WKLNPVVGTV
210 220 230 240 250
YGPEFYAVTS FPYPTTGTAV AYRGAHLRGR GRAVYNTFRA APPPPPIPTY
260 270 280 290 300
GAALEQTLVK MPVPWAGLAP CPLPPQQTPE PAYPTSPAFP PLSCPFASRV
310 320 330 340 350
VYQDGFYGAE IYGGYAAYRY AQPAAATAAA YSDSYGRVYA AADPYHHTIG
360 370
PTATYSIGTM ASLCRGGYSR FTPY
Length:374
Mass (Da):40,610
Last modified:September 2, 2008 - v2
Checksum:iAC1454ADBCD2B810
GO
Isoform 2 (identifier: Q8BIF2-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     361-374: Missing.

Show »
Length:360
Mass (Da):39,051
Checksum:i789CC518B9F6CC92
GO
Isoform 3 (identifier: Q8BIF2-3) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     139-169: Missing.
     361-374: Missing.

Show »
Length:329
Mass (Da):35,638
Checksum:iBB7BA1021A5216D6
GO
Isoform 4 (identifier: Q8BIF2-4) [UniParc]FASTAAdd to basket
Also known as: Fox3v3

The sequence of this isoform differs from the canonical sequence as follows:
     253-299: Missing.
     361-374: Missing.

Show »
Length:313
Mass (Da):34,068
Checksum:i664AB23CC03D9B7A
GO
Isoform 5 (identifier: Q8BIF2-5) [UniParc]FASTAAdd to basket
Also known as: Fox3v2, Fox-3-S

The sequence of this isoform differs from the canonical sequence as follows:
     253-299: Missing.

Show »
Length:327
Mass (Da):35,628
Checksum:i2952868AD8C8E39A
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti266A → V in BAC37531 (PubMed:19713214).Curated1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_035219139 – 169Missing in isoform 3. 1 PublicationAdd BLAST31
Alternative sequenceiVSP_043949253 – 299Missing in isoform 4 and isoform 5. 1 PublicationAdd BLAST47
Alternative sequenceiVSP_035220361 – 374Missing in isoform 2, isoform 3 and isoform 4. 2 PublicationsAdd BLAST14

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
FJ958310 mRNA. Translation: ACY91937.1.
FJ958311 mRNA. Translation: ACY91938.1.
AK079086 mRNA. Translation: BAC37531.1.
AK160816 mRNA. Translation: BAE36031.1.
AL591514 Genomic DNA. No translation available.
AL591544 Genomic DNA. No translation available.
AL591075 Genomic DNA. Translation: CAM15761.1.
AL591075 Genomic DNA. Translation: CAM15760.1.
AL591075 Genomic DNA. Translation: CAM15762.1.
AL591075 Genomic DNA. Translation: CAX16099.1.
AL591075 Genomic DNA. Translation: CAX16100.1.
CH466558 Genomic DNA. Translation: EDL34674.1.
BC054403 mRNA. Translation: AAH54403.1.
CCDSiCCDS25705.1. [Q8BIF2-4]
CCDS25706.1. [Q8BIF2-1]
CCDS70358.1. [Q8BIF2-3]
CCDS70360.1. [Q8BIF2-2]
RefSeqiNP_001020102.2. NM_001024931.2. [Q8BIF2-4]
NP_001034256.1. NM_001039167.1. [Q8BIF2-1]
NP_001034257.1. NM_001039168.1.
NP_001272365.1. NM_001285436.1. [Q8BIF2-2]
NP_001272366.1. NM_001285437.1. [Q8BIF2-3]
NP_001272367.1. NM_001285438.1. [Q8BIF2-4]
XP_006533785.1. XM_006533722.3. [Q8BIF2-1]
XP_006533788.1. XM_006533725.3. [Q8BIF2-1]
XP_006533790.1. XM_006533727.3. [Q8BIF2-5]
XP_017170150.1. XM_017314661.1. [Q8BIF2-1]
XP_017170151.1. XM_017314662.1. [Q8BIF2-1]
XP_017170152.1. XM_017314663.1. [Q8BIF2-2]
UniGeneiMm.341103.

Genome annotation databases

EnsembliENSMUST00000017576; ENSMUSP00000017576; ENSMUSG00000025576. [Q8BIF2-1]
ENSMUST00000069343; ENSMUSP00000069598; ENSMUSG00000025576. [Q8BIF2-3]
ENSMUST00000103023; ENSMUSP00000099312; ENSMUSG00000025576. [Q8BIF2-4]
ENSMUST00000106278; ENSMUSP00000101885; ENSMUSG00000025576. [Q8BIF2-4]
ENSMUST00000117731; ENSMUSP00000113636; ENSMUSG00000025576. [Q8BIF2-2]
ENSMUST00000120061; ENSMUSP00000113987; ENSMUSG00000025576. [Q8BIF2-5]
GeneIDi52897.
KEGGimmu:52897.
UCSCiuc007mpl.1. mouse. [Q8BIF2-4]
uc007mpm.1. mouse. [Q8BIF2-5]
uc007mpn.1. mouse. [Q8BIF2-1]
uc007mpp.1. mouse. [Q8BIF2-3]

