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

Ciclev10000976m

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

ARF

Protein Properties

Length: 485aa MW: 53502.3 Da PI: 7.4054

Description

ARF family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Ciclev10000976m	genome	ICGC	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	B3	77.4	1.6e-24	141	242	1	99
EEEE-..-HHHHTT-EE--HHH.HTT.......---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE-SS CS B3 1 ffkvltpsdvlksgrlvlpkkfaeeh.......ggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfvvFkldgr 87 f+k+lt sd+++ g +++p++ ae++ + ++ s++l+ +d++g +W++++iyr++++r++lt+GW+ Fv+ ++L +gD v+F + Ciclev10000976m 141 FCKTLTASDTSTYGGFSVPRRAAEDCfppldymQ--QRPSQQLVAKDLHGVEWKFRHIYRGQPRRHLLTTGWSAFVNKKKLVSGDAVLFL--RG 230 99***************************743..345568********************************************..44 PP SEE..EEEEE-S CS B3 88 sefelvvkvfrk 99 +++el+++++r+ Ciclev10000976m 231 EDGELKIGIRRA 242 99*****996 PP
2	Auxin_resp	116.6	2.1e-38	267	348	1	82
Auxin_resp 1 aahaastksvFevvYnPrastseFvvkvekvekalkvkvsvGmRfkmafetedsserrlsGtvvgvsdldpvrWpnSkWrsL 82 +++a++ k +F++ YnPras+seFv++v+k++k+++++++ GmRfkm+ eted++err+sG++vgvsd+dpvrWp+SkWr+L Ciclev10000976m 267 VVDAIARKRAFSISYNPRASASEFVIPVNKFLKSIDHPFAEGMRFKMRSETEDAAERRCSGMIVGVSDTDPVRWPGSKWRCL 348 578999***************************************************************************9 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Gene3D	G3DSA:2.40.330.10	1.1E-39	132	244	IPR015300	DNA-binding pseudobarrel domain
SuperFamily	SSF101936	7.06E-42	134	257	IPR015300	DNA-binding pseudobarrel domain
CDD	cd10017	6.56E-23	139	241	No hit	No description
Pfam	PF02362	2.3E-22	141	242	IPR003340	B3 DNA binding domain
SMART	SM01019	5.2E-22	141	243	IPR003340	B3 DNA binding domain
PROSITE profile	PS50863	13.352	141	243	IPR003340	B3 DNA binding domain
Pfam	PF06507	3.7E-33	268	348	IPR010525	Auxin response factor

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0006355	Biological Process	regulation of transcription, DNA-templated
GO:0009725	Biological Process	response to hormone
GO:0005634	Cellular Component	nucleus
GO:0003677	Molecular Function	DNA binding

Sequence ? help Back to Top
Protein Sequence Length: 485 aa Download sequence Send to blast
MVGLIDLNKT KDDENPSSGS LASASASASG VSSELWHACA GPLIFLPKRG SVVVYFPQGH 60 LEHVSDFSAA ASTAYDLPPH LFCRVADVKL HADAASDEVY AQVSLVHDEL IEQKVRKGKI 120 KEDGDEESVE VAAKSSTTHM FCKTLTASDT STYGGFSVPR RAAEDCFPPL DYMQQRPSQQ 180 LVAKDLHGVE WKFRHIYRGQ PRRHLLTTGW SAFVNKKKLV SGDAVLFLRG EDGELKIGIR 240 RAAQVKNGAT FPSFCNQHSS TSSVTEVVDA IARKRAFSIS YNPRASASEF VIPVNKFLKS 300 IDHPFAEGMR FKMRSETEDA AERRCSGMIV GVSDTDPVRW PGSKWRCLLV RWDDVESNRH 360 NRVSPWEIEP SGSNILVTSG LRRTRIGLPL WRPEFPVPEG IGVTDFGESL RFQTVLQGQE 420 ISPKSPYGRA PTNNEAHDIG SLGISDGLQE VWTREHMYLS DAEATKMRVN DGVTVLEGRG 480 CARR*

