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

AT4G00180.2

Common Name

YAB3

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

YABBY

Protein Properties

Length: 209aa MW: 23171.4 Da PI: 9.7567

Description

YABBY family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
AT4G00180.2	genome	TAIR	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	YABBY	241.4	1.9e-74	2	170	18	170
YABBY 18 CntilavsvPstslfkvvtvrCGhCtsllsvnlakasqllaaeshldeslkee........lleelkveeenlksnvekeesastsvssekl...... 101 C+ vsvP +slfk+vtvrCGhC++llsv++++++ ll+++s+l++s+ ++ llee+++ ++n+++n++++++as+++++e+l AT4G00180.2 2 CDINWQVSVPPSSLFKTVTVRCGHCSNLLSVTVSMRALLLPSVSNLGHSFLPPpppppppnLLEEMRSGGQNINMNMMMSHHASAHHPNEHLvmatrn 99 888889*******************************************9999********************************99* PP YABBY 102 ..senedeevprvppvirPPekrqrvPsaynrfikeeiqrikasnPdishreafsaaaknWahfPkihfgl 170 s ++ +e+pr+pp++rPPekrqrvPsaynrfikeeiqrika+nPdishreafsaaaknWahfP+ihfgl AT4G00180.2 100 grSVDHLQEMPRPPPANRPPEKRQRVPSAYNRFIKEEIQRIKAGNPDISHREAFSAAAKNWAHFPHIHFGL 170 *******************************************************************97 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Pfam	PF04690	1.1E-56	1	170	IPR006780	YABBY protein
SuperFamily	SSF47095	5.63E-8	115	163	IPR009071	High mobility group box domain
Gene3D	G3DSA:1.10.30.10	7.1E-5	118	164	IPR009071	High mobility group box domain

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0006355	Biological Process	regulation of transcription, DNA-templated
GO:0009944	Biological Process	polarity specification of adaxial/abaxial axis
GO:0010154	Biological Process	fruit development
GO:0010158	Biological Process	abaxial cell fate specification
GO:1902183	Biological Process	regulation of shoot apical meristem development
GO:2000024	Biological Process	regulation of leaf development
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:0046872	Molecular Function	metal ion binding

Plant Ontology ? help Back to Top
PO Term	PO Category	PO Description
PO:0000013	anatomy	cauline leaf
PO:0000037	anatomy	shoot apex
PO:0000293	anatomy	guard cell
PO:0008019	anatomy	leaf lamina base
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:0020137	anatomy	leaf apex
PO:0025022	anatomy	collective leaf structure
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: 209 aa Download sequence Send to blast
MCDINWQVSV PPSSLFKTVT VRCGHCSNLL SVTVSMRALL LPSVSNLGHS FLPPPPPPPP 60 PNLLEEMRSG GQNINMNMMM SHHASAHHPN EHLVMATRNG RSVDHLQEMP RPPPANRPPE 120 KRQRVPSAYN RFIKEEIQRI KAGNPDISHR EAFSAAAKNW AHFPHIHFGL MADHPPTKKA 180 NVRQQEGEDG MMGREGFYGS AANVGVAHN

Expression -- UniGene ? help Back to Top
UniGene ID	E-value	Expressed in
At.11867	0.0	root\| seed

Expression -- Microarray ? help Back to Top
Source	ID	E-value
Genevisible	255709_at	0.0
Expression Atlas	AT4G00180	-
AtGenExpress	AT4G00180	-
ATTED-II	AT4G00180	-

Expression -- Description ? help Back to Top
Source	Description
Uniprot	DEVELOPMENTAL STAGE: Expressed in subepidermal cells of anlagen regions, then in abaxial part of primordia and finally in differentiating organs. Levels decrease in differentiated organs. In embryo the expression starts during the heart stage in the cotyledon anlagen. Later, expression expands to abaxial domain of the cotyledon primordia and decrease as the embryo matures. In stamen, expression restricted to the abaxial region differentiating into the connective. In gynoecium, expressed in the abaxial cell layers differentiating into the valves. {ECO:0000269\|PubMed:10457020}.
Uniprot	TISSUE SPECIFICITY: Expressed in abaxial regions of lateral aerial organ primordia leading to cotyledons, leaves, flower meristems, sepals, petals, stamen and carpels, but not in roots. {ECO:0000269\|PubMed:10457020, ECO:0000269\|PubMed:12417699}.

