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

GSVIVT01009865001

Common Name

VIT_18s0001g13930

Organism

Vitis vinifera

Taxonomic ID

29760

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; rosids incertae sedis; Vitales; Vitaceae; Vitis

Family

ARF

Protein Properties

Length: 908aa MW: 100064 Da PI: 4.988

Description

ARF family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
GSVIVT01009865001	genome	Genoscope	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	B3	70.9	1.7e-22	148	249	1	99
EEEE-..-HHHHTT-EE--HHH.HTT......---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE-S CS B3 1 ffkvltpsdvlksgrlvlpkkfaeeh......ggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfvvFkldg 86 f+k+lt sd++++g +++p++ ae+ ++++++ ++l+++d++ ++++++iyr++++r++lt+GW+ Fv+a++L++gD v+F + GSVIVT01009865001 148 FCKTLTASDTSTHGGFSVPRRAAEKLfppldySMQPPT-QELIVRDLHDITYTFRHIYRGQPKRHLLTTGWSVFVSAKRLRAGDAVLFI--R 236 99*******************999*9555554.49**********************************************..4 PP SSEE..EEEEE-S CS B3 87 rsefelvvkvfrk 99 +++ +l+++v+r+ GSVIVT01009865001 237 DEKSQLLLGVRRA 249 5677789999997 PP
2	Auxin_resp	104.9	9.4e-35	274	362	1	83
Auxin_resp 1 aahaastksvFevvYnPr.....astseFvvkvekvekalk.vkvsvGmRfkmafetedsserrlsGtvvgvsdldpvrWpnSkWrsLk 83 aahaa+++s+F+++YnPr a++seFv++++k++k+++ +++svGmRf m+fete+s +rr++Gt+vg+sdldp++Wp+SkWr+L+ GSVIVT01009865001 274 AAHAAANRSPFTIFYNPRhafflACPSEFVIPLAKYRKSVYgTQISVGMRFGMMFETEESGKRRYMGTIVGISDLDPLSWPGSKWRNLQ 362 79**************55555579***********9*******************************************97 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SuperFamily	SSF101936	1.57E-46	135	277	IPR015300	DNA-binding pseudobarrel domain
Gene3D	G3DSA:2.40.330.10	1.2E-40	141	262	IPR015300	DNA-binding pseudobarrel domain
CDD	cd10017	2.11E-21	147	248	No hit	No description
Pfam	PF02362	6.3E-20	148	249	IPR003340	B3 DNA binding domain
PROSITE profile	PS50863	11.603	148	250	IPR003340	B3 DNA binding domain
SMART	SM01019	2.7E-23	148	250	IPR003340	B3 DNA binding domain
Pfam	PF06507	9.4E-30	274	362	IPR010525	Auxin response factor
Pfam	PF02309	2.6E-10	796	884	IPR033389	AUX/IAA domain
PROSITE profile	PS51745	24.937	797	881	IPR000270	PB1 domain
SuperFamily	SSF54277	1.9E-8	813	876	No hit	No description

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0006355	Biological Process	regulation of transcription, DNA-templated
GO:0009734	Biological Process	auxin-activated signaling pathway
GO:0009908	Biological Process	flower development
GO:0009942	Biological Process	longitudinal axis specification
GO:0010305	Biological Process	leaf vascular tissue pattern formation
GO:0048364	Biological Process	root development
GO:0048507	Biological Process	meristem development
GO:0005634	Cellular Component	nucleus
GO:0016020	Cellular Component	membrane
GO:0042802	Molecular Function	identical protein binding
GO:0044212	Molecular Function	transcription regulatory region DNA binding

