Reviewed, UniProtKB/Swiss-Prot Q9FE22 (HFR1_ARATH)

Names and origin

Protein names

Recommended name:
    Transcription factor HFR1
Alternative name(s):
    Protein LONG HYPOCOTYL IN FAR-RED 1
    Protein REDUCED PHYTOCHROME SIGNALING
    Transcription factor EN 68
    bHLH transcription factor bHLH026
    Basic helix-loop-helix protein 26
      Short name=bHLH 26
      Short name=AtbHLH26
    Reduced sensitivity to far-red light

Gene names

Name:	HFR1
Synonyms:	BHLH26, EN68, FBI1, REP1, RSF1
Ordered Locus Names:	At1g02340
ORF Names:	T6A9.4, T6A9_13

Organism

Arabidopsis thaliana (Mouse-ear cress) [Complete proteome]

Taxonomic identifier

3702 [NCBI]

Taxonomic lineage

Eukaryota › Viridiplantae › Streptophyta › Embryophyta › Tracheophyta › Spermatophyta › Magnoliophyta › eudicotyledons › core eudicotyledons › rosids › eurosids II › Brassicales › Brassicaceae › Arabidopsis

Protein attributes

Sequence length	292 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is not processed.
Protein existence	Evidence at protein level.

General annotation (Comments)

Function	May be a transcription factor acting positively in the phytochrome A signaling pathway.
Subunit structure	Homodimer and heterodimer with PIF3. Do not interact alone with either phytochrome A (phyA) or B (phyB), but REP1/PIF3 complex binds to phyA and phyB, preferentially to the Pfr forms.
Subcellular location	Nucleus.
Tissue specificity	Expressed constitutively in roots, leaves, stems, and flowers. Ref.7
Induction	Twofold induction by far-red light and 14-fold suppression by red light.
Sequence similarities	Contains 1 basic helix-loop-helix (bHLH) domain.
Sequence caution	The sequence AAG00886.1 differs from that shown. Reason: Erroneous gene model prediction.

Ontologies

Keywords
Biological process	Phytochrome signaling pathway Transcription Transcription regulation
Cellular component	Nucleus
Ligand	DNA-binding
Technical term	Complete proteome
Gene Ontology (GO)
Biological process	blue light signaling pathway Traceable author statement. Source: TAIR red or far red light signaling pathway Inferred from electronic annotation. Source: UniProtKB-KW red, far-red light phototransduction Traceable author statement. Source: TAIR regulation of transcription, DNA-dependent Inferred from electronic annotation. Source: UniProtKB-KW response to light intensity Inferred from expression pattern. Source: TAIR transcription Inferred from electronic annotation. Source: UniProtKB-KW
Cellular component	nucleus Ref.2 Inferred from direct assay. Source: TAIR
Molecular function	DNA binding Inferred from electronic annotation. Source: UniProtKB-KW identical protein binding Inferred from physical interaction. Source: IntAct transcription regulator activity Inferred from electronic annotation. Source: InterPro
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
itself		1	EBI-626001,EBI-626001
COP1	P43254	3	EBI-626001,EBI-301649
LAF1	Q9M0K4	3	EBI-626001,EBI-1543309
PIF3	O80536	1	EBI-626001,EBI-625701
SPA1	Q9SYX2	1	EBI-626001,EBI-626992

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 292	292	Transcription factor HFR1		PRO_0000127430
Regions
	Domain	148 – 188	41	Helix-loop-helix motif
	DNA binding	131 – 147	17	Basic motif By similarity

Sequences

	Sequence		Length	Mass (Da)
	Q9FE22-1 [UniParc]. Last modified March 1, 2001. Version 1. Checksum: BC75C5EB26E10A20	FASTA	292	33,615
	10 20 30 40 50 60 MSNNQAFMEL GWRNDVGSLA VKDQGMMSER ARSDEDRLIN GLKWGYGYFD HDQTDNYLQI 70 80 90 100 110 120 VPEIHKEVEN AKEDLLVVVP DEHSETDDHH HIKDFSERSD HRFYLRNKHE NPKKRRIQVL 130 140 150 160 170 180 SSDDESEEFT REVPSVTRKG SKRRRRDEKM SNKMRKLQQL VPNCHKTDKV SVLDKTIEYM 190 200 210 220 230 240 KNLQLQLQMM STVGVNPYFL PATLGFGMHN HMLTAMASAH GLNPANHMMP SPLIPALNWP 250 260 270 280 290 LPPFTNISFP HSSSQSLFLT TSSPASSPQS LHGLVPYFPS FLDFSSHAMR RL

