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P48381

- RFX3_MOUSE

UniProt

P48381 - RFX3_MOUSE

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Protein

Transcription factor RFX3

Gene

Rfx3

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

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. sequence-specific DNA binding transcription factor activity Source: BHF-UCL
  2. 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
Complete GO annotation...

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
Complete GO annotation...

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

MaxQBiP48381.
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

BgeeiP48381.
ExpressionAtlasiP48381. baseline and differential.
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

        10         20         30         40         50
MQTSETGSDT GSTVTLQTSV ASQAAVPTQV VQQVPVQQQV QQVQTVQQVQ
60 70 80 90 100
HVYPAQVQYV EGSDTVYTNG AIRTTTYPYT ETQMYSQNTG GNYFDTQGSS
110 120 130 140 150
AQVTTVVSSH SMVGTGGIQM GVTGGQLISS SGGTYLIGNS MENSGHSVTH
160 170 180 190 200
TTRASPATIE MAIETLQKSD GLSTHRSSLL NSHLQWLLDN YETAEGVSLP
210 220 230 240 250
RSTLYNHYLR HCQEHKLDPV NAASFGKLIR SIFMGLRTRR LGTRGNSKYH
260 270 280 290 300
YYGIRVKPDS PLNRLQEDMQ YMAMRQQPMQ QKQRYKPMQK VDGVADGFTG
310 320 330 340 350
SGQQTGTSVE QTVIAQSQHH QQFLDASRAL PEFGEVEISS LPDGTTFEDI
360 370 380 390 400
KSLQSLYREH CEAILDVVVN LQFSLIEKLW QTFWRYSPST PADGTTITES
410 420 430 440 450
SNLSEIESRL PKAKLITLCK HESILKWMCN CDHGMYQALV EILIPDVLRP
460 470 480 490 500
IPSALTQAIR NFAKSLEGWL SNAMNNIPQR MIQTKVAAVS AFAQTLRRYT
510 520 530 540 550
SLNHLAQAAR AVLQNTSQIN QMLSDLNRVD FANVQEQASW VCQCDDNMVQ
560 570 580 590 600
RLETDFKMTL QQQSTLEQWA AWLDNVMMQA LKPYEGRPSF PKAARQFLLK
610 620 630 640 650
WSFYSSMVIR DLTLRSAASF GSFHLIRLLY DEYMFYLVEH RVAQVTGETP
660 670 680 690 700
IAVMGEFGDL NAVSPGNLDK DEGSEVESET DEDLDDSSEP RAKREKTELS
710 720 730 740
QAFPVGCMQP VLESAVQPSL LNPLHSEHIV TSTQTIRQCS ATGNTYTAV
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:
EMBLi
GenBanki
DDBJi
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:
EMBLi
GenBanki
DDBJi
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

MaxQBi P48381.
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

Bgeei P48381.
ExpressionAtlasi P48381. baseline and differential.
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

« Hide 'large scale' publications
  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 29, 2014
This is version 114 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