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Q7TNK1

- RFX4_MOUSE

UniProt

Q7TNK1 - RFX4_MOUSE

Protein

Transcription factor RFX4

Gene

Rfx4

Organism
Mus musculus (Mouse)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 91 (01 Oct 2014)
      Sequence version 1 (01 Oct 2003)
      Previous versions | rss
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    Functioni

    Plays a role in early brain development. May activate transcription by interacting directly with the X-box. May activate transcription from CX3CL1 promoter through the X-box during brain development.2 Publications

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    DNA bindingi44 – 12683Add
    BLAST
    DNA bindingi61 – 13676RFX-type winged-helixPROSITE-ProRule annotationAdd
    BLAST

    GO - Molecular functioni

    1. chromatin binding Source: MGI
    2. DNA binding Source: UniProtKB-KW
    3. protein binding Source: MGI

    GO - Biological processi

    1. cerebellar cortex morphogenesis Source: MGI
    2. cilium assembly Source: MGI
    3. dorsal spinal cord development Source: MGI
    4. forebrain development Source: MGI
    5. midbrain development Source: MGI
    6. negative regulation of smoothened signaling pathway involved in ventral spinal cord patterning Source: MGI
    7. positive regulation of transcription from RNA polymerase II promoter Source: MGI
    8. regulation of protein processing Source: MGI
    9. regulation of transcription from RNA polymerase II promoter Source: MGI
    10. telencephalon development Source: MGI
    11. transcription, DNA-templated Source: UniProtKB-KW

    Keywords - Molecular functioni

    Activator

    Keywords - Biological processi

    Transcription, Transcription regulation

    Keywords - Ligandi

    DNA-binding

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Transcription factor RFX4
    Alternative name(s):
    Regulatory factor X 4
    Gene namesi
    Name:Rfx4
    OrganismiMus musculus (Mouse)
    Taxonomic identifieri10090 [NCBI]
    Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeMusMus
    ProteomesiUP000000589: Chromosome 10

    Organism-specific databases

    MGIiMGI:1918387. Rfx4.

    Subcellular locationi

    Nucleus 1 PublicationPROSITE-ProRule annotation

    GO - Cellular componenti

    1. nucleus Source: MGI

    Keywords - Cellular componenti

    Nucleus

    Pathology & Biotechi

    Disruption phenotypei

    Mice with an insertion of a cardiac-specific epoxygenase transgene into an intron in the Rfx4 locus develop head swelling and rapid neurological decline in young adulthood, and have marked hydrocephalus of the lateral and third ventricles. Interruption of two alleles results in profound failure of dorsal midline brain structure formation and perinatal death. Interruption of a single allele prevents formation of the subcommissural organ, a structure important for cerebrospinal fluid flow through the aqueduct of Sylvius and results in congenital hydrocephalus.2 Publications

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 735735Transcription factor RFX4PRO_0000314238Add
    BLAST

    Proteomic databases

    PRIDEiQ7TNK1.

    Expressioni

    Tissue specificityi

    Isoform 1 is brain-specific. Isoform 2 is testis-specific. Isoform 1 is highly expressed in the suprachiasmatic nucleus (at protein level), the central pacemaker site of the circadian clock.2 Publications

    Developmental stagei

    At E8.5, detected in most of the neural plate but is excluded from the presumptive forebrain region. At E9.5, its expression is mostly restricted to two large regions, the caudal diencephalon/mesencephalon and the spinal cord. By E10.5, is present throughout the neural tube, and it is also detected in the cerebral cortex. It is also strongly expressed in the developing subcommissural organ (SCO) from E14.5 to birth.1 Publication

    Inductioni

    Isoform 1 is induced in a subjective night-specific manner.1 Publication

    Gene expression databases

    BgeeiQ7TNK1.
    GenevestigatoriQ7TNK1.

    Interactioni

    Subunit structurei

    Homodimer. Heterodimer with RFX2 and RFX3. Binds DNA By similarity.By similarity

    Protein-protein interaction databases

    BioGridi214500. 3 interactions.

