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P48381 (RFX3_MOUSE) Reviewed, UniProtKB/Swiss-Prot

Last modified March 19, 2014. Version 108. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (2) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Alt products·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Transcription factor RFX3
Alternative name(s):
Regulatory factor X 3
Gene names
Name:Rfx3
OrganismMus musculus (Mouse) [Reference proteome]
Taxonomic identifier10090 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeMusMus

Protein attributes

Sequence length749 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

Transcription factor required for ciliogenesis and islet cell differentiation during endocrine pancreas development. Essential for the differentiation of nodal monocilia and left-right asymmetry specification during embryogenesis. Required for the biogenesis of motile cilia by governing growth and beating efficiency of motile cells. Also required for ciliated ependymal cell differentiation. Together with RFX6, participates in the differentiation of 4 of the 5 islet cell types during endocrine pancreas development, with the exception of pancreatic PP (polypeptide-producing) cells. Regulates transcription by forming a heterodimer with another RFX protein and binding to the X-box in the promoter of target genes. Regulates the expression of genes involved in ciliary assembly (DYNC2LI1, FOXJ1 and BBS4) and genes involved in ciliary motility (DNAH11, DNAH9 and DNAH5). Represses transcription of MAP1A in non-neuronal cells but not in neuronal cells. Ref.4 Ref.5 Ref.6 Ref.7

Subunit structure

Interacts with RFX6 By similarity.

Subcellular location

Nucleus Ref.7.

Tissue specificity

Expressed in ciliated cells of the node and in the ciliated ependymal cells of the subcommissural organ (SCO), choroid plexuses (CP) and ventricular walls during embryonic and postnatal development. Expressed in developing and mature pancreatic endocrine cells during embryogenesis and in adults (at protein level). Ref.4 Ref.5 Ref.6

Disruption phenotype

High rate of embryonic lethality. 2 peaks of death are observed: approximately half of the embryos die around days 11 or 12 of embryonic development. Of the embryos that survive past this stage, approximately two-thirds die at birth. Surviving mice are systematically smaller. Their body weights at birth are approximately one-third lower. This growth retardation increases with age, and the body weights that adult male or female mice attain are less than half those of wild-type mice. Mice exhibit a pronounced defect in nodal cilia: cilia are present but remain markedly stunted. Mice also suffer from hydrocephalus without stenosis of the aqueduct of Sylvius. In pancreatic endocrine cells, primary cilia are reduced in number and severely stunted: this ciliary abnormality is associated with a developmental defect leading to an altered cellular composition of the islets of Langerhans. Just before birth, islets contain considerably less insulin-, glucagon-, and ghrelin-producing cells, whereas pancreatic PP (polypeptide-producing) cells are markedly increased in number. In adult mice, the defect leads to small and disorganized islets, reduced insulin production, and impaired glucose tolerance. Ref.4 Ref.5 Ref.6

Sequence similarities

Belongs to the RFX family.

Contains 1 RFX-type winged-helix DNA-binding domain.

Ontologies

Keywords
   Biological processDifferentiation
Transcription
Transcription regulation
   Cellular componentNucleus
   Coding sequence diversityAlternative splicing
   LigandDNA-binding
   Molecular functionDevelopmental protein
Repressor
   Technical termComplete proteome
Reference proteome
Gene Ontology (GO)
   Biological_processciliary cell motility

Inferred from mutant phenotype Ref.7. Source: UniProtKB

cilium assembly

Inferred from mutant phenotype PubMed 20413507. Source: BHF-UCL

epithelial cilium movement involved in determination of left/right asymmetry

Inferred from mutant phenotype Ref.4. Source: UniProtKB

negative regulation of transcription, DNA-templated

Inferred from sequence or structural similarity. Source: UniProtKB

positive regulation of transcription from RNA polymerase II promoter

Inferred from mutant phenotype PubMed 20413507. Source: BHF-UCL

positive regulation of type B pancreatic cell development

Inferred from mutant phenotype PubMed 20413507. Source: BHF-UCL

regulation of insulin secretion

Inferred from mutant phenotype Ref.6. Source: UniProtKB

transcription, DNA-templated

Inferred from mutant phenotype Ref.7. Source: UniProtKB

type B pancreatic cell maturation

Inferred from mutant phenotype PubMed 20413507. Source: BHF-UCL

   Cellular_componentnuclear chromatin

Inferred from direct assay PubMed 20413507. Source: BHF-UCL

transcription factor complex

Inferred by curator PubMed 20413507. Source: BHF-UCL

   Molecular_functionsequence-specific DNA binding transcription factor activity

Inferred from direct assay PubMed 20413507. Source: BHF-UCL

transcription regulatory region DNA binding

Inferred from direct assay Ref.7. Source: UniProtKB

Complete GO annotation...

