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Protein

Transcription factor RFX4

Gene

Rfx4

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

Functioni

Isoform 1: Transcription factor that 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.3 Publications

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
DNA bindingi44 – 126Add BLAST83
DNA bindingi61 – 136RFX-type winged-helixPROSITE-ProRule annotationAdd BLAST76

GO - Molecular functioni

GO - Biological processi

Keywordsi

Molecular functionActivator, DNA-binding
Biological processTranscription, Transcription regulation

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 lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaMyomorphaMuroideaMuridaeMurinaeMusMus
Proteomesi
  • UP000000589 Componenti: Chromosome 10

Organism-specific databases

MGIiMGI:1918387 Rfx4

Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

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)DescriptionActionsGraphical viewLength
ChainiPRO_00003142381 – 735Transcription factor RFX4Add BLAST735

Proteomic databases

PaxDbiQ7TNK1
PeptideAtlasiQ7TNK1
PRIDEiQ7TNK1

PTM databases

PhosphoSitePlusiQ7TNK1

Expressioni

Tissue specificityi

Isoform 1: Brain-specific. Isoform 2: Testis-specific. Isoform 1: Highly expressed in the suprachiasmatic nucleus, the central pacemaker site of the circadian clock (at protein level).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: Induced in a subjective night-specific manner.1 Publication

Gene expression databases

BgeeiENSMUSG00000020037 Expressed in 125 organ(s), highest expression level in brain
GenevisibleiQ7TNK1 MM

Interactioni

Subunit structurei

Homodimer. Heterodimer with RFX2 and RFX3. Binds DNA (By similarity). Interacts with GPS2 (PubMed:18218630).By similarity1 Publication

Protein-protein interaction databases

BioGridi214500, 4 interactors
STRINGi10090.ENSMUSP00000051107

Structurei

3D structure databases

ProteinModelPortaliQ7TNK1
SMRiQ7TNK1
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni315 – 487Necessary for dimerizationAdd BLAST173

Sequence similaritiesi

Belongs to the RFX family.PROSITE-ProRule annotation

Phylogenomic databases

eggNOGiENOG410IT81 Eukaryota
ENOG410XSKJ LUCA
GeneTreeiENSGT00550000074532
HOGENOMiHOG000013104
HOVERGENiHBG101271
InParanoidiQ7TNK1
KOiK09174
OMAiPPMQSQY
OrthoDBiEOG091G01JI
PhylomeDBiQ7TNK1
TreeFamiTF321340

Family and domain databases

Gene3Di1.10.10.10, 1 hit
InterProiView protein in InterPro
IPR003150 DNA-bd_RFX
IPR039779 RFX-like
IPR036388 WH-like_DNA-bd_sf
IPR036390 WH_DNA-bd_sf
PANTHERiPTHR12619 PTHR12619, 1 hit
PfamiView protein in Pfam
PF02257 RFX_DNA_binding, 1 hit
SUPFAMiSSF46785 SSF46785, 1 hit
PROSITEiView protein in PROSITE
PS51526 RFX_DBD, 1 hit

Sequences (4)i

Sequence statusi: Complete.

This entry describes 4 isoformsi produced by alternative splicing. AlignAdd to basket
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
        10         20         30         40         50
MHCGLLEEPD MDSTESWIER CLNESENKRY SSHTSLGNVS NDENEEKENN
60 70 80 90 100
RASKPHSTPA TLQWLEENYE IAEGVCIPRS ALYMHYLDFC EKNDTQPVNA
110 120 130 140 150
ASFGKIIRQQ FPQLTTRRLG TRGQSKYHYY GIAVKESSQY YDVMYSKKGA
160 170 180 190 200
AWVSETGKRE VTKQTVAYSP RSKLGTLLPD FPNVKDLNLP ASLPEEKVST
210 220 230 240 250
FIMMYRTHCQ RILDTVIRAN FDEVQSFLLH FWQGMPPHML PVLGSSTVVN
260 270 280 290 300
IVGVCDSILY KAISGVLMPT VLQALPDSLT QVIRKFAKQL DEWLKVALHD
310 320 330 340 350
LPENLRNIKF ELSRRFSQIL RRQTSLNHLC QASRTVIHSA DITFQMLEDW
360 370 380 390 400
RNVDLSSITK QTLYTMEDSR DEHRRLIIQL YQEFDHLLEE QSPIESYIEW
410 420 430 440 450
LDTMVDRCVV KVAAKRQGSL KKVAQQFLLM WSCFGTRVIR DMTLHSAPSF
460 470 480 490 500
GSFHLIHLMF DDYVLYLLES LHCQERANEL MRAMKGEGST AEAQEEIILT
510 520 530 540 550
EATPPTPSPG PSFSPAKSAT SVEVPPPSSP VSNPSPEYTG LSTAGAMQSY
560 570 580 590 600
TWSLTYTVTT AAGSPAENSQ QLPCMRSTHM PSSSVTHRIP VYSHREEHGY
610 620 630 640 650
TGSYNYGSYG NQHPHPLQNQ YPALPHDTAI SGPLHYSPYH RSSAQYPFNS
660 670 680 690 700
PTSRMEPCLM SSTPRLHPTP VTPRWPEVPT ANACYTSPSV HSTRYGNSSD
710 720 730
MYTPLTTRRN SEYEHMQHFP GFAYINGEAS TGWAK
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 differs from that shown. Reason: Erroneous initiation.Curated

