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Protein

Transcription factor RFX4

Gene

RFX4

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

May activate transcription by interacting directly with the X-box.By similarity

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

Complete GO annotation...

Keywords - Molecular functioni

Activator

Keywords - Biological processi

Transcription, Transcription regulation

Keywords - Ligandi

DNA-binding

Enzyme and pathway databases

SIGNORiQ33E94.

Names & Taxonomyi

Protein namesi
Recommended name:
Transcription factor RFX4
Alternative name(s):
Regulatory factor X 4
Testis development protein NYD-SP10
Gene namesi
Name:RFX4
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 12

Organism-specific databases

HGNCiHGNC:9985. RFX4.

Subcellular locationi

  • Nucleus PROSITE-ProRule annotation

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Nucleus

Pathology & Biotechi

Organism-specific databases

DisGeNETi5992.
OpenTargetsiENSG00000111783.
PharmGKBiPA34355.

Polymorphism and mutation databases

BioMutaiRFX4.
DMDMi332278145.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00003142371 – 735Transcription factor RFX4Add BLAST735

Proteomic databases

PaxDbiQ33E94.
PeptideAtlasiQ33E94.
PRIDEiQ33E94.

PTM databases

iPTMnetiQ33E94.
PhosphoSitePlusiQ33E94.

Expressioni

Tissue specificityi

Isoform 4 is testis-specific. Isoform 1 is expressed in brain and gliomas. Isoform 2 and isoform 3 are testis-specific (at protein level). Isoform 1 is expressed in brain (at protein level). Isoform 3 is expressed at a higher level in adult testes and ejaculated spematozoa than in fetal testes.3 Publications

Gene expression databases

BgeeiENSG00000111783.
ExpressionAtlasiQ33E94. baseline and differential.
GenevisibleiQ33E94. HS.

Organism-specific databases

HPAiHPA050527.

Interactioni

Subunit structurei

Homodimer. Heterodimer with RFX2 and RFX3. Binds DNA.

Binary interactionsi

WithEntry#Exp.IntActNotes
taxP140793EBI-9675925,EBI-9675698From a different organism.

Protein-protein interaction databases

BioGridi111924. 4 interactors.
IntActiQ33E94. 1 interactor.
STRINGi9606.ENSP00000350552.

Structurei

3D structure databases

ProteinModelPortaliQ33E94.
SMRiQ33E94.
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
Contains 1 RFX-type winged-helix DNA-binding domain.PROSITE-ProRule annotation

Phylogenomic databases

eggNOGiENOG410IT81. Eukaryota.
ENOG410XSKJ. LUCA.
GeneTreeiENSGT00550000074532.
HOGENOMiHOG000013104.
HOVERGENiHBG101271.
InParanoidiQ33E94.
KOiK09174.
OMAiQLPCMRS.
OrthoDBiEOG091G01JI.
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]
SUPFAMiSSF46785. SSF46785. 1 hit.
PROSITEiPS51526. RFX_DBD. 1 hit.
[Graphical view]

Sequences (4)i

Sequence statusi: Complete.

This entry describes 4 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 1 (identifier: Q33E94-1) [UniParc]FASTAAdd to basket
Also known as: RFX4-D, 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
AWVSETGKKE VSKQTVAYSP RSKLGTLLPE 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
RNVDLNSITK QTLYTMEDSR DEHRKLITQL YQEFDHLLEE QSPIESYIEW
410 420 430 440 450
LDTMVDRCVV KVAAKRQGSL KKVAQQFLLM WSCFGTRVIR DMTLHSAPSF
460 470 480 490 500
GSFHLIHLMF DDYVLYLLES LHCQERANEL MRAMKGEGST AEVREEIILT
510 520 530 540 550
EAAAPTPSPV PSFSPAKSAT SVEVPPPSSP VSNPSPEYTG LSTTGAMQSY
560 570 580 590 600
TWSLTYTVTT AAGSPAENSQ QLPCMRNTHV PSSSVTHRIP VYPHREEHGY
610 620 630 640 650
TGSYNYGSYG NQHPHPMQSQ YPALPHDTAI SGPLHYAPYH RSSAQYPFNS
660 670 680 690 700
PTSRMEPCLM SSTPRLHPTP VTPRWPEVPS ANTCYTSPSV HSARYGNSSD
710 720 730
MYTPLTTRRN SEYEHMQHFP GFAYINGEAS TGWAK
Length:735
Mass (Da):83,368
Last modified:May 3, 2011 - v2
Checksum:i9C2422428B9D7E8B
GO
Isoform 2 (identifier: Q33E94-2) [UniParc]FASTAAdd to basket
Also known as: RFX4-C, RFX4_v4

