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Q33E94 (RFX4_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Last modified July 9, 2014. Version 85. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (5) | 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
Testis development protein NYD-SP10
Gene names
Name:RFX4
OrganismHomo sapiens (Human) [Reference proteome]
Taxonomic identifier9606 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo

Protein attributes

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

General annotation (Comments)

Function

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

Subunit structure

Homodimer. Heterodimer with RFX2 and RFX3. Binds DNA.

Subcellular location

Nucleus By similarity.

Tissue specificity

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. Ref.2 Ref.3 Ref.8

Sequence similarities

Belongs to the RFX family.

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

Sequence caution

The sequence BAB59001.1 differs from that shown. Reason: Probable intron retention.

The sequence BAC11288.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.

The sequence BAE48237.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.

The sequence BAE48238.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.

Alternative products

This entry describes 4 isoforms produced by alternative splicing. [Align] [Select]
Isoform 1 (identifier: Q33E94-1)

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.
Isoform 2 (identifier: Q33E94-2)

Also known as: RFX4-C; RFX4_v4;

The sequence of this isoform differs from the canonical sequence as follows:
     1-12: MHCGLLEEPDMD → MIKRRAHPGAGGDRTRPRRRR
Isoform 3 (identifier: Q33E94-3)

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
Isoform 4 (identifier: Q33E94-4)

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

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 735735Transcription factor RFX4
PRO_0000314237

Regions

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

Natural variations

Alternative sequence1 – 9494Missing in isoform 3.
VSP_030242
Alternative sequence1 – 1212MHCGL…EPDMD → MIKRRAHPGAGGDRTRPRRR R in isoform 2 and isoform 4.
VSP_030243
Alternative sequence95 – 12632TQPVN…RGQSK → MNWAAFGGSEFFIPEGIQID SRCPLSRNITEW in isoform 3.
VSP_030244
Alternative sequence546 – 5549AMQSYTWSL → NGKSFKNFG in isoform 4.
VSP_030245
Alternative sequence555 – 735181Missing in isoform 4.
VSP_030246
Natural variant6871S → N. Ref.2 Ref.3
VAR_037873
Natural variant6981S → A.
Corresponds to variant rs17038766 [ dbSNP | Ensembl ].
VAR_057152

Experimental info

Sequence conflict4171Q → R in AAK17191. Ref.3
Sequence conflict4231V → E in BAC11288. Ref.4
Sequence conflict4771A → T in AAH28582. Ref.7
Sequence conflict5221V → M in AAM52484. Ref.1
Sequence conflict5491S → A in BAE48231. Ref.2
Sequence conflict5491S → A in BAE48237. Ref.2
Sequence conflict5491S → A in BAE48238. Ref.2
Sequence conflict5491S → A in AAK17191. Ref.3

Sequences

Sequence LengthMass (Da)Tools
Isoform 1 (RFX4-D) (RFX4_v3) [UniParc].

Last modified May 3, 2011. Version 2.
Checksum: 9C2422428B9D7E8B

FASTA73583,368
        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 AWVSETGKKE VSKQTVAYSP RSKLGTLLPE 

       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 RNVDLNSITK 

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

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

       490        500        510        520        530        540 
MRAMKGEGST AEVREEIILT EAAAPTPSPV PSFSPAKSAT SVEVPPPSSP VSNPSPEYTG 

       550        560        570        580        590        600 
LSTTGAMQSY TWSLTYTVTT AAGSPAENSQ QLPCMRNTHV PSSSVTHRIP VYPHREEHGY 

       610        620        630        640        650        660 
TGSYNYGSYG NQHPHPMQSQ YPALPHDTAI SGPLHYAPYH RSSAQYPFNS PTSRMEPCLM 

       670        680        690        700        710        720 
SSTPRLHPTP VTPRWPEVPS ANTCYTSPSV HSARYGNSSD MYTPLTTRRN SEYEHMQHFP 

       730 
GFAYINGEAS TGWAK 

« Hide

Isoform 2 (RFX4-C) (RFX4_v4) [UniParc].

Checksum: 5A36FF5CB5D8EFB7
Show »

FASTA74484,479
Isoform 3 (RFX4-A) (RFX4_v1) [UniParc].

Checksum: 55FD9787E6771AF8
Show »

FASTA64172,561
Isoform 4 [UniParc].