    Structurei

    3D structure databases

    ProteinModelPortaliQ7TNK1.
    SMRiQ7TNK1. Positions 61-135.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni315 – 487173Necessary for dimerizationAdd
    BLAST

    Sequence similaritiesi

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

    Phylogenomic databases

    eggNOGiNOG243313.
    GeneTreeiENSGT00550000074532.
    HOGENOMiHOG000013104.
    HOVERGENiHBG101271.
    InParanoidiQ7TNK1.
    KOiK09174.
    OMAiGAMQSYT.
    OrthoDBiEOG79CXXT.
    PhylomeDBiQ7TNK1.
    TreeFamiTF321340.

    Family and domain databases

    Gene3Di1.10.10.10. 1 hit.
    InterProiIPR003150. DNA-bd_RFX.
    IPR011991. WHTH_DNA-bd_dom.
    [Graphical view]
    PfamiPF02257. RFX_DNA_binding. 1 hit.
    [Graphical view]
    PROSITEiPS51526. RFX_DBD. 1 hit.
    [Graphical view]

    Sequences (4)i

    Sequence statusi: Complete.

    This entry describes 4 isoformsi produced by alternative splicing. Align

    Isoform 1 (identifier: Q7TNK1-1) [UniParc]FASTAAdd to Basket

    Also known as: bRFX4, RFX4_v3

    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

    MHCGLLEEPD MDSTESWIER CLNESENKRY SSHTSLGNVS NDENEEKENN    50
    RASKPHSTPA TLQWLEENYE IAEGVCIPRS ALYMHYLDFC EKNDTQPVNA 100
    ASFGKIIRQQ FPQLTTRRLG TRGQSKYHYY GIAVKESSQY YDVMYSKKGA 150
    AWVSETGKRE VTKQTVAYSP RSKLGTLLPD FPNVKDLNLP ASLPEEKVST 200
    FIMMYRTHCQ RILDTVIRAN FDEVQSFLLH FWQGMPPHML PVLGSSTVVN 250
    IVGVCDSILY KAISGVLMPT VLQALPDSLT QVIRKFAKQL DEWLKVALHD 300
    LPENLRNIKF ELSRRFSQIL RRQTSLNHLC QASRTVIHSA DITFQMLEDW 350
    RNVDLSSITK QTLYTMEDSR DEHRRLIIQL YQEFDHLLEE QSPIESYIEW 400
    LDTMVDRCVV KVAAKRQGSL KKVAQQFLLM WSCFGTRVIR DMTLHSAPSF 450
    GSFHLIHLMF DDYVLYLLES LHCQERANEL MRAMKGEGST AEAQEEIILT 500
    EATPPTPSPG PSFSPAKSAT SVEVPPPSSP VSNPSPEYTG LSTAGAMQSY 550
    TWSLTYTVTT AAGSPAENSQ QLPCMRSTHM PSSSVTHRIP VYSHREEHGY 600
    TGSYNYGSYG NQHPHPLQNQ YPALPHDTAI SGPLHYSPYH RSSAQYPFNS 650
    PTSRMEPCLM SSTPRLHPTP VTPRWPEVPT ANACYTSPSV HSTRYGNSSD 700
    MYTPLTTRRN SEYEHMQHFP GFAYINGEAS TGWAK 735
    Length:735
    Mass (Da):83,371
    Last modified:October 1, 2003 - v1
    Checksum:i5D51484CC26A8338
    GO
    Isoform 2 (identifier: Q7TNK1-2) [UniParc]FASTAAdd to Basket

    The sequence of this isoform differs from the canonical sequence as follows:
         1-94: Missing.
         95-126: TQPVNAASFGKIIRQQFPQLTTRRLGTRGQSK → MNWAAFGGPEFFIPGGMKMEASCPLGRNFTEW

    Show »
    Length:641
    Mass (Da):72,471
    Checksum:iA7B08624C1BAB370
    GO
    Isoform 3 (identifier: Q7TNK1-3) [UniParc]FASTAAdd to Basket

    The sequence of this isoform differs from the canonical sequence as follows:
         1-143: Missing.

    Note: No experimental confirmation available.

