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

orange1.1g027215m

Common Name

CISIN_1g027215mg

Organism

Citrus sinensis

Taxonomic ID

2711

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Sapindales; Rutaceae; Aurantioideae; Citrus

Family

YABBY

Protein Properties

Length: 227aa MW: 25103.8 Da PI: 8.1652

Description

YABBY family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
orange1.1g027215m	genome	ICGC	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	YABBY	230.1	5.7e-71	12	187	2	170
YABBY 2 dvfssseqvCyvqCnfCntila........vsvPstslfkvvtvrCGhCtsllsvnlakasqllaaeshldeslkee..lleelkveeenlk 83 d+ ssseq+Cyv+C+fC+t+la vsvP tslfk+vtvrCGhCt+llsvn++ a + hl++ + + llee ++ + orange1.1g027215m 12 DHLSSSEQLCYVHCTFCDTVLAvpyhfifsVSVPCTSLFKTVTVRCGHCTNLLSVNMRGLLLPAANQLHLGHPFFTPqnLLEEIRNVPA--N 101 7899*************9873333333369******************98888777777777777777655224444444443..3 PP YABBY 84 snvekeesastsvsseklsenedeevprvppvirPPekrqrvPsaynrfikeeiqrikasnPdishreafsaaaknWahfPkihfgl 170 + +++ ++ +++s++ + +++e+p+ p v+rPPekrqrvPsaynrfik+eiqrika+nPdishreafsaaaknWahfP+ihfgl orange1.1g027215m 102 MLMINPPNP-ADQSVMPVRVVDHQEIPKSPVVNRPPEKRQRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWAHFPHIHFGL 187 444443333.44455567889999***********************************************************97 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Pfam	PF04690	1.9E-66	16	187	IPR006780	YABBY protein
SuperFamily	SSF47095	6.55E-8	131	180	IPR009071	High mobility group box domain
Gene3D	G3DSA:1.10.30.10	2.3E-4	136	179	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: 227 aa Download sequence Send to blast
MSSSTPAALS PDHLSSSEQL CYVHCTFCDT VLAVPYHFIF SVSVPCTSLF KTVTVRCGHC 60 TNLLSVNMRG LLLPAANQLH LGHPFFTPQN LLEEIRNVPA NMLMINPPNP ADQSVMPVRV 120 VDHQEIPKSP VVNRPPEKRQ RVPSAYNRFI KDEIQRIKAG NPDISHREAF SAAAKNWAHF 180 PHIHFGLMPS DQPVKKTSVR QQQEGEDAMI KDGFFAPAAN VGVTPY*

Expression -- UniGene ? help Back to Top
UniGene ID	E-value	Expressed in
Csi.546	0.0	flower\| fruit

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

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	AB938212	1e-57	AB938212.1 Sarracenia purpurea FIL mRNA for filamentous flower, complete cds.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_006445302.1	1e-159	axial regulator YABBY 1
Refseq	XP_006490878.1	1e-159	axial regulator YABBY 1
Swissprot	O22152	1e-94	YAB1_ARATH; Axial regulator YABBY 1
TrEMBL	A0A067HD73	1e-168	A0A067HD73_CITSI; Uncharacterized protein
STRING	XP_006490878.1	1e-159	(Citrus sinensis)
STRING	XP_006445302.1	1e-159	(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	5e-97	YABBY family protein

Link Out ? help Back to Top
Phytozome	orange1.1g027215m

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]