Checksum: 67D9817BB0BC6B9E
Show »

FASTA56364,181

References

« Hide 'large scale' references
[1]"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).
Tissue: Brain.
[2]"Identification of glioma-specific RFX4-E and -F isoforms and humoral immune response in patients."
Matsushita H., Uenaka A., Ono T., Hasegawa K., Sato S., Koizumi F., Nakagawa K., Toda M., Shingo T., Ichikawa T., Noguchi Y., Tamiya T., Furuta T., Kawase T., Date I., Nakayama E.
Cancer Sci. 96:801-809(2005) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORMS 1 AND 2), TISSUE SPECIFICITY, VARIANT ASN-687.
Tissue: Astrocytoma and Testis.
[3]"Identification of a novel substrate for tyrosine kinase in human testes."
Huang X., Zhou Z., Yin L., Zhu H., Wang L., Lin M., Zhou Y., Sha J.
J. Nanosci. Nanotechnol. 5:1236-1239(2005) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 3), TISSUE SPECIFICITY, VARIANT ASN-687.
Tissue: Testis.
[4]"Complete sequencing and characterization of 21,243 full-length human cDNAs."
Ota T., Suzuki Y., Nishikawa T., Otsuki T., Sugiyama T., Irie R., Wakamatsu A., Hayashi K., Sato H., Nagai K., Kimura K., Makita H., Sekine M., Obayashi M., Nishi T., Shibahara T., Tanaka T., Ishii S. expand/collapse author list , Yamamoto J., Saito K., Kawai Y., Isono Y., Nakamura Y., Nagahari K., Murakami K., Yasuda T., Iwayanagi T., Wagatsuma M., Shiratori A., Sudo H., Hosoiri T., Kaku Y., Kodaira H., Kondo H., Sugawara M., Takahashi M., Kanda K., Yokoi T., Furuya T., Kikkawa E., Omura Y., Abe K., Kamihara K., Katsuta N., Sato K., Tanikawa M., Yamazaki M., Ninomiya K., Ishibashi T., Yamashita H., Murakawa K., Fujimori K., Tanai H., Kimata M., Watanabe M., Hiraoka S., Chiba Y., Ishida S., Ono Y., Takiguchi S., Watanabe S., Yosida M., Hotuta T., Kusano J., Kanehori K., Takahashi-Fujii A., Hara H., Tanase T.-O., Nomura Y., Togiya S., Komai F., Hara R., Takeuchi K., Arita M., Imose N., Musashino K., Yuuki H., Oshima A., Sasaki N., Aotsuka S., Yoshikawa Y., Matsunawa H., Ichihara T., Shiohata N., Sano S., Moriya S., Momiyama H., Satoh N., Takami S., Terashima Y., Suzuki O., Nakagawa S., Senoh A., Mizoguchi H., Goto Y., Shimizu F., Wakebe H., Hishigaki H., Watanabe T., Sugiyama A., Takemoto M., Kawakami B., Yamazaki M., Watanabe K., Kumagai A., Itakura S., Fukuzumi Y., Fujimori Y., Komiyama M., Tashiro H., Tanigami A., Fujiwara T., Ono T., Yamada K., Fujii Y., Ozaki K., Hirao M., Ohmori Y., Kawabata A., Hikiji T., Kobatake N., Inagaki H., Ikema Y., Okamoto S., Okitani R., Kawakami T., Noguchi S., Itoh T., Shigeta K., Senba T., Matsumura K., Nakajima Y., Mizuno T., Morinaga M., Sasaki M., Togashi T., Oyama M., Hata H., Watanabe M., Komatsu T., Mizushima-Sugano J., Satoh T., Shirai Y., Takahashi Y., Nakagawa K., Okumura K., Nagase T., Nomura N., Kikuchi H., Masuho Y., Yamashita R., Nakai K., Yada T., Nakamura Y., Ohara O., Isogai T., Sugano S.
Nat. Genet. 36:40-45(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORMS 1 AND 3).
Tissue: Brain and Testis.
[5]"The finished DNA sequence of human chromosome 12."
Scherer S.E., Muzny D.M., Buhay C.J., Chen R., Cree A., Ding Y., Dugan-Rocha S., Gill R., Gunaratne P., Harris R.A., Hawes A.C., Hernandez J., Hodgson A.V., Hume J., Jackson A., Khan Z.M., Kovar-Smith C., Lewis L.R. expand/collapse author list , Lozado R.J., Metzker M.L., Milosavljevic A., Miner G.R., Montgomery K.T., Morgan M.B., Nazareth L.V., Scott G., Sodergren E., Song X.-Z., Steffen D., Lovering R.C., Wheeler D.A., Worley K.C., Yuan Y., Zhang Z., Adams C.Q., Ansari-Lari M.A., Ayele M., Brown M.J., Chen G., Chen Z., Clerc-Blankenburg K.P., Davis C., Delgado O., Dinh H.H., Draper H., Gonzalez-Garay M.L., Havlak P., Jackson L.R., Jacob L.S., Kelly S.H., Li L., Li Z., Liu J., Liu W., Lu J., Maheshwari M., Nguyen B.