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

Ciclev10019044m

Common Name

CICLE_v10019039mg

Organism

Citrus clementina

Taxonomic ID

85681

Taxonomic Lineage

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

Family

Protein Properties

Length: 726aa MW: 80532.1 Da PI: 6.62

Description

B3 family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Ciclev10019044m	genome	ICGC	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	B3	66.3	4.5e-21	582	678	2	95
EEE-..-HHHHTT-EE--HHH.HTT..---..--SEEEEEE.TTS-EEEEEE....EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE-SS.SE CS B3 2 fkvltpsdvlksgrlvlpkkfaeeh..ggkkeesktltled.esgrsWevkliy..rkksgryvltkGWkeFvkangLkegDfvvFkldgr.se 89 +kvl++sdv+++gr+vlpkk ae+h +++ + ++ + +ed ++r+W++++++ ++ks++y+l+ ++ +FvkangL+egDf+v++ ++ ++ Ciclev10019044m 582 QKVLKQSDVGNLGRIVLPKKEAETHlpELEARDGISIAMEDiGTSRVWNMRYRFwpNNKSRMYLLE-NTGDFVKANGLQEGDFIVIY--SDvKC 672 79***********************999999****7778***99777777777777.******************..55599 PP E..EEE CS B3 90 felvvk 95 ++++++ Ciclev10019044m 673 GKYLIR 678 988776 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Gene3D	G3DSA:2.40.330.10	2.0E-28	576	688	IPR015300	DNA-binding pseudobarrel domain
CDD	cd10015	1.02E-37	579	680	No hit	No description
SuperFamily	SSF101936	5.49E-23	580	674	IPR015300	DNA-binding pseudobarrel domain
SMART	SM01019	2.3E-20	581	683	IPR003340	B3 DNA binding domain
PROSITE profile	PS50863	10.898	581	683	IPR003340	B3 DNA binding domain
Pfam	PF02362	4.3E-17	582	677	IPR003340	B3 DNA binding domain

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0009657	Biological Process	plastid organization
GO:0009733	Biological Process	response to auxin
GO:0009737	Biological Process	response to abscisic acid
GO:0009793	Biological Process	embryo development ending in seed dormancy
GO:0031930	Biological Process	mitochondria-nucleus signaling pathway
GO:0045893	Biological Process	positive regulation of transcription, DNA-templated
GO:0005634	Cellular Component	nucleus
GO:0005829	Cellular Component	cytosol
GO:0001076	Molecular Function	transcription factor activity, RNA polymerase II transcription factor binding
GO:0003677	Molecular Function	DNA binding
GO:0003700	Molecular Function	transcription factor activity, sequence-specific DNA binding

Sequence ? help Back to Top
Protein Sequence Length: 726 aa Download sequence Send to blast
MKNLQLYGED LHVRSKIEAN NHTGFQAMTE EQVTGAGAER EIYMQDDLLD VDDASIFYAD 60 FPPLPDFPCM SSSSSSSSTP AAVKAITSSA SSSSASSSSS AASWAVLRSD AEEDVDKKNH 120 QDQSGDAATQ PALSSTASMD ISQATDTGIN GVGVDCMDVM ENFVFMDLLD NNDLFDPSSI 180 FNQDDSQPFE GYQQQQQQNQ PQHEHRQQER DQELMMQSNN GDNSNEDGGA SDDLAMVFLE 240 WLKSNKETVS AEDLRNVKIK KSTIECAAKR LGGGKEAMKQ LLKLILEWVQ TNHLQKRRMR 300 EALLPASNNN NNLPHQQHFQ DTFQNPNPNP NPNHIPNPNL NCNPIPPEPN PCFAQSSWIG 360 QPSFIHDPAT MVTGFPTPAV GYMGDSFANG MSNINGHGYA APPSEYHMLE TTRSWPNSQF 420 GLASNYNSFS DNNLHPAPLH PQAFTGYGNQ YPYPYLPGHG EQRLMRMGSS ATKEARKKRM 480 ARQRRLSTHP RHQHHHNNQQ NQLQGQNADQ HARFGSDNCN PAAQANSGNW VFWPASAGGP 540 AAVSPLSPVD RQPMQPQNYQ RQPASDRRQG WKPEKNLRFL LQKVLKQSDV GNLGRIVLPK 600 KEAETHLPEL EARDGISIAM EDIGTSRVWN MRYRFWPNNK SRMYLLENTG DFVKANGLQE 660 GDFIVIYSDV KCGKYLIRGV KVRQPGPKSE TKRTGKSQRN QHANPPSAAM GNGSSSSLQV 720 PQTVK*

