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UniProtKB - Q8BIF2 (RFOX3_MOUSE)

Protein

RNA binding protein fox-1 homolog 3

Gene

Rbfox3

Organism
Mus musculus (Mouse)
Status
Reviewed-Annotation score: -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

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

GO - Molecular functioni

  • DNA binding Source: MGI
  • mRNA binding Source: GO_Central
View the complete GO annotation on QuickGO ...

GO - Biological processi

View the complete GO annotation on QuickGO ...

Keywordsi

Molecular functionRNA-binding
Biological processmRNA processing, mRNA splicing

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 lineageiEukaryota › Metazoa › Chordata › Craniata › Vertebrata › Euteleostomi › Mammalia › Eutheria › Euarchontoglires › Glires › Rodentia › Myomorpha › Muroidea › Muridae › Murinae › Mus › Mus
Proteomesi
  • UP000000589 Componenti: Chromosome 11

Organism-specific databases

MGIiMGI:106368 Rbfox3

Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

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

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 Expressed in 134 organ(s), highest expression level in lumbar subsegment of spinal cord
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

Protein-protein interaction databases

IntActiQ8BIF2, 4 interactors
MINTiQ8BIF2
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

Phylogenomic databases

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

Family and domain databases

CDDicd12407 RRM_FOX1_like, 1 hit
Gene3Di3.30.70.330, 1 hit
InterProiView protein in InterPro
IPR025670 Fox-1_C_dom
IPR034237 FOX1_RRM
IPR012677 Nucleotide-bd_a/b_plait_sf
IPR035979 RBD_domain_sf
IPR017325 RNA-bd_Fox-1
IPR000504 RRM_dom
PfamiView protein in Pfam
PF12414 Fox-1_C, 2 hits
PF00076 RRM_1, 1 hit
PIRSFiPIRSF037932 Ataxin_2_bd_A2BP, 1 hit
SMARTiView protein in SMART
SM00360 RRM, 1 hit
SUPFAMiSSF54928 SSF54928, 1 hit
PROSITEiView protein in PROSITE
PS50102 RRM, 1 hit

Sequences (5+)i

Sequence statusi: Complete.

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

This entry has 5 described isoforms and 2 potential isoforms that are computationally mapped.iShow all

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

Computationally mapped potential isoform sequencesi

There are 2 potential isoforms mapped to this entry.BLASTAlignShow allAdd to basket
EntryEntry nameProtein names
Gene namesLengthAnnotation
A2A4W9A2A4W9_MOUSE
RNA-binding protein fox-1 homolog 3
Rbfox3
169Annotation score:
B7ZC11B7ZC11_MOUSE
RNA-binding protein fox-1 homolog 3
Rbfox3
145Annotation score:

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

Similar proteinsi

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
MINTiQ8BIF2
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
OMAiWHPASKM
OrthoDBiEOG091G15X5
PhylomeDBiQ8BIF2
TreeFamiTF315942

Miscellaneous databases

PROiPR:Q8BIF2
SOURCEiSearch...

Gene expression databases

BgeeiENSMUSG00000025576 Expressed in 134 organ(s), highest expression level in lumbar subsegment of spinal cord
ExpressionAtlasiQ8BIF2 baseline and differential
GenevisibleiQ8BIF2 MM

Family and domain databases

CDDicd12407 RRM_FOX1_like, 1 hit
Gene3Di3.30.70.330, 1 hit
InterProiView protein in InterPro
IPR025670 Fox-1_C_dom
IPR034237 FOX1_RRM
IPR012677 Nucleotide-bd_a/b_plait_sf
IPR035979 RBD_domain_sf
IPR017325 RNA-bd_Fox-1
IPR000504 RRM_dom
PfamiView protein in Pfam
PF12414 Fox-1_C, 2 hits
PF00076 RRM_1, 1 hit
PIRSFiPIRSF037932 Ataxin_2_bd_A2BP, 1 hit
SMARTiView protein in SMART
SM00360 RRM, 1 hit
SUPFAMiSSF54928 SSF54928, 1 hit
PROSITEiView protein in PROSITE
PS50102 RRM, 1 hit
ProtoNetiSearch...

Entry informationi

Entry nameiRFOX3_MOUSE
AccessioniPrimary (citable) accession number: Q8BIF2
Secondary accession number(s): A2A4W7
, A2A4W8, B7ZC12, B7ZC13, D1GI07, Q3TUE0, Q7TQI4
Entry historyiIntegrated into UniProtKB/Swiss-Prot: September 2, 2008
Last sequence update: September 2, 2008
Last modified: September 12, 2018
This is version 121 of the entry and version 2 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Direct protein sequencing, Reference proteome
UniProt is an ELIXIR core data resource
Main funding by: National Institutes of Health

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