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

Rsa1.0_02534.1_g00001.1

Organism

Raphanus sativus

Taxonomic ID

3726

Taxonomic Lineage

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

Family

YABBY

Protein Properties

Length: 239aa MW: 26785.6 Da PI: 8.154

Description

YABBY family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Rsa1.0_02534.1_g00001.1	genome	RGD	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	YABBY	248.8	1e-76	17	200	2	170
YABBY 2 dvfssseqvCyvqCnfCntilavsvPstslfkvvtvrCGhCtsllsvnlakasqllaaeshldeslkee.......lleelkveee 80 ++ s s+++CyvqCnfC+tilavsvP+ts+fk+vtvrCG+Ct+llsv +++s l+a+++l+ +l ++ +leel+++ + Rsa1.0_02534.1_g00001.1 17 EHLSPSDHLCYVQCNFCETILAVSVPYTSMFKTVTVRCGCCTNLLSV--NMRSAGLPASNQLQLQLGPHsyfntqnILEELRDAPS 100 67899***************************************5..5778899********99************ PP YABBY 81 nlksnvekeesastsvsseklsenedeevprvppvir...........PPekrqrvPsaynrfikeeiqrikasnPdishreafsa 155 n++++v++++ ++++++s++ + ++++e+p++ppv+r PekrqrvPsaynrfikeeiqrika+nPdishreafsa Rsa1.0_02534.1_g00001.1 101 NMNMMVMNQHPNMNDIPSFM-NIHQQHEIPKAPPVNRrkmlvsfsflfAPEKRQRVPSAYNRFIKEEIQRIKAGNPDISHREAFSA 185 **************65.**********99566665555556********************************* PP YABBY 156 aaknWahfPkihfgl 170 aaknWahfP+ihfgl Rsa1.0_02534.1_g00001.1 186 AAKNWAHFPHIHFGL 200 ***********97 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Pfam	PF04690	1.5E-66	21	200	IPR006780	YABBY protein
SuperFamily	SSF47095	1.83E-7	147	193	IPR009071	High mobility group box domain
Gene3D	G3DSA:1.10.30.10	1.5E-4	149	194	IPR009071	High mobility group box domain

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0009909	Biological Process	regulation of flower development
GO:0009933	Biological Process	meristem structural organization
GO:0009944	Biological Process	polarity specification of adaxial/abaxial axis
GO:0010093	Biological Process	specification of floral organ identity
GO:0010154	Biological Process	fruit development
GO:0010158	Biological Process	abaxial cell fate specification
GO:0010159	Biological Process	specification of organ position
GO:0010450	Biological Process	inflorescence meristem growth
GO:1902183	Biological Process	regulation of shoot apical meristem development
GO:2000024	Biological Process	regulation of leaf development

Sequence ? help Back to Top
Protein Sequence Length: 239 aa Download sequence Send to blast
MSMSSMSSPS SAVFSPEHLS PSDHLCYVQC NFCETILAVS VPYTSMFKTV TVRCGCCTNL 60 LSVNMRSAGL PASNQLQLQL GPHSYFNTQN ILEELRDAPS NMNMMVMNQH PNMNDIPSFM 120 NIHQQHEIPK APPVNRRKML VSFSFLFAPE KRQRVPSAYN RFIKEEIQRI KAGNPDISHR 180 EAFSAAAKNW AHFPHIHFGL APDNQPVKKT NMPQQEGEDN VGMKEGFYAP AANIGVAPY

