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P48381

- RFX3_MOUSE

UniProt

P48381 - RFX3_MOUSE

Protein

Transcription factor RFX3

Gene

Rfx3

Organism
Mus musculus (Mouse)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 113 (01 Oct 2014)
      Sequence version 2 (20 Jun 2003)
      Previous versions | rss
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    Functioni

    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.4 Publications

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    DNA bindingi183 – 25876RFX-type winged-helixPROSITE-ProRule annotationAdd
    BLAST

    GO - Molecular functioni

    1. protein binding Source: UniProtKB
    2. sequence-specific DNA binding transcription factor activity Source: BHF-UCL
    3. transcription regulatory region DNA binding Source: UniProtKB

    GO - Biological processi

    1. cell maturation Source: BHF-UCL
    2. cilium assembly Source: BHF-UCL
    3. cilium-dependent cell motility Source: UniProtKB
    4. determination of left/right symmetry Source: MGI
    5. endocrine pancreas development Source: UniProtKB
    6. epithelial cilium movement involved in determination of left/right asymmetry Source: UniProtKB
    7. negative regulation of transcription, DNA-templated Source: UniProtKB
    8. positive regulation of transcription, DNA-templated Source: BHF-UCL
    9. positive regulation of transcription from RNA polymerase II promoter Source: BHF-UCL
    10. positive regulation of type B pancreatic cell development Source: BHF-UCL
    11. regulation of insulin secretion Source: UniProtKB
    12. regulation of transcription, DNA-templated Source: UniProtKB
    13. transcription, DNA-templated Source: UniProtKB
    14. type B pancreatic cell maturation Source: BHF-UCL

    Keywords - Molecular functioni

    Developmental protein, Repressor

    Keywords - Biological processi

    Differentiation, Transcription, Transcription regulation

    Keywords - Ligandi

    DNA-binding

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Transcription factor RFX3
    Alternative name(s):
    Regulatory factor X 3
    Gene namesi
    Name:Rfx3
    OrganismiMus musculus (Mouse)
    Taxonomic identifieri10090 [NCBI]
    Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeMusMus
    ProteomesiUP000000589: Chromosome 19

    Organism-specific databases

    MGIiMGI:106582. Rfx3.

    Subcellular locationi

    Nucleus 1 PublicationPROSITE-ProRule annotation

    GO - Cellular componenti

    1. nuclear chromatin Source: BHF-UCL
    2. transcription factor complex Source: BHF-UCL

    Keywords - Cellular componenti

    Nucleus

    Pathology & Biotechi

    Disruption phenotypei

    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.3 Publications

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 749749Transcription factor RFX3PRO_0000215291Add
    BLAST

    Proteomic databases

    PaxDbiP48381.
    PRIDEiP48381.

    PTM databases

    PhosphoSiteiP48381.

    Expressioni

    Tissue specificityi

    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).3 Publications

    Gene expression databases

    ArrayExpressiP48381.
    BgeeiP48381.
    GenevestigatoriP48381.

    Interactioni

    Subunit structurei

    Interacts with RFX6.By similarity

    Protein-protein interaction databases

    BioGridi202874. 1 interaction.
    IntActiP48381. 1 interaction.

    Structurei

    3D structure databases

    ProteinModelPortaliP48381.
    SMRiP48381. Positions 184-257.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Sequence similaritiesi

    Belongs to the RFX family.PROSITE-ProRule annotation
    Contains 1 RFX-type winged-helix DNA-binding domain.PROSITE-ProRule annotation

    Phylogenomic databases

    eggNOGiNOG264634.
    GeneTreeiENSGT00550000074532.
    HOGENOMiHOG000294091.
    HOVERGENiHBG002753.
    InParanoidiP48381.
    KOiK09173.
    OMAiAFQVGCM.
    PhylomeDBiP48381.
    TreeFamiTF321340.

