PlantTFDB - Plant Transcription Factor Database @ CBI, PKU

PlantRegMap/PlantTFDB v5.0

Plant Transcription Factor Database

Transcription Factor Information

Basic Information | Signature Domain | Sequence |

Basic Information? help Back to Top

TF ID

AT5G08130.1

Common Name

BIM1

Organism

Arabidopsis thaliana

Taxonomic ID

3702

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis

Family

bHLH

Protein Properties

Length: 409aa MW: 45545.4 Da PI: 7.2412

Description

bHLH family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
AT5G08130.1	genome	TAIR	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	HLH	56.1	6.7e-18	158	207	2	55
HHHHHHHHHHHHHHHHHHHHHHHCTSCCC...TTS-STCHHHHHHHHHHHHHHH CS HLH 2 rrahnerErrRRdriNsafeeLrellPkaskapskKlsKaeiLekAveYIksLq 55 r +h++ E+rRR++iN++f+ Lr+l+P++ ++K +Ka+ L +++eYI+ Lq AT5G08130.1 158 RSKHSATEQRRRSKINDRFQMLRQLIPNS----DQKRDKASFLLEVIEYIQFLQ 207 889***********************9....9*****************9 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Gene3D	G3DSA:4.10.280.10	1.9E-23	155	227	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
PROSITE profile	PS50888	17.225	156	206	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
SuperFamily	SSF47459	8.24E-19	157	226	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
CDD	cd00083	2.19E-14	158	209	No hit	No description
Pfam	PF00010	2.2E-15	158	207	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
SMART	SM00353	3.4E-13	162	212	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0006351	Biological Process	transcription, DNA-templated
GO:0006355	Biological Process	regulation of transcription, DNA-templated
GO:0009742	Biological Process	brassinosteroid mediated signaling pathway
GO:1902448	Biological Process	positive regulation of shade avoidance
GO:0005634	Cellular Component	nucleus
GO:0003677	Molecular Function	DNA binding
GO:0003700	Molecular Function	transcription factor activity, sequence-specific DNA binding
GO:0005515	Molecular Function	protein binding
GO:0046983	Molecular Function	protein dimerization activity

Plant Ontology ? help Back to Top
PO Term	PO Category	PO Description
PO:0000013	anatomy	cauline leaf
PO:0000037	anatomy	shoot apex
PO:0000230	anatomy	inflorescence meristem
PO:0000293	anatomy	guard cell
PO:0008019	anatomy	leaf lamina base
PO:0009005	anatomy	root
PO:0009006	anatomy	shoot system
PO:0009009	anatomy	plant embryo
PO:0009010	anatomy	seed
PO:0009025	anatomy	vascular leaf
PO:0009029	anatomy	stamen
PO:0009030	anatomy	carpel
PO:0009031	anatomy	sepal
PO:0009032	anatomy	petal
PO:0009046	anatomy	flower
PO:0009047	anatomy	stem
PO:0009052	anatomy	flower pedicel
PO:0020030	anatomy	cotyledon
PO:0020038	anatomy	petiole
PO:0020100	anatomy	hypocotyl
PO:0020137	anatomy	leaf apex
PO:0025022	anatomy	collective leaf structure
PO:0025281	anatomy	pollen
PO:0001054	developmental stage	vascular leaf senescent stage
PO:0001078	developmental stage	plant embryo cotyledonary stage
PO:0001081	developmental stage	mature plant embryo stage
PO:0001185	developmental stage	plant embryo globular stage
PO:0004507	developmental stage	plant embryo bilateral stage
PO:0007064	developmental stage	LP.12 twelve leaves visible stage
PO:0007095	developmental stage	LP.08 eight leaves visible stage
PO:0007098	developmental stage	LP.02 two leaves visible stage
PO:0007103	developmental stage	LP.10 ten leaves visible stage
PO:0007115	developmental stage	LP.04 four leaves visible stage
PO:0007123	developmental stage	LP.06 six leaves visible stage
PO:0007611	developmental stage	petal differentiation and expansion stage
PO:0007616	developmental stage	flowering stage

Sequence ? help Back to Top
Protein Sequence Length: 409 aa Download sequence Send to blast
MMFNANERNV LDENSNSNCS SYAAASSGFT LWDESASGKK GQTRKENSVG ERVNMRADVA 60 ATVGQWPVAE RRSQSLTNNH MSGFSSLSSS QGSVLKSQSF MDMIRSAKGS SQEDDLDDEE 120 DFIMKKESSS TSQSHRVDLR VKADVRGSPN DQKLNTPRSK HSATEQRRRS KINDRFQMLR 180 QLIPNSDQKR DKASFLLEVI EYIQFLQEKA DKYVTSYQGW NHEPAKLLNW QSNNNQQLVP 240 EGVAFAPKLE EEKNNIPVSV LATAQGVVID HPTTATTSPF PLSIQSNSFF SPVIAGNPVP 300 QFHARVASSE AVEPSPSSRS QKEEEDEEVL EGNIRISSVY SQGLVKTLRE ALENSGVDLT 360 KASISVEIEL AKQSSSSSFK DHEVREPVSR TRNDNVKQTR KPKRLKTGQ

