P48380 (RFX3_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Transcription factor RFX3

Alternative name(s):
Regulatory factor X 3

Gene names

Name:

RFX3

Organism

Homo sapiens (Human) [Reference proteome]

Taxonomic identifier

9606 [NCBI]

Taxonomic lineage

cellular organisms › Eukaryota › Opisthokonta › Metazoa › Eumetazoa › Bilateria › Deuterostomia › Chordata › Craniata › Vertebrata › Gnathostomata › Teleostomi › Euteleostomi › Sarcopterygii › Tetrapoda › Amniota › Mammalia › Theria › Eutheria › Euarchontoglires › Primates › Haplorrhini › Simiiformes › Catarrhini › Hominoidea › Hominidae › Homininae › Homo

Protein attributes

Sequence length	749 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Transcription factor required for ciliogenesis and islet cell differentiation during endocrine pancreas development. Essential for the differentiation of nodal monocilia and left-right asymmetry specification during embryogenesis. Required for the biogenesis of motile cilia by governing growth and beating efficiency of motile cells. Also required for ciliated ependymal cell differentiation. Regulates the expression of genes involved in ciliary assembly (DYNC2LI1, FOXJ1 and BBS4) and genes involved in ciliary motility (DNAH11, DNAH9 and DNAH5) By similarity. Together with RFX6, participates in the differentiation of 4 of the 5 islet cell types during endocrine pancreas development, with the exception of pancreatic PP (polypeptide-producing) cells. Regulates transcription by forming a heterodimer with another RFX protein and binding to the X-box in the promoter of target genes. Acts as a transcription factor. Represses transcription of MAP1A in non-neuronal cells but not in neuronal cells. Ref.6 Ref.7
Subcellular location	Nucleus Probable.
Sequence similarities	Belongs to the RFX family. Contains 1 RFX-type winged-helix DNA-binding domain.

Ontologies

Keywords
Biological process	Differentiation Transcription Transcription regulation
Cellular component	Nucleus
Coding sequence diversity	Alternative splicing
Ligand	DNA-binding
Molecular function	Developmental protein Repressor
Technical term	Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	cell maturation Inferred from sequence or structural similarity PubMed 20413507. Source: BHF-UCL ciliary cell motility Inferred from sequence or structural similarity. Source: UniProtKB cilium assembly Inferred from sequence or structural similarity PubMed 20413507. Source: BHF-UCL endocrine pancreas development Inferred from sequence or structural similarity. Source: UniProtKB epithelial cilium movement involved in determination of left/right asymmetry Inferred from sequence or structural similarity. Source: UniProtKB negative regulation of transcription, DNA-dependent Inferred from direct assay Ref.6. Source: UniProtKB positive regulation of transcription from RNA polymerase II promoter Inferred from sequence or structural similarity PubMed 20413507. Source: BHF-UCL positive regulation of type B pancreatic cell development Inferred from sequence or structural similarity PubMed 20413507. Source: BHF-UCL regulation of insulin secretion Inferred from sequence or structural similarity. Source: UniProtKB type B pancreatic cell maturation Inferred from electronic annotation. Source: Compara
Cellular_component	nuclear chromatin Inferred from direct assay PubMed 20413507. Source: BHF-UCL transcription factor complex Inferred by curator PubMed 20413507. Source: BHF-UCL
Molecular_function	RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity Traceable author statement Ref.1. Source: ProtInc transcription regulatory region DNA binding Inferred from direct assay Ref.7. Source: UniProtKB
Complete GO annotation...

Alternative products

This entry describes 3 isoforms produced by alternative splicing. [Align] [Select]

Isoform 1 (identifier: P48380-1)

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.

Note: No experimental confirmation available.

Isoform 2 (identifier: P48380-2)

The sequence of this isoform differs from the canonical sequence as follows:
     657-707: FGDLNAVSPG...ELSQAFPVGC → VREAERAVTH...RDCGVIARVP
     708-749: Missing.

Isoform 3 (identifier: P48380-3)

The sequence of this isoform differs from the canonical sequence as follows:
     401-413: SNLSEIESRLPKA → RSESTSFPIHFHG
     414-749: Missing.

Note: No experimental confirmation available.