    Family and domain databases

    Gene3Di1.10.10.10. 1 hit.
    InterProiIPR003150. DNA-bd_RFX.
    IPR007668. RFX1_trans_act.
    IPR011991. WHTH_DNA-bd_dom.
    [Graphical view]
    PfamiPF04589. RFX1_trans_act. 1 hit.
    PF02257. RFX_DNA_binding. 1 hit.
    [Graphical view]
    PROSITEiPS51526. RFX_DBD. 1 hit.
    [Graphical view]

    Sequences (2)i

    Sequence statusi: Complete.

    This entry describes 2 isoformsi produced by alternative splicing. Align

    Isoform 1 (identifier: P48381-1) [UniParc]FASTAAdd to Basket

    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

    MQTSETGSDT GSTVTLQTSV ASQAAVPTQV VQQVPVQQQV QQVQTVQQVQ    50
    HVYPAQVQYV EGSDTVYTNG AIRTTTYPYT ETQMYSQNTG GNYFDTQGSS 100
    AQVTTVVSSH SMVGTGGIQM GVTGGQLISS SGGTYLIGNS MENSGHSVTH 150
    TTRASPATIE MAIETLQKSD GLSTHRSSLL NSHLQWLLDN YETAEGVSLP 200
    RSTLYNHYLR HCQEHKLDPV NAASFGKLIR SIFMGLRTRR LGTRGNSKYH 250
    YYGIRVKPDS PLNRLQEDMQ YMAMRQQPMQ QKQRYKPMQK VDGVADGFTG 300
    SGQQTGTSVE QTVIAQSQHH QQFLDASRAL PEFGEVEISS LPDGTTFEDI 350
    KSLQSLYREH CEAILDVVVN LQFSLIEKLW QTFWRYSPST PADGTTITES 400
    SNLSEIESRL PKAKLITLCK HESILKWMCN CDHGMYQALV EILIPDVLRP 450
    IPSALTQAIR NFAKSLEGWL SNAMNNIPQR MIQTKVAAVS AFAQTLRRYT 500
    SLNHLAQAAR AVLQNTSQIN QMLSDLNRVD FANVQEQASW VCQCDDNMVQ 550
    RLETDFKMTL QQQSTLEQWA AWLDNVMMQA LKPYEGRPSF PKAARQFLLK 600
    WSFYSSMVIR DLTLRSAASF GSFHLIRLLY DEYMFYLVEH RVAQVTGETP 650
    IAVMGEFGDL NAVSPGNLDK DEGSEVESET DEDLDDSSEP RAKREKTELS 700
    QAFPVGCMQP VLESAVQPSL LNPLHSEHIV TSTQTIRQCS ATGNTYTAV 749
    Length:749
    Mass (Da):83,512
    Last modified:June 20, 2003 - v2
    Checksum:i5527A5F3826D32AA
    GO
    Isoform 2 (identifier: P48381-2) [UniParc]FASTAAdd to Basket

    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.

    Show »
    Length:388
    Mass (Da):42,900
    Checksum:iCDA2971DA0E4DE79
    GO

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti372 – 3721Q → K in BAC26730. (PubMed:16141072)Curated
    Sequence conflicti459 – 4591I → V in BAC26730. (PubMed:16141072)Curated
    Sequence conflicti494 – 4941Q → H in BAC26730. (PubMed:16141072)Curated

    Alternative sequence

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Alternative sequencei159 – 18325Missing in isoform 2. 1 PublicationVSP_007628Add
    BLAST
    Alternative sequencei401 – 41313SNLSE…RLPKA → RSESIGLSDLFSR in isoform 2. 1 PublicationVSP_007629Add
    BLAST
    Alternative sequencei414 – 749336Missing in isoform 2. 1 PublicationVSP_007630Add
    BLAST

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AK030008 mRNA. Translation: BAC26730.1.
    AK041120 mRNA. Translation: BAC30829.1.
    BC017598 mRNA. Translation: AAH17598.1.
    X76090 mRNA. Translation: CAA53704.1.
    CCDSiCCDS29725.1. [P48381-1]
    PIRiE55926.
    RefSeqiNP_001159886.1. NM_001166414.1. [P48381-1]
    NP_035395.2. NM_011265.3. [P48381-1]
    XP_006526844.1. XM_006526781.1. [P48381-1]
    XP_006526845.1. XM_006526782.1. [P48381-1]
    UniGeneiMm.313321.

