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Database: UniProt
Entry: RFX4_MOUSE
LinkDB: RFX4_MOUSE
Original site: RFX4_MOUSE 
ID   RFX4_MOUSE              Reviewed;         735 AA.
AC   Q7TNK1; B2RS52; Q3V158; Q76KT2; Q8HWA6; Q9D453;
DT   15-JAN-2008, integrated into UniProtKB/Swiss-Prot.
DT   01-OCT-2003, sequence version 1.
DT   05-DEC-2018, entry version 118.
DE   RecName: Full=Transcription factor RFX4;
DE   AltName: Full=Regulatory factor X 4;
GN   Name=Rfx4;
OS   Mus musculus (Mouse).
OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
OC   Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha;
OC   Muroidea; Muridae; Murinae; Mus; Mus.
OX   NCBI_TaxID=10090;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1).
RA   Belaoussoff M., Dohrmann C.E., Armsen W., Gruss P.;
RT   "Mouse Rfx4, a gene expressed in the proliferative zones of the
RT   central nervous system.";
RL   Submitted (JUL-2003) to the EMBL/GenBank/DDBJ databases.
RN   [2]
RP   NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1), FUNCTION, TISSUE SPECIFICITY,
RP   DEVELOPMENTAL STAGE, AND DISRUPTION PHENOTYPE.
RC   STRAIN=C57BL/6J; TISSUE=Brain;
RX   PubMed=12925582; DOI=10.1242/dev.00661;
RA   Blackshear P.J., Graves J.P., Stumpo D.J., Cobos I.,
RA   Rubenstein J.L.R., Zeldin D.C.;
RT   "Graded phenotypic response to partial and complete deficiency of a
RT   brain-specific transcript variant of the winged helix transcription
RT   factor RFX4.";
RL   Development 130:4539-4552(2003).
RN   [3]
RP   NUCLEOTIDE SEQUENCE [MRNA] (ISOFORMS 1 AND 2), SUBCELLULAR LOCATION,
RP   INDUCTION, AND TISSUE SPECIFICITY.
RC   STRAIN=C57BL/6J; TISSUE=Suprachiasmatic nucleus, and Testis;
RX   PubMed=14701801; DOI=10.1074/jbc.M312761200;
RA   Araki R., Takahashi H., Fukumura R., Sun F., Umeda N., Sujino M.,
RA   Inouye S.T., Saito T., Abe M.;
RT   "Restricted expression and photic induction of a novel mouse
RT   regulatory factor X4 transcript in the suprachiasmatic nucleus.";
RL   J. Biol. Chem. 279:10237-10242(2004).
RN   [4]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORMS 1; 3 AND 4).
RC   STRAIN=C57BL/6J; TISSUE=Diencephalon, and Testis;
RX   PubMed=16141072; DOI=10.1126/science.1112014;
RA   Carninci P., Kasukawa T., Katayama S., Gough J., Frith M.C., Maeda N.,
RA   Oyama R., Ravasi T., Lenhard B., Wells C., Kodzius R., Shimokawa K.,
RA   Bajic V.B., Brenner S.E., Batalov S., Forrest A.R., Zavolan M.,
RA   Davis M.J., Wilming L.G., Aidinis V., Allen J.E.,
RA   Ambesi-Impiombato A., Apweiler R., Aturaliya R.N., Bailey T.L.,
RA   Bansal M., Baxter L., Beisel K.W., Bersano T., Bono H., Chalk A.M.,
RA   Chiu K.P., Choudhary V., Christoffels A., Clutterbuck D.R.,
RA   Crowe M.L., Dalla E., Dalrymple B.P., de Bono B., Della Gatta G.,
RA   di Bernardo D., Down T., Engstrom P., Fagiolini M., Faulkner G.,
RA   Fletcher C.F., Fukushima T., Furuno M., Futaki S., Gariboldi M.,
RA   Georgii-Hemming P., Gingeras T.R., Gojobori T., Green R.E.,
RA   Gustincich S., Harbers M., Hayashi Y., Hensch T.K., Hirokawa N.,
RA   Hill D., Huminiecki L., Iacono M., Ikeo K., Iwama A., Ishikawa T.,