The sequence of this isoform differs from the canonical sequence as follows:
     1-12: MHCGLLEEPDMD → MIKRRAHPGAGGDRTRPRRRR

Show »
Length:744
Mass (Da):84,479
Checksum:i5A36FF5CB5D8EFB7
GO
Isoform 3 (identifier: Q33E94-3) [UniParc]FASTAAdd to basket
Also known as: RFX4-A, RFX4_v1

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

Show »
Length:641
Mass (Da):72,561
Checksum:i55FD9787E6771AF8
GO
Isoform 4 (identifier: Q33E94-4) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     1-12: MHCGLLEEPDMD → MIKRRAHPGAGGDRTRPRRRR
     546-554: AMQSYTWSL → NGKSFKNFG
     555-735: Missing.

Show »
Length:563
Mass (Da):64,181
Checksum:i67D9817BB0BC6B9E
GO

Sequence cautioni

The sequence BAB59001 differs from that shown. Probable intron retention.Curated
The sequence BAC11288 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.Curated
The sequence BAE48237 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.Curated
The sequence BAE48238 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.Curated

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti417Q → R in AAK17191 (PubMed:16193984).Curated1
Sequence conflicti423V → E in BAC11288 (PubMed:14702039).Curated1
Sequence conflicti477A → T in AAH28582 (PubMed:15489334).Curated1
Sequence conflicti522V → M in AAM52484 (PubMed:12925582).Curated1
Sequence conflicti549S → A in BAE48231 (PubMed:16271074).Curated1
Sequence conflicti549S → A in BAE48237 (PubMed:16271074).Curated1
Sequence conflicti549S → A in BAE48238 (PubMed:16271074).Curated1
Sequence conflicti549S → A in AAK17191 (PubMed:16193984).Curated1

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_037873687S → N.2 Publications1
Natural variantiVAR_057152698S → A.Corresponds to variant rs17038766dbSNPEnsembl.1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_0302421 – 94Missing in isoform 3. 3 PublicationsAdd BLAST94
Alternative sequenceiVSP_0302431 – 12MHCGL…EPDMD → MIKRRAHPGAGGDRTRPRRR R in isoform 2 and isoform 4. 2 PublicationsAdd BLAST12
Alternative sequenceiVSP_03024495 – 126TQPVN…RGQSK → MNWAAFGGSEFFIPEGIQID SRCPLSRNITEW in isoform 3. 3 PublicationsAdd BLAST32
Alternative sequenceiVSP_030245546 – 554AMQSYTWSL → NGKSFKNFG in isoform 4. 1 Publication9
Alternative sequenceiVSP_030246555 – 735Missing in isoform 4. 1 PublicationAdd BLAST181

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AY102009 mRNA. Translation: AAM52484.1.
AB095365 mRNA. Translation: BAE48231.1.
AB095366 mRNA. Translation: BAE48232.1.
AB195784 mRNA. Translation: BAE48237.1. Different initiation.
AB195785 mRNA. Translation: BAE48238.1. Different initiation.
AF332192 mRNA. Translation: AAK17191.1.
AK074913 mRNA. Translation: BAC11288.1. Different initiation.
AK291445 mRNA. Translation: BAF84134.1.
AK315698 mRNA. Translation: BAG38061.1.
AC009721 Genomic DNA. No translation available.
AC079385 Genomic DNA. No translation available.
CH471054 Genomic DNA. Translation: EAW97783.1.
CH471054 Genomic DNA. Translation: EAW97784.1.
CH471054 Genomic DNA. Translation: EAW97782.1.
BC028582 mRNA. Translation: AAH28582.1.
BC030644 mRNA. Translation: AAH30644.1.
AB044245 mRNA. Translation: BAB59001.1. Sequence problems.
AL833921 mRNA. Translation: CAD38777.1.
CCDSiCCDS55880.1. [Q33E94-2]
CCDS9106.1. [Q33E94-1]
CCDS9108.1. [Q33E94-3]
RefSeqiNP_001193620.1. NM_001206691.1. [Q33E94-2]
NP_115880.2. NM_032491.5. [Q33E94-3]
NP_998759.1. NM_213594.2. [Q33E94-1]
UniGeneiHs.388827.

