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

RrC3289_p2

Organism

Raphanus raphanistrum

Taxonomic ID

109996

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Brassiceae; Raphanus

Family

ARF

Protein Properties

Length: 830aa MW: 92161.5 Da PI: 6.6279

Description

ARF family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
RrC3289_p2	genome	MSU	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	B3	35.1	2.3e-11	147	234	1	99
EEEE-..-HHHHTT-EE--HHH.HTT---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE-SSSEE..EEEEE-S CS B3 1 ffkvltpsdvlksgrlvlpkkfaeehggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfvvFkldgrsefelvvkvfrk 99 f+k+lt sd++++g +++ +++a+e+ +++ l l++ + ++ +++ ++ s +++ ++GW+ Fv++++L +gD ++F + +++el+v+v+r+ RrC3289_p2 147 FCKTLTASDTSTHGGFSVLRRHADEI-----CHFNLLLRS-WLQKICMQM--SGVS-GIFSESGWSVFVSSKRLVAGDAFIFL--RGENGELRVGVRRA 234 99*******************877.....444566554.555666666..4444.488999****************..449999***996 PP
2	Auxin_resp	50.2	1.1e-17	270	334	30	83
Auxin_resp 30 kvekalkvkvsvGmRfkmafetedsserr...........lsGtvvgvsdldpvrWpnSkWrsLk 83 +++++k+++s+GmRfkm+fe+e+++e+r ++Gt+vg++d+dp +W +SkWrsLk RrC3289_p2 270 TYMESVKKNYSIGMRFKMRFEGEEAPEQRrssltvltcirFTGTIVGIEDSDPRSWAKSKWRSLK 334 699********************99753333333322259*******************96 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-18	143	248	IPR015300	DNA-binding pseudobarrel domain
SuperFamily	SSF101936	5.62E-17	143	262	IPR015300	DNA-binding pseudobarrel domain
CDD	cd10017	2.45E-9	145	233	No hit	No description
SMART	SM01019	1.8E-8	147	235	IPR003340	B3 DNA binding domain
Pfam	PF02362	2.6E-9	147	234	IPR003340	B3 DNA binding domain
PROSITE profile	PS50863	8.966	180	235	IPR003340	B3 DNA binding domain
Pfam	PF06507	1.1E-14	270	334	IPR010525	Auxin response factor
Pfam	PF02309	4.2E-5	615	728	IPR033389	AUX/IAA domain
PROSITE profile	PS51745	21.017	692	773	IPR000270	PB1 domain
SuperFamily	SSF54277	1.18E-9	694	765	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:0009725	Biological Process	response to hormone
GO:0005634	Cellular Component	nucleus
GO:0003677	Molecular Function	DNA binding
GO:0005515	Molecular Function	protein binding

Sequence ? help Back to Top
Protein Sequence Length: 830 aa Download sequence Send to blast
MTSSVKGNHH HGGENDAVSS VVVVAGEGQN SHLNRVEAAI YRELWHACAG PLVTVPRRDD 60 RVFYFPQGHI EQVEASTNQA AEHQMPLYDL PSKLLCRVIN VDLKAEVDTD EVYAQITLLP 120 EPNQDENAIE KEAPPLPPPP RFQVHSFCKT LTASDTSTHG GFSVLRRHAD EICHFNLLLR 180 SWLQKICMQM SGVSGIFSES GWSVFVSSKR LVAGDAFIFL RGENGELRVG VRRAMRQQGN 240 VPSSVISSHS MHLGVLATAW HAISTGTMFT YMESVKKNYS IGMRFKMRFE GEEAPEQRRS 300 SLTVLTCIRF TGTIVGIEDS DPRSWAKSKW RSLKVRWDET STIPRPERVS PWKIEPALAP 360 PALSPVPMAR PKRPRSNMAP SSPDSSMHIK EGSSKANLYP LPASGLSRVL QGQEYPTLRT 420 KHTESAECDA PETSVVWQSS ADDDKVDVAS RRYDNWMSSG RHEASYTDLL SGFGANGDPS 480 HGHQIPFYDN HSSSPSVTAK KILSEQDAKF DYLANQWQMM HSGLSLKLHE SPKIPAASDA 540 SFTQGQGNAR YGEYPVLHAL TTETAGSNWP IRPRALNYFE EAVHAQTQAQ AQAQARENVT 600 KQPAVVQEET AKPGDGNCRL FGIPLVNNVN KTDSTMSQRN KLNETSGFTQ LASPRVQDLS 660 DHSKGSKSTN DHREQSKPSQ AKDGHCKTNS SRSCTKVHKQ GIVLGRSVDL SKFQNYEELI 720 AELDMLFEFN GELMARKKDW LVVYTDDEDD MMLVGDDPWQ EFCCMIFIYT KEVVMKMNSG 780 TLSCRSEEEV AVVGEGSDAK DAKSASNPSL SSELLNQKNQ LQAEVCMLLN