Sequence ? help Back to Top
Protein Sequence Length: 908 aa Download sequence Send to blast
MMSSVEENIK AGGLVSGTQT TLIEEMKLLK EMQDQSGPRK AINSELWHAC AGPLVSLPQV 60 GSLVYYFPQG HSEQVAVSTK RTATSQIPNY PNLPSQLMCQ VHNVTLHADK DTDEIYAQMS 120 LQPVNSEKDI FPIPDFGLKP SKHPSEFFCK TLTASDTSTH GGFSVPRRAA EKLFPPLDYS 180 MQPPTQELIV RDLHDITYTF RHIYRGQPKR HLLTTGWSVF VSAKRLRAGD AVLFIRDEKS 240 QLLLGVRRAN RQQTSLPSSV LSADSMHIGV LAAAAHAAAN RSPFTIFYNP RHAFFLACPS 300 EFVIPLAKYR KSVYGTQISV GMRFGMMFET EESGKRRYMG TIVGISDLDP LSWPGSKWRN 360 LQVEWDESGC GDKQSRVSSW EIETPESLFI FPSLTSSLKR PMHAGFLGGE AEWGSLMKRP 420 FIRVLENGNG VLPYPTIPNI CSEQLMKMLL KPQLVNPPGT LTPAFQDSGV KAASLQEARI 480 IEGMIKQQPP PIPSENKLLQ NQNHPQPCLD QPDATNSDLP SQPNLVGQVQ PLNKLENQTP 540 SGNAEKSNIE PVHTADQLSQ LTSTGQGDEE KLAKSPKNPQ NLTNSFMQPH LESSIFHAQQ 600 ISAPPFDSNP NALSPYIDTD EWILYPSANQ SFGGVLRSPG PLSTFSLQDP SVVFPEAINP 660 TLPSMGQEIW DHQLNNAKYL SDDSNNQSGI YSCLNFDVSN GGSTVVDPSV SSTILDEFCT 720 FKDADFPDPS DCLVGNFSTS QDVQSQITSV SLADSQAFSR PDFLDNSGGT SSSNVDFDES 780 SLLQNSSWQQ VAPPPMRTYT KVQKMGSVGR SIDVASFKNY EELCSAIECM FGLEGLLNDQ 840 KGSGWKLVYV DYENDVLLVG DDPWKEFVGC VRCIRILSPS EVQQMSEEGM QLLNSTAIEG 900 INDSIRR*

Sequence ? help Back to Top

Protein Sequence Length: 908 aa Download sequence Send to blast

MMSSVEENIK AGGLVSGTQT TLIEEMKLLK EMQDQSGPRK AINSELWHAC AGPLVSLPQV  60
GSLVYYFPQG HSEQVAVSTK RTATSQIPNY PNLPSQLMCQ VHNVTLHADK DTDEIYAQMS  120
LQPVNSEKDI FPIPDFGLKP SKHPSEFFCK TLTASDTSTH GGFSVPRRAA EKLFPPLDYS  180
MQPPTQELIV RDLHDITYTF RHIYRGQPKR HLLTTGWSVF VSAKRLRAGD AVLFIRDEKS  240
QLLLGVRRAN RQQTSLPSSV LSADSMHIGV LAAAAHAAAN RSPFTIFYNP RHAFFLACPS  300
EFVIPLAKYR KSVYGTQISV GMRFGMMFET EESGKRRYMG TIVGISDLDP LSWPGSKWRN  360
LQVEWDESGC GDKQSRVSSW EIETPESLFI FPSLTSSLKR PMHAGFLGGE AEWGSLMKRP  420
FIRVLENGNG VLPYPTIPNI CSEQLMKMLL KPQLVNPPGT LTPAFQDSGV KAASLQEARI  480
IEGMIKQQPP PIPSENKLLQ NQNHPQPCLD QPDATNSDLP SQPNLVGQVQ PLNKLENQTP  540
SGNAEKSNIE PVHTADQLSQ LTSTGQGDEE KLAKSPKNPQ NLTNSFMQPH LESSIFHAQQ  600
ISAPPFDSNP NALSPYIDTD EWILYPSANQ SFGGVLRSPG PLSTFSLQDP SVVFPEAINP  660
TLPSMGQEIW DHQLNNAKYL SDDSNNQSGI YSCLNFDVSN GGSTVVDPSV SSTILDEFCT  720
FKDADFPDPS DCLVGNFSTS QDVQSQITSV SLADSQAFSR PDFLDNSGGT SSSNVDFDES  780
SLLQNSSWQQ VAPPPMRTYT KVQKMGSVGR SIDVASFKNY EELCSAIECM FGLEGLLNDQ  840
KGSGWKLVYV DYENDVLLVG DDPWKEFVGC VRCIRILSPS EVQQMSEEGM QLLNSTAIEG  900
INDSIRR*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
4ldu_A	0.0	2	387	5	392	Auxin response factor 5
Search in ModeBase

