Q9FE22 (HFR1_ARATH) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Transcription factor HFR1

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

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)

Taxonomic identifier

3702 [NCBI]

Taxonomic lineage

Eukaryota › Viridiplantae › Streptophyta › Embryophyta › Tracheophyta › Spermatophyta › Magnoliophyta › eudicotyledons › core eudicotyledons › rosids › malvids › Brassicales › Brassicaceae › Camelineae › Arabidopsis

Protein attributes

Sequence length	292 AA.
Sequence status	Complete.
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.8
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 Reference proteome
Gene Ontology (GO)
Biological process	abscisic acid mediated signaling pathway Inferred from mutant phenotype. Source: TAIR blue light signaling pathway Traceable author statement. Source: TAIR 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, DNA-dependent Inferred from electronic annotation. Source: UniProtKB-KW
Cellular component	cytosol Inferred from direct assay. Source: TAIR nucleus Inferred from direct assay. Source: TAIR
Molecular function	DNA binding Inferred from electronic annotation. Source: UniProtKB-KW protein binding Inferred from physical interaction Ref.2. Source: IntAct transcription cofactor activity Inferred from mutant phenotype. Source: TAIR
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
ATJ13	Q39079	3	EBI-626001,EBI-2461966
COP1	P43254	6	EBI-626001,EBI-301649
LAF1	Q9M0K4	6	EBI-626001,EBI-1543309
PIF3	O80536	6	EBI-626001,EBI-625701
SPA1	Q9SYX2	3	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 [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]	The Arabidopsis Information Resource (TAIR) Submitted (APR-2011) to the EMBL/GenBank/DDBJ databases Cited for: GENOME REANNOTATION. Strain: cv. Columbia.
[7]	"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.
[8]	"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.
[9]	"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.
+	Additional computationally mapped references.

Cross-references

Sequence databases
EMBL GenBank DDBJ	AF288287 mRNA. Translation: AAG45733.1. AF324245 mRNA. Translation: AAG40617.1. AF323182 mRNA. Translation: AAK15282.1. AC064879 Genomic DNA. Translation: AAG00886.1. Sequence problems. CP002684 Genomic DNA. Translation: AEE27418.1. AK117248 mRNA. Translation: BAC41923.1.
IPI	IPI00545685.
PIR	G86153.
RefSeq	NP_563650.1. NM_100115.2.
UniGene	At.24795.
3D structure databases
ProteinModelPortal	Q9FE22.
SMR	Q9FE22. Positions 147-192.
ModBase	Search...
Protein-protein interaction databases
IntAct	Q9FE22. 10 interactions.
STRING	Q9FE22.
Proteomic databases
PRIDE	Q9FE22.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblPlants	AT1G02340.1; AT1G02340.1; AT1G02340.
GeneID	839300.
GenomeReviews	Gene locus AT1G02340 in contig CT485782_GR.
KEGG	ath:AT1G02340.
NMPDR	fig|3702.1.peg.353.
Organism-specific databases
TAIR	At1g02340.
Phylogenomic databases
GeneTree	EPGT00050000008845.
OMA	FSSHAMR.
PhylomeDB	Q9FE22.
ProtClustDB	CLSN2916946.
Gene expression databases
ArrayExpress	Q9FE22.
Genevestigator	Q9FE22.
GermOnline	AT1G02340. Arabidopsis thaliana.
Family and domain databases
InterPro	IPR011598. HLH_DNA-bd. [Graphical view]
Gene3D	G3DSA:4.10.280.10. HLH_DNA_bd. 1 hit.
Pfam	PF00010. HLH. 1 hit. [Graphical view]
SMART	SM00353. HLH. 1 hit. [Graphical view]
SUPFAM	SSF47459. HLH_basic. 1 hit.
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:	January 25, 2012
This is version 89 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Plant Protein Annotation Program