Sequence ? help Back to Top

Protein Sequence Length: 485 aa Download sequence Send to blast

MVGLIDLNKT KDDENPSSGS LASASASASG VSSELWHACA GPLIFLPKRG SVVVYFPQGH  60
LEHVSDFSAA ASTAYDLPPH LFCRVADVKL HADAASDEVY AQVSLVHDEL IEQKVRKGKI  120
KEDGDEESVE VAAKSSTTHM FCKTLTASDT STYGGFSVPR RAAEDCFPPL DYMQQRPSQQ  180
LVAKDLHGVE WKFRHIYRGQ PRRHLLTTGW SAFVNKKKLV SGDAVLFLRG EDGELKIGIR  240
RAAQVKNGAT FPSFCNQHSS TSSVTEVVDA IARKRAFSIS YNPRASASEF VIPVNKFLKS  300
IDHPFAEGMR FKMRSETEDA AERRCSGMIV GVSDTDPVRW PGSKWRCLLV RWDDVESNRH  360
NRVSPWEIEP SGSNILVTSG LRRTRIGLPL WRPEFPVPEG IGVTDFGESL RFQTVLQGQE  420
ISPKSPYGRA PTNNEAHDIG SLGISDGLQE VWTREHMYLS DAEATKMRVN DGVTVLEGRG  480
CARR*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
4ldu_A	1e-107	31	373	51	392	Auxin response factor 5
Search in ModeBase

Expression -- Description ? help Back to Top
Source	Description
Uniprot	DEVELOPMENTAL STAGE: Detected during gynoecium development.
Uniprot	TISSUE SPECIFICITY: Expressed in the whole plant. {ECO:0000269\|PubMed:10476078, ECO:0000269\|PubMed:9409666}.

Functional Description ? help Back to Top
Source	Description
UniProt	Auxin response factors (ARFs) are transcriptional factors that bind specifically to the DNA sequence 5'-TGTCTC-3' found in the auxin-responsive promoter elements (AuxREs). Could act as transcriptional activator or repressor. Formation of heterodimers with Aux/IAA proteins may alter their ability to modulate early auxin response genes expression. Involved in the establishment or elaboration of tissue patterning during gynoecial development. {ECO:0000269\|PubMed:10952886, ECO:0000269\|PubMed:12036261}.

Regulation -- Description ? help Back to Top
Source	Description
UniProt	INDUCTION: Negatively regulated by AHL21/GIK. {ECO:0000269\|PubMed:19956801}.

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

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_024040951.1	0.0	auxin response factor 3 isoform X3
Swissprot	O23661	0.0	ARFC_ARATH; Auxin response factor 3
TrEMBL	A0A067F6V9	0.0	A0A067F6V9_CITSI; Auxin response factor
STRING	XP_006471168.1	0.0	(Citrus sinensis)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM4924	28	49

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT2G33860.1	0.0	ARF family protein