RA   Jakt M., Kanapin A., Katoh M., Kawasawa Y., Kelso J., Kitamura H.,
RA   Kitano H., Kollias G., Krishnan S.P., Kruger A., Kummerfeld S.K.,
RA   Kurochkin I.V., Lareau L.F., Lazarevic D., Lipovich L., Liu J.,
RA   Liuni S., McWilliam S., Madan Babu M., Madera M., Marchionni L.,
RA   Matsuda H., Matsuzawa S., Miki H., Mignone F., Miyake S., Morris K.,
RA   Mottagui-Tabar S., Mulder N., Nakano N., Nakauchi H., Ng P.,
RA   Nilsson R., Nishiguchi S., Nishikawa S., Nori F., Ohara O.,
RA   Okazaki Y., Orlando V., Pang K.C., Pavan W.J., Pavesi G., Pesole G.,
RA   Petrovsky N., Piazza S., Reed J., Reid J.F., Ring B.Z., Ringwald M.,
RA   Rost B., Ruan Y., Salzberg S.L., Sandelin A., Schneider C.,
RA   Schoenbach C., Sekiguchi K., Semple C.A., Seno S., Sessa L., Sheng Y.,
RA   Shibata Y., Shimada H., Shimada K., Silva D., Sinclair B.,
RA   Sperling S., Stupka E., Sugiura K., Sultana R., Takenaka Y., Taki K.,
RA   Tammoja K., Tan S.L., Tang S., Taylor M.S., Tegner J., Teichmann S.A.,
RA   Ueda H.R., van Nimwegen E., Verardo R., Wei C.L., Yagi K.,
RA   Yamanishi H., Zabarovsky E., Zhu S., Zimmer A., Hide W., Bult C.,
RA   Grimmond S.M., Teasdale R.D., Liu E.T., Brusic V., Quackenbush J.,
RA   Wahlestedt C., Mattick J.S., Hume D.A., Kai C., Sasaki D., Tomaru Y.,
RA   Fukuda S., Kanamori-Katayama M., Suzuki M., Aoki J., Arakawa T.,
RA   Iida J., Imamura K., Itoh M., Kato T., Kawaji H., Kawagashira N.,
RA   Kawashima T., Kojima M., Kondo S., Konno H., Nakano K., Ninomiya N.,
RA   Nishio T., Okada M., Plessy C., Shibata K., Shiraki T., Suzuki S.,
RA   Tagami M., Waki K., Watahiki A., Okamura-Oho Y., Suzuki H., Kawai J.,
RA   Hayashizaki Y.;
RT   "The transcriptional landscape of the mammalian genome.";
RL   Science 309:1559-1563(2005).
RN   [5]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2).
RC   TISSUE=Brain;
RX   PubMed=15489334; DOI=10.1101/gr.2596504;
RG   The MGC Project Team;
RT   "The status, quality, and expansion of the NIH full-length cDNA
RT   project: the Mammalian Gene Collection (MGC).";
RL   Genome Res. 14:2121-2127(2004).
RN   [6]
RP   FUNCTION, AND DISRUPTION PHENOTYPE.
RX   PubMed=16893423; DOI=10.1111/j.1471-4159.2006.03930.x;
RA   Zhang D., Stumpo D.J., Graves J.P., DeGraff L.M., Grissom S.F.,
RA   Collins J.B., Li L., Zeldin D.C., Blackshear P.J.;
RT   "Identification of potential target genes for RFX4_v3, a transcription
RT   factor critical for brain development.";
RL   J. Neurochem. 98:860-875(2006).
RN   [7]
RP   FUNCTION, SUBCELLULAR LOCATION, AND INTERACTION WITH GPS2.
RX   PubMed=18218630; DOI=10.1074/jbc.M708209200;
RA   Zhang D., Harry G.J., Blackshear P.J., Zeldin D.C.;
RT   "G-protein pathway suppressor 2 (GPS2) interacts with the regulatory
RT   factor X4 variant 3 (RFX4_v3) and functions as a transcriptional co-
RT   activator.";
RL   J. Biol. Chem. 283:8580-8590(2008).
CC   -!- FUNCTION: Isoform 1: Transcription factor that plays a role in
CC       early brain development. May activate transcription by interacting
CC       directly with the X-box. May activate transcription from CX3CL1
CC       promoter through the X-box during brain development.