Sequence ? help Back to Top

Protein Sequence Length: 409 aa Download sequence Send to blast

MMFNANERNV LDENSNSNCS SYAAASSGFT LWDESASGKK GQTRKENSVG ERVNMRADVA  60
ATVGQWPVAE RRSQSLTNNH MSGFSSLSSS QGSVLKSQSF MDMIRSAKGS SQEDDLDDEE  120
DFIMKKESSS TSQSHRVDLR VKADVRGSPN DQKLNTPRSK HSATEQRRRS KINDRFQMLR  180
QLIPNSDQKR DKASFLLEVI EYIQFLQEKA DKYVTSYQGW NHEPAKLLNW QSNNNQQLVP  240
EGVAFAPKLE EEKNNIPVSV LATAQGVVID HPTTATTSPF PLSIQSNSFF SPVIAGNPVP  300
QFHARVASSE AVEPSPSSRS QKEEEDEEVL EGNIRISSVY SQGLVKTLRE ALENSGVDLT  360
KASISVEIEL AKQSSSSSFK DHEVREPVSR TRNDNVKQTR KPKRLKTGQ

Expression -- UniGene ? help Back to Top
UniGene ID	E-value	Expressed in
At.20960	0.0	bud\| flower\| root\| seed

Expression -- Microarray ? help Back to Top
Source	ID	E-value
Genevisible	250569_at	0.0
Expression Atlas	AT5G08130	-
AtGenExpress	AT5G08130	-
ATTED-II	AT5G08130	-

Expression -- Description ? help Back to Top
Source	Description
Uniprot	TISSUE SPECIFICITY: Expressed constitutively in roots. {ECO:0000269\|PubMed:12679534}.

Functional Description ? help Back to Top
Source	Description
TAIR	Arabidopsis thaliana basic helix-loop-helix (bHLH) family protein involved in brassinosteroid signaling. It synergistically interacts with BES1 to bind to E box sequences (CANNTG).
UniProt	Positive brassinosteroid-signaling protein. Transcription factor that bind specifically to the DNA sequence 5'-CANNTG-3'(E box). Can bind individually to the promoter as a homodimer or synergistically as a heterodimer with BZR2/BES1. Does not itself activate transcription but enhances BZR2/BES1-mediated target gene activation. {ECO:0000269\|PubMed:15680330}.

Function -- GeneRIF ? help Back to Top
role of BIM1 in embryonic development not only implicates a function for brassinosteroids in this process, but the interaction of BIM1 with DRN, involved with auxin signalling, represents a possible point of hormonal crosstalk in embryonic patterning [PMID: 18830673] UVR8-BES1/BIM1 interaction represents an early photoreceptor signaling mechanism in plants and serves as an important module integrating light and brassinosteroid signaling [PMID: 29398622]

Binding Motif ? help Back to Top
Motif ID	Method	Source	Motif file
MP00498	DAP	27203113	Download

Cis-element ? help Back to Top
Source	Link
PlantRegMap	AT5G08130.1

Regulation -- Description ? help Back to Top
Source	Description
UniProt	INDUCTION: Repressed by cold treatment. {ECO:0000269\|PubMed:12679534}.

Regulation -- PlantRegMap ? help Back to Top
Source	Upstream Regulator	Target Gene
PlantRegMap	Retrieve	Retrieve

Regulation -- ATRM (Manually Curated Upstream Regulators) ? help Back to Top
Source	Upstream Regulator (A: Activate/R: Repress)
ATRM	AT2G20180 (A)

Regulation -- ATRM (Manually Curated Target Genes) ? help Back to Top
Source	Target Gene (A: Activate/R: Repress)
ATRM	AT4G38850(A)

Regulation -- Hormone ? help Back to Top
Source	Hormone
AHD	brassinosteroid

Interaction -- BIND ? help Back to Top
Source	Intact With	Description
BIND	AT1G19350	An unspecified isoform of BES1 interacts with BIM1.