Sequence ? help Back to Top

Protein Sequence Length: 726 aa Download sequence Send to blast

MKNLQLYGED LHVRSKIEAN NHTGFQAMTE EQVTGAGAER EIYMQDDLLD VDDASIFYAD  60
FPPLPDFPCM SSSSSSSSTP AAVKAITSSA SSSSASSSSS AASWAVLRSD AEEDVDKKNH  120
QDQSGDAATQ PALSSTASMD ISQATDTGIN GVGVDCMDVM ENFVFMDLLD NNDLFDPSSI  180
FNQDDSQPFE GYQQQQQQNQ PQHEHRQQER DQELMMQSNN GDNSNEDGGA SDDLAMVFLE  240
WLKSNKETVS AEDLRNVKIK KSTIECAAKR LGGGKEAMKQ LLKLILEWVQ TNHLQKRRMR  300
EALLPASNNN NNLPHQQHFQ DTFQNPNPNP NPNHIPNPNL NCNPIPPEPN PCFAQSSWIG  360
QPSFIHDPAT MVTGFPTPAV GYMGDSFANG MSNINGHGYA APPSEYHMLE TTRSWPNSQF  420
GLASNYNSFS DNNLHPAPLH PQAFTGYGNQ YPYPYLPGHG EQRLMRMGSS ATKEARKKRM  480
ARQRRLSTHP RHQHHHNNQQ NQLQGQNADQ HARFGSDNCN PAAQANSGNW VFWPASAGGP  540
AAVSPLSPVD RQPMQPQNYQ RQPASDRRQG WKPEKNLRFL LQKVLKQSDV GNLGRIVLPK  600
KEAETHLPEL EARDGISIAM EDIGTSRVWN MRYRFWPNNK SRMYLLENTG DFVKANGLQE  660
GDFIVIYSDV KCGKYLIRGV KVRQPGPKSE TKRTGKSQRN QHANPPSAAM GNGSSSSLQV  720
PQTVK*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
6j9b_A	4e-37	577	684	1	108	B3 domain-containing transcription factor FUS3
6j9b_D	4e-37	577	684	1	108	B3 domain-containing transcription factor FUS3
Search in ModeBase

Expression -- Description ? help Back to Top
Source	Description
Uniprot	DEVELOPMENTAL STAGE: Expressed in the embryos, endosperm, and outer teguments of the seed throughout seed development. {ECO:0000269\|PubMed:12657652}.
Uniprot	TISSUE SPECIFICITY: Isoform 2 accumulates only at the end of seed maturation. {ECO:0000269\|PubMed:20525852}.

Functional Description ? help Back to Top
Source	Description
UniProt	Participates in abscisic acid-regulated gene expression during seed development. Regulates the transcription of SGR1 and SGR2 that are involved in leaf and embryo degreening. {ECO:0000269\|PubMed:19531597, ECO:0000269\|PubMed:24043799}.

Binding Motif ? help Back to Top
Motif ID	Method	Source	Motif file
MP00083	PBM	Transfer from AT3G24650	Download

Regulation -- Description ? help Back to Top
Source	Description
UniProt	INDUCTION: Repressed by silencing mediated by polycomb group (PcG) protein complex containing EMF1 and EMF2. {ECO:0000269\|PubMed:19783648}.