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 749	749	Transcription factor RFX3		PRO_0000215290
Regions
	DNA binding	183 – 258	76	RFX-type winged-helix Ref.7
Natural variations
	Alternative sequence	401 – 413	13	SNLSE…RLPKA → RSESTSFPIHFHG in isoform 3.		VSP_015162
	Alternative sequence	414 – 749	336	Missing in isoform 3.		VSP_015163
	Alternative sequence	657 – 707	51	FGDLN…FPVGC → VREAERAVTHWVIKNKPELH FSLNTLLIKTMVPNQVSLRA RRDCGVIARVP in isoform 2.		VSP_007626
	Alternative sequence	708 – 749	42	Missing in isoform 2.		VSP_007627
Experimental info
	Sequence conflict	150	1	H → P in BAF82229. Ref.2
	Sequence conflict	310	1	E → G in AAH67778. Ref.5

Sequences

	Sequence		Length	Mass (Da)
	Isoform 1 [UniParc]. Last modified June 20, 2003. Version 2. Checksum: 531F5CFCA7A707C7	FASTA	749	83,530
	10 20 30 40 50 60 MQTSETGSDT GSTVTLQTSV ASQAAVPTQV VQQVPVQQQV QQVQTVQQVQ HVYPAQVQYV 70 80 90 100 110 120 EGSDTVYTNG AIRTTTYPYT ETQMYSQNTG GNYFDTQGSS AQVTTVVSSH SMVGTGGIQM 130 140 150 160 170 180 GVTGGQLISS SGGTYLIGNS MENSGHSVTH TTRASPATIE MAIETLQKSD GLSTHRSSLL 190 200 210 220 230 240 NSHLQWLLDN YETAEGVSLP RSTLYNHYLR HCQEHKLDPV NAASFGKLIR SIFMGLRTRR 250 260 270 280 290 300 LGTRGNSKYH YYGIRVKPDS PLNRLQEDMQ YMAMRQQPMQ QKQRYKPMQK VDGVADGFTG 310 320 330 340 350 360 SGQQTGTSVE QTVIAQSQHH QQFLDASRAL PEFGEVEISS LPDGTTFEDI KSLQSLYREH 370 380 390 400 410 420 CEAILDVVVN LQFSLIEKLW QTFWRYSPST PTDGTTITES SNLSEIESRL PKAKLITLCK 430 440 450 460 470 480 HESILKWMCN CDHGMYQALV EILIPDVLRP IPSALTQAIR NFAKSLEGWL SNAMNNIPQR 490 500 510 520 530 540 MIQTKVAAVS AFAQTLRRYT SLNHLAQAAR AVLQNTSQIN QMLSDLNRVD FANVQEQASW 550 560 570 580 590 600 VCQCDDNMVQ RLETDFKMTL QQQSTLEQWA AWLDNVMMQA LKPYEGRPSF PKAARQFLLK 610 620 630 640 650 660 WSFYSSMVIR DLTLRSAASF GSFHLIRLLY DEYMFYLVEH RVAQATGETP IAVMGEFGDL 670 680 690 700 710 720 NAVSPGNLDK DEGSEVESEM DEELDDSSEP QAKREKTELS QAFPVGCMQP VLETGVQPSL 730 740 LNPIHSEHIV TSTQTIRQCS ATGNTYTAV
	Isoform 2 [UniParc]. Checksum: A1959E3F23E0D8F0	FASTA	707	79,357
	10 20 30 40 50 60 MQTSETGSDT GSTVTLQTSV ASQAAVPTQV VQQVPVQQQV QQVQTVQQVQ HVYPAQVQYV 70 80 90 100 110 120 EGSDTVYTNG AIRTTTYPYT ETQMYSQNTG GNYFDTQGSS AQVTTVVSSH SMVGTGGIQM 130 140 150 160 170 180 GVTGGQLISS SGGTYLIGNS MENSGHSVTH TTRASPATIE MAIETLQKSD GLSTHRSSLL 190 200 210 220 230 240 NSHLQWLLDN YETAEGVSLP RSTLYNHYLR HCQEHKLDPV NAASFGKLIR SIFMGLRTRR 250 260 270 280 290 300 LGTRGNSKYH YYGIRVKPDS PLNRLQEDMQ YMAMRQQPMQ QKQRYKPMQK VDGVADGFTG 310 320 330 340 350 360 SGQQTGTSVE QTVIAQSQHH QQFLDASRAL PEFGEVEISS LPDGTTFEDI KSLQSLYREH 370 380 390 400 410 420 CEAILDVVVN LQFSLIEKLW QTFWRYSPST PTDGTTITES SNLSEIESRL PKAKLITLCK 430 440 450 460 470 480 HESILKWMCN CDHGMYQALV EILIPDVLRP IPSALTQAIR NFAKSLEGWL SNAMNNIPQR 490 500 510 520 530 540 MIQTKVAAVS AFAQTLRRYT SLNHLAQAAR AVLQNTSQIN QMLSDLNRVD FANVQEQASW 550 560 570 580 590 600 VCQCDDNMVQ RLETDFKMTL QQQSTLEQWA AWLDNVMMQA LKPYEGRPSF PKAARQFLLK 610 620 630 640 650 660 WSFYSSMVIR DLTLRSAASF GSFHLIRLLY DEYMFYLVEH RVAQATGETP IAVMGEVREA 670 680 690 700 ERAVTHWVIK NKPELHFSLN TLLIKTMVPN QVSLRARRDC GVIARVP
	Isoform 3 [UniParc]. Checksum: 8C355CDF0E4837D7	FASTA	413	45,715
	10 20 30 40 50 60 MQTSETGSDT GSTVTLQTSV ASQAAVPTQV VQQVPVQQQV QQVQTVQQVQ HVYPAQVQYV 70 80 90 100 110 120 EGSDTVYTNG AIRTTTYPYT ETQMYSQNTG GNYFDTQGSS AQVTTVVSSH SMVGTGGIQM 130 140 150 160 170 180 GVTGGQLISS SGGTYLIGNS MENSGHSVTH TTRASPATIE MAIETLQKSD GLSTHRSSLL 190 200 210 220 230 240 NSHLQWLLDN YETAEGVSLP RSTLYNHYLR HCQEHKLDPV NAASFGKLIR SIFMGLRTRR 250 260 270 280 290 300 LGTRGNSKYH YYGIRVKPDS PLNRLQEDMQ YMAMRQQPMQ QKQRYKPMQK VDGVADGFTG 310 320 330 340 350 360 SGQQTGTSVE QTVIAQSQHH QQFLDASRAL PEFGEVEISS LPDGTTFEDI KSLQSLYREH 370 380 390 400 410 CEAILDVVVN LQFSLIEKLW QTFWRYSPST PTDGTTITES RSESTSFPIH FHG