    Show »
    Length:592
    Mass (Da):66,842
    Checksum:iAEC52710E9D358F9
    GO
    Isoform 4 (identifier: Q7TNK1-4) [UniParc]FASTAAdd to Basket

    The sequence of this isoform differs from the canonical sequence as follows:
         1-94: Missing.
         95-126: TQPVNAASFGKIIRQQFPQLTTRRLGTRGQSK → MNWAAFGGPEFFIPGGMKMEASCPLGRNFTEW
         452-476: SFHLIHLMFDDYVLYLLESLHCQER → LFYCPASKATLLGQGWEAPCDLSGT
         477-735: Missing.

    Note: No experimental confirmation available.

    Show »
    Length:382
    Mass (Da):43,743
    Checksum:iD5CF5B41DE9B3466
    GO

    Sequence cautioni

    The sequence BAC28598.1 differs from that shown. Reason: Erroneous initiation.

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti227 – 2271F → L in BAB30432. (PubMed:16141072)Curated
    Sequence conflicti578 – 5781T → N in BAE21294. (PubMed:16141072)Curated

    Alternative sequence

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Alternative sequencei1 – 143143Missing in isoform 3. 1 PublicationVSP_030247Add
    BLAST
    Alternative sequencei1 – 9494Missing in isoform 2 and isoform 4. 3 PublicationsVSP_030248Add
    BLAST
    Alternative sequencei95 – 12632TQPVN…RGQSK → MNWAAFGGPEFFIPGGMKME ASCPLGRNFTEW in isoform 2 and isoform 4. 3 PublicationsVSP_030249Add
    BLAST
    Alternative sequencei452 – 47625SFHLI…HCQER → LFYCPASKATLLGQGWEAPC DLSGT in isoform 4. 1 PublicationVSP_030250Add
    BLAST
    Alternative sequencei477 – 735259Missing in isoform 4. 1 PublicationVSP_030251Add
    BLAST

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AY342003 mRNA. Translation: AAQ17042.1.
    AY102010 mRNA. Translation: AAM52485.2.
    AB086957 mRNA. Translation: BAD07408.1.
    AB089184 mRNA. Translation: BAD07409.1.
    AK016791 mRNA. Translation: BAB30432.1.
    AK034131 mRNA. Translation: BAC28598.1. Different initiation.
    AK132673 mRNA. Translation: BAE21294.1.
    BC138719 mRNA. Translation: AAI38720.1.
    BC138720 mRNA. Translation: AAI38721.1.
    CCDSiCCDS24082.1. [Q7TNK1-1]
    CCDS24083.1. [Q7TNK1-2]
    RefSeqiNP_001020089.1. NM_001024918.1. [Q7TNK1-1]
    NP_081965.2. NM_027689.3. [Q7TNK1-2]
    UniGeneiMm.79070.

    Genome annotation databases

    EnsembliENSMUST00000060397; ENSMUSP00000051107; ENSMUSG00000020037. [Q7TNK1-1]
    ENSMUST00000095388; ENSMUSP00000093035; ENSMUSG00000020037. [Q7TNK1-2]
    ENSMUST00000166696; ENSMUSP00000128690; ENSMUSG00000020037. [Q7TNK1-3]
    GeneIDi71137.
    KEGGimmu:71137.
    UCSCiuc007gkv.1. mouse. [Q7TNK1-1]
    uc007gkw.1. mouse. [Q7TNK1-2]

    Keywords - Coding sequence diversityi

    Alternative splicing

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AY342003 mRNA. Translation: AAQ17042.1 .
    AY102010 mRNA. Translation: AAM52485.2 .
    AB086957 mRNA. Translation: BAD07408.1 .
    AB089184 mRNA. Translation: BAD07409.1 .
    AK016791 mRNA. Translation: BAB30432.1 .
    AK034131 mRNA. Translation: BAC28598.1 . Different initiation.
    AK132673 mRNA. Translation: BAE21294.1 .
    BC138719 mRNA. Translation: AAI38720.1 .
    BC138720 mRNA. Translation: AAI38721.1 .
    CCDSi CCDS24082.1. [Q7TNK1-1 ]
    CCDS24083.1. [Q7TNK1-2 ]
    RefSeqi NP_001020089.1. NM_001024918.1. [Q7TNK1-1 ]
    NP_081965.2. NM_027689.3. [Q7TNK1-2 ]
    UniGenei Mm.79070.

