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

AT5G06070.1

Common Name

K16F4.3, RAB, RBE

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

C2H2

Protein Properties

Length: 226aa MW: 25337.6 Da PI: 7.8286

Description

C2H2 family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
AT5G06070.1	genome	TAIR	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	zf-C2H2	17.3	1.3e-05	55	77	1	23
EEETTTTEEESSHHHHHHHHHHT CS zf-C2H2 1 ykCpdCgksFsrksnLkrHirtH 23 y+C+ Cg+ F++ L H+++H AT5G06070.1 55 YSCSFCGREFKSAQALGGHMNVH 77 99*******************99 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SuperFamily	SSF57667	1.1E-6	52	81	No hit	No description
Gene3D	G3DSA:3.30.160.60	2.3E-4	53	79	IPR013087	Zinc finger C2H2-type/integrase DNA-binding domain
SMART	SM00355	0.0017	55	77	IPR015880	Zinc finger, C2H2-like
PROSITE profile	PS50157	12.154	55	82	IPR007087	Zinc finger, C2H2
Pfam	PF13912	3.4E-6	55	78	IPR007087	Zinc finger, C2H2
PROSITE pattern	PS00028	0	57	77	IPR007087	Zinc finger, C2H2

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0006355	Biological Process	regulation of transcription, DNA-templated
GO:0009409	Biological Process	response to cold
GO:0009934	Biological Process	regulation of meristem structural organization
GO:0030154	Biological Process	cell differentiation
GO:0048441	Biological Process	petal development
GO:0005634	Cellular Component	nucleus
GO:0003700	Molecular Function	transcription factor activity, sequence-specific DNA binding
GO:0008270	Molecular Function	zinc ion binding
GO:0043565	Molecular Function	sequence-specific DNA binding
GO:0044212	Molecular Function	transcription regulatory region DNA binding

Plant Ontology ? help Back to Top
PO Term	PO Category	PO Description
PO:0000021	anatomy	petal primordium
PO:0009046	anatomy	flower
PO:0009052	anatomy	flower pedicel
PO:0020022	anatomy	inner integument
PO:0020023	anatomy	outer integument
PO:0007611	developmental stage	petal differentiation and expansion stage
PO:0007616	developmental stage	flowering stage

Sequence ? help Back to Top
Protein Sequence Length: 226 aa Download sequence Send to blast
MMDRGECLMS MKLRPMVTRP SSDGTLFWPF REERAFASAE EYGGGGGCMW PPRSYSCSFC 60 GREFKSAQAL GGHMNVHRRD RARLKQQSLS PSSTDQATPP ECDRQQQVLD VGSKVLVQEE 120 TRKPNGTKRE ISDVCNNNVL ESSMKRYEHD NGEVKTDLSV GLLSTEFDPR KKQLINGSSS 180 SWKRAKTDVS RFPMMLGLVI GISEINGHHE ELDLELRLGA DPPKVN

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
1njq_A	3e-12	50	77	2	29	superman protein
2l1o_A	3e-12	50	77	2	29	Transcriptional regulator SUPERMAN
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Expression -- UniGene ? help Back to Top
UniGene ID	E-value	Expressed in
At.32906	0.0	flower

Expression -- Microarray ? help Back to Top
Source	ID	E-value
GEO	145357692	0.0
Genevisible	250708_at	0.0
Expression Atlas	AT5G06070	-
AtGenExpress	AT5G06070	-
ATTED-II	AT5G06070	-

Expression -- Description ? help Back to Top
Source	Description
Uniprot	DEVELOPMENTAL STAGE: Not expressed in the inflorescence meristem or in the flowers at stages 1 and 2. First expressed in the precursor cells of petal primordia in stage 3 flowers and in the developing petal primordia up to stage 6. Not expressed at later stages. {ECO:0000269\|PubMed:14681191}.
Uniprot	TISSUE SPECIFICITY: Strongly expressed in inflorescences and flowers, and weakly in siliques, seedlings and roots. In flowers, it is expressed in petal primordia and their precursor cells. Also expressed in the lateral root caps and the basal cells of lateral roots. {ECO:0000269\|PubMed:14681191}.

Functional Description ? help Back to Top
Source	Description
TAIR	Isolated as a mutation defective in petal development with specific effects on adaxial petals which are filamentous or absent. Encodes a Superman (SUP) like protein with zinc finger motifs. Transcript is detected in petal primordia and protein is localized to the nucleus.
UniProt	Probable transcriptional regulator essential for petal development. Required for the early development of the organ primordia of the second whorl. Acts downstream of AP1 and PTL. {ECO:0000269\|PubMed:14681191}.