CC       {ECO:0000269|PubMed:12925582, ECO:0000269|PubMed:16893423,
CC       ECO:0000269|PubMed:18218630}.
CC   -!- SUBUNIT: Homodimer. Heterodimer with RFX2 and RFX3. Binds DNA (By
CC       similarity). Interacts with GPS2 (PubMed:18218630).
CC       {ECO:0000250|UniProtKB:Q33E94, ECO:0000269|PubMed:18218630}.
CC   -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000255|PROSITE-
CC       ProRule:PRU00858, ECO:0000269|PubMed:14701801,
CC       ECO:0000269|PubMed:18218630}.
CC   -!- ALTERNATIVE PRODUCTS:
CC       Event=Alternative splicing; Named isoforms=4;
CC       Name=1; Synonyms=bRFX4, RFX4_v3;
CC         IsoId=Q7TNK1-1; Sequence=Displayed;
CC       Name=2;
CC         IsoId=Q7TNK1-2; Sequence=VSP_030248, VSP_030249;
CC       Name=3;
CC         IsoId=Q7TNK1-3; Sequence=VSP_030247;
CC         Note=No experimental confirmation available.;
CC       Name=4;
CC         IsoId=Q7TNK1-4; Sequence=VSP_030248, VSP_030249, VSP_030250,
CC                                  VSP_030251;
CC         Note=No experimental confirmation available.;
CC   -!- TISSUE SPECIFICITY: Isoform 1: Brain-specific. Isoform 2: Testis-
CC       specific. Isoform 1: Highly expressed in the suprachiasmatic
CC       nucleus, the central pacemaker site of the circadian clock (at
CC       protein level). {ECO:0000269|PubMed:12925582,
CC       ECO:0000269|PubMed:14701801}.
CC   -!- DEVELOPMENTAL STAGE: At E8.5, detected in most of the neural plate
CC       but is excluded from the presumptive forebrain region. At E9.5,
CC       its expression is mostly restricted to two large regions, the
CC       caudal diencephalon/mesencephalon and the spinal cord. By E10.5,
CC       is present throughout the neural tube, and it is also detected in
CC       the cerebral cortex. It is also strongly expressed in the
CC       developing subcommissural organ (SCO) from E14.5 to birth.
CC       {ECO:0000269|PubMed:12925582}.
CC   -!- INDUCTION: Isoform 1: Induced in a subjective night-specific
CC       manner. {ECO:0000269|PubMed:14701801}.
CC   -!- DISRUPTION PHENOTYPE: Mice with an insertion of a cardiac-specific
CC       epoxygenase transgene into an intron in the Rfx4 locus develop
CC       head swelling and rapid neurological decline in young adulthood,
CC       and have marked hydrocephalus of the lateral and third ventricles.
CC       Interruption of two alleles results in profound failure of dorsal
CC       midline brain structure formation and perinatal death.
CC       Interruption of a single allele prevents formation of the
CC       subcommissural organ, a structure important for cerebrospinal
CC       fluid flow through the aqueduct of Sylvius and results in
CC       congenital hydrocephalus. {ECO:0000269|PubMed:12925582,
CC       ECO:0000269|PubMed:16893423}.
CC   -!- SIMILARITY: Belongs to the RFX family. {ECO:0000255|PROSITE-
CC       ProRule:PRU00858}.
CC   -!- SEQUENCE CAUTION:
CC       Sequence=BAC28598.1; Type=Erroneous initiation; Evidence={ECO:0000305};
DR   EMBL; AY342003; AAQ17042.1; -; mRNA.
DR   EMBL; AY102010; AAM52485.2; -; mRNA.
DR   EMBL; AB086957; BAD07408.1; -; mRNA.
DR   EMBL; AB089184; BAD07409.1; -; mRNA.
DR   EMBL; AK016791; BAB30432.1; -; mRNA.
DR   EMBL; AK034131; BAC28598.1; ALT_INIT; mRNA.
DR   EMBL; AK132673; BAE21294.1; -; mRNA.
DR   EMBL; BC138719; AAI38720.1; -; mRNA.
DR   EMBL; BC138720; AAI38721.1; -; mRNA.
