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

XP_013607047.1

Organism

Brassica oleracea

Taxonomic ID

3712

Taxonomic Lineage

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

Family

YABBY

Protein Properties

Length: 270aa MW: 29916.4 Da PI: 9.2646

Description

YABBY family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
XP_013607047.1	genome	NCBI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	YABBY	269.1	5.8e-83	74	257	2	170
YABBY 2 dvfssseqvCyvqCnfCntilavsvPstslfkvvtvrCGhCtsllsvnlakasqllaaeshldeslkee........lleelkveeenlksnvek 88 d+ sss+q+Cyv+C+fC+t+lavsvP +slfk+vtvrCGhC++llsv++++++ ll+++s++++ + ++ llee+++ ++n+++n+++ XP_013607047.1 74 DHISSSDQLCYVHCSFCDTVLAVSVPPSSLFKTVTVRCGHCSNLLSVTVNMRALLLPSVSNIGHPFLPSpppppppsLLEEMRNGGQNINMNMMM 168 7899*************************************************************9999******************** PP YABBY 89 eesastsvssekl......senedeevprvppvirP.PekrqrvPsaynrfikeeiqrikasnPdishreafsaaaknWahfPkihfgl 170 +++a +++s+e++ + + +e+pr+pp++rP PekrqrvPsaynrfikeeiqrika+nPdishreafsaaaknWahfP+ihfgl XP_013607047.1 169 SHHAAAHHSNESFvmatrnGSVDLQEMPRPPPANRPaPEKRQRVPSAYNRFIKEEIQRIKAGNPDISHREAFSAAAKNWAHFPHIHFGL 257 ****99887778776556789******999***********************************************97 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Pfam	PF04690	4.8E-67	78	257	IPR006780	YABBY protein
SuperFamily	SSF47095	1.3E-7	200	250	IPR009071	High mobility group box domain
Gene3D	G3DSA:1.10.30.10	1.5E-4	206	251	IPR009071	High mobility group box domain

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
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

Sequence ? help Back to Top
Protein Sequence Length: 270 aa Download sequence Send to blast
MLPNCLGTVS LHVYINRIKS LSPPHLPLYS PPFFPFSLWN STSGELLNIY KEKQKESMSS 60 MSMSSSSAPA YPPDHISSSD QLCYVHCSFC DTVLAVSVPP SSLFKTVTVR CGHCSNLLSV 120 TVNMRALLLP SVSNIGHPFL PSPPPPPPPS LLEEMRNGGQ NINMNMMMSH HAAAHHSNES 180 FVMATRNGSV DLQEMPRPPP ANRPAPEKRQ RVPSAYNRFI KEEIQRIKAG NPDISHREAF 240 SAAAKNWAHF PHIHFGLMPD HPPTKKANVR

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
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}.

Cis-element ? help Back to Top
Source	Link
PlantRegMap	XP_013607047.1

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

Annotation -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	AF136540	0.0	AF136540.1 Arabidopsis thaliana YABBY3 (YABBY3) mRNA, complete cds.
GenBank	AY037186	0.0	AY037186.1 Arabidopsis thaliana AT4g00180/F6N15_22 mRNA, complete cds.
GenBank	BT002662	0.0	BT002662.1 Arabidopsis thaliana At4g00180/F6N15_22 gene, complete cds.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_013607047.1	0.0	PREDICTED: axial regulator YABBY 3 isoform X1
Swissprot	Q9XFB1	1e-118	YAB3_ARATH; Axial regulator YABBY 3
TrEMBL	A0A078JBF7	1e-124	A0A078JBF7_BRANA; BnaAnng18530D protein
TrEMBL	A0A397XXC6	1e-124	A0A397XXC6_BRACM; Uncharacterized protein
TrEMBL	M4F8A8	1e-124	M4F8A8_BRARP; Uncharacterized protein
STRING	Bra037320.1-P	1e-125	(Brassica rapa)

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
AT4G00180.1	3e-95	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] Yadav RK, et al. Plant stem cell maintenance involves direct transcriptional repression of differentiation program. Mol. Syst. Biol., 2013. 9: p. 654 [PMID:23549482]