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"RFX1, a transactivator of hepatitis B virus enhancer I, belongs to a novel family of homodimeric and heterodimeric DNA-binding proteins." Reith W., Ucla C., Barras E., Gaud A., Durand B., Herrero-Sanchez C., Kobr M., Mach B. Mol. Cell. Biol. 14:1230-1244(1994) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 2).
[2]	"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. , 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] (ISOFORM 1). Tissue: Cerebellum.
[3]	"DNA sequence and analysis of human chromosome 9." Humphray S.J., Oliver K., Hunt A.R., Plumb R.W., Loveland J.E., Howe K.L., Andrews T.D., Searle S., Hunt S.E., Scott C.E., Jones M.C., Ainscough R., Almeida J.P., Ambrose K.D., Ashwell R.I.S., Babbage A.K., Babbage S., Bagguley C.L. , Bailey J., Banerjee R., Barker D.J., Barlow K.F., Bates K., Beasley H., Beasley O., Bird C.P., Bray-Allen S., Brown A.J., Brown J.Y., Burford D., Burrill W., Burton J., Carder C., Carter N.P., Chapman J.C., Chen Y., Clarke G., Clark S.Y., Clee C.M., Clegg S., Collier R.E., Corby N., Crosier M., Cummings A.T., Davies J., Dhami P., Dunn M., Dutta I., Dyer L.W., Earthrowl M.E., Faulkner L., Fleming C.J., Frankish A., Frankland J.A., French L., Fricker D.G., Garner P., Garnett J., Ghori J., Gilbert J.G.R., Glison C., Grafham D.V., Gribble S., Griffiths C., Griffiths-Jones S., Grocock R., Guy J., Hall R.E., Hammond S., Harley J.L., Harrison E.S.I., Hart E.A., Heath P.D., Henderson C.D., Hopkins B.L., Howard P.J., Howden P.J., Huckle E., Johnson C., Johnson D., Joy A.A., Kay M., Keenan S., Kershaw J.K., Kimberley A.M., King A., Knights A., Laird G.K., Langford C., Lawlor S., Leongamornlert D.A., Leversha M., Lloyd C., Lloyd D.M., Lovell J., Martin S., Mashreghi-Mohammadi M., Matthews L., McLaren S., McLay K.E., McMurray A., Milne S., Nickerson T., Nisbett J., Nordsiek G., Pearce A.V., Peck A.I., Porter K.M., Pandian R., Pelan S., Phillimore B., Povey S., Ramsey Y., Rand V., Scharfe M., Sehra H.K., Shownkeen R., Sims S.K., Skuce C.D., Smith M., Steward C.A., Swarbreck D., Sycamore N., Tester J., Thorpe A., Tracey A., Tromans A., Thomas D.W., Wall M., Wallis J.M., West A.P., Whitehead S.L., Willey D.L., Williams S.A., Wilming L., Wray P.W., Young L., Ashurst J.L., Coulson A., Blocker H., Durbin R.M., Sulston J.E., Hubbard T., Jackson M.J., Bentley D.R., Beck S., Rogers J., Dunham I. Nature 429:369-374(2004) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[4]	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. , 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 (SEP-2005) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[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] (ISOFORMS 1 AND 3). Tissue: Muscle and Testis.
[6]	"Role for RFX transcription factors in non-neuronal cell-specific inactivation of the microtubule-associated protein MAP1A promoter." Nakayama A., Murakami H., Maeyama N., Yamashiro N., Sakakibara A., Mori N., Takahashi M. J. Biol. Chem. 278:233-240(2003) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION.
[7]	"Rfx6 directs islet formation and insulin production in mice and humans." Smith S.B., Qu H.Q., Taleb N., Kishimoto N.Y., Scheel D.W., Lu Y., Patch A.M., Grabs R., Wang J., Lynn F.C., Miyatsuka T., Mitchell J., Seerke R., Desir J., Eijnden S.V., Abramowicz M., Kacet N., Weill J. , Renard M.E., Gentile M., Hansen I., Dewar K., Hattersley A.T., Wang R., Wilson M.E., Johnson J.D., Polychronakos C., German M.S. Nature 463:775-780(2010) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION, DNA-BINDING, INTERACTION WITH RFX6.
+	Additional computationally mapped references.