DR   CCDS; CCDS24082.1; -. [Q7TNK1-1]
DR   CCDS; CCDS24083.1; -. [Q7TNK1-2]
DR   RefSeq; NP_001020089.1; NM_001024918.1. [Q7TNK1-1]
DR   RefSeq; NP_081965.2; NM_027689.3. [Q7TNK1-2]
DR   UniGene; Mm.79070; -.
DR   ProteinModelPortal; Q7TNK1; -.
DR   SMR; Q7TNK1; -.
DR   BioGrid; 214500; 4.
DR   STRING; 10090.ENSMUSP00000051107; -.
DR   PhosphoSitePlus; Q7TNK1; -.
DR   PaxDb; Q7TNK1; -.
DR   PeptideAtlas; Q7TNK1; -.
DR   PRIDE; Q7TNK1; -.
DR   Ensembl; ENSMUST00000060397; ENSMUSP00000051107; ENSMUSG00000020037. [Q7TNK1-1]
DR   Ensembl; ENSMUST00000095388; ENSMUSP00000093035; ENSMUSG00000020037. [Q7TNK1-2]
DR   Ensembl; ENSMUST00000166696; ENSMUSP00000128690; ENSMUSG00000020037. [Q7TNK1-3]
DR   GeneID; 71137; -.
DR   KEGG; mmu:71137; -.
DR   UCSC; uc007gkv.1; mouse. [Q7TNK1-1]
DR   UCSC; uc007gkw.1; mouse. [Q7TNK1-2]
DR   CTD; 5992; -.
DR   MGI; MGI:1918387; Rfx4.
DR   eggNOG; ENOG410IT81; Eukaryota.
DR   eggNOG; ENOG410XSKJ; LUCA.
DR   GeneTree; ENSGT00940000153688; -.
DR   HOGENOM; HOG000013104; -.
DR   HOVERGEN; HBG101271; -.
DR   InParanoid; Q7TNK1; -.
DR   KO; K09174; -.
DR   OMA; PPMQSQY; -.
DR   OrthoDB; EOG091G01JI; -.
DR   PhylomeDB; Q7TNK1; -.
DR   TreeFam; TF321340; -.
DR   PRO; PR:Q7TNK1; -.
DR   Proteomes; UP000000589; Chromosome 10.
DR   Bgee; ENSMUSG00000020037; Expressed in 125 organ(s), highest expression level in brain.
DR   Genevisible; Q7TNK1; MM.
DR   GO; GO:0005634; C:nucleus; IDA:MGI.
DR   GO; GO:0003682; F:chromatin binding; IDA:MGI.
DR   GO; GO:0003700; F:DNA-binding transcription factor activity; IBA:GO_Central.
DR   GO; GO:0001077; F:proximal promoter DNA-binding transcription activator activity, RNA polymerase II-specific; ISO:MGI.
DR   GO; GO:0000978; F:RNA polymerase II proximal promoter sequence-specific DNA binding; ISO:MGI.
DR   GO; GO:0021696; P:cerebellar cortex morphogenesis; IMP:MGI.
DR   GO; GO:0060271; P:cilium assembly; IMP:MGI.
DR   GO; GO:0021516; P:dorsal spinal cord development; IMP:MGI.
DR   GO; GO:0030900; P:forebrain development; IMP:MGI.
DR   GO; GO:0030901; P:midbrain development; IMP:MGI.
DR   GO; GO:0021914; P:negative regulation of smoothened signaling pathway involved in ventral spinal cord patterning; IMP:MGI.
DR   GO; GO:0045944; P:positive regulation of transcription by RNA polymerase II; IDA:MGI.
DR   GO; GO:0070613; P:regulation of protein processing; IMP:MGI.
DR   GO; GO:0006357; P:regulation of transcription by RNA polymerase II; IDA:MGI.
DR   GO; GO:0021537; P:telencephalon development; IMP:MGI.
DR   Gene3D; 1.10.10.10; -; 1.
DR   InterPro; IPR003150; DNA-bd_RFX.
DR   InterPro; IPR039779; RFX-like.
DR   InterPro; IPR036388; WH-like_DNA-bd_sf.
DR   InterPro; IPR036390; WH_DNA-bd_sf.
DR   PANTHER; PTHR12619; PTHR12619; 1.
DR   Pfam; PF02257; RFX_DNA_binding; 1.
DR   SUPFAM; SSF46785; SSF46785; 1.