-V., Okwuonu G.O., Pasternak S., Perez L.M., Plopper F.J.H., Santibanez J., Shen H., Tabor P.E., Verduzco D., Waldron L., Wang Q., Williams G.A., Zhang J., Zhou J., Allen C.C., Amin A.G., Anyalebechi V., Bailey M., Barbaria J.A., Bimage K.E., Bryant N.P., Burch P.E., Burkett C.E., Burrell K.L., Calderon E., Cardenas V., Carter K., Casias K., Cavazos I., Cavazos S.R., Ceasar H., Chacko J., Chan S.N., Chavez D., Christopoulos C., Chu J., Cockrell R., Cox C.D., Dang M., Dathorne S.R., David R., Davis C.M., Davy-Carroll L., Deshazo D.R., Donlin J.E., D'Souza L., Eaves K.A., Egan A., Emery-Cohen A.J., Escotto M., Flagg N., Forbes L.D., Gabisi A.M., Garza M., Hamilton C., Henderson N., Hernandez O., Hines S., Hogues M.E., Huang M., Idlebird D.G., Johnson R., Jolivet A., Jones S., Kagan R., King L.M., Leal B., Lebow H., Lee S., LeVan J.M., Lewis L.C., London P., Lorensuhewa L.M., Loulseged H., Lovett D.A., Lucier A., Lucier R.L., Ma J., Madu R.C., Mapua P., Martindale A.D., Martinez E., Massey E., Mawhiney S., Meador M.G., Mendez S., Mercado C., Mercado I.C., Merritt C.E., Miner Z.L., Minja E., Mitchell T., Mohabbat F., Mohabbat K., Montgomery B., Moore N., Morris S., Munidasa M., Ngo R.N., Nguyen N.B., Nickerson E., Nwaokelemeh O.O., Nwokenkwo S., Obregon M., Oguh M., Oragunye N., Oviedo R.J., Parish B.J., Parker D.N., Parrish J., Parks K.L., Paul H.A., Payton B.A., Perez A., Perrin W., Pickens A., Primus E.L., Pu L.-L., Puazo M., Quiles M.M., Quiroz J.B., Rabata D., Reeves K., Ruiz S.J., Shao H., Sisson I., Sonaike T., Sorelle R.P., Sutton A.E., Svatek A.F., Svetz L.A., Tamerisa K.S., Taylor T.R., Teague B., Thomas N., Thorn R.D., Trejos Z.Y., Trevino B.K., Ukegbu O.N., Urban J.B., Vasquez L.I., Vera V.A., Villasana D.M., Wang L., Ward-Moore S., Warren J.T., Wei X., White F., Williamson A.L., Wleczyk R., Wooden H.S., Wooden S.H., Yen J., Yoon L., Yoon V., Zorrilla S.E., Nelson D., Kucherlapati R., Weinstock G., Gibbs R.A.
Nature 440:346-351(2006) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[6]Mural R.J., Istrail S., Sutton G.G., Florea L., Halpern A.L., Mobarry C.M., Lippert R., Walenz B., Shatkay H., Dew I., Miller J.R., Flanigan M.J., Edwards N.J., Bolanos R., Fasulo D., Halldorsson B.V., Hannenhalli S., Turner R. expand/collapse author list , Yooseph S., Lu F., Nusskern D.R., Shue B.C., Zheng X.H., Zhong F., Delcher A.L., Huson D.H., Kravitz S.A., Mouchard L., Reinert K., Remington K.A., Clark A.G., Waterman M.S., Eichler E.E., Adams M.D., Hunkapiller M.W., Myers E.W., Venter J.C.
Submitted (JUL-2005) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[7]"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 3).
Tissue: Testis.
[8]"Human regulatory factor X 4 (RFX4) is a testis-specific dimeric DNA-binding protein that cooperates with other human RFX members."
Morotomi-Yano K., Yano K., Saito H., Sun Z., Iwama A., Miki Y.
J. Biol. Chem. 277:836-842(2002) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA] OF 1-545 (ISOFORM 4), TISSUE SPECIFICITY, INTERACTION WITH RFX2 AND RFX3.
[9]"The full-ORF clone resource of the German cDNA consortium."
Bechtel S., Rosenfelder H., Duda A., Schmidt C.P., Ernst U., Wellenreuther R., Mehrle A., Schuster C., Bahr A., Bloecker H., Heubner D., Hoerlein A., Michel G., Wedler H., Koehrer K., Ottenwaelder B., Poustka A., Wiemann S., Schupp I.
BMC Genomics 8:399-399(2007) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 256-735 (ISOFORM 1).
Tissue: Testis.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
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.
CCDSCCDS55880.1. [Q33E94-2]
CCDS9106.1. [Q33E94-1]
CCDS9108.1. [Q33E94-3]
RefSeqNP_001193620.1. NM_001206691.1. [Q33E94-2]
NP_115880.2. NM_032491.5. [Q33E94-3]
NP_998759.1. NM_213594.2. [Q33E94-1]
UniGeneHs.388827.