Alternative products

This entry describes 2 isoforms produced by alternative splicing. [Align] [Select]
Isoform 1 (identifier: P48381-1)

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.
Isoform 2 (identifier: P48381-2)

The sequence of this isoform differs from the canonical sequence as follows:
     159-183: Missing.
     401-413: SNLSEIESRLPKA → RSESIGLSDLFSR
     414-749: Missing.
Note: No experimental confirmation available.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 749749Transcription factor RFX3
PRO_0000215291

Regions

DNA binding183 – 25876RFX-type winged-helix Ref.7

Natural variations

Alternative sequence159 – 18325Missing in isoform 2.
VSP_007628
Alternative sequence401 – 41313SNLSE…RLPKA → RSESIGLSDLFSR in isoform 2.
VSP_007629
Alternative sequence414 – 749336Missing in isoform 2.
VSP_007630

Experimental info

Sequence conflict3721Q → K in BAC26730. Ref.1
Sequence conflict4591I → V in BAC26730. Ref.1
Sequence conflict4941Q → H in BAC26730. Ref.1

Sequences

Sequence LengthMass (Da)Tools
Isoform 1 [UniParc].

Last modified June 20, 2003. Version 2.
Checksum: 5527A5F3826D32AA

FASTA74983,512
        10         20         30         40         50         60 
MQTSETGSDT GSTVTLQTSV ASQAAVPTQV VQQVPVQQQV QQVQTVQQVQ HVYPAQVQYV 

        70         80         90        100        110        120 
EGSDTVYTNG AIRTTTYPYT ETQMYSQNTG GNYFDTQGSS AQVTTVVSSH SMVGTGGIQM 

       130        140        150        160        170        180 
GVTGGQLISS SGGTYLIGNS MENSGHSVTH TTRASPATIE MAIETLQKSD GLSTHRSSLL 

       190        200        210        220        230        240 
NSHLQWLLDN YETAEGVSLP RSTLYNHYLR HCQEHKLDPV NAASFGKLIR SIFMGLRTRR 

       250        260        270        280        290        300 
LGTRGNSKYH YYGIRVKPDS PLNRLQEDMQ YMAMRQQPMQ QKQRYKPMQK VDGVADGFTG 

       310        320        330        340        350        360 
SGQQTGTSVE QTVIAQSQHH QQFLDASRAL PEFGEVEISS LPDGTTFEDI KSLQSLYREH 

       370        380        390        400        410        420 
CEAILDVVVN LQFSLIEKLW QTFWRYSPST PADGTTITES SNLSEIESRL PKAKLITLCK 

       430        440        450        460        470        480 
HESILKWMCN CDHGMYQALV EILIPDVLRP IPSALTQAIR NFAKSLEGWL SNAMNNIPQR 

       490        500        510        520        530        540 
MIQTKVAAVS AFAQTLRRYT SLNHLAQAAR AVLQNTSQIN QMLSDLNRVD FANVQEQASW 

       550        560        570        580        590        600 
VCQCDDNMVQ RLETDFKMTL QQQSTLEQWA AWLDNVMMQA LKPYEGRPSF PKAARQFLLK 

       610        620        630        640        650        660 
WSFYSSMVIR DLTLRSAASF GSFHLIRLLY DEYMFYLVEH RVAQVTGETP IAVMGEFGDL 

       670        680        690        700        710        720 
NAVSPGNLDK DEGSEVESET DEDLDDSSEP RAKREKTELS QAFPVGCMQP VLESAVQPSL 

       730        740 
LNPLHSEHIV TSTQTIRQCS ATGNTYTAV 

« Hide

Isoform 2 [UniParc].

