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Q7TNK1 (RFX4_MOUSE) Reviewed, UniProtKB/Swiss-Prot

Last modified July 9, 2014. Version 90. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (2) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Alt products·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Transcription factor RFX4
Alternative name(s):
Regulatory factor X 4
Gene names
Name:Rfx4
OrganismMus musculus (Mouse) [Reference proteome]
Taxonomic identifier10090 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeMusMus

Protein attributes

Sequence length735 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

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. Ref.2 Ref.6

Subunit structure

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

Subcellular location

Nucleus Ref.3.

Tissue specificity

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. Ref.2 Ref.3

Developmental stage

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. Ref.2

Induction

Isoform 1 is induced in a subjective night-specific manner. Ref.3

Disruption phenotype

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. Ref.2 Ref.6

Sequence similarities

Belongs to the RFX family.

Contains 1 RFX-type winged-helix DNA-binding domain.

Sequence caution

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

Ontologies

Keywords
   Biological processTranscription
Transcription regulation
   Cellular componentNucleus
   Coding sequence diversityAlternative splicing
   LigandDNA-binding
   Molecular functionActivator
   Technical termComplete proteome
Reference proteome
Gene Ontology (GO)
   Biological_processcerebellar cortex morphogenesis

Inferred from mutant phenotype Ref.2. Source: MGI

cilium assembly

Inferred from mutant phenotype PubMed 19887680. Source: MGI

dorsal spinal cord development

Inferred from mutant phenotype Ref.2. Source: MGI

forebrain development

Inferred from mutant phenotype Ref.2. Source: MGI

midbrain development

Inferred from mutant phenotype Ref.2. Source: MGI

negative regulation of smoothened signaling pathway involved in ventral spinal cord patterning

Inferred from mutant phenotype PubMed 19887680. Source: MGI

positive regulation of transcription from RNA polymerase II promoter

Inferred from direct assay Ref.6PubMed 18218630. Source: MGI

regulation of protein processing

Inferred from mutant phenotype PubMed 19887680. Source: MGI

regulation of transcription from RNA polymerase II promoter

Inferred from direct assay Ref.6PubMed 18218630. Source: MGI

telencephalon development

Inferred from mutant phenotype PubMed 19887680. Source: MGI

transcription, DNA-templated

Inferred from electronic annotation. Source: UniProtKB-KW

   Cellular_componentnucleus

Inferred from direct assay Ref.6PubMed 18218630. Source: MGI

   Molecular_functionDNA binding

Inferred from electronic annotation. Source: UniProtKB-KW

chromatin binding

Inferred from direct assay Ref.6. Source: MGI

protein binding

Inferred from physical interaction PubMed 18218630. Source: MGI

Complete GO annotation...

Alternative products

This entry describes 4 isoforms produced by alternative splicing. [Align] [Select]
Isoform 1 (identifier: Q7TNK1-1)

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.
Isoform 2 (identifier: Q7TNK1-2)

The sequence of this isoform differs from the canonical sequence as follows:
     1-94: Missing.
     95-126: TQPVNAASFGKIIRQQFPQLTTRRLGTRGQSK → MNWAAFGGPEFFIPGGMKMEASCPLGRNFTEW
Isoform 3 (identifier: Q7TNK1-3)

The sequence of this isoform differs from the canonical sequence as follows:
     1-143: Missing.
Note: No experimental confirmation available.
Isoform 4 (identifier: Q7TNK1-4)

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.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 735735Transcription factor RFX4
PRO_0000314238

Regions

DNA binding44 – 12683
DNA binding61 – 13676RFX-type winged-helix
Region315 – 487173Necessary for dimerization

Natural variations

Alternative sequence1 – 143143Missing in isoform 3.
VSP_030247
Alternative sequence1 – 9494Missing in isoform 2 and isoform 4.
VSP_030248
Alternative sequence95 – 12632TQPVN…RGQSK → MNWAAFGGPEFFIPGGMKME ASCPLGRNFTEW in isoform 2 and isoform 4.
VSP_030249
Alternative sequence452 – 47625SFHLI…HCQER → LFYCPASKATLLGQGWEAPC DLSGT in isoform 4.
VSP_030250
Alternative sequence477 – 735259Missing in isoform 4.
VSP_030251

Experimental info

Sequence conflict2271F → L in BAB30432. Ref.4
Sequence conflict5781T → N in BAE21294. Ref.4

Sequences

Sequence LengthMass (Da)Tools
Isoform 1 (bRFX4) (RFX4_v3) [UniParc].