Link Out ? help Back to Top
Phytozome	Ciclev10000976m

Publications ? help Back to Top
Ozerova LV,Krasnikova MS,Troitsky AV,Solovyev AG,Morozov SY TAS3 Genes for small ta-siARF RNAs in plants belonging to subtribe Senecioninae: occurrence of prematurely terminated RNA precursors. Mol. Gen. Mikrobiol. Virusol., 2013. [PMID:24003511] Thoma R,Chandler JW Polarity in the early floral meristem of Arabidopsis. Plant Signal Behav, 2015. 10(4): p. e992733 [PMID:25806573] Lora J,Hormaza JI,Herrero M Transition from two to one integument in Prunus species: expression pattern of INNER NO OUTER (INO), ABERRANT TESTA SHAPE (ATS) and ETTIN (ETT). New Phytol., 2015. 208(2): p. 584-95 [PMID:25991552] Machida C,Nakagawa A,Kojima S,Takahashi H,Machida Y The complex of ASYMMETRIC LEAVES (AS) proteins plays a central role in antagonistic interactions of genes for leaf polarity specification in Arabidopsis. Wiley Interdiscip Rev Dev Biol, 2015 Nov-Dec. 4(6): p. 655-71 [PMID:26108442] Cabrera J, et al. Differentially expressed small RNAs in Arabidopsis galls formed by Meloidogyne javanica: a functional role for miR390 and its TAS3-derived tasiRNAs. New Phytol., 2016. 209(4): p. 1625-40 [PMID:26542733] Husbands AY,Benkovics AH,Nogueira FT,Lodha M,Timmermans MC The ASYMMETRIC LEAVES Complex Employs Multiple Modes of Regulation to Affect Adaxial-Abaxial Patterning and Leaf Complexity. Plant Cell, 2015. 27(12): p. 3321-35 [PMID:26589551] Yamaguchi N,Wu MF,Winter CM,Wagner D LEAFY and Polar Auxin Transport Coordinately Regulate Arabidopsis Flower Development. Plants (Basel), 2014. 3(2): p. 251-65 [PMID:27135503] Matsumura Y, et al. A genetic link between epigenetic repressor AS1-AS2 and a putative small subunit processome in leaf polarity establishment of Arabidopsis. Biol Open, 2016. 5(7): p. 942-54 [PMID:27334696] Simonini S, et al. A noncanonical auxin-sensing mechanism is required for organ morphogenesis in Arabidopsis. Genes Dev., 2016. 30(20): p. 2286-2296 [PMID:27898393] Pfannebecker KC,Lange M,Rupp O,Becker A An Evolutionary Framework for Carpel Developmental Control Genes. Mol. Biol. Evol., 2017. 34(2): p. 330-348 [PMID:28049761] Wójcikowska B,Gaj MD Expression profiling of AUXIN RESPONSE FACTOR genes during somatic embryogenesis induction in Arabidopsis. Plant Cell Rep., 2017. 36(6): p. 843-858 [PMID:28255787] Su Z, et al. The THO Complex Non-Cell-Autonomously Represses Female Germline Specification through the TAS3-ARF3 Module. Curr. Biol., 2017. 27(11): p. 1597-1609.e2 [PMID:28552357] Simonini S,Bencivenga S,Trick M,Østergaard L Auxin-Induced Modulation of ETTIN Activity Orchestrates Gene Expression in Arabidopsis. Plant Cell, 2017. 29(8): p. 1864-1882 [PMID:28804059] Guan C, et al. Spatial Auxin Signaling Controls Leaf Flattening in Arabidopsis. Curr. Biol., 2017. 27(19): p. 2940-2950.e4 [PMID:28943086] Simonini S, et al. Corrigendum: A noncanonical auxin-sensing mechanism is required for organ morphogenesis in Arabidopsis. Genes Dev., 2017. 31(17): p. 1821 [PMID:28982764] Zhang K, et al. AUXIN RESPONSE FACTOR3 Regulates Floral Meristem Determinacy by Repressing Cytokinin Biosynthesis and Signaling. Plant Cell, 2018. 30(2): p. 324-346 [PMID:29371438] Vial-Pradel S, et al. Arabidopsis Zinc-Finger-Like Protein ASYMMETRIC LEAVES2 (AS2) and Two Nucleolar Proteins Maintain Gene Body DNA Methylation in the Leaf Polarity Gene ETTIN (ARF3). Plant Cell Physiol., 2018. 59(7): p. 1385-1397 [PMID:29415182] Simonini S,Stephenson P,Østergaard L A molecular framework controlling style morphology in Brassicaceae. Development, 2018. [PMID:29440299] Andres-Robin A, et al. Evidence for the Regulation of Gynoecium Morphogenesis by ETTIN via Cell Wall Dynamics. Plant Physiol., 2018. 178(3): p. 1222-1232 [PMID:30237208] Hablak SG Features inheritance of root system Arabidopsis thaliana (L.) Heynh. the interaction of genes CTR1 AND ALF3, NPH4 and IAR2. Tsitol. Genet., 2019. [PMID:30484609]