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_009142322.1

Organism

Brassica rapa

Taxonomic ID

3711

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: 231aa MW: 25899.6 Da PI: 7.2024

Description

YABBY family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
XP_009142322.1	genome	NCBI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	YABBY	257.3	2.4e-79	25	192	5	170
YABBY 5 ssseqvCyvqCnfCntilavsvPstslfkvvtvrCGhCtsllsvnlakasqllaaeshldeslkee.......lleelkveeenlksnvekeesa 92 s seq+CyvqCn+C+tilavsvP+ts+fk+vtvrCG+Ct+l+s ++++s +l+a+++l+ +l ++ +leelk++ +n+++++++++ + XP_009142322.1 25 SPSEQLCYVQCNYCETILAVSVPYTSMFKTVTVRCGCCTNLIS--VNMRSLVLPASNQLQLQLGPHsyftpqnILEELKDAPSNMNMMMMNQHPN 117 789**************************************..5678999*************************************** PP YABBY 93 stsvsseklsenedeevprvppvirPPekrqrvPsaynrfikeeiqrikasnPdishreafsaaaknWahfPkihfgl 170 +++++s+ ++ ++++e+p++ppv+r +krqrvPsaynrfikeeiqrika+nPdishreafsaaaknWahfP+ihfgl XP_009142322.1 118 MNDIPSF-MDLHQQHEIPKAPPVNR--QKRQRVPSAYNRFIKEEIQRIKAGNPDISHREAFSAAAKNWAHFPHIHFGL 192 **6.5***********9..7**********************************************97 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Pfam	PF04690	1.4E-66	26	192	IPR006780	YABBY protein
SuperFamily	SSF47095	1.96E-7	135	185	IPR009071	High mobility group box domain
Gene3D	G3DSA:1.10.30.10	2.7E-4	145	186	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: 231 aa Download sequence Send to blast
MSMSSMSSPS SAVFSPENLS PDPLSPSEQL CYVQCNYCET ILAVSVPYTS MFKTVTVRCG 60 CCTNLISVNM RSLVLPASNQ LQLQLGPHSY FTPQNILEEL KDAPSNMNMM MMNQHPNMND 120 IPSFMDLHQQ HEIPKAPPVN RQKRQRVPSA YNRFIKEEIQ RIKAGNPDIS HREAFSAAAK 180 NWAHFPHIHF GLAPDNQPVK KTNMPQQEGE DNMGMKEGFY APAANVGVIP Y

Expression -- UniGene ? help Back to Top
UniGene ID	E-value	Expressed in
Bra.10772	0.0	bud

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 transition between globular and heart stages in the cotyledon anlagen. From the heart stage, 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 young lateral aerial organs, and in primordia leading to cotyledons, leaves, flower meristems, sepals, petals, stamen and carpels, but not in roots. {ECO:0000269\|PubMed:10323860, ECO:0000269\|PubMed:10457020, ECO:0000269\|PubMed:14555697, ECO:0000269\|Ref.3}.

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	XP_009142322.1

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	FJ868216	0.0	FJ868216.1 Brassica rapa subsp. pekinensis cultivar CMS7311 DBC43-3-2 (DBC43-3-2) mRNA, complete cds.
GenBank	JQ234918	0.0	JQ234918.1 Brassica rapa subsp. pekinensis clone 5-696 putative male sterile protein mRNA, complete cds.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_009142322.1	1e-174	PREDICTED: axial regulator YABBY 1 isoform X2
Refseq	XP_013688136.1	1e-174	axial regulator YABBY 1-like isoform X2
Swissprot	O22152	1e-137	YAB1_ARATH; Axial regulator YABBY 1
TrEMBL	A0A397ZXP8	1e-172	A0A397ZXP8_BRACM; Uncharacterized protein
STRING	Bra040322.1-P	1e-149	(Brassica rapa)

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT2G45190.1	1e-133	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]