Expression -- UniGene ? help Back to Top
UniGene ID	E-value	Expressed in
Vvi.1321	0.0	fruit\| leaf

Expression -- Description ? help Back to Top
Source	Description
Uniprot	DEVELOPMENTAL STAGE: In early embryo and during organ development.
Uniprot	TISSUE SPECIFICITY: Expressed in the whole plant with a lower expression in leaves. Detected in embryo axis, provascular tissues, procambium and some differentiated vascular regions of mature organs. {ECO:0000269\|PubMed:10476078}.

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). Seems to act as transcriptional activator. Formation of heterodimers with Aux/IAA proteins may alter their ability to modulate early auxin response genes expression. Mediates embryo axis formation and vascular tissues differentiation. Functionally redundant with ARF7. May be necessary to counteract AMP1 activity. {ECO:0000269\|PubMed:12036261, ECO:0000269\|PubMed:14973283, ECO:0000269\|PubMed:17553903}.

Binding Motif ? help Back to Top
Motif ID	Method	Source	Motif file
MP00153	DAP	Transfer from AT1G19850	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	AM444797	0.0	AM444797.1 Vitis vinifera, whole genome shotgun sequence, contig VV78X074140.10, clone ENTAV 115.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_003634382.2	0.0	PREDICTED: auxin response factor 5
Refseq	XP_010664787.1	0.0	PREDICTED: auxin response factor 5
Swissprot	P93024	0.0	ARFE_ARATH; Auxin response factor 5
TrEMBL	F6H071	0.0	F6H071_VITVI; Auxin response factor
STRING	VIT_18s0001g13930.t01	0.0	(Vitis vinifera)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Representative plant	OGRP8260	12	16

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT1G19850.1	0.0	ARF family protein