Function -- GeneRIF ? help Back to Top
RBE acts to maintain two different types of spatial boundaries in young flowers: boundaries between organ primordia within a whorl and boundaries of homeotic gene expression between whorls. [PMID: 16412084] These results indicate that one role of RBE is to fine-tune miR164 expression to regulate the CUC1 and CUC2 effector genes, which, in turn, regulate developmental events required for sepal and petal organogenesis. [PMID: 22573623] restriction of expression to the petal precursor cells crucial for flower development [PMID: 24366683] RBE promotes cell division and negatively regulates the expression of TCP5, TCP13, and TCP17 in young petals. [PMID: 26073137] regulates the transcription of TCP4 during petal development [PMID: 27838638]

Cis-element ? help Back to Top
Source	Link
PlantRegMap	AT5G06070.1

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	AT5G03680 (A)

Regulation -- ATRM (Manually Curated Target Genes) ? help Back to Top
Source	Target Gene (A: Activate/R: Repress)
ATRM	AT4G18960(R)

Phenotype -- Mutation ? help Back to Top
Source	ID
T-DNA Express	AT5G06070

Annotation -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	AB107371	0.0	AB107371.1 Arabidopsis thaliana RBE mRNA for one finger-type zinc finger protein for RABBIT EARS, complete cds.
GenBank	AP002030	0.0	AP002030.1 Arabidopsis thaliana genomic DNA, chromosome 5, TAC clone:K16F4.
GenBank	AY088861	0.0	AY088861.1 Arabidopsis thaliana clone 97505 mRNA, complete sequence.
GenBank	CP002688	0.0	CP002688.1 Arabidopsis thaliana chromosome 5 sequence.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	NP_568161.1	1e-169	C2H2 and C2HC zinc fingers superfamily protein
Swissprot	Q9LHS9	1e-170	RBE_ARATH; Probable transcriptional regulator RABBIT EARS
TrEMBL	A0A384KSD2	1e-168	A0A384KSD2_ARATH; RBE
TrEMBL	Q1LYT2	1e-168	Q1LYT2_ARATH; At5g06070
STRING	AT5G06070.1	1e-169	(Arabidopsis thaliana)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM5128	25	44
Representative plant	OGRP576	15	81

Link Out ? help Back to Top
Phytozome	AT5G06070.1
Entrez Gene	830494
iHOP	AT5G06070
wikigenes	AT5G06070

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] Takeda S,Matsumoto N,Okada K RABBIT EARS, encoding a SUPERMAN-like zinc finger protein, regulates petal development in Arabidopsis thaliana. Development, 2004. 131(2): p. 425-34 [PMID:14681191] Krizek BA,Lewis MW,Fletcher JC RABBIT EARS is a second-whorl repressor of AGAMOUS that maintains spatial boundaries in Arabidopsis flowers. Plant J., 2006. 45(3): p. 369-83 [PMID:16412084] Haas TJ, et al. The Arabidopsis AAA ATPase SKD1 is involved in multivesicular endosome function and interacts with its positive regulator LYST-INTERACTING PROTEIN5. Plant Cell, 2007. 19(4): p. 1295-312 [PMID:17468262] Gon PpRab1, a Rab GTPase from maritime pine is differentially expressed during embryogenesis. Mol. Genet. Genomics, 2007. 278(3): p. 273-82 [PMID:17562081] Dacks JB,Poon PP,Field MC Phylogeny of endocytic components yields insight into the process of nonendosymbiotic organelle evolution. Proc. Natl. Acad. Sci. U.S.A., 2008. 105(2): p. 588-93 [PMID:18182495] Alvim Kamei CL, et al. The PRA1 gene family in Arabidopsis. Plant Physiol., 2008. 147(4): p. 1735-49 [PMID:18583532] Irish VF The flowering of Arabidopsis flower development. Plant J., 2010. 61(6): p. 1014-28 [PMID:20409275] Heo JB,Yi YB,Bahk JD Rice GDP dissociation inhibitor 3 inhibits OsMAPK2 activity through physical interaction. Biochem. Biophys. Res. Commun., 2011. 414(4): p. 814-9 [PMID:22020099] Huang T,L RBE controls microRNA164 expression to effect floral organogenesis. Development, 2012. 139(12): p. 2161-9 [PMID:22573623] Lampugnani ER,Kilinc A,Smyth DR Auxin controls petal initiation in Arabidopsis. Development, 2013. 140(1): p. 185-94 [PMID:23175631] Takeda S,Noguchi M,Hamamura Y,Higashiyama T Spatial distribution of the RABBIT EARS protein and effects of its ectopic expression in Arabidopsis thaliana flowers. Planta, 2014. 239(3): p. 707-15 [PMID:24366683] 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] Huang T,Irish VF Temporal Control of Plant Organ Growth by TCP Transcription Factors. Curr. Biol., 2015. 25(13): p. 1765-70 [PMID:26073137] Li J, et al. RABBIT EARS regulates the transcription of TCP4 during petal development in Arabidopsis. J. Exp. Bot., 2016. 67(22): p. 6473-6480 [PMID:27838638] Lång V,Palva ET The expression of a rab-related gene, rab 18, is induced by abscisic acid during the cold acclimation process of Arabidopsis thaliana (L.) Heynh. Plant Mol. Biol., 1993. 21(3): p. 581-2 [PMID:8443352]