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

AT2G28350.1

Common Name

ARF10, T1B3.13

Organism

Arabidopsis thaliana

Taxonomic ID

3702

Taxonomic Lineage

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

Family

ARF

Protein Properties

Length: 693aa MW: 76720.9 Da PI: 7.794

Description

auxin response factor 10

Gene Model

Gene Model ID	Type	Source	Coding Sequence
AT2G28350.1	genome	TAIR	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	B3	76.5	2.9e-24	115	216	1	99
EEEE-..-HHHHTT-EE--HHH.HTT.......---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE-SSSEE. CS B3 1 ffkvltpsdvlksgrlvlpkkfaeeh.......ggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfvvFkldgrsefe 91 f k+lt+sd+++ g +++p+ +ae++ +++ + t++ +d +g++W++++iyr++++r++lt+GW+ Fv++++L +gD++vF +++++ AT2G28350.1 115 FAKTLTQSDANNGGGFSVPRYCAETIfprldysAEPPVQ--TVIAKDIHGETWKFRHIYRGTPRRHLLTTGWSTFVNQKKLIAGDSIVFL--RSESGD 208 89**************************986445444..8********************************************..458999 PP .EEEEE-S CS B3 92 lvvkvfrk 99 l+v+++r+ AT2G28350.1 209 LCVGIRRA 216 9**997 PP
2	Auxin_resp	114.6	8.8e-38	277	360	1	83
Auxin_resp 1 aahaastksvFevvYnPrastseFvvkvekvekalkvkvsvGmRfkmafetedsserrl.sGtvvgvsdldpvrWpnSkWrsLk 83 a+ +a+ +++FevvY+Prast+eF+vk+++v++a++++++ GmRfkmafetedss++++ +Gtv++v+ +dp+rWpnS+Wr+L+ AT2G28350.1 277 AVARAACGQAFEVVYYPRASTPEFCVKAADVRSAMRIRWCSGMRFKMAFETEDSSRISWfMGTVSAVQVADPIRWPNSPWRLLQ 360 56778899**************************************************************************97 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Gene3D	G3DSA:2.40.330.10	2.2E-37	108	219	IPR015300	DNA-binding pseudobarrel domain
SuperFamily	SSF101936	2.22E-29	110	216	IPR015300	DNA-binding pseudobarrel domain
CDD	cd10017	3.86E-21	114	215	No hit	No description
SMART	SM01019	1.2E-21	115	217	IPR003340	B3 DNA binding domain
PROSITE profile	PS50863	13.183	115	217	IPR003340	B3 DNA binding domain
Pfam	PF02362	3.7E-22	115	216	IPR003340	B3 DNA binding domain
Pfam	PF06507	2.7E-32	278	360	IPR010525	Auxin response factor
PROSITE profile	PS51745	19.444	580	668	IPR000270	PB1 domain

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0006355	Biological Process	regulation of transcription, DNA-templated
GO:0007389	Biological Process	pattern specification process
GO:0009734	Biological Process	auxin-activated signaling pathway
GO:0009738	Biological Process	abscisic acid-activated signaling pathway
GO:0009743	Biological Process	response to carbohydrate
GO:0010154	Biological Process	fruit development
GO:0031540	Biological Process	regulation of anthocyanin biosynthetic process
GO:0048366	Biological Process	leaf development
GO:0048441	Biological Process	petal development
GO:0048442	Biological Process	sepal development
GO:0048589	Biological Process	developmental growth
GO:0048829	Biological Process	root cap development
GO:0051301	Biological Process	cell division
GO:0005634	Cellular Component	nucleus
GO:0003677	Molecular Function	DNA binding
GO:0003700	Molecular Function	transcription factor activity, sequence-specific DNA binding
GO:0005515	Molecular Function	protein binding
GO:0035198	Molecular Function	miRNA binding