Link Out ? help Back to Top
Phytozome	GSVIVT01009865001

Publications ? help Back to Top
Chen MK,Wilson RL,Palme K,Ditengou FA,Shpak ED ERECTA family genes regulate auxin transport in the shoot apical meristem and forming leaf primordia. Plant Physiol., 2013. 162(4): p. 1978-91 [PMID:23821653] Huang JB, et al. ROP3 GTPase contributes to polar auxin transport and auxin responses and is important for embryogenesis and seedling growth in Arabidopsis. Plant Cell, 2014. 26(9): p. 3501-18 [PMID:25217509] Qi J, et al. Auxin depletion from leaf primordia contributes to organ patterning. Proc. Natl. Acad. Sci. U.S.A., 2014. 111(52): p. 18769-74 [PMID:25512543] Crawford BC, et al. Plant development. Genetic control of distal stem cell fate within root and embryonic meristems. Science, 2015. 347(6222): p. 655-9 [PMID:25612610] Zhang Y, et al. Regulation of oncogene expression in T-DNA-transformed host plant cells. PLoS Pathog., 2015. 11(1): p. e1004620 [PMID:25615824] Robert HS, et al. Plant embryogenesis requires AUX/LAX-mediated auxin influx. Development, 2015. 142(4): p. 702-11 [PMID:25617434] Krogan NT,Berleth T The identification and characterization of specific ARF-Aux/IAA regulatory modules in plant growth and development. Plant Signal Behav, 2015. 10(4): p. e992748 [PMID:25830553] Ckurshumova W,Berleth T Overcoming recalcitrance - Auxin response factor functions in plant regeneration. Plant Signal Behav, 2015. 10(7): p. e993293 [PMID:26098229] Wendrich JR, et al. A set of domain-specific markers in the Arabidopsis embryo. Plant Reprod, 2015. 28(3-4): p. 153-60 [PMID:26216537] Wu MF, et al. Auxin-regulated chromatin switch directs acquisition of flower primordium founder fate. Elife, 2015. 4: p. e09269 [PMID:26460543] Yamaguchi N,Jeong CW,Nole-Wilson S,Krizek BA,Wagner D AINTEGUMENTA and AINTEGUMENTA-LIKE6/PLETHORA3 Induce LEAFY Expression in Response to Auxin to Promote the Onset of Flower Formation in Arabidopsis. Plant Physiol., 2016. 170(1): p. 283-93 [PMID:26537561] Müller CJ, et al. PHABULOSA Mediates an Auxin Signaling Loop to Regulate Vascular Patterning in Arabidopsis. Plant Physiol., 2016. 170(2): p. 956-70 [PMID:26637548] Herud O,Weijers D,Lau S,Jürgens G Auxin responsiveness of the MONOPTEROS-BODENLOS module in primary root initiation critically depends on the nuclear import kinetics of the Aux/IAA inhibitor BODENLOS. Plant J., 2016. 85(2): p. 269-77 [PMID:26714008] Luo S, et al. Constitutive Expression of OsIAA9 Affects Starch Granules Accumulation and Root Gravitropic Response in Arabidopsis. Front Plant Sci, 2015. 6: p. 1156 [PMID:26734051] 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] Krogan NT,Marcos D,Weiner AI,Berleth T The auxin response factor MONOPTEROS controls meristem function and organogenesis in both the shoot and root through the direct regulation of PIN genes. New Phytol., 2016. 212(1): p. 42-50 [PMID:27441727] Fendrych M,Leung J,Friml J TIR1/AFB-Aux/IAA auxin perception mediates rapid cell wall acidification and growth of Arabidopsis hypocotyls. Elife, 2018. [PMID:27627746] Matthes M,Torres-Ruiz RA Boronic acid treatment phenocopies monopteros by affecting PIN1 membrane stability and polar auxin transport in Arabidopsis thaliana embryos. Development, 2016. 143(21): p. 4053-4062 [PMID:27697905] Bhatia N, et al. Auxin Acts through MONOPTEROS to Regulate Plant Cell Polarity and Pattern Phyllotaxis. Curr. Biol., 2016. 26(23): p. 3202-3208 [PMID:27818174] 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] Möller BK, et al. Auxin response cell-autonomously controls ground tissue initiation in the early Arabidopsis embryo. Proc. Natl. Acad. Sci. U.S.A., 2017. 114(12): p. E2533-E2539 [PMID:28265057] Carey NS,Krogan NT The role of AUXIN RESPONSE FACTORs in the development and differential growth of inflorescence stems. Plant Signal Behav, 2017. 12(4): p. e1307492 [PMID:28340328] Guan C, et al. Spatial Auxin Signaling Controls Leaf Flattening in Arabidopsis. Curr. Biol., 2017. 27(19): p. 2940-2950.e4 [PMID:28943086] Gaillochet C, et al. Control of plant cell fate transitions by transcriptional and hormonal signals. Elife, 2018. [PMID:29058667] Zheng K, et al. Involvement of PACLOBUTRAZOL RESISTANCE6/KIDARI, an Atypical bHLH Transcription Factor, in Auxin Responses in Arabidopsis. Front Plant Sci, 2017. 8: p. 1813 [PMID:29114256] Liu Z, et al. ARF2-ARF4 and ARF5 are Essential for Female and Male Gametophyte Development in Arabidopsis. Plant Cell Physiol., 2018. 59(1): p. 179-189 [PMID:29145642]