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"REP1, a basic helix-loop-helix protein, is required for a branch pathway of phytochrome A signaling in Arabidopsis." Soh M.-S., Kim Y.-M., Han S.-J., Song P.-S. Plant Cell 12:2061-2074(2000) [PubMed: 11090209] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA].
[2]	"HFR1 encodes an atypical bHLH protein that acts in phytochrome A signal transduction." Fairchild C.D., Schumaker M.A., Quail P.H. Genes Dev. 14:2377-2391(2000) [PubMed: 10995393] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA]. Strain: cv. Landsberg erecta. Tissue: Hypocotyl.
[3]	"Cloning of the Arabidopsis RSF1 gene by using a mapping strategy based on high-density DNA arrays and denaturing high-performance liquid chromatography." Spiegelman J.I., Mindrinos M.N., Fankhauser C., Richards D., Lutes J., Chory J., Oefner P.J. Plant Cell 12:2485-2498(2000) [PubMed: 11148292] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[4]	"FBI1, an Arabidopsis bHLH protein involved in both cryptochrome 1 and phytochrome A signaling." Wu Y., Liu D., Yang H., Tang R., Cashmore A.R. Submitted (NOV-2000) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [MRNA].
[5]	"Sequence and analysis of chromosome 1 of the plant Arabidopsis thaliana." Theologis A., Ecker J.R., Palm C.J., Federspiel N.A., Kaul S., White O., Alonso J., Altafi H., Araujo R., Bowman C.L., Brooks S.Y., Buehler E., Chan A., Chao Q., Chen H., Cheuk R.F., Chin C.W., Chung M.K. , Conn L., Conway A.B., Conway A.R., Creasy T.H., Dewar K., Dunn P., Etgu P., Feldblyum T.V., Feng J.-D., Fong B., Fujii C.Y., Gill J.E., Goldsmith A.D., Haas B., Hansen N.F., Hughes B., Huizar L., Hunter J.L., Jenkins J., Johnson-Hopson C., Khan S., Khaykin E., Kim C.J., Koo H.L., Kremenetskaia I., Kurtz D.B., Kwan A., Lam B., Langin-Hooper S., Lee A., Lee J.M., Lenz C.A., Li J.H., Li Y.-P., Lin X., Liu S.X., Liu Z.A., Luros J.S., Maiti R., Marziali A., Militscher J., Miranda M., Nguyen M., Nierman W.C., Osborne B.I., Pai G., Peterson J., Pham P.K., Rizzo M., Rooney T., Rowley D., Sakano H., Salzberg S.L., Schwartz J.R., Shinn P., Southwick A.M., Sun H., Tallon L.J., Tambunga G., Toriumi M.J., Town C.D., Utterback T., Van Aken S., Vaysberg M., Vysotskaia V.S., Walker M., Wu D., Yu G., Fraser C.M., Venter J.C., Davis R.W. Nature 408:816-820(2000) [PubMed: 11130712] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: cv. Columbia.
[6]	"Functional annotation of a full-length Arabidopsis cDNA collection." Seki M., Narusaka M., Kamiya A., Ishida J., Satou M., Sakurai T., Nakajima M., Enju A., Akiyama K., Oono Y., Muramatsu M., Hayashizaki Y., Kawai J., Carninci P., Itoh M., Ishii Y., Arakawa T., Shibata K., Shinagawa A., Shinozaki K. Science 296:141-145(2002) [PubMed: 11910074] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 150-292. Strain: cv. Columbia.
[7]	"The basic helix-loop-helix transcription factor family in plants: a genome-wide study of protein structure and functional diversity." Heim M.A., Jakoby M., Werber M., Martin C., Weisshaar B., Bailey P.C. Mol. Biol. Evol. 20:735-747(2003) [PubMed: 12679534] [Abstract] Cited for: TISSUE SPECIFICITY, GENE FAMILY, NOMENCLATURE.
[8]	"The Arabidopsis basic/helix-loop-helix transcription factor family." Toledo-Ortiz G., Huq E., Quail P.H. Plant Cell 15:1749-1770(2003) [PubMed: 12897250] [Abstract] Cited for: GENE FAMILY.

Cross-references

Sequence databases
EMBLGenBankDDBJ	AF288287 mRNA. Translation: AAG45733.1. AF324245 mRNA. Translation: AAG40617.1. AF323182 mRNA. Translation: AAK15282.1. AC064879 Genomic DNA. Translation: AAG00886.1. Sequence problems. AK117248 mRNA. Translation: BAC41923.1.
IPI	IPI00545685.
PIR	G86153.
RefSeq	NP_563650.1.
UniGene	At.24795
3D structure databases
ModBase	Search...
Protein-protein interaction databases
IntAct	Q9FE22. 8 interactions.
Genome annotation databases
GeneID	839300.
GenomeReviews	Gene locus AT1G02340 in contig CT485782_GR.
KEGG	ath:AT1G02340.
NMPDR	fig|3702.1.peg.353.
Organism-specific databases
TAIR	At1g02340.
Gene expression databases
ArrayExpress	Q9FE22.
GermOnline	AT1G02340. Arabidopsis thaliana.
Family and domain databases
InterPro	IPR001092. HLH_basic. [Graphical view]
Pfam	PF00010. HLH. 1 hit. [Graphical view]
SMART	SM00353. HLH. 1 hit. [Graphical view]
PROSITE	PS50888. HLH. 1 hit. [Graphical view]
ProtoNet	Search...

Entry information

Entry name

HFR1_ARATH

Accession

Primary (citable) accession number: Q9FE22
Secondary accession number(s): Q8GZ25, Q9FZ26

Entry history

Integrated into UniProtKB/Swiss-Prot:	May 10, 2002
Last sequence update:	March 1, 2001
Last modified:	June 16, 2009
This is version 62 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

PPAP (Plant Proteome Annotation Project)