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

Tp57577_TGAC_v2_mRNA1034

Organism

Trifolium pratense

Taxonomic ID

57577

Taxonomic Lineage

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

Family

ARF

Protein Properties

Length: 229aa MW: 26282.8 Da PI: 5.637

Description

ARF family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Tp57577_TGAC_v2_mRNA1034	genome	JGI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	B3	71.2	1.3e-22	20	117	3	99
EE-..-HHHHTT-EE--HHH.HTT.......---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EE CS B3 3 kvltpsdvlksgrlvlpkkfaeeh.......ggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfv 80 k l ++ + l++pk++a+++ g+++ + +l+++d++g +W++++iy+ ++++++lt+GW++Fv++++L gD++ Tp57577_TGAC_v2_mRNA1034 20 KML-ET-STHAAGLYIPKEHADRCfptlditGQPPMQ--DLVMKDLHGIEWNFRHIYCDHQKAHYLTSGWSKFVNSKKLVPGDSC 100 333.33.344456***************6555544..8***************************************** PP EEEE-SSSEE..EEEEE-S CS B3 81 vFkldgrsefelvvkvfrk 99 +F + +++e ++++r+ Tp57577_TGAC_v2_mRNA1034 101 IFA--RGENGEIGIGIRRA 117 *..34888888999885 PP
2	Auxin_resp	71	3.6e-24	140	215	4	81
Auxin_resp 4 aastksvFevvYnPrastseFvvkvekvekalkvkvsvGmRfkmafetedsserrlsGtvvgvsdldpvrWpnSkWrs 81 a+ t+++F+v Y+P+ ++ eF+++++ +++++++ + +G+R++ + e+s++r +Gt+vg +d+dp+rWp+S+Wr+ Tp57577_TGAC_v2_mRNA1034 140 AVLTGTMFTVQYYPWITPFEFMIPLKTYVESIERDYPIGTRVRRLSQDEESARR--YGTIVGNEDIDPIRWPGSEWRC 215 67799************************************77777766665..5******************9 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Gene3D	G3DSA:2.40.330.10	6.0E-30	13	122	IPR015300	DNA-binding pseudobarrel domain
SuperFamily	SSF101936	5.1E-26	14	123	IPR015300	DNA-binding pseudobarrel domain
CDD	cd10017	2.59E-18	16	116	No hit	No description
PROSITE profile	PS50863	12.816	16	118	IPR003340	B3 DNA binding domain
SMART	SM01019	1.1E-16	18	118	IPR003340	B3 DNA binding domain
Pfam	PF02362	7.6E-20	23	117	IPR003340	B3 DNA binding domain
Pfam	PF06507	3.8E-21	138	215	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:0009725	Biological Process	response to hormone
GO:0005634	Cellular Component	nucleus
GO:0003677	Molecular Function	DNA binding

Sequence ? help Back to Top
Protein Sequence Length: 229 aa Download sequence Send to blast
MEEENDPVDD SLSEVFTFTK MLETSTHAAG LYIPKEHADR CFPTLDITGQ PPMQDLVMKD 60 LHGIEWNFRH IYCDHQKAHY LTSGWSKFVN SKKLVPGDSC IFARGENGEI GIGIRRAMKQ 120 DSDIWKTSST FAPMGVASFA VLTGTMFTVQ YYPWITPFEF MIPLKTYVES IERDYPIGTR 180 VRRLSQDEES ARRYGTIVGN EDIDPIRWPG SEWRCAMGFQ TTKYFYRT*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
4ldy_A	6e-48	15	214	121	329	Auxin response factor 1
4ldy_B	6e-48	15	214	121	329	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. 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}.

Cis-element ? help Back to Top
Source	Link
PlantRegMap	Tp57577_TGAC_v2_mRNA1034

Regulation -- PlantRegMap ? help Back to Top
Source	Upstream Regulator	Target Gene
PlantRegMap	Retrieve	-

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_013445290.1	2e-99	auxin response factor 2
Swissprot	Q94JM3	5e-57	ARFB_ARATH; Auxin response factor 2
TrEMBL	A0A2Z6MVN7	1e-127	A0A2Z6MVN7_TRISU; Auxin response factor
STRING	XP_004511136.1	1e-87	(Cicer arietinum)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Fabids	OGEF28004	2	3

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT5G62000.3	1e-49	auxin response factor 2

Link Out ? help Back to Top
Phytozome	Tp57577_TGAC_v2_mRNA1034

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]