DR   PROSITE; PS51526; RFX_DBD; 1.
PE   1: Evidence at protein level;
KW   Activator; Alternative splicing; Complete proteome; DNA-binding;
KW   Nucleus; Reference proteome; Transcription; Transcription regulation.
FT   CHAIN         1    735       Transcription factor RFX4.
FT                                /FTId=PRO_0000314238.
FT   DNA_BIND     44    126
FT   DNA_BIND     61    136       RFX-type winged-helix.
FT                                {ECO:0000255|PROSITE-ProRule:PRU00858}.
FT   REGION      315    487       Necessary for dimerization.
FT   VAR_SEQ       1    143       Missing (in isoform 3).
FT                                {ECO:0000303|PubMed:16141072}.
FT                                /FTId=VSP_030247.
FT   VAR_SEQ       1     94       Missing (in isoform 2 and isoform 4).
FT                                {ECO:0000303|PubMed:14701801,
FT                                ECO:0000303|PubMed:15489334,
FT                                ECO:0000303|PubMed:16141072}.
FT                                /FTId=VSP_030248.
FT   VAR_SEQ      95    126       TQPVNAASFGKIIRQQFPQLTTRRLGTRGQSK -> MNWAA
FT                                FGGPEFFIPGGMKMEASCPLGRNFTEW (in isoform 2
FT                                and isoform 4).
FT                                {ECO:0000303|PubMed:14701801,
FT                                ECO:0000303|PubMed:15489334,
FT                                ECO:0000303|PubMed:16141072}.
FT                                /FTId=VSP_030249.
FT   VAR_SEQ     452    476       SFHLIHLMFDDYVLYLLESLHCQER -> LFYCPASKATLL
FT                                GQGWEAPCDLSGT (in isoform 4).
FT                                {ECO:0000303|PubMed:16141072}.
FT                                /FTId=VSP_030250.
FT   VAR_SEQ     477    735       Missing (in isoform 4).
FT                                {ECO:0000303|PubMed:16141072}.
FT                                /FTId=VSP_030251.
FT   CONFLICT    227    227       F -> L (in Ref. 4; BAB30432).
FT                                {ECO:0000305}.
FT   CONFLICT    578    578       T -> N (in Ref. 4; BAE21294).
FT                                {ECO:0000305}.
SQ   SEQUENCE   735 AA;  83371 MW;  5D51484CC26A8338 CRC64;
     MHCGLLEEPD MDSTESWIER CLNESENKRY SSHTSLGNVS NDENEEKENN RASKPHSTPA
     TLQWLEENYE IAEGVCIPRS ALYMHYLDFC EKNDTQPVNA ASFGKIIRQQ FPQLTTRRLG
     TRGQSKYHYY GIAVKESSQY YDVMYSKKGA AWVSETGKRE VTKQTVAYSP RSKLGTLLPD
     FPNVKDLNLP ASLPEEKVST FIMMYRTHCQ RILDTVIRAN FDEVQSFLLH FWQGMPPHML
     PVLGSSTVVN IVGVCDSILY KAISGVLMPT VLQALPDSLT QVIRKFAKQL DEWLKVALHD
     LPENLRNIKF ELSRRFSQIL RRQTSLNHLC QASRTVIHSA DITFQMLEDW RNVDLSSITK
     QTLYTMEDSR DEHRRLIIQL YQEFDHLLEE QSPIESYIEW LDTMVDRCVV KVAAKRQGSL
     KKVAQQFLLM WSCFGTRVIR DMTLHSAPSF GSFHLIHLMF DDYVLYLLES LHCQERANEL
     MRAMKGEGST AEAQEEIILT EATPPTPSPG PSFSPAKSAT SVEVPPPSSP VSNPSPEYTG
     LSTAGAMQSY TWSLTYTVTT AAGSPAENSQ QLPCMRSTHM PSSSVTHRIP VYSHREEHGY
     TGSYNYGSYG NQHPHPLQNQ YPALPHDTAI SGPLHYSPYH RSSAQYPFNS PTSRMEPCLM
     SSTPRLHPTP VTPRWPEVPT ANACYTSPSV HSTRYGNSSD MYTPLTTRRN SEYEHMQHFP
     GFAYINGEAS TGWAK
//
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