Checksum: CDA2971DA0E4DE79
Show »

FASTA38842,900

References

« Hide 'large scale' references
[1]"The transcriptional landscape of the mammalian genome."
Carninci P., Kasukawa T., Katayama S., Gough J., Frith M.C., Maeda N., Oyama R., Ravasi T., Lenhard B., Wells C., Kodzius R., Shimokawa K., Bajic V.B., Brenner S.E., Batalov S., Forrest A.R., Zavolan M., Davis M.J. expand/collapse author list , Wilming L.G., Aidinis V., Allen J.E., Ambesi-Impiombato A., Apweiler R., Aturaliya R.N., Bailey T.L., Bansal M., Baxter L., Beisel K.W., Bersano T., Bono H., Chalk A.M., Chiu K.P., Choudhary V., Christoffels A., Clutterbuck D.R., Crowe M.L., Dalla E., Dalrymple B.P., de Bono B., Della Gatta G., di Bernardo D., Down T., Engstrom P., Fagiolini M., Faulkner G., Fletcher C.F., Fukushima T., Furuno M., Futaki S., Gariboldi M., Georgii-Hemming P., Gingeras T.R., Gojobori T., Green R.E., Gustincich S., Harbers M., Hayashi Y., Hensch T.K., Hirokawa N., Hill D., Huminiecki L., Iacono M., Ikeo K., Iwama A., Ishikawa T., Jakt M., Kanapin A., Katoh M., Kawasawa Y., Kelso J., Kitamura H., Kitano H., Kollias G., Krishnan S.P., Kruger A., Kummerfeld S.K., Kurochkin I.V., Lareau L.F., Lazarevic D., Lipovich L., Liu J., Liuni S., McWilliam S., Madan Babu M., Madera M., Marchionni L., Matsuda H., Matsuzawa S., Miki H., Mignone F., Miyake S., Morris K., Mottagui-Tabar S., Mulder N., Nakano N., Nakauchi H., Ng P., Nilsson R., Nishiguchi S., Nishikawa S., Nori F., Ohara O., Okazaki Y., Orlando V., Pang K.C., Pavan W.J., Pavesi G., Pesole G., Petrovsky N., Piazza S., Reed J., Reid J.F., Ring B.Z., Ringwald M., Rost B., Ruan Y., Salzberg S.L., Sandelin A., Schneider C., Schoenbach C., Sekiguchi K., Semple C.A., Seno S., Sessa L., Sheng Y., Shibata Y., Shimada H., Shimada K., Silva D., Sinclair B., Sperling S., Stupka E., Sugiura K., Sultana R., Takenaka Y., Taki K., Tammoja K., Tan S.L., Tang S., Taylor M.S., Tegner J., Teichmann S.A., Ueda H.R., van Nimwegen E., Verardo R., Wei C.L., Yagi K., Yamanishi H., Zabarovsky E., Zhu S., Zimmer A., Hide W., Bult C., Grimmond S.M., Teasdale R.D., Liu E.T., Brusic V., Quackenbush J., Wahlestedt C., Mattick J.S., Hume D.A., Kai C., Sasaki D., Tomaru Y., Fukuda S., Kanamori-Katayama M., Suzuki M., Aoki J., Arakawa T., Iida J., Imamura K., Itoh M., Kato T., Kawaji H., Kawagashira N., Kawashima T., Kojima M., Kondo S., Konno H., Nakano K., Ninomiya N., Nishio T., Okada M., Plessy C., Shibata K., Shiraki T., Suzuki S., Tagami M., Waki K., Watahiki A., Okamura-Oho Y., Suzuki H., Kawai J., Hayashizaki Y.
Science 309:1559-1563(2005) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORMS 1 AND 2).
Strain: C57BL/6J.
Tissue: Aorta and Vein.
[2]"The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
The MGC Project Team
Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
Tissue: Mammary gland.
[3]"RFX1, a transactivator of hepatitis B virus enhancer I, belongs to a novel family of homodimeric and heterodimeric DNA-binding proteins."
Reith W., Ucla C., Barras E., Gaud A., Durand B., Herrero-Sanchez C., Kobr M., Mach B.
Mol. Cell. Biol. 14:1230-1244(1994) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA] OF 137-325 (ISOFORM 1).
Strain: BALB/c.
Tissue: Spleen.
[4]"The transcription factor RFX3 directs nodal cilium development and left-right asymmetry specification."
Bonnafe E., Touka M., Ait-Lounis A., Baas D., Barras E., Ucla C., Moreau A., Flamant F., Dubruille R., Couble P., Collignon J., Durand B., Reith W.
Mol. Cell. Biol. 24:4417-4427(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION, TISSUE SPECIFICITY, DISRUPTION PHENOTYPE.
[5]"A deficiency in RFX3 causes hydrocephalus associated with abnormal differentiation of ependymal cells."
Baas D., Meiniel A., Benadiba C., Bonnafe E., Meiniel O., Reith W., Durand B.
Eur. J. Neurosci. 24:1020-1030(2006) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION, TISSUE SPECIFICITY, DISRUPTION PHENOTYPE.
[6]"Novel function of the ciliogenic transcription factor RFX3 in development of the endocrine pancreas."
Ait-Lounis A., Baas D., Barras E., Benadiba C., Charollais A., Nlend Nlend R., Liegeois D., Meda P., Durand B., Reith W.
Diabetes 56:950-959(2007) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION, TISSUE SPECIFICITY, DISRUPTION PHENOTYPE.
[7]"RFX3 governs growth and beating efficiency of motile cilia in mouse and controls the expression of genes involved in human ciliopathies."
El Zein L., Ait-Lounis A., Morle L., Thomas J., Chhin B., Spassky N., Reith W., Durand B.
J. Cell Sci. 122:3180-3189(2009) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION, DNA-BINDING, SUBCELLULAR LOCATION.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
AK030008 mRNA. Translation: BAC26730.1.
AK041120 mRNA. Translation: BAC30829.1.
BC017598 mRNA. Translation: AAH17598.1.
X76090 mRNA. Translation: CAA53704.1.
PIRE55926.
RefSeqNP_001159886.1. NM_001166414.1.
NP_035395.2. NM_011265.3.
XP_006526844.1. XM_006526781.1.
XP_006526845.1. XM_006526782.1.
UniGeneMm.313321.