Plant Ontology ? help Back to Top
PO Term	PO Category	PO Description
PO:0000013	anatomy	cauline leaf
PO:0000037	anatomy	shoot apex
PO:0000084	anatomy	plant sperm cell
PO:0000230	anatomy	inflorescence meristem
PO:0000293	anatomy	guard cell
PO:0008019	anatomy	leaf lamina base
PO:0009005	anatomy	root
PO:0009006	anatomy	shoot system
PO:0009009	anatomy	plant embryo
PO:0009010	anatomy	seed
PO:0009025	anatomy	vascular leaf
PO:0009029	anatomy	stamen
PO:0009030	anatomy	carpel
PO:0009031	anatomy	sepal
PO:0009032	anatomy	petal
PO:0009046	anatomy	flower
PO:0009047	anatomy	stem
PO:0009049	anatomy	inflorescence
PO:0009052	anatomy	flower pedicel
PO:0020030	anatomy	cotyledon
PO:0020031	anatomy	radicle
PO:0020038	anatomy	petiole
PO:0020100	anatomy	hypocotyl
PO:0020137	anatomy	leaf apex
PO:0025022	anatomy	collective leaf structure
PO:0025281	anatomy	pollen
PO:0001054	developmental stage	vascular leaf senescent stage
PO:0001078	developmental stage	plant embryo cotyledonary stage
PO:0001081	developmental stage	mature plant embryo stage
PO:0001185	developmental stage	plant embryo globular stage
PO:0004507	developmental stage	plant embryo bilateral stage
PO:0007015	developmental stage	radicle emergence stage
PO:0007064	developmental stage	LP.12 twelve leaves visible stage
PO:0007095	developmental stage	LP.08 eight leaves visible stage
PO:0007098	developmental stage	LP.02 two leaves visible stage
PO:0007103	developmental stage	LP.10 ten leaves visible stage
PO:0007115	developmental stage	LP.04 four leaves visible stage
PO:0007123	developmental stage	LP.06 six leaves visible stage
PO:0007131	developmental stage	seedling development stage
PO:0007611	developmental stage	petal differentiation and expansion stage
PO:0007616	developmental stage	flowering stage

Sequence ? help Back to Top
Protein Sequence Length: 693 aa Download sequence Send to blast
MEQEKSLDPQ LWHACAGSMV QIPSLNSTVF YFAQGHTEHA HAPPDFHAPR VPPLILCRVV 60 SVKFLADAET DEVFAKITLL PLPGNDLDLE NDAVLGLTPP SSDGNGNGKE KPASFAKTLT 120 QSDANNGGGF SVPRYCAETI FPRLDYSAEP PVQTVIAKDI HGETWKFRHI YRGTPRRHLL 180 TTGWSTFVNQ KKLIAGDSIV FLRSESGDLC VGIRRAKRGG LGSNAGSDNP YPGFSGFLRD 240 DESTTTTSKL MMMKRNGNND GNAAATGRVR VEAVAEAVAR AACGQAFEVV YYPRASTPEF 300 CVKAADVRSA MRIRWCSGMR FKMAFETEDS SRISWFMGTV SAVQVADPIR WPNSPWRLLQ 360 VAWDEPDLLQ NVKRVSPWLV ELVSNMPTIH LSPFSPRKKI RIPQPFEFPF HGTKFPIFSP 420 GFANNGGGES MCYLSNDNNN APAGIQGARQ AQQLFGSPSP SLLSDLNLSS YTGNNKLHSP 480 AMFLSSFNPR HHHYQARDSE NSNNISCSLT MGNPAMVQDK KKSVGSVKTH QFVLFGQPIL 540 TEQQVMNRKR FLEEEAEAEE EKGLVARGLT WNYSLQGLET GHCKVFMESE DVGRTLDLSV 600 IGSYQELYRK LAEMFHIEER SDLLTHVVYR DANGVIKRIG DEPFSDFMKA TKRLTIKMDI 660 GGDNVRKTWI TGIRTGENGI DASTKTGPLS IFA

Sequence ? help Back to Top

Protein Sequence Length: 693 aa Download sequence Send to blast

MEQEKSLDPQ LWHACAGSMV QIPSLNSTVF YFAQGHTEHA HAPPDFHAPR VPPLILCRVV  60
SVKFLADAET DEVFAKITLL PLPGNDLDLE NDAVLGLTPP SSDGNGNGKE KPASFAKTLT  120
QSDANNGGGF SVPRYCAETI FPRLDYSAEP PVQTVIAKDI HGETWKFRHI YRGTPRRHLL  180
TTGWSTFVNQ KKLIAGDSIV FLRSESGDLC VGIRRAKRGG LGSNAGSDNP YPGFSGFLRD  240
DESTTTTSKL MMMKRNGNND GNAAATGRVR VEAVAEAVAR AACGQAFEVV YYPRASTPEF  300
CVKAADVRSA MRIRWCSGMR FKMAFETEDS SRISWFMGTV SAVQVADPIR WPNSPWRLLQ  360
VAWDEPDLLQ NVKRVSPWLV ELVSNMPTIH LSPFSPRKKI RIPQPFEFPF HGTKFPIFSP  420
GFANNGGGES MCYLSNDNNN APAGIQGARQ AQQLFGSPSP SLLSDLNLSS YTGNNKLHSP  480
AMFLSSFNPR HHHYQARDSE NSNNISCSLT MGNPAMVQDK KKSVGSVKTH QFVLFGQPIL  540
TEQQVMNRKR FLEEEAEAEE EKGLVARGLT WNYSLQGLET GHCKVFMESE DVGRTLDLSV  600
IGSYQELYRK LAEMFHIEER SDLLTHVVYR DANGVIKRIG DEPFSDFMKA TKRLTIKMDI  660
GGDNVRKTWI TGIRTGENGI DASTKTGPLS IFA