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

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_006443662.1	0.0	B3 domain-containing transcription factor ABI3
Refseq	XP_006480255.1	0.0	B3 domain-containing transcription factor ABI3 isoform X2
Swissprot	Q01593	0.0	ABI3_ARATH; B3 domain-containing transcription factor ABI3
TrEMBL	V4TTV1	0.0	V4TTV1_9ROSI; Uncharacterized protein
STRING	XP_006480255.1	0.0	(Citrus sinensis)

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT3G24650.1	1e-155	B3 family protein

Link Out ? help Back to Top
Phytozome	Ciclev10019044m
Entrez Gene	18046559

Publications ? help Back to Top
Zeng Y,Kermode AR A gymnosperm ABI3 gene functions in a severe abscisic acid-insensitive mutant of Arabidopsis (abi3-6) to restore the wild-type phenotype and demonstrates a strong synergistic effect with sugar in the inhibition of post-germinative growth. Plant Mol. Biol., 2004. 56(5): p. 731-46 [PMID:15803411] Seifert M,Keilwagen J,Strickert M,Grosse I Utilizing gene pair orientations for HMM-based analysis of promoter array ChIP-chip data. Bioinformatics, 2009. 25(16): p. 2118-25 [PMID:19401402] Yang C, et al. VAL- and AtBMI1-mediated H2Aub initiate the switch from embryonic to postgerminative growth in Arabidopsis. Curr. Biol., 2013. 23(14): p. 1324-9 [PMID:23810531] Duarte GT, et al. Involvement of microRNA-related regulatory pathways in the glucose-mediated control of Arabidopsis early seedling development. J. Exp. Bot., 2013. 64(14): p. 4301-12 [PMID:23997203] Jia H,McCarty DR,Suzuki M Distinct roles of LAFL network genes in promoting the embryonic seedling fate in the absence of VAL repression. Plant Physiol., 2013. 163(3): p. 1293-305 [PMID:24043445] Bu Q, et al. Regulation of drought tolerance by the F-box protein MAX2 in Arabidopsis. Plant Physiol., 2014. 164(1): p. 424-39 [PMID:24198318] Gao DY, et al. Functional analyses of an E3 ligase gene AIP2 from wheat in Arabidopsis revealed its roles in seed germination and pre-harvest sprouting. J Integr Plant Biol, 2014. 56(5): p. 480-91 [PMID:24279988] Kim HU, et al. Ectopic overexpression of castor bean LEAFY COTYLEDON2 (LEC2) in Arabidopsis triggers the expression of genes that encode regulators of seed maturation and oil body proteins in vegetative tissues. FEBS Open Bio, 2013. 4: p. 25-32 [PMID:24363987] Molitor AM,Bu Z,Yu Y,Shen WH Arabidopsis AL PHD-PRC1 complexes promote seed germination through H3K4me3-to-H3K27me3 chromatin state switch in repression of seed developmental genes. PLoS Genet., 2014. 10(1): p. e1004091 [PMID:24465219] Suzuki M,Wu S,Li Q,McCarty DR Distinct functions of COAR and B3 domains of maize VP1 in induction of ectopic gene expression and plant developmental phenotypes in Arabidopsis. Plant Mol. Biol., 2014. 85(1-2): p. 179-91 [PMID:24473899] Xie M, et al. AtWNK9 is regulated by ABA and dehydration and is involved in drought tolerance in Arabidopsis. Plant Physiol. Biochem., 2014. 77: p. 73-83 [PMID:24561249] Chen C, et al. ASCORBATE PEROXIDASE6 protects Arabidopsis desiccating and germinating seeds from stress and mediates cross talk between reactive oxygen species, abscisic acid, and auxin. Plant Physiol., 2014. 166(1): p. 370-83 [PMID:25049361] Rikiishi K,Maekawa M Seed maturation regulators are related to the control of seed dormancy in wheat (Triticum aestivum L.). PLoS ONE, 2014. 