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

Glyma.13G234200.1.p

Common Name

GLYMA_13G234200, LOC100789906

Organism

Glycine max

Taxonomic ID

3847

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; fabids; Fabales; Fabaceae; Papilionoideae; Phaseoleae; Glycine; Soja

Family

ARF

Protein Properties

Length: 737aa MW: 80446.5 Da PI: 6.6967

Description

ARF family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Glyma.13G234200.1.p	genome	JGI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	B3	77.2	1.7e-24	158	259	1	99
EEEE-..-HHHHTT-EE--HHH.HTT......---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE CS B3 1 ffkvltpsdvlksgrlvlpkkfaeeh......ggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfvvFkl 84 f+k+lt sd++++g +++p++ ae++ + +++ s++l+ +d++g +W++++iyr++++r++lt+GW+ Fv+ ++L +gD v+F Glyma.13G234200.1.p 158 FCKTLTASDTSTHGGFSVPRRAAEDCfppldyS-QQRPSQELVAKDLHGLEWRFRHIYRGQPRRHLLTTGWSAFVNKKKLVSGDAVLFL- 245 99**************************963.3445679********************************************. PP -SSSEE..EEEEE-S CS B3 85 dgrsefelvvkvfrk 99 + +++el+++++r+ Glyma.13G234200.1.p 246 -RGDDGELRLGIRRA 259 .3489999**996 PP
2	Auxin_resp	117.8	8.9e-39	284	365	1	82
Auxin_resp 1 aahaastksvFevvYnPrastseFvvkvekvekalkvkvsvGmRfkmafetedsserrlsGtvvgvsdldpvrWpnSkWrsL 82 +++a+st+++F+v+YnPr s+seF+++v+k++k+l++++svGmRf+m+feted++err++G+++g+sd+dpvrW +SkWr+L Glyma.13G234200.1.p 284 VVNALSTRCAFSVCYNPRFSSSEFIIPVHKFLKSLDCSYSVGMRFRMRFETEDAAERRCTGLIAGISDVDPVRWLGSKWRCL 365 6899*****************************************************************************9 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SuperFamily	SSF101936	9.55E-43	151	265	IPR015300	DNA-binding pseudobarrel domain
Gene3D	G3DSA:2.40.330.10	2.9E-40	153	261	IPR015300	DNA-binding pseudobarrel domain
CDD	cd10017	1.46E-22	156	258	No hit	No description
Pfam	PF02362	1.4E-22	158	259	IPR003340	B3 DNA binding domain
PROSITE profile	PS50863	13.394	158	260	IPR003340	B3 DNA binding domain
SMART	SM01019	3.4E-23	158	260	IPR003340	B3 DNA binding domain
Pfam	PF06507	1.9E-33	285	365	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:0009734	Biological Process	auxin-activated signaling pathway
GO:0010050	Biological Process	vegetative phase change
GO:0010158	Biological Process	abaxial cell fate specification
GO:0010582	Biological Process	floral meristem determinacy
GO:0005634	Cellular Component	nucleus
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: 737 aa Download sequence Send to blast
MGLIDLNTTE DDEAAPLSAS SPASYSSSSS HSGISTSAST LVVPPTPPSV CLELWHACAG 60 PLISLPKKGS VVVYLPQGHF EHVQDFPVTA YDIPPHVFCR VLDVKLHAEE GSDEVYCQVL 120 LVPESEQVEQ SLREGEIVAD GEEEDTEAIV KSTTPHMFCK TLTASDTSTH GGFSVPRRAA 180 EDCFPPLDYS QQRPSQELVA KDLHGLEWRF RHIYRGQPRR HLLTTGWSAF VNKKKLVSGD 240 AVLFLRGDDG ELRLGIRRAA QLKSAGSFAV PSGQQLNPAT LKGVVNALST RCAFSVCYNP 300 RFSSSEFIIP VHKFLKSLDC SYSVGMRFRM RFETEDAAER RCTGLIAGIS DVDPVRWLGS 360 KWRCLLVRWD DIEAARRNRV SPWEIEPSGS ASNSSNLMSA GLKRTRIGMT SVKLEFPTPD 420 GIGASDFGES LRFRKVLQGQ EILGVNTPFD GINAQSPRLY ELGRCYPGSN CSGIPPTGNN 480 IRMPHPASDF SCNGIGFSES FRFQKVLQGQ EILPSQPYGR VLSIEEARAN GCYGLYDGCQ 540 LLNTRNGWSA QMHDNAPYLH ASVTPAQVSS PSSVLMFQQA VNPVSNCDYN KNKRDKEMEG 600 RVHYQGLYTS EVKGRTFASS PFDDPILSTL APEGASSLGM FDVHNQLGSS RPHESVSALR 660 SSQELVSSCK SSCRLFGFSL TEDTHLAKKE ASASTITLPL SSGPSFTRLV EDEFHPGHSL 720 PSKGVGSNCT KGVLQY*

