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

Neem_4411_f_2

Organism

Azadirachta indica

Taxonomic ID

124943

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Sapindales; Meliaceae; Azadirachta

Family

YABBY

Protein Properties

Length: 237aa MW: 26317.3 Da PI: 8.2298

Description

YABBY family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Neem_4411_f_2	genome	NGD	View Nucleic Acid

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	YABBY	103.4	4.7e-32	11	123	2	117
YABBY 2 dvfssseqvCyvqCnfCntilavsvPstslfkvvtvrCGhCtsllsvnlakasqllaaeshldeslkeelleelkveeenlksnvekeesastsvs 97 d+ ssseq+Cyv+CnfC+t+lavsvP tslfk+vtvrCGhCt+llsvn++ a + hl++++ ++ ++ +++ +++ ++++ +++ ++ Neem_4411_f_2 11 DHLSSSEQLCYVHCNFCDTVLAVSVPCTSLFKTVTVRCGHCTNLLSVNMRGLLLPAANQLHLGHAFFTPQNLLEEIRNTPTNMLMINQPNPT--EP 104 7899******************************************9988887777777788888776644333444444445555554444..44 PP YABBY 98 seklsenedeevprvppvir 117 ++ + d+e+p++p v+r Neem_4411_f_2 105 VMP-VRGIDQEIPKPPVVNR 123 433.4678889998777776 PP
2	YABBY	121.3	1.5e-37	146	199	117	170
YABBY 117 rPPekrqrvPsaynrfikeeiqrikasnPdishreafsaaaknWahfPkihfgl 170 PekrqrvPsaynrfik+eiqrika+nPdishreafsaaaknWahfP+ihfgl Neem_4411_f_2 146 ETPEKRQRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWAHFPHIHFGL 199 67**************************************************97 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Pfam	PF04690	5.4E-65	15	199	IPR006780	YABBY protein
SuperFamily	SSF47095	1.31E-7	144	192	IPR009071	High mobility group box domain
Gene3D	G3DSA:1.10.30.10	2.2E-4	148	191	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: 237 aa Download sequence Send to blast
MSSSTSAFSP DHLSSSEQLC YVHCNFCDTV LAVSVPCTSL FKTVTVRCGH CTNLLSVNMR 60 GLLLPAANQL HLGHAFFTPQ NLLEEIRNTP TNMLMINQPN PTEPVMPVRG IDQEIPKPPV 120 VNRQKLAKAL ACCPPAFTVD IFAFKETPEK RQRVPSAYNR FIKDEIQRIK AGNPDISHRE 180 AFSAAAKNWA HFPHIHFGLM PSDQPVKKTS IRQQEGEDAM NMKDGFFAPA NVGVSPY

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

Annotation -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	AM468296	4e-44	AM468296.2 Vitis vinifera contig VV78X023826.39, whole genome shotgun sequence.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_006445302.1	1e-130	axial regulator YABBY 1
Refseq	XP_006490878.1	1e-130	axial regulator YABBY 1
Swissprot	O22152	1e-92	YAB1_ARATH; Axial regulator YABBY 1
TrEMBL	A0A067H4B3	1e-129	A0A067H4B3_CITSI; Uncharacterized protein
TrEMBL	A0A2H5NP36	1e-129	A0A2H5NP36_CITUN; Uncharacterized protein
TrEMBL	V4TY63	1e-129	V4TY63_9ROSI; Uncharacterized protein
STRING	XP_006490878.1	1e-130	(Citrus sinensis)
STRING	XP_006445302.1	1e-130	(Citrus clementina)

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	6e-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] 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]