Cross-references

Sequence databases
EMBL GenBank DDBJ	X76092 mRNA. Translation: CAA53706.1. AK289540 mRNA. Translation: BAF82229.1. AL365202, AL133549, AL354941 Genomic DNA. Translation: CAI13403.1. AL365202, AL133549, AL354941 Genomic DNA. Translation: CAI13404.1. AL133549, AL354941, AL365202 Genomic DNA. Translation: CAI40199.1. AL133549, AL354941, AL365202 Genomic DNA. Translation: CAI40200.1. AL354941, AL133549, AL365202 Genomic DNA. Translation: CAI41215.1. AL354941, AL133549, AL365202 Genomic DNA. Translation: CAI41216.1. CH471071 Genomic DNA. Translation: EAW58795.1. CH471071 Genomic DNA. Translation: EAW58796.1. CH471071 Genomic DNA. Translation: EAW58798.1. CH471071 Genomic DNA. Translation: EAW58799.1. BC022191 mRNA. Translation: AAH22191.1. BC067778 mRNA. Translation: AAH67778.1.
IPI	IPI00009298. IPI00102829. IPI00646621.
PIR	D55926.
RefSeq	NP_002910.1. NM_002919.2. NP_602304.1. NM_134428.1.
UniGene	Hs.136829.
3D structure databases
ProteinModelPortal	P48380.
ModBase	Search...
Protein-protein interaction databases
IntAct	P48380. 2 interactions.
STRING	9606.ENSP00000371434.
PTM databases
PhosphoSite	P48380.
Polymorphism databases
DMDM	32172437.
Proteomic databases
PaxDb	P48380.
PRIDE	P48380.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
Ensembl	ENST00000302303; ENSP00000303847; ENSG00000080298. ENST00000358730; ENSP00000351574; ENSG00000080298. ENST00000382004; ENSP00000371434; ENSG00000080298.
GeneID	5991.
KEGG	hsa:5991.
UCSC	uc003zhr.3. human. uc003zhs.1. human. uc003zht.1. human.
Organism-specific databases
CTD	5991.
GeneCards	GC09M003214.
HGNC	HGNC:9984. RFX3.
HPA	HPA035689.
MIM	601337. gene.
neXtProt	NX_P48380.
PharmGKB	PA34354.
GenAtlas	Search...
Phylogenomic databases
eggNOG	NOG264634.
HOVERGEN	HBG002753.
InParanoid	P48380.
KO	K09173.
OMA	MQTPEAG.
OrthoDB	EOG49ZXNR.
PhylomeDB	P48380.
Gene expression databases
ArrayExpress	P48380.
Bgee	P48380.
CleanEx	HS_RFX3.
Genevestigator	P48380.
GermOnline	ENSG00000080298. Homo sapiens.
Family and domain databases
Gene3D	1.10.10.10. 1 hit.
InterPro	IPR003150. DNA-bd_RFX. IPR007668. RFX1_trans_act. IPR011991. WHTH_DNA-bd_dom. [Graphical view]
Pfam	PF04589. RFX1_trans_act. 1 hit. PF02257. RFX_DNA_binding. 1 hit. [Graphical view]
PROSITE	PS51526. RFX_DBD. 1 hit. [Graphical view]
ProtoNet	Search...
Other
GenomeRNAi	5991.
NextBio	23335.
SOURCE	Search...

Entry information

Entry name

RFX3_HUMAN

Accession

Primary (citable) accession number: P48380
Secondary accession number(s): A8K0H5 , D3DRH8, D3DRH9, Q5JTL7, Q5JTL8, Q6NW13, Q8WTU4, Q95HL5, Q95HL6

Entry history

Integrated into UniProtKB/Swiss-Prot:	February 1, 1996
Last sequence update:	June 20, 2003
Last modified:	May 1, 2013
This is version 111 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Chordata Protein Annotation Program

Disclaimer

Any 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.