3D structure databases

ProteinModelPortalP48381.
SMRP48381. Positions 184-257.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid202874. 1 interaction.
IntActP48381. 1 interaction.

PTM databases

PhosphoSiteP48381.

Proteomic databases

PaxDbP48381.
PRIDEP48381.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblENSMUST00000165566; ENSMUSP00000126313; ENSMUSG00000040929. [P48381-1]
ENSMUST00000172907; ENSMUSP00000134141; ENSMUSG00000040929. [P48381-1]
ENSMUST00000174850; ENSMUSP00000133461; ENSMUSG00000040929. [P48381-1]
GeneID19726.
KEGGmmu:19726.
UCSCuc008hcb.2. mouse. [P48381-1]
uc008hcd.3. mouse. [P48381-2]

Organism-specific databases

CTD5991.
MGIMGI:106582. Rfx3.

Phylogenomic databases

eggNOGNOG264634.
GeneTreeENSGT00550000074532.
HOGENOMHOG000294091.
HOVERGENHBG002753.
InParanoidP48381.
KOK09173.
OMAYSEPQLY.
TreeFamTF321340.

Gene expression databases

ArrayExpressP48381.
BgeeP48381.
GenevestigatorP48381.

Family and domain databases

Gene3D1.10.10.10. 1 hit.
InterProIPR003150. DNA-bd_RFX.
IPR007668. RFX1_trans_act.
IPR011991. WHTH_DNA-bd_dom.
[Graphical view]
PfamPF04589. RFX1_trans_act. 1 hit.
PF02257. RFX_DNA_binding. 1 hit.
[Graphical view]
PROSITEPS51526. RFX_DBD. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

NextBio297136.
PROP48381.
SOURCESearch...

Entry information

Entry nameRFX3_MOUSE
AccessionPrimary (citable) accession number: P48381
Secondary accession number(s): Q8BLW2, Q8C0R3, Q8VBY6
Entry history
Integrated into UniProtKB/Swiss-Prot: February 1, 1996
Last sequence update: June 20, 2003
Last modified: March 19, 2014
This is version 108 of the entry and version 2 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

MGD cross-references

Mouse Genome Database (MGD) cross-references in UniProtKB/Swiss-Prot