Functional Description ? help Back to Top
Source	Description
TAIR	YABBY gene family member, likely has transcription factor activity, involved in specifying abaxial cell fate. Along with FIL, involved in patterning of the fruit. GUS reporter gene expression in seedlings is observed in the young leaves and as the leaf matures, expression is restricted to the abaxial tissues of leaves, expression is also observed on either side of the leaf margin in the younger tissues of leaf blades.
UniProt	Involved in the abaxial cell fate determination during embryogenesis and organogenesis. Regulates the initiation of embryonic shoot apical meristem (SAM) development (PubMed:10457020, PubMed:12417699, PubMed:19837869). Contributes to the repression of KNOX genes (STM, KNAT1/BP and KNAT2) to avoid ectopic meristems. Binds DNA without sequence specificity (PubMed:10457020, PubMed:12417699). {ECO:0000269\|PubMed:10457020, ECO:0000269\|PubMed:12417699, ECO:0000269\|PubMed:19837869}.

Function -- GeneRIF ? help Back to Top
Data show that mutations in the YABBY3 (YAB3) cause an array of defects, including aberrant phyllotaxis. [PMID: 18469164] YAB3 interact with LUG and LUH. Together these proteins maintain leaf polarity and meristem activity in Arabidopsis. [PMID: 19837869] Mutation of these YAB and KNOX1 genes together causes nearly complete suppression of bop1 bop2 ectopic organ outgrowth at the morphological and cellular levels. [PMID: 20610407]

Cis-element ? help Back to Top
Source	Link
PlantRegMap	AT4G00180.2

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	AT1G65620 (R), AT2G28610 (R), AT4G37750 (A)

Regulation -- ATRM (Manually Curated Target Genes) ? help Back to Top
Source	Target Gene (A: Activate/R: Repress)
ATRM	AT1G62360(R), AT1G65620(R), AT5G60910(A)

Interaction -- BIND ? help Back to Top
Source	Intact With	Description
BIND	AT4G27330	NZZ interacts with YAB3.

Interaction ? help Back to Top
Source	Intact With
BioGRID	AT4G27330, AT1G18570

Phenotype -- Mutation ? help Back to Top
Source	ID
T-DNA Express	AT4G00180

Annotation -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	AK316696	0.0	AK316696.1 Arabidopsis thaliana AT4G00180 mRNA, complete cds, clone: RAFL06-81-K07.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	NP_001078337.1	1e-154	Plant-specific transcription factor YABBY family protein
Swissprot	Q9XFB1	1e-150	YAB3_ARATH; Axial regulator YABBY 3
TrEMBL	A8MRG7	1e-153	A8MRG7_ARATH; AT4G00180 protein
STRING	AT4G00180.1	1e-149	(Arabidopsis thaliana)

Link Out ? help Back to Top
Phytozome	AT4G00180.2
Entrez Gene	827914
iHOP	AT4G00180
wikigenes	AT4G00180