Last modified October 1, 2003. Version 1.
Checksum: 5D51484CC26A8338

FASTA73583,371
        10         20         30         40         50         60 
MHCGLLEEPD MDSTESWIER CLNESENKRY SSHTSLGNVS NDENEEKENN RASKPHSTPA 

        70         80         90        100        110        120 
TLQWLEENYE IAEGVCIPRS ALYMHYLDFC EKNDTQPVNA ASFGKIIRQQ FPQLTTRRLG 

       130        140        150        160        170        180 
TRGQSKYHYY GIAVKESSQY YDVMYSKKGA AWVSETGKRE VTKQTVAYSP RSKLGTLLPD 

       190        200        210        220        230        240 
FPNVKDLNLP ASLPEEKVST FIMMYRTHCQ RILDTVIRAN FDEVQSFLLH FWQGMPPHML 

       250        260        270        280        290        300 
PVLGSSTVVN IVGVCDSILY KAISGVLMPT VLQALPDSLT QVIRKFAKQL DEWLKVALHD 

       310        320        330        340        350        360 
LPENLRNIKF ELSRRFSQIL RRQTSLNHLC QASRTVIHSA DITFQMLEDW RNVDLSSITK 

       370        380        390        400        410        420 
QTLYTMEDSR DEHRRLIIQL YQEFDHLLEE QSPIESYIEW LDTMVDRCVV KVAAKRQGSL 

       430        440        450        460        470        480 
KKVAQQFLLM WSCFGTRVIR DMTLHSAPSF GSFHLIHLMF DDYVLYLLES LHCQERANEL 

       490        500        510        520        530        540 
MRAMKGEGST AEAQEEIILT EATPPTPSPG PSFSPAKSAT SVEVPPPSSP VSNPSPEYTG 

       550        560        570        580        590        600 
LSTAGAMQSY TWSLTYTVTT AAGSPAENSQ QLPCMRSTHM PSSSVTHRIP VYSHREEHGY 

       610        620        630        640        650        660 
TGSYNYGSYG NQHPHPLQNQ YPALPHDTAI SGPLHYSPYH RSSAQYPFNS PTSRMEPCLM 

       670        680        690        700        710        720 
SSTPRLHPTP VTPRWPEVPT ANACYTSPSV HSTRYGNSSD MYTPLTTRRN SEYEHMQHFP 

       730 
GFAYINGEAS TGWAK 

« Hide

Isoform 2 [UniParc].

Checksum: A7B08624C1BAB370
Show »

FASTA64172,471
Isoform 3 [UniParc].

Checksum: AEC52710E9D358F9
Show »

FASTA59266,842
Isoform 4 [UniParc].

Checksum: D5CF5B41DE9B3466
Show »

FASTA38243,743

References

« Hide 'large scale' references
[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. expand/collapse author list , 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.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
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.
CCDSCCDS24082.1. [Q7TNK1-1]
CCDS24083.1. [Q7TNK1-2]
RefSeqNP_001020089.1. NM_001024918.1. [Q7TNK1-1]
NP_081965.2. NM_027689.3. [Q7TNK1-2]
UniGeneMm.79070.

3D structure databases

ProteinModelPortalQ7TNK1.
SMRQ7TNK1. Positions 61-135.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid214500. 3 interactions.

Proteomic databases

PRIDEQ7TNK1.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblENSMUST00000060397; ENSMUSP00000051107; ENSMUSG00000020037. [Q7TNK1-1]
ENSMUST00000095388; ENSMUSP00000093035; ENSMUSG00000020037. [Q7TNK1-2]
ENSMUST00000166696; ENSMUSP00000128690; ENSMUSG00000020037. [Q7TNK1-3]
GeneID71137.
KEGGmmu:71137.
UCSCuc007gkv.1. mouse. [Q7TNK1-1]
uc007gkw.1. mouse. [Q7TNK1-2]

Organism-specific databases

CTD5992.
MGIMGI:1918387. Rfx4.

Phylogenomic databases

eggNOGNOG243313.
GeneTreeENSGT00550000074532.
HOGENOMHOG000013104.
HOVERGENHBG101271.
InParanoidQ7TNK1.
KOK09174.
OMAGAMQSYT.
OrthoDBEOG79CXXT.
PhylomeDBQ7TNK1.
TreeFamTF321340.

Gene expression databases

BgeeQ7TNK1.
GenevestigatorQ7TNK1.

Family and domain databases

Gene3D1.10.10.10. 1 hit.
InterProIPR003150. DNA-bd_RFX.
IPR011991. WHTH_DNA-bd_dom.
[Graphical view]
PfamPF02257. RFX_DNA_binding. 1 hit.
[Graphical view]
PROSITEPS51526. RFX_DBD. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

NextBio333097.
PROQ7TNK1.
SOURCESearch...

Entry information

Entry nameRFX4_MOUSE
AccessionPrimary (citable) accession number: Q7TNK1
Secondary accession number(s): B2RS52 expand/collapse secondary AC list , Q3V158, Q76KT2, Q8HWA6, Q9D453
Entry history
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 statusReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

MGD cross-references

Mouse Genome Database (MGD) cross-references in UniProtKB/Swiss-Prot