    Genome annotation databases

    EnsembliENSMUST00000165566; ENSMUSP00000126313; ENSMUSG00000040929. [P48381-1]
    ENSMUST00000172907; ENSMUSP00000134141; ENSMUSG00000040929. [P48381-1]
    ENSMUST00000174850; ENSMUSP00000133461; ENSMUSG00000040929. [P48381-1]
    GeneIDi19726.
    KEGGimmu:19726.
    UCSCiuc008hcb.2. mouse. [P48381-1]
    uc008hcd.3. mouse. [P48381-2]

    Keywords - Coding sequence diversityi

    Alternative splicing

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AK030008 mRNA. Translation: BAC26730.1 .
    AK041120 mRNA. Translation: BAC30829.1 .
    BC017598 mRNA. Translation: AAH17598.1 .
    X76090 mRNA. Translation: CAA53704.1 .
    CCDSi CCDS29725.1. [P48381-1 ]
    PIRi E55926.
    RefSeqi NP_001159886.1. NM_001166414.1. [P48381-1 ]
    NP_035395.2. NM_011265.3. [P48381-1 ]
    XP_006526844.1. XM_006526781.1. [P48381-1 ]
    XP_006526845.1. XM_006526782.1. [P48381-1 ]
    UniGenei Mm.313321.

    3D structure databases

    ProteinModelPortali P48381.
    SMRi P48381. Positions 184-257.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    BioGridi 202874. 1 interaction.
    IntActi P48381. 1 interaction.

    PTM databases

    PhosphoSitei P48381.

    Proteomic databases

    PaxDbi P48381.
    PRIDEi P48381.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    Ensembli ENSMUST00000165566 ; ENSMUSP00000126313 ; ENSMUSG00000040929 . [P48381-1 ]
    ENSMUST00000172907 ; ENSMUSP00000134141 ; ENSMUSG00000040929 . [P48381-1 ]
    ENSMUST00000174850 ; ENSMUSP00000133461 ; ENSMUSG00000040929 . [P48381-1 ]
    GeneIDi 19726.
    KEGGi mmu:19726.
    UCSCi uc008hcb.2. mouse. [P48381-1 ]
    uc008hcd.3. mouse. [P48381-2 ]

    Organism-specific databases

    CTDi 5991.
    MGIi MGI:106582. Rfx3.

    Phylogenomic databases

    eggNOGi NOG264634.
    GeneTreei ENSGT00550000074532.
    HOGENOMi HOG000294091.
    HOVERGENi HBG002753.
    InParanoidi P48381.
    KOi K09173.
    OMAi AFQVGCM.
    PhylomeDBi P48381.
    TreeFami TF321340.

    Miscellaneous databases

    NextBioi 297136.
    PROi P48381.
    SOURCEi Search...

    Gene expression databases

    ArrayExpressi P48381.
    Bgeei P48381.
    Genevestigatori P48381.

    Family and domain databases

    Gene3Di 1.10.10.10. 1 hit.
    InterProi IPR003150. DNA-bd_RFX.
    IPR007668. RFX1_trans_act.
    IPR011991. WHTH_DNA-bd_dom.
    [Graphical view ]
    Pfami PF04589. RFX1_trans_act. 1 hit.
    PF02257. RFX_DNA_binding. 1 hit.
    [Graphical view ]
    PROSITEi PS51526. RFX_DBD. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    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.
      , 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.

    Entry informationi

    Entry nameiRFX3_MOUSE
    AccessioniPrimary (citable) accession number: P48381
    Secondary accession number(s): Q8BLW2, Q8C0R3, Q8VBY6
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: February 1, 1996
    Last sequence update: June 20, 2003
    Last modified: October 1, 2014
    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

    Keywords - Technical termi

    Complete proteome, 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

    External Data

    Dasty 3