9(9): p. e107618 [PMID:25211528] Yamamoto A, et al. Cell-by-cell developmental transition from embryo to post-germination phase revealed by heterochronic gene expression and ER-body formation in Arabidopsis leafy cotyledon mutants. Plant Cell Physiol., 2014. 55(12): p. 2112-25 [PMID:25282558] Bello B, et al. Cloning of Gossypium hirsutum sucrose non-fermenting 1-related protein kinase 2 gene (GhSnRK2) and its overexpression in transgenic Arabidopsis escalates drought and low temperature tolerance. PLoS ONE, 2014. 9(11): p. e112269 [PMID:25393623] Chen C,Twito S,Miller G New cross talk between ROS, ABA and auxin controlling seed maturation and germination unraveled in APX6 deficient Arabidopsis seeds. Plant Signal Behav, 2014. 9(12): p. e976489 [PMID:25482750] Shen Y,Devic M,Lepiniec L,Zhou DX Chromodomain, Helicase and DNA-binding CHD1 protein, CHR5, are involved in establishing active chromatin state of seed maturation genes. Plant Biotechnol. J., 2015. 13(6): p. 811-20 [PMID:25581843] Zhao M,Yang S,Liu X,Wu K Arabidopsis histone demethylases LDL1 and LDL2 control primary seed dormancy by regulating DELAY OF GERMINATION 1 and ABA signaling-related genes. Front Plant Sci, 2015. 6: p. 159 [PMID:25852712] Mukhopadhyay P,Tyagi AK OsTCP19 influences developmental and abiotic stress signaling by modulating ABI4-mediated pathways. Sci Rep, 2015. 5: p. 9998 [PMID:25925167] Ma X, et al. CYCLIN-DEPENDENT KINASE G2 regulates salinity stress response and salt mediated flowering in Arabidopsis thaliana. Plant Mol. Biol., 2015. 88(3): p. 287-99 [PMID:25948280] Zhang GZ, et al. Ectopic expression of UGT75D1, a glycosyltransferase preferring indole-3-butyric acid, modulates cotyledon development and stress tolerance in seed germination of Arabidopsis thaliana. Plant Mol. Biol., 2016. 90(1-2): p. 77-93 [PMID:26496910] Kim H, et al. ABA-HYPERSENSITIVE BTB/POZ PROTEIN 1 functions as a negative regulator in ABA-mediated inhibition of germination in Arabidopsis. Plant Mol. Biol., 2016. 90(3): p. 303-15 [PMID:26667153] Dekkers BJ, et al. The Arabidopsis DELAY OF GERMINATION 1 gene affects ABSCISIC ACID INSENSITIVE 5 (ABI5) expression and genetically interacts with ABI3 during Arabidopsis seed development. Plant J., 2016. 85(4): p. 451-65 [PMID:26729600] Huang Y,Feng CZ,Ye Q,Wu WH,Chen YF Arabidopsis WRKY6 Transcription Factor Acts as a Positive Regulator of Abscisic Acid Signaling during Seed Germination and Early Seedling Development. PLoS Genet., 2016. 12(2): p. e1005833 [PMID:26829043] Abraham Z, et al. A Developmental Switch of Gene Expression in the Barley Seed Mediated by HvVP1 (Viviparous-1) and HvGAMYB Interactions. Plant Physiol., 2016. 170(4): p. 2146-58 [PMID:26858366] Salas-Muñoz S,Rodríguez-Hernández AA,Ortega-Amaro MA,Salazar-Badillo FB,Jiménez-Bremont JF Arabidopsis AtDjA3 Null Mutant Shows Increased Sensitivity to Abscisic Acid, Salt, and Osmotic Stress in Germination and Post-germination Stages. Front Plant Sci, 2016. 7: p. 220 [PMID:26941772] Kim SI,Kwak JS,Song JT,Seo HS The E3 SUMO ligase AtSIZ1 functions in seed germination in Arabidopsis. Physiol Plant, 2016. 158(3): p. 256-271 [PMID:27130140] Baud S, et al. Deciphering the Molecular Mechanisms Underpinning the Transcriptional Control of Gene Expression by Master Transcriptional Regulators in Arabidopsis Seed. Plant Physiol., 2016. 171(2): p. 1099-112 [PMID:27208266] Bedi S,Sengupta S,Ray A,Nag Chaudhuri R ABI3 mediates dehydration stress recovery response in Arabidopsis thaliana by regulating expression of downstream genes. Plant Sci., 2016. 