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

KHN15502.1

Organism

Glycine soja

Taxonomic ID

3848

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: 715aa MW: 79080.1 Da PI: 8.0285

Description

ARF family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
KHN15502.1	genome	TCUHK	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	B3	79.4	3.6e-25	99	200	1	99
EEEE-..-HHHHTT-EE--HHH.HTT......---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE-SSSEE..E CS B3 1 ffkvltpsdvlksgrlvlpkkfaeeh......ggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfvvFkldgrsefelv 93 f+k+lt sd++++g +++p++ ae++ + +++ s++l+ +d++g++W++++iyr++++r++lt+GW+ Fv+ ++L +gD v+F + +++el+ KHN15502.1 99 FCKTLTASDTSTHGGFSVPRRAAEDCfppldyS-QQRPSQELVAKDLHGQEWRFRHIYRGQPRRHLLTTGWSAFVNKKKLVSGDAVLFL--RGEDGELR 194 99**************************963.3445679********************************************..449999 PP EEEE-S CS B3 94 vkvfrk 99 ++++r+ KHN15502.1 195 LGIRRA 200 ***996 PP
2	Auxin_resp	114.8	7.8e-38	225	306	1	82
Auxin_resp 1 aahaastksvFevvYnPrastseFvvkvekvekalkvkvsvGmRfkmafetedsserrlsGtvvgvsdldpvrWpnSkWrsL 82 +++a+s +++F++ YnPr+stseF++++++++k+l+ ++s+GmRf+m+feted++err++G++vg+ d+dpvrWp+SkWr+L KHN15502.1 225 VVNALSARCAFSIHYNPRVSTSEFIIPIHRFLKSLDYSYSAGMRFRMRFETEDAAERRFTGLIVGIADVDPVRWPGSKWRCL 306 6899*****************************************************************************9 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SuperFamily	SSF101936	4.19E-43	92	208	IPR015300	DNA-binding pseudobarrel domain
Gene3D	G3DSA:2.40.330.10	1.4E-41	93	203	IPR015300	DNA-binding pseudobarrel domain
CDD	cd10017	1.76E-23	97	199	No hit	No description
SMART	SM01019	1.3E-23	99	201	IPR003340	B3 DNA binding domain
Pfam	PF02362	3.3E-23	99	200	IPR003340	B3 DNA binding domain
PROSITE profile	PS50863	13.704	99	201	IPR003340	B3 DNA binding domain
Pfam	PF06507	2.5E-32	226	306	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: 715 aa Download sequence Send to blast
MISLPKKGSV VVYFPQGHLE QHLHDFPLPA SANIPSHVFC RVLDVKLHAE EGSDEVHCQV 60 VLVPETEQVH QKLREGEFDA DGEEEDAEAV MKSTTPHMFC KTLTASDTST HGGFSVPRRA 120 AEDCFPPLDY SQQRPSQELV AKDLHGQEWR FRHIYRGQPR RHLLTTGWSA FVNKKKLVSG 180 DAVLFLRGED GELRLGIRRA AQLKSGSTFS ALSGQQLSPT SLMDVVNALS ARCAFSIHYN 240 PRVSTSEFII PIHRFLKSLD YSYSAGMRFR MRFETEDAAE RRFTGLIVGI ADVDPVRWPG 300 SKWRCLMVRW DDLEVTRHNR VSPWEIEPSG SASTANNLMS AGLKRTKIGL PSAKLEFPVS 360 NVIGTSDFGE SLRFQKVLQG QEMLGVNPTY DSINAQSHQV SDLRRCYPVS NYPRIAATGN 420 NIGIPQVSSN VSSNGIGFSE SFRFQKVLQG QEIFPSQPYG RALSVDEACG NSRCGLFDGY 480 QVMRSRNGWC SDMSNNSSNL HPPVPSGQVS SPSSVLMFQQ AVNLVSNSDY NNKISQVMGG 540 KFHQRVPYAS DVKGGKFVST PYEPLLCGLA KEGTNSFGLS NFHNQLDSSR SHDSISVLRA 600 NQELVPSCKS SCRVFGFSLT EVAPIANKEA ADSSSVACSG PSFTRHVDDD FHPGHSLRSK 660 AVASYCTKTR FDFFGLGSNT AIRSMKMLRN SHPLKVCCNI DYEITMYAST DAGIR

Sequence ? help Back to Top

Protein Sequence Length: 715 aa Download sequence Send to blast

MISLPKKGSV VVYFPQGHLE QHLHDFPLPA SANIPSHVFC RVLDVKLHAE EGSDEVHCQV  60
VLVPETEQVH QKLREGEFDA DGEEEDAEAV MKSTTPHMFC KTLTASDTST HGGFSVPRRA  120
AEDCFPPLDY SQQRPSQELV AKDLHGQEWR FRHIYRGQPR RHLLTTGWSA FVNKKKLVSG  180
DAVLFLRGED GELRLGIRRA AQLKSGSTFS ALSGQQLSPT SLMDVVNALS ARCAFSIHYN  240
PRVSTSEFII PIHRFLKSLD YSYSAGMRFR MRFETEDAAE RRFTGLIVGI ADVDPVRWPG  300
SKWRCLMVRW DDLEVTRHNR VSPWEIEPSG SASTANNLMS AGLKRTKIGL PSAKLEFPVS  360
NVIGTSDFGE SLRFQKVLQG QEMLGVNPTY DSINAQSHQV SDLRRCYPVS NYPRIAATGN  420
NIGIPQVSSN VSSNGIGFSE SFRFQKVLQG QEIFPSQPYG RALSVDEACG NSRCGLFDGY  480
QVMRSRNGWC SDMSNNSSNL HPPVPSGQVS SPSSVLMFQQ AVNLVSNSDY NNKISQVMGG  540
KFHQRVPYAS DVKGGKFVST PYEPLLCGLA KEGTNSFGLS NFHNQLDSSR SHDSISVLRA  600
NQELVPSCKS SCRVFGFSLT EVAPIANKEA ADSSSVACSG PSFTRHVDDD FHPGHSLRSK  660
AVASYCTKTR FDFFGLGSNT AIRSMKMLRN SHPLKVCCNI DYEITMYAST DAGIR

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
4ldy_A	1e-104	1	333	31	359	Auxin response factor 1
4ldy_B	1e-104	1	333	31	359	Auxin response factor 1
Search in ModeBase

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	KHN15502.1

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_028241110.1	0.0	auxin response factor 3-like
Swissprot	O23661	0.0	ARFC_ARATH; Auxin response factor 3
TrEMBL	A0A0B2Q6Q3	0.0	A0A0B2Q6Q3_GLYSO; Auxin response factor
STRING	GLYMA07G32300.2	0.0	(Glycine max)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Fabids	OGEF4576	33	55

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT2G33860.1	1e-176	ARF family protein

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] Qi X, et al. Identification of a novel salt tolerance gene in wild soybean by whole-genome sequencing. Nat Commun, 2014. 5: p. 4340 [PMID:25004933] 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]