3D structure databases

ProteinModelPortalQ33E94.
SMRQ33E94. Positions 61-135.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid111924. 3 interactions.

PTM databases

PhosphoSiteQ33E94.

Polymorphism databases

DMDM332278145.

Proteomic databases

PaxDbQ33E94.
PRIDEQ33E94.

Protocols and materials databases

DNASU5992.
StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblENST00000229387; ENSP00000229387; ENSG00000111783. [Q33E94-3]
ENST00000357881; ENSP00000350552; ENSG00000111783. [Q33E94-2]
ENST00000392842; ENSP00000376585; ENSG00000111783. [Q33E94-1]
GeneID5992.
KEGGhsa:5992.
UCSCuc001tlr.3. human. [Q33E94-1]
uc001tls.3. human. [Q33E94-4]
uc001tlt.3. human. [Q33E94-2]
uc001tlv.3. human. [Q33E94-3]

Organism-specific databases

CTD5992.
GeneCardsGC12P106976.
H-InvDBHIX0037058.
HGNCHGNC:9985. RFX4.
HPAHPA050527.
MIM603958. gene.
neXtProtNX_Q33E94.
PharmGKBPA34355.
GenAtlasSearch...

Phylogenomic databases

eggNOGNOG243313.
HOVERGENHBG101271.
KOK09174.
OMAGAMQSYT.
OrthoDBEOG79CXXT.
TreeFamTF321340.

Gene expression databases

ArrayExpressQ33E94.
BgeeQ33E94.
GenevestigatorQ33E94.

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

GeneWikiRFX4.
GenomeRNAi5992.
NextBio23341.
PROQ33E94.
SOURCESearch...

Entry information

Entry nameRFX4_HUMAN
AccessionPrimary (citable) accession number: Q33E94
Secondary accession number(s): A8K5Y0 expand/collapse secondary AC list , B2RDW4, Q33DW6, Q33DW7, Q33E95, Q6YM53, Q8MHQ1, Q8NC78, Q8NDF9, Q8SNA1, Q96S80, Q9BXI0
Entry history
Integrated into UniProtKB/Swiss-Prot: January 15, 2008
Last sequence update: May 3, 2011
Last modified: July 9, 2014
This is version 85 of the entry and version 2 of the sequence. [Complete history]
Entry statusReviewed (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.

Relevant documents

SIMILARITY comments

Index of protein domains and families

MIM cross-references

Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot

Human polymorphisms and disease mutations

Index of human polymorphisms and disease mutations

Human entries with polymorphisms or disease mutations

List of human entries with polymorphisms or disease mutations

Human chromosome 12

Human chromosome 12: entries, gene names and cross-references to MIM