Functional Description ? help Back to Top
Source	Description
UniProt	Involved in the abaxial cell fate determination during embryogenesis and organogenesis. Regulates the initiation of embryonic shoot apical meristem (SAM) development (PubMed:10323860, PubMed:10331982, PubMed:10457020, PubMed:11812777, PubMed:12417699, PubMed:9878633, Ref.3, Ref.6, PubMed:19837869). Required during flower formation and development, particularly for the patterning of floral organs. Positive regulator of class B (AP3 and PI) activity in whorls 2 and 3. Negative regulator of class B activity in whorl 1 and of SUP activity in whorl 3. Interacts with class A proteins (AP1, AP2 and LUG) to repress class C (AG) activity in whorls 1 and 2. Contributes to the repression of KNOX genes (STM, KNAT1/BP and KNAT2) to avoid ectopic meristems. Binds DNA without sequence specificity. In vitro, can compete and displace the AP1 protein binding to DNA containing CArG box (PubMed:10323860, PubMed:10331982, PubMed:10457020, PubMed:11812777, PubMed:12417699, PubMed:9878633, Ref.3, Ref.6). {ECO:0000269\|PubMed:10323860, ECO:0000269\|PubMed:10331982, ECO:0000269\|PubMed:10457020, ECO:0000269\|PubMed:11812777, ECO:0000269\|PubMed:12417699, ECO:0000269\|PubMed:19837869, ECO:0000269\|PubMed:9878633, ECO:0000269\|Ref.3, ECO:0000269\|Ref.6}.

Binding Motif ? help Back to Top
Motif ID	Method	Source	Motif file
MP00620	PBM	Transfer from AT2G45190	Download

Cis-element ? help Back to Top
Source	Link
PlantRegMap	Rsa1.0_02534.1_g00001.1

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

Annotation -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	AF074948	1e-143	AF074948.1 Arabidopsis thaliana FIL mRNA, complete cds.
GenBank	AF087015	1e-143	AF087015.1 Arabidopsis thaliana abnormal floral organs protein (AFO) mRNA, complete cds.
GenBank	AF136538	1e-143	AF136538.1 Arabidopsis thaliana YABBY1 (YABBY1) mRNA, complete cds.
GenBank	BT026409	1e-143	BT026409.1 Arabidopsis thaliana At2g45190 mRNA, complete cds.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_018476406.1	1e-180	PREDICTED: axial regulator YABBY 1 isoform X1
Swissprot	O22152	1e-138	YAB1_ARATH; Axial regulator YABBY 1
TrEMBL	A0A3P6G8H8	1e-142	A0A3P6G8H8_BRAOL; Uncharacterized protein
STRING	Bostr.25993s0255.1.p	1e-150	(Boechera stricta)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM2217	28	77

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT2G45190.1	1e-140	YABBY family protein

Publications ? help Back to Top
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] Lian H,Li X,Liu Z,He Y HYL1 is required for establishment of stamen architecture with four microsporangia in Arabidopsis. J. Exp. Bot., 2013. 64(11): p. 3397-410 [PMID:23918970] Tameshige T, et al. Pattern dynamics in adaxial-abaxial specific gene expression are modulated by a plastid retrograde signal during Arabidopsis thaliana leaf development. PLoS Genet., 2013. 9(7): p. e1003655 [PMID:23935517] Boter M, et al. FILAMENTOUS FLOWER Is a Direct Target of JAZ3 and Modulates Responses to Jasmonate. Plant Cell, 2015. 27(11): p. 3160-74 [PMID:26530088] Douglas SJ,Li B,Kliebenstein DJ,Nambara E,Riggs CD A novel Filamentous Flower mutant suppresses brevipedicellus developmental defects and modulates glucosinolate and auxin levels. PLoS ONE, 2017. 12(5): p. e0177045 [PMID:28493925] Tanaka W,Toriba T,Hirano HY Three TOB1-related YABBY genes are required to maintain proper function of the spikelet and branch meristems in rice. New Phytol., 2017. 215(2): p. 825-839 [PMID:28556940] Silverblatt-Buser EW,Frick MA,Rabeler C,Kaplinsky NJ Genetic Interactions Between BOB1 and Multiple 26S Proteasome Subunits Suggest a Role for Proteostasis in Regulating Arabidopsis Development. G3 (Bethesda), 2018. 8(4): p. 1379-1390 [PMID:29487187]