Sequence ? help Back to Top

Protein Sequence Length: 737 aa Download sequence Send to blast

MGLIDLNTTE DDEAAPLSAS SPASYSSSSS HSGISTSAST LVVPPTPPSV CLELWHACAG  60
PLISLPKKGS VVVYLPQGHF EHVQDFPVTA YDIPPHVFCR VLDVKLHAEE GSDEVYCQVL  120
LVPESEQVEQ SLREGEIVAD GEEEDTEAIV KSTTPHMFCK TLTASDTSTH GGFSVPRRAA  180
EDCFPPLDYS QQRPSQELVA KDLHGLEWRF RHIYRGQPRR HLLTTGWSAF VNKKKLVSGD  240
AVLFLRGDDG ELRLGIRRAA QLKSAGSFAV PSGQQLNPAT LKGVVNALST RCAFSVCYNP  300
RFSSSEFIIP VHKFLKSLDC SYSVGMRFRM RFETEDAAER RCTGLIAGIS DVDPVRWLGS  360
KWRCLLVRWD DIEAARRNRV SPWEIEPSGS ASNSSNLMSA GLKRTRIGMT SVKLEFPTPD  420
GIGASDFGES LRFRKVLQGQ EILGVNTPFD GINAQSPRLY ELGRCYPGSN CSGIPPTGNN  480
IRMPHPASDF SCNGIGFSES FRFQKVLQGQ EILPSQPYGR VLSIEEARAN GCYGLYDGCQ  540
LLNTRNGWSA QMHDNAPYLH ASVTPAQVSS PSSVLMFQQA VNPVSNCDYN KNKRDKEMEG  600
RVHYQGLYTS EVKGRTFASS PFDDPILSTL APEGASSLGM FDVHNQLGSS RPHESVSALR  660
SSQELVSSCK SSCRLFGFSL TEDTHLAKKE ASASTITLPL SSGPSFTRLV EDEFHPGHSL  720
PSKGVGSNCT KGVLQY*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
4ldy_A	1e-112	49	394	18	361	Auxin response factor 1
4ldy_B	1e-112	49	394	18	361	Auxin response factor 1
Search in ModeBase

Expression -- UniGene ? help Back to Top
UniGene ID	E-value	Expressed in
Gma.13491	0.0	cotyledon\| leaf\| meristem

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}.

Binding Motif ? help Back to Top
Motif ID	Method	Source	Motif file
MP00021	PBM	Transfer from AT2G33860	Download

Cis-element ? help Back to Top
Source	Link
PlantRegMap	Glyma.13G234200.1.p

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	Retrieve

Annotation -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	BT093691	0.0	BT093691.1 Soybean clone JCVI-FLGm-17L13 unknown mRNA.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_003543018.1	0.0	auxin response factor 3
Refseq	XP_028190353.1	0.0	auxin response factor 3-like
Swissprot	O23661	0.0	ARFC_ARATH; Auxin response factor 3
TrEMBL	A0A445I9B2	0.0	A0A445I9B2_GLYSO; Auxin response factor
TrEMBL	I1M1Y1	0.0	I1M1Y1_SOYBN; Auxin response factor
STRING	GLYMA13G30750.1	0.0	(Glycine max)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Fabids	OGEF4576	33	55
Representative plant	OGRP6685	10	18

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	Glyma.13G234200.1.p
Entrez Gene	100789906

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]