Genome annotation databases

EnsembliENST00000229387; ENSP00000229387; ENSG00000111783. [Q33E94-3]
ENST00000357881; ENSP00000350552; ENSG00000111783. [Q33E94-2]
ENST00000392842; ENSP00000376585; ENSG00000111783. [Q33E94-1]
GeneIDi5992.
KEGGihsa:5992.
UCSCiuc001tlr.4. human. [Q33E94-1]

Keywords - Coding sequence diversityi

Alternative splicing, Polymorphism

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AY102009 mRNA. Translation: AAM52484.1.
AB095365 mRNA. Translation: BAE48231.1.
AB095366 mRNA. Translation: BAE48232.1.
AB195784 mRNA. Translation: BAE48237.1. Different initiation.
AB195785 mRNA. Translation: BAE48238.1. Different initiation.
AF332192 mRNA. Translation: AAK17191.1.
AK074913 mRNA. Translation: BAC11288.1. Different initiation.
AK291445 mRNA. Translation: BAF84134.1.
AK315698 mRNA. Translation: BAG38061.1.
AC009721 Genomic DNA. No translation available.
AC079385 Genomic DNA. No translation available.
CH471054 Genomic DNA. Translation: EAW97783.1.
CH471054 Genomic DNA. Translation: EAW97784.1.
CH471054 Genomic DNA. Translation: EAW97782.1.
BC028582 mRNA. Translation: AAH28582.1.
BC030644 mRNA. Translation: AAH30644.1.
AB044245 mRNA. Translation: BAB59001.1. Sequence problems.
AL833921 mRNA. Translation: CAD38777.1.
CCDSiCCDS55880.1. [Q33E94-2]
CCDS9106.1. [Q33E94-1]
CCDS9108.1. [Q33E94-3]
RefSeqiNP_001193620.1. NM_001206691.1. [Q33E94-2]
NP_115880.2. NM_032491.5. [Q33E94-3]
NP_998759.1. NM_213594.2. [Q33E94-1]
UniGeneiHs.388827.

3D structure databases

ProteinModelPortaliQ33E94.
SMRiQ33E94.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi111924. 4 interactors.
IntActiQ33E94. 1 interactor.
STRINGi9606.ENSP00000350552.

PTM databases

iPTMnetiQ33E94.
PhosphoSitePlusiQ33E94.

Polymorphism and mutation databases

BioMutaiRFX4.
DMDMi332278145.

Proteomic databases

PaxDbiQ33E94.
PeptideAtlasiQ33E94.
PRIDEiQ33E94.

Protocols and materials databases

DNASUi5992.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000229387; ENSP00000229387; ENSG00000111783. [Q33E94-3]
ENST00000357881; ENSP00000350552; ENSG00000111783. [Q33E94-2]
ENST00000392842; ENSP00000376585; ENSG00000111783. [Q33E94-1]
GeneIDi5992.
KEGGihsa:5992.
UCSCiuc001tlr.4. human. [Q33E94-1]

Organism-specific databases

CTDi5992.
DisGeNETi5992.
GeneCardsiRFX4.
H-InvDBHIX0037058.
HGNCiHGNC:9985. RFX4.
HPAiHPA050527.
MIMi603958. gene.
neXtProtiNX_Q33E94.
OpenTargetsiENSG00000111783.
PharmGKBiPA34355.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiENOG410IT81. Eukaryota.
ENOG410XSKJ. LUCA.
GeneTreeiENSGT00550000074532.
HOGENOMiHOG000013104.
HOVERGENiHBG101271.
InParanoidiQ33E94.
KOiK09174.
OMAiQLPCMRS.
OrthoDBiEOG091G01JI.
TreeFamiTF321340.

Enzyme and pathway databases

SIGNORiQ33E94.

Miscellaneous databases

GeneWikiiRFX4.
GenomeRNAii5992.
PROiQ33E94.
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000111783.
ExpressionAtlasiQ33E94. baseline and differential.
GenevisibleiQ33E94. HS.

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]
SUPFAMiSSF46785. SSF46785. 1 hit.
PROSITEiPS51526. RFX_DBD. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiRFX4_HUMAN
AccessioniPrimary (citable) accession number: Q33E94
Secondary accession number(s): A8K5Y0
, B2RDW4, Q33DW6, Q33DW7, Q33E95, Q6YM53, Q8MHQ1, Q8NC78, Q8NDF9, Q8SNA1, Q96S80, Q9BXI0
Entry historyi
Integrated into UniProtKB/Swiss-Prot: January 15, 2008
Last sequence update: May 3, 2011
Last modified: November 2, 2016
This is version 104 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Human chromosome 12
    Human chromosome 12: entries, gene names and cross-references to MIM
  2. Human entries with polymorphisms or disease mutations
    List of human entries with polymorphisms or disease mutations
  3. Human polymorphisms and disease mutations
    Index of human polymorphisms and disease mutations
  4. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  5. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.