    3D structure databases

    ProteinModelPortali Q7TNK1.
    SMRi Q7TNK1. Positions 61-135.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    BioGridi 214500. 3 interactions.

    Proteomic databases

    PRIDEi Q7TNK1.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    Ensembli ENSMUST00000060397 ; ENSMUSP00000051107 ; ENSMUSG00000020037 . [Q7TNK1-1 ]
    ENSMUST00000095388 ; ENSMUSP00000093035 ; ENSMUSG00000020037 . [Q7TNK1-2 ]
    ENSMUST00000166696 ; ENSMUSP00000128690 ; ENSMUSG00000020037 . [Q7TNK1-3 ]
    GeneIDi 71137.
    KEGGi mmu:71137.
    UCSCi uc007gkv.1. mouse. [Q7TNK1-1 ]
    uc007gkw.1. mouse. [Q7TNK1-2 ]

    Organism-specific databases

    CTDi 5992.
    MGIi MGI:1918387. Rfx4.

    Phylogenomic databases

    eggNOGi NOG243313.
    GeneTreei ENSGT00550000074532.
    HOGENOMi HOG000013104.
    HOVERGENi HBG101271.
    InParanoidi Q7TNK1.
    KOi K09174.
    OMAi GAMQSYT.
    OrthoDBi EOG79CXXT.
    PhylomeDBi Q7TNK1.
    TreeFami TF321340.

    Miscellaneous databases

    NextBioi 333097.
    PROi Q7TNK1.
    SOURCEi Search...

    Gene expression databases

    Bgeei Q7TNK1.
    Genevestigatori Q7TNK1.

    Family and domain databases

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

    Publicationsi

    1. "Mouse Rfx4, a gene expressed in the proliferative zones of the central nervous system."
      Belaoussoff M., Dohrmann C.E., Armsen W., Gruss P.
      Submitted (JUL-2003) to the EMBL/GenBank/DDBJ databases
      Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1).
    2. "Graded phenotypic response to partial and complete deficiency of a brain-specific transcript variant of the winged helix transcription factor RFX4."
      Blackshear P.J., Graves J.P., Stumpo D.J., Cobos I., Rubenstein J.L.R., Zeldin D.C.
      Development 130:4539-4552(2003) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1), FUNCTION, TISSUE SPECIFICITY, DEVELOPMENTAL STAGE, DISRUPTION PHENOTYPE.
      Strain: C57BL/6.
      Tissue: Brain.
    3. "Restricted expression and photic induction of a novel mouse regulatory factor X4 transcript in the suprachiasmatic nucleus."
      Araki R., Takahashi H., Fukumura R., Sun F., Umeda N., Sujino M., Inouye S.T., Saito T., Abe M.
      J. Biol. Chem. 279:10237-10242(2004) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORMS 1 AND 2), SUBCELLULAR LOCATION, INDUCTION, TISSUE SPECIFICITY.
      Strain: C57BL/6.
      Tissue: Suprachiasmatic nucleus and Testis.
    4. "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; 3 AND 4).
      Strain: C57BL/6J.
      Tissue: Diencephalon and Testis.
    5. "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 2).
      Tissue: Brain.
    6. "Identification of potential target genes for RFX4_v3, a transcription factor critical for brain development."
      Zhang D., Stumpo D.J., Graves J.P., DeGraff L.M., Grissom S.F., Collins J.B., Li L., Zeldin D.C., Blackshear P.J.
      J. Neurochem. 98:860-875(2006) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, DISRUPTION PHENOTYPE.

    Entry informationi

    Entry nameiRFX4_MOUSE
    AccessioniPrimary (citable) accession number: Q7TNK1
    Secondary accession number(s): B2RS52
    , Q3V158, Q76KT2, Q8HWA6, Q9D453
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: January 15, 2008
    Last sequence update: October 1, 2003
    Last modified: October 1, 2014
    This is version 91 of the entry and version 1 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