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti227F → L in BAB30432 (PubMed:16141072).Curated1
Sequence conflicti578T → N in BAE21294 (PubMed:16141072).Curated1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_0302471 – 143Missing in isoform 3. 1 PublicationAdd BLAST143
Alternative sequenceiVSP_0302481 – 94Missing in isoform 2 and isoform 4. 3 PublicationsAdd BLAST94
Alternative sequenceiVSP_03024995 – 126TQPVN…RGQSK → MNWAAFGGPEFFIPGGMKME ASCPLGRNFTEW in isoform 2 and isoform 4. 3 PublicationsAdd BLAST32
Alternative sequenceiVSP_030250452 – 476SFHLI…HCQER → LFYCPASKATLLGQGWEAPC DLSGT in isoform 4. 1 PublicationAdd BLAST25
Alternative sequenceiVSP_030251477 – 735Missing in isoform 4. 1 PublicationAdd BLAST259

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
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

Similar proteinsi

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
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

3D structure databases

ProteinModelPortaliQ7TNK1
SMRiQ7TNK1
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi214500, 4 interactors
STRINGi10090.ENSMUSP00000051107

PTM databases

PhosphoSitePlusiQ7TNK1

Proteomic databases

PaxDbiQ7TNK1
PeptideAtlasiQ7TNK1
PRIDEiQ7TNK1

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

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]

Organism-specific databases

CTDi5992
MGIiMGI:1918387 Rfx4

Phylogenomic databases

eggNOGiENOG410IT81 Eukaryota
ENOG410XSKJ LUCA
GeneTreeiENSGT00550000074532
HOGENOMiHOG000013104
HOVERGENiHBG101271
InParanoidiQ7TNK1
KOiK09174
OMAiPPMQSQY
OrthoDBiEOG091G01JI
PhylomeDBiQ7TNK1
TreeFamiTF321340

Miscellaneous databases

PROiPR:Q7TNK1
SOURCEiSearch...

Gene expression databases

BgeeiENSMUSG00000020037 Expressed in 125 organ(s), highest expression level in brain
GenevisibleiQ7TNK1 MM

Family and domain databases

Gene3Di1.10.10.10, 1 hit
InterProiView protein in InterPro
IPR003150 DNA-bd_RFX
IPR039779 RFX-like
IPR036388 WH-like_DNA-bd_sf
IPR036390 WH_DNA-bd_sf
PANTHERiPTHR12619 PTHR12619, 1 hit
PfamiView protein in Pfam
PF02257 RFX_DNA_binding, 1 hit
SUPFAMiSSF46785 SSF46785, 1 hit
PROSITEiView protein in PROSITE
PS51526 RFX_DBD, 1 hit
ProtoNetiSearch...

Entry informationi

Entry nameiRFX4_MOUSE
AccessioniPrimary (citable) accession number: Q7TNK1
Secondary accession number(s): B2RS52
, Q3V158, Q76KT2, Q8HWA6, Q9D453
Entry historyiIntegrated into UniProtKB/Swiss-Prot: January 15, 2008
Last sequence update: October 1, 2003
Last modified: November 7, 2018
This is version 117 of the entry and version 1 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families
  2. MGD cross-references
    Mouse Genome Database (MGD) cross-references in UniProtKB/Swiss-Prot
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