250: p. 125-140 [PMID:27457990] Fatihi A, et al. Deciphering and modifying LAFL transcriptional regulatory network in seed for improving yield and quality of storage compounds. Plant Sci., 2016. 250: p. 198-204 [PMID:27457996] Zhu Z, et al. Overexpression of AtEDT1/HDG11 in Chinese Kale (Brassica oleracea var. alboglabra) Enhances Drought and Osmotic Stress Tolerance. Front Plant Sci, 2016. 7: p. 1285 [PMID:27625663] Feng J,Chen D,Berr A,Shen WH ZRF1 Chromatin Regulators Have Polycomb Silencing and Independent Roles in Development. Plant Physiol., 2016. 172(3): p. 1746-1759 [PMID:27630184] Wu JR, et al. The Arabidopsis heat-intolerant 5 (hit5)/enhanced response to aba 1 (era1) mutant reveals the crucial role of protein farnesylation in plant responses to heat stress. New Phytol., 2017. 213(3): p. 1181-1193 [PMID:27673599] Gu L, et al. An RRM-containing mei2-like MCT1 plays a negative role in the seed germination and seedling growth of Arabidopsis thaliana in the presence of ABA. Plant Physiol. Biochem., 2016. 109: p. 273-279 [PMID:27771580] Chen YS, et al. Two MYB-related transcription factors play opposite roles in sugar signaling in Arabidopsis. Plant Mol. Biol., 2017. 93(3): p. 299-311 [PMID:27866313] Xu J, et al. A Novel RNA-Binding Protein Involves ABA Signaling by Post-transcriptionally Repressing ABI2. Front Plant Sci, 2017. 8: p. 24 [PMID:28174577] Restovic F,Espinoza-Corral R,Gómez I,Vicente-Carbajosa J,Jordana X An active Mitochondrial Complex II Present in Mature Seeds Contains an Embryo-Specific Iron-Sulfur Subunit Regulated by ABA and bZIP53 and Is Involved in Germination and Seedling Establishment. Front Plant Sci, 2017. 8: p. 277 [PMID:28293251] Le Hir R, et al. AtbHLH68 transcription factor contributes to the regulation of ABA homeostasis and drought stress tolerance in Arabidopsis thaliana. Physiol Plant, 2017. 160(3): p. 312-327 [PMID:28369972] Han JD, et al. Evolutionary Analysis of the LAFL Genes Involved in the Land Plant Seed Maturation Program. Front Plant Sci, 2017. 8: p. 439 [PMID:28421087] Li K,Yang F,Miao Y,Song CP Abscisic acid signaling is involved in regulating the mitogen-activated protein kinase cascade module, AIK1-MKK5-MPK6. Plant Signal Behav, 2017. 12(5): p. e1321188 [PMID:28494202] Bi B,Tang J,Han S,Guo J,Miao Y Sinapic acid or its derivatives interfere with abscisic acid homeostasis during Arabidopsis thaliana seed germination. BMC Plant Biol., 2017. 17(1): p. 99 [PMID:28587634] Xiao X,Cheng X,Yin K,Li H,Qiu JL Abscisic acid negatively regulates post-penetration resistance of Arabidopsis to the biotrophic powdery mildew fungus. Sci China Life Sci, 2017. 60(8): p. 891-901 [PMID:28702742] Horstman A, et al. The BABY BOOM Transcription Factor Activates the LEC1-ABI3-FUS3-LEC2 Network to Induce Somatic Embryogenesis. Plant Physiol., 2017. 175(2): p. 848-857 [PMID:28830937] Hanano A,Almousally I,Shaban M,Murphy DJ Arabidopsis plants exposed to dioxin result in a WRINKLED seed phenotype due to 20S proteasomal degradation of WRI1. J. Exp. Bot., 2018. 69(7): p. 1781-1794 [PMID:29394403] Cheng Y,Zhang X,Sun T,Tian Q,Zhang WH Glutamate Receptor Homolog3.4 is Involved in Regulation of Seed Germination Under Salt Stress in Arabidopsis. Plant Cell Physiol., 2018. 59(5): p. 978-988 [PMID:29432559] Chen N,Veerappan V,Abdelmageed H,Kang M,Allen RD HSI2/VAL1 Silences AGL15 to Regulate the Developmental Transition from Seed Maturation to Vegetative Growth in Arabidopsis. Plant Cell, 2018. 30(3): p. 600-619 [PMID:29475938]