Sequence ? help Back to Top

Protein Sequence Length: 830 aa Download sequence Send to blast

MTSSVKGNHH HGGENDAVSS VVVVAGEGQN SHLNRVEAAI YRELWHACAG PLVTVPRRDD  60
RVFYFPQGHI EQVEASTNQA AEHQMPLYDL PSKLLCRVIN VDLKAEVDTD EVYAQITLLP  120
EPNQDENAIE KEAPPLPPPP RFQVHSFCKT LTASDTSTHG GFSVLRRHAD EICHFNLLLR  180
SWLQKICMQM SGVSGIFSES GWSVFVSSKR LVAGDAFIFL RGENGELRVG VRRAMRQQGN  240
VPSSVISSHS MHLGVLATAW HAISTGTMFT YMESVKKNYS IGMRFKMRFE GEEAPEQRRS  300
SLTVLTCIRF TGTIVGIEDS DPRSWAKSKW RSLKVRWDET STIPRPERVS PWKIEPALAP  360
PALSPVPMAR PKRPRSNMAP SSPDSSMHIK EGSSKANLYP LPASGLSRVL QGQEYPTLRT  420
KHTESAECDA PETSVVWQSS ADDDKVDVAS RRYDNWMSSG RHEASYTDLL SGFGANGDPS  480
HGHQIPFYDN HSSSPSVTAK KILSEQDAKF DYLANQWQMM HSGLSLKLHE SPKIPAASDA  540
SFTQGQGNAR YGEYPVLHAL TTETAGSNWP IRPRALNYFE EAVHAQTQAQ AQAQARENVT  600
KQPAVVQEET AKPGDGNCRL FGIPLVNNVN KTDSTMSQRN KLNETSGFTQ LASPRVQDLS  660
DHSKGSKSTN DHREQSKPSQ AKDGHCKTNS SRSCTKVHKQ GIVLGRSVDL SKFQNYEELI  720
AELDMLFEFN GELMARKKDW LVVYTDDEDD MMLVGDDPWQ EFCCMIFIYT KEVVMKMNSG  780
TLSCRSEEEV AVVGEGSDAK DAKSASNPSL SSELLNQKNQ LQAEVCMLLN

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
4ldv_A	1e-125	39	356	18	354	Auxin response factor 1
4ldw_A	1e-125	39	356	18	354	Auxin response factor 1
4ldw_B	1e-125	39	356	18	354	Auxin response factor 1
4ldx_A	1e-125	39	356	18	354	Auxin response factor 1
4ldx_B	1e-125	39	356	18	354	Auxin response factor 1
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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. Promotes flowering, stamen development, floral organ abscission and fruit dehiscence. Functions independently of ethylene and cytokinin response pathways. May act as a repressor of cell division and organ growth. {ECO:0000269\|PubMed:12036261, ECO:0000269\|PubMed:15960614, ECO:0000269\|PubMed:16176952, ECO:0000269\|PubMed:16339187}.

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	JN979459	0.0	JN979459.1 Brassica rapa subsp. pekinensis auxin response factor 2-1 (ARF2-1) mRNA, complete cds.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_018439789.1	0.0	PREDICTED: auxin response factor 2-like
Swissprot	Q94JM3	0.0	ARFB_ARATH; Auxin response factor 2
TrEMBL	A0A078JPD8	0.0	A0A078JPD8_BRANA; Auxin response factor
STRING	Bo2g161810.1	0.0	(Brassica oleracea)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM5348	26	47

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT5G62000.3	0.0	auxin response factor 2

Publications ? help Back to Top
Chao WS,Doğramaci M,Foley ME,Horvath DP,Anderson JV Selection and validation of endogenous reference genes for qRT-PCR analysis in leafy spurge (Euphorbia esula). PLoS ONE, 2012. 7(8): p. e42839 [PMID:22916167] 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] Li C, et al. Ectopic expression of a maize hybrid down-regulated gene ZmARF25 decreases organ size by affecting cellular proliferation in Arabidopsis. PLoS ONE, 2014. 9(4): p. e94830 [PMID:24756087] Lyons R, et al. Fusarium oxysporum triggers tissue-specific transcriptional reprogramming in Arabidopsis thaliana. PLoS ONE, 2015. 10(4): p. e0121902 [PMID:25849296] Roodbarkelari F,Du F,Truernit E,Laux T ZLL/AGO10 maintains shoot meristem stem cells during Arabidopsis embryogenesis by down-regulating ARF2-mediated auxin response. BMC Biol., 2015. 13: p. 74 [PMID:26358077] Meng LS,Wang ZB,Yao SQ,Liu A The ARF2-ANT-COR15A gene cascade regulates ABA-signaling-mediated resistance of large seeds to drought in Arabidopsis. J. Cell. Sci., 2015. 128(21): p. 3922-32 [PMID:26395398] Zhao S,Zhang ML,Ma TL,Wang Y Phosphorylation of ARF2 Relieves Its Repression of Transcription of the K+ Transporter Gene HAK5 in Response to Low Potassium Stress. Plant Cell, 2016. 28(12): p. 3005-3019 [PMID:27895227] Promchuea S,Zhu Y,Chen Z,Zhang J,Gong Z ARF2 coordinates with PLETHORAs and PINs to orchestrate ABA-mediated root meristem activity in Arabidopsis . J Integr Plant Biol, 2017. 59(1): p. 30-43 [PMID:28074634] 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] Sanz-Fernández M, et al. Screening Arabidopsis mutants in genes useful for phytoremediation. J. Hazard. Mater., 2017. 335: p. 143-151 [PMID:28441590] Zhang M,Hu X,Zhu M,Xu M,Wang L Transcription factors NF-YA2 and NF-YA10 regulate leaf growth via auxin signaling in Arabidopsis. Sci Rep, 2017. 7(1): p. 1395 [PMID:28469131] Guan C, et al. Spatial Auxin Signaling Controls Leaf Flattening in Arabidopsis. Curr. Biol., 2017. 27(19): p. 2940-2950.e4 [PMID:28943086] 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] Sarkar Das S, et al. Expression dynamics of miRNAs and their targets in seed germination conditions reveals miRNA-ta-siRNA crosstalk as regulator of seed germination. Sci Rep, 2018. 8(1): p. 1233 [PMID:29352229]