Publications ? help Back to Top
Siegfried KR, et al. Members of the YABBY gene family specify abaxial cell fate in Arabidopsis. Development, 1999. 126(18): p. 4117-28 [PMID:10457020] Riechmann JL, et al. Arabidopsis transcription factors: genome-wide comparative analysis among eukaryotes. Science, 2000. 290(5499): p. 2105-10 [PMID:11118137] Lin WC,Shuai B,Springer PS The Arabidopsis LATERAL ORGAN BOUNDARIES-domain gene ASYMMETRIC LEAVES2 functions in the repression of KNOX gene expression and in adaxial-abaxial patterning. Plant Cell, 2003. 15(10): p. 2241-52 [PMID:14508003] Engstrom EM,Izhaki A,Bowman JL Promoter bashing, microRNAs, and Knox genes. New insights, regulators, and targets-of-regulation in the establishment of lateral organ polarity in Arabidopsis. Plant Physiol., 2004. 135(2): p. 685-94 [PMID:15208415] Sieber P,Petrascheck M,Barberis A,Schneitz K Organ polarity in Arabidopsis. NOZZLE physically interacts with members of the YABBY family. Plant Physiol., 2004. 135(4): p. 2172-85 [PMID:15299139] Dinneny JR,Weigel D,Yanofsky MF A genetic framework for fruit patterning in Arabidopsis thaliana. Development, 2005. 132(21): p. 4687-96 [PMID:16192305] Duarte JM, et al. Expression pattern shifts following duplication indicative of subfunctionalization and neofunctionalization in regulatory genes of Arabidopsis. Mol. Biol. Evol., 2006. 23(2): p. 469-78 [PMID:16280546] Nole-Wilson S,Krizek BA AINTEGUMENTA contributes to organ polarity and regulates growth of lateral organs in combination with YABBY genes. Plant Physiol., 2006. 141(3): p. 977-87 [PMID:16714408] Dai M,Hu Y,Zhao Y,Liu H,Zhou DX A WUSCHEL-LIKE HOMEOBOX gene represses a YABBY gene expression required for rice leaf development. Plant Physiol., 2007. 144(1): p. 380-90 [PMID:17351053] Fu Y, et al. Genetic interactions between leaf polarity-controlling genes and ASYMMETRIC LEAVES1 and 2 in Arabidopsis leaf patterning. Plant Cell Physiol., 2007. 48(5): p. 724-35 [PMID:17395603] Gallagher TL,Gasser CS Independence and interaction of regions of the INNER NO OUTER protein in growth control during ovule development. Plant Physiol., 2008. 147(1): p. 306-15 [PMID:18326791] Goldshmidt A,Alvarez JP,Bowman JL,Eshed Y Signals derived from YABBY gene activities in organ primordia regulate growth and partitioning of Arabidopsis shoot apical meristems. Plant Cell, 2008. 20(5): p. 1217-30 [PMID:18469164] Mummenhoff K,Polster A,M Lepidium as a model system for studying the evolution of fruit development in Brassicaceae. J. Exp. Bot., 2009. 60(5): p. 1503-13 [PMID:19052256] Dai M,Hu Y,Zhao Y,Zhou DX Regulatory Networks Involving YABBY Genes in Rice Shoot Development. Plant Signal Behav, 2007. 2(5): p. 399-400 [PMID:19704613] Stahle MI,Kuehlich J,Staron L,von Arnim AG,Golz JF YABBYs and the transcriptional corepressors LEUNIG and LEUNIG_HOMOLOG maintain leaf polarity and meristem activity in Arabidopsis. Plant Cell, 2009. 21(10): p. 3105-18 [PMID:19837869] Ha CM,Jun JH,Fletcher JC Control of Arabidopsis leaf morphogenesis through regulation of the YABBY and KNOX families of transcription factors. Genetics, 2010. 186(1): p. 197-206 [PMID:20610407] Hanada K, et al. Functional compensation of primary and secondary metabolites by duplicate genes in Arabidopsis thaliana. Mol. Biol. Evol., 2011. 28(1): p. 377-82 [PMID:20736450] McKeown PC, et al. Identification of imprinted genes subject to parent-of-origin specific expression in Arabidopsis thaliana seeds. BMC Plant Biol., 2011. 11: p. 113 [PMID:21838868] Bonaccorso O,Lee JE,Puah L,Scutt CP,Golz JF FILAMENTOUS FLOWER controls lateral organ development by acting as both an activator and a repressor. BMC Plant Biol., 2012. 12: p. 176 [PMID:23025792] Gonz Antagonistic gene activities determine the formation of pattern elements along the mediolateral axis of the Arabidopsis fruit. PLoS Genet., 2012. 8(11): p. e1003020 [PMID:23133401] Yadav RK, et al. Plant stem cell maintenance involves direct transcriptional repression of differentiation program. Mol. Syst. Biol., 2013. 9: p. 654 [PMID:23549482] Xiang J, et al. Isolation and characterization of two VpYABBY genes from wild Chinese Vitis pseudoreticulata. Protoplasma, 2013. 250(6): p. 1315-25 [PMID:23728789] Frerigmann H,Berger B,Gigolashvili T bHLH05 is an interaction partner of MYB51 and a novel regulator of glucosinolate biosynthesis in Arabidopsis. Plant Physiol., 2014. 166(1): p. 349-69 [PMID:25049362] 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]