Interaction ? help Back to Top
Source	Intact With
BioGRID	AT1G12980, AT1G19350, AT1G24590, AT1G30490

Phenotype -- Mutation ? help Back to Top
Source	ID
T-DNA Express	AT5G08130

Annotation -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	BT029780	0.0	BT029780.1 Arabidopsis thaliana At5g08130 mRNA, complete cds.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	NP_001318507.1	0.0	basic helix-loop-helix (bHLH) DNA-binding superfamily protein
Swissprot	Q9LEZ3	0.0	BIM1_ARATH; Transcription factor BIM1
TrEMBL	C0SVN9	0.0	C0SVN9_ARATH; Uncharacterized protein At5g08130 (Fragment)
STRING	AT5G08130.5	0.0	(Arabidopsis thaliana)

Link Out ? help Back to Top
Phytozome	AT5G08130.1
Entrez Gene	830708
iHOP	AT5G08130
wikigenes	AT5G08130

Publications ? help Back to Top
Riechmann JL, et al. Arabidopsis transcription factors: genome-wide comparative analysis among eukaryotes. Science, 2000. 290(5499): p. 2105-10 [PMID:11118137] Yin Y, et al. BES1 accumulates in the nucleus in response to brassinosteroids to regulate gene expression and promote stem elongation. Cell, 2002. 109(2): p. 181-91 [PMID:12007405] R Rapid identification of Arabidopsis insertion mutants by non-radioactive detection of T-DNA tagged genes. Plant J., 2002. 32(2): p. 243-53 [PMID:12383089] Heim MA, et al. The basic helix-loop-helix transcription factor family in plants: a genome-wide study of protein structure and functional diversity. Mol. Biol. Evol., 2003. 20(5): p. 735-47 [PMID:12679534] Toledo-Ortiz G,Huq E,Quail PH The Arabidopsis basic/helix-loop-helix transcription factor family. Plant Cell, 2003. 15(8): p. 1749-70 [PMID:12897250] Bailey PC, et al. Update on the basic helix-loop-helix transcription factor gene family in Arabidopsis thaliana. Plant Cell, 2003. 15(11): p. 2497-502 [PMID:14600211] Czechowski T,Bari RP,Stitt M,Scheible WR,Udvardi MK Real-time RT-PCR profiling of over 1400 Arabidopsis transcription factors: unprecedented sensitivity reveals novel root- and shoot-specific genes. Plant J., 2004. 38(2): p. 366-79 [PMID:15078338] Yin Y, et al. A new class of transcription factors mediates brassinosteroid-regulated gene expression in Arabidopsis. Cell, 2005. 120(2): p. 249-59 [PMID:15680330] Gao M,Li G,McCombie WR,Quiros CF Comparative analysis of a transposon-rich Brassica oleracea BAC clone with its corresponding sequence in A. thaliana. Theor. Appl. Genet., 2005. 111(5): p. 949-55 [PMID:16044267] Ohashi-Ito K,Bergmann DC Regulation of the Arabidopsis root vascular initial population by LONESOME HIGHWAY. Development, 2007. 134(16): p. 2959-68 [PMID:17626058] Gampala SS, et al. An essential role for 14-3-3 proteins in brassinosteroid signal transduction in Arabidopsis. Dev. Cell, 2007. 13(2): p. 177-89 [PMID:17681130] Catala R, et al. The Arabidopsis E3 SUMO ligase SIZ1 regulates plant growth and drought responses. Plant Cell, 2007. 19(9): p. 2952-66 [PMID:17905899] Chandler JW,Cole M,Flier A,Werr W BIM1, a bHLH protein involved in brassinosteroid signalling, controls Arabidopsis embryonic patterning via interaction with DORNROSCHEN and DORNROSCHEN-LIKE. Plant Mol. Biol., 2009. 69(1-2): p. 57-68 [PMID:18830673] Oh E, et al. Genome-wide analysis of genes targeted by PHYTOCHROME INTERACTING FACTOR 3-LIKE5 during seed germination in Arabidopsis. Plant Cell, 2009. 21(2): p. 403-19 [PMID:19244139] Elrouby N,Coupland G Proteome-wide screens for small ubiquitin-like modifier (SUMO) substrates identify Arabidopsis proteins implicated in diverse biological processes. Proc. Natl. Acad. Sci. U.S.A., 2010. 107(40): p. 17415-20 [PMID:20855607] Efroni I, et al. Regulation of leaf maturation by chromatin-mediated modulation of cytokinin responses. Dev. Cell, 2013. 24(4): p. 438-45 [PMID:23449474] Cifuentes-Esquivel N, et al. The bHLH proteins BEE and BIM positively modulate the shade avoidance syndrome in Arabidopsis seedlings. Plant J., 2013. 75(6): p. 989-1002 [PMID:23763263] Jin J, et al. An Arabidopsis Transcriptional Regulatory Map Reveals Distinct Functional and Evolutionary Features of Novel Transcription Factors. Mol. Biol. Evol., 2015. 32(7): p. 1767-73 [PMID:25750178] Liang T, et al. UVR8 Interacts with BES1 and BIM1 to Regulate Transcription and Photomorphogenesis in Arabidopsis. Dev. Cell, 2018. 44(4): p. 512-523.e5 [PMID:29398622]