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.13G174000.3.p

Common Name

GLYMA_13G174000

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: 608aa MW: 66857.7 Da PI: 8.664

Description

ARF family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Glyma.13G174000.3.p	genome	JGI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	B3	79.8	2.8e-25	33	134	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.13G174000.3.p 33 FCKTLTASDTSTHGGFSVPRRAAEDCfppldyS-QQRPSQELVAKDLHGQEWRFRHIYRGQPRRHLLTTGWSAFVNKKKLVSGDAVLFL- 120 99**************************963.3445679********************************************. PP -SSSEE..EEEEE-S CS B3 85 dgrsefelvvkvfrk 99 + +++el+++++r+ Glyma.13G174000.3.p 121 -RGEDGELRLGIRRA 134 .449999***996 PP
2	Auxin_resp	113.6	1.8e-37	159	240	1	82
Auxin_resp 1 aahaastksvFevvYnPrastseFvvkvekvekalkvkvsvGmRfkmafetedsserrlsGtvvgvsdldpvrWpnSkWrsL 82 +++a+s +++F++ YnPr+s+seF++++++++k+l+ ++s+GmRf+m+feted++err++G++vg+ d+dpvrWp+S+Wr+L Glyma.13G174000.3.p 159 VVNALSARCAFSIHYNPRVSSSEFIIPIHRFVKSLDYSYSAGMRFRMRFETEDAAERRFTGLIVGIADVDPVRWPGSRWRCL 240 6899*****************************************************************************9 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SuperFamily	SSF101936	2.75E-43	25	146	IPR015300	DNA-binding pseudobarrel domain
Gene3D	G3DSA:2.40.330.10	1.1E-41	27	137	IPR015300	DNA-binding pseudobarrel domain
CDD	cd10017	7.54E-24	31	133	No hit	No description
SMART	SM01019	1.3E-23	33	135	IPR003340	B3 DNA binding domain
Pfam	PF02362	2.6E-23	33	134	IPR003340	B3 DNA binding domain
PROSITE profile	PS50863	13.704	33	135	IPR003340	B3 DNA binding domain
Pfam	PF06507	5.1E-32	160	240	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:0005634	Cellular Component	nucleus
GO:0003677	Molecular Function	DNA binding

Sequence ? help Back to Top
Protein Sequence Length: 608 aa Download sequence Send to blast
MQVQQKLREG EFDADGEEED AEAVMKSTTP HMFCKTLTAS DTSTHGGFSV PRRAAEDCFP 60 PLDYSQQRPS QELVAKDLHG QEWRFRHIYR GQPRRHLLTT GWSAFVNKKK LVSGDAVLFL 120 RGEDGELRLG IRRAAQLKSG STFSALSGQQ GSPTSLMDVV NALSARCAFS IHYNPRVSSS 180 EFIIPIHRFV KSLDYSYSAG MRFRMRFETE DAAERRFTGL IVGIADVDPV RWPGSRWRCL 240 MVRWDDLEAT RHNRVSPWEI EPSGSASTAN NLMSAGLKRT KIGLPSAKLD FPVSNAIGTS 300 DFGESLRFQK VLQGQEMLGV NTTYDSFNAQ SHQLSDLRRC YPGSNYPRIA ATGNSIGISQ 360 VSSNVSNNGI GFSESFRFQK VLQGQEILPS QPYGRALSVD EACGNGRFGL FDGFQAMRSR 420 NGWSSHVSNN SSHLHPPVPS GQVSSPSSVF MFQQAVNPVL NSDYNNQIGQ VMGDKVHQRV 480 SYASEVKGGK FVSTPYEPLL RGLSQEGTNS FGLSNFHNQL DSSRSHDSVS VLRASQELVP 540 SCKSRCRVFG FSLTEGAPVA SKEATDSSAV ACAGPSFTRH VEDDFHPGHS LRSKAVASYC 600 TKGVLQY*

Sequence ? help Back to Top

Protein Sequence Length: 608 aa Download sequence Send to blast

MQVQQKLREG EFDADGEEED AEAVMKSTTP HMFCKTLTAS DTSTHGGFSV PRRAAEDCFP  60
PLDYSQQRPS QELVAKDLHG QEWRFRHIYR GQPRRHLLTT GWSAFVNKKK LVSGDAVLFL  120
RGEDGELRLG IRRAAQLKSG STFSALSGQQ GSPTSLMDVV NALSARCAFS IHYNPRVSSS  180
EFIIPIHRFV KSLDYSYSAG MRFRMRFETE DAAERRFTGL IVGIADVDPV RWPGSRWRCL  240
MVRWDDLEAT RHNRVSPWEI EPSGSASTAN NLMSAGLKRT KIGLPSAKLD FPVSNAIGTS  300
DFGESLRFQK VLQGQEMLGV NTTYDSFNAQ SHQLSDLRRC YPGSNYPRIA ATGNSIGISQ  360
VSSNVSNNGI GFSESFRFQK VLQGQEILPS QPYGRALSVD EACGNGRFGL FDGFQAMRSR  420
NGWSSHVSNN SSHLHPPVPS GQVSSPSSVF MFQQAVNPVL NSDYNNQIGQ VMGDKVHQRV  480
SYASEVKGGK FVSTPYEPLL RGLSQEGTNS FGLSNFHNQL DSSRSHDSVS VLRASQELVP  540
SCKSRCRVFG FSLTEGAPVA SKEATDSSAV ACAGPSFTRH VEDDFHPGHS LRSKAVASYC  600
TKGVLQY*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
4ldy_A	6e-86	29	267	120	359	Auxin response factor 1
4ldy_B	6e-86	29	267	120	359	Auxin response factor 1
Search in ModeBase

Expression -- UniGene ? help Back to Top
UniGene ID	E-value	Expressed in
Gma.21378	0.0	hypocotyl\| leaf\| meristem\| stem

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}.

Cis-element ? help Back to Top
Source	Link
PlantRegMap	Glyma.13G174000.3.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	-

Annotation -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	AC158503	0.0	AC158503.31 Glycine max cultivar Williams 82 clone gmw2-133d1, complete sequence.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_003542716.1	0.0	auxin response factor 3 isoform X1
Swissprot	O23661	1e-151	ARFC_ARATH; Auxin response factor 3
TrEMBL	A0A0R0GQJ8	0.0	A0A0R0GQJ8_SOYBN; Auxin response factor
STRING	GLYMA13G24240.1	0.0	(Glycine max)

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT2G33860.1	1e-145	ARF family protein

Link Out ? help Back to Top
Phytozome	Glyma.13G174000.3.p

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]