Keywords - Coding sequence diversityi

Alternative splicing

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
FJ958310 mRNA. Translation: ACY91937.1.
FJ958311 mRNA. Translation: ACY91938.1.
AK079086 mRNA. Translation: BAC37531.1.
AK160816 mRNA. Translation: BAE36031.1.
AL591514 Genomic DNA. No translation available.
AL591544 Genomic DNA. No translation available.
AL591075 Genomic DNA. Translation: CAM15761.1.
AL591075 Genomic DNA. Translation: CAM15760.1.
AL591075 Genomic DNA. Translation: CAM15762.1.
AL591075 Genomic DNA. Translation: CAX16099.1.
AL591075 Genomic DNA. Translation: CAX16100.1.
CH466558 Genomic DNA. Translation: EDL34674.1.
BC054403 mRNA. Translation: AAH54403.1.
CCDSiCCDS25705.1. [Q8BIF2-4]
CCDS25706.1. [Q8BIF2-1]
CCDS70358.1. [Q8BIF2-3]
CCDS70360.1. [Q8BIF2-2]
RefSeqiNP_001020102.2. NM_001024931.2. [Q8BIF2-4]
NP_001034256.1. NM_001039167.1. [Q8BIF2-1]
NP_001034257.1. NM_001039168.1.
NP_001272365.1. NM_001285436.1. [Q8BIF2-2]
NP_001272366.1. NM_001285437.1. [Q8BIF2-3]
NP_001272367.1. NM_001285438.1. [Q8BIF2-4]
XP_006533785.1. XM_006533722.3. [Q8BIF2-1]
XP_006533788.1. XM_006533725.3. [Q8BIF2-1]
XP_006533790.1. XM_006533727.3. [Q8BIF2-5]
XP_017170150.1. XM_017314661.1. [Q8BIF2-1]
XP_017170151.1. XM_017314662.1. [Q8BIF2-1]
XP_017170152.1. XM_017314663.1. [Q8BIF2-2]
UniGeneiMm.341103.

3D structure databases

ProteinModelPortaliQ8BIF2.
SMRiQ8BIF2.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

IntActiQ8BIF2. 4 interactors.
MINTiMINT-4110740.
STRINGi10090.ENSMUSP00000017576.

PTM databases

iPTMnetiQ8BIF2.
PhosphoSitePlusiQ8BIF2.

Proteomic databases

PaxDbiQ8BIF2.
PeptideAtlasiQ8BIF2.
PRIDEiQ8BIF2.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSMUST00000017576; ENSMUSP00000017576; ENSMUSG00000025576. [Q8BIF2-1]
ENSMUST00000069343; ENSMUSP00000069598; ENSMUSG00000025576. [Q8BIF2-3]
ENSMUST00000103023; ENSMUSP00000099312; ENSMUSG00000025576. [Q8BIF2-4]
ENSMUST00000106278; ENSMUSP00000101885; ENSMUSG00000025576. [Q8BIF2-4]
ENSMUST00000117731; ENSMUSP00000113636; ENSMUSG00000025576. [Q8BIF2-2]
ENSMUST00000120061; ENSMUSP00000113987; ENSMUSG00000025576. [Q8BIF2-5]
GeneIDi52897.
KEGGimmu:52897.
UCSCiuc007mpl.1. mouse. [Q8BIF2-4]
uc007mpm.1. mouse. [Q8BIF2-5]
uc007mpn.1. mouse. [Q8BIF2-1]
uc007mpp.1. mouse. [Q8BIF2-3]

Organism-specific databases

CTDi146713.
MGIiMGI:106368. Rbfox3.

Phylogenomic databases

eggNOGiKOG0125. Eukaryota.
ENOG4111WJT. LUCA.
GeneTreeiENSGT00390000013767.
HOGENOMiHOG000230971.
HOVERGENiHBG000044.
InParanoidiQ8BIF2.
KOiK14946.
OMAiHTIGPTA.
OrthoDBiEOG091G15X5.
PhylomeDBiQ8BIF2.
TreeFamiTF315942.

Miscellaneous databases

PROiQ8BIF2.
SOURCEiSearch...

Gene expression databases

BgeeiENSMUSG00000025576.
ExpressionAtlasiQ8BIF2. baseline and differential.
GenevisibleiQ8BIF2. MM.

Family and domain databases

Gene3Di3.30.70.330. 1 hit.
InterProiIPR025670. Fox-1_C_dom.
IPR012677. Nucleotide-bd_a/b_plait.
IPR017325. RNA-bd_Fox-1.
IPR000504. RRM_dom.
[Graphical view]
PfamiPF12414. Fox-1_C. 2 hits.
PF00076. RRM_1. 1 hit.
[Graphical view]
PIRSFiPIRSF037932. Ataxin_2_bd_A2BP. 1 hit.
SMARTiSM00360. RRM. 1 hit.
[Graphical view]
SUPFAMiSSF54928. SSF54928. 1 hit.
PROSITEiPS50102. RRM. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiRFOX3_MOUSE
AccessioniPrimary (citable) accession number: Q8BIF2
Secondary accession number(s): A2A4W7
, A2A4W8, B7ZC12, B7ZC13, D1GI07, Q3TUE0, Q7TQI4
Entry historyi
Integrated into UniProtKB/Swiss-Prot: September 2, 2008
Last sequence update: September 2, 2008
Last modified: November 2, 2016
This is version 113 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Caution

Initial characterization was derived from usage of a monoclonal antibody (A60) directed to an unknown protein called NeuN (PubMed:15605376 and PubMed:1483388), but later identified as RBFOX3.1 Publication

Keywords - Technical termi

Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. MGD cross-references
    Mouse Genome Database (MGD) cross-references in UniProtKB/Swiss-Prot
  2. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.