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Q7TNK1

- RFX4_MOUSE

UniProt

Q7TNK1 - RFX4_MOUSE

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Protein
Transcription factor RFX4
Gene
Rfx4
Organism
Mus musculus (Mouse)
Status
Reviewed - Annotation score: 5 out of 5 - Experimental evidence at protein leveli

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 – 12683
Add
BLAST
DNA bindingi61 – 13676RFX-type winged-helix
Add
BLAST

GO - Molecular functioni

  1. DNA binding Source: UniProtKB-KW
  2. chromatin binding Source: MGI
  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
Complete GO annotation...

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 Publication

GO - Cellular componenti

  1. nucleus Source: MGI
Complete GO annotation...

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 RFX4
PRO_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.

Protein-protein interaction databases

BioGridi214500. 3 interactions.

Structurei

3D structure databases

ProteinModelPortaliQ7TNK1.
SMRiQ7TNK1. Positions 61-135.

Family & Domainsi

Region

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

Sequence similaritiesi

Belongs to the RFX family.

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.

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei1 – 143143Missing in isoform 3.
VSP_030247Add
BLAST
Alternative sequencei1 – 9494Missing in isoform 2 and isoform 4.
VSP_030248Add
BLAST
Alternative sequencei95 – 12632TQPVN…RGQSK → MNWAAFGGPEFFIPGGMKME ASCPLGRNFTEW in isoform 2 and isoform 4.
VSP_030249Add
BLAST
Alternative sequencei452 – 47625SFHLI…HCQER → LFYCPASKATLLGQGWEAPC DLSGT in isoform 4.
VSP_030250Add
BLAST
Alternative sequencei477 – 735259Missing in isoform 4.
VSP_030251Add
BLAST

Sequence conflict

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti227 – 2271F → L in BAB30432. 1 Publication
Sequence conflicti578 – 5781T → N in BAE21294. 1 Publication

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

« Hide 'large scale' publications
  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: July 9, 2014
This is version 90 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

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