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
4ldu_A	1e-79	7	381	51	388	Auxin response factor 5
Search in ModeBase

Expression -- UniGene ? help Back to Top
UniGene ID	E-value	Expressed in
At.13730	0.0	bud\| cell culture\| flower

Expression -- Microarray ? help Back to Top
Source	ID	E-value
GEO	145360418	0.0
Genevisible	265272_at	0.0
Expression Atlas	AT2G28350	-
AtGenExpress	AT2G28350	-
ATTED-II	AT2G28350	-

Expression -- Description ? help Back to Top
Source	Description
Uniprot	TISSUE SPECIFICITY: Expressed in the whole plant. {ECO:0000269\|PubMed:10476078}.

Functional Description ? help Back to Top
Source	Description
TAIR	Involved in root cap cell differentiation.
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. {ECO:0000269\|PubMed:12036261}.

Function -- GeneRIF ? help Back to Top
In root, auxin and miR160 regulate the expression of ARF10 genes independently, generating a pattern consistent with root cap development. [PMID: 16006581] negative regulation of ARF10 by miR160 plays a critical role in seed germination and post-embryonic developmental programs [PMID: 17672844] Phenotypic plasticity of adventitious rooting is controlled by complex regulation of AUXIN RESPONSE FACTOR transcripts and microRNA abundance. Repressor/Activator Balance Is Unaltered by Disruptions to ARF10 and ARF16. [PMID: 19820192] miR160 negatively affects the expression of ARF10 during shoot regeneration. [PMID: 22335436] Auxin recruits AUXIN RESPONSE FACTOR 10 and AUXIN RESPONSE FACTOR 16 to control the expression of ABI3 during seed germination. [PMID: 23986496]

Cis-element ? help Back to Top
Source	Link
PlantRegMap	AT2G28350.1

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

Regulation -- ATRM (Manually Curated Target Genes) ? help Back to Top
Source	Target Gene (A: Activate/R: Repress)
ATRM	AT3G11260(R)

Regulation -- MicroRNA ? help Back to Top
Source	Description
miRTarBase	Regulated by ath-miR160c, ath-miR160b, ath-miR160a

Regulation -- Hormone ? help Back to Top
Source	Hormone
AHD	abscisic acid, auxin

Interaction ? help Back to Top
Source	Intact With
BioGRID	AT5G60450
IntAct	Search Q9SKN5

Phenotype -- Mutation ? help Back to Top
Source	ID
T-DNA Express	AT2G28350

Annotation -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	AF325073	0.0	AF325073.1 Arabidopsis thaliana unknown protein (At2g28350) mRNA, complete cds.
GenBank	AF336919	0.0	AF336919.1 Arabidopsis thaliana clone C00034 (b) auxin response factor 10 (At2g28350) mRNA, complete cds.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	NP_180402.1	0.0	auxin response factor 10
Swissprot	Q9SKN5	0.0	ARFJ_ARATH; Auxin response factor 10
TrEMBL	A0A384K881	0.0	A0A384K881_ARATH; Auxin response factor
TrEMBL	C0SV66	0.0	C0SV66_ARATH; Auxin response factor (Fragment)
STRING	AT2G28350.1	0.0	(Arabidopsis thaliana)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM580	27	130
Representative plant	OGRP526	15	78

Link Out ? help Back to Top
Phytozome	AT2G28350.1
Entrez Gene	817382
iHOP	AT2G28350
wikigenes	AT2G28350

Publications ? help Back to Top
Ulmasov T,Hagen G,Guilfoyle TJ Dimerization and DNA binding of auxin response factors. Plant J., 1999. 19(3): p. 309-19 [PMID:10476078] Riechmann JL, et al. Arabidopsis transcription factors: genome-wide comparative analysis among eukaryotes. Science, 2000. 290(5499): p. 2105-10 [PMID:11118137] Hagen G,Guilfoyle T Auxin-responsive gene expression: genes, promoters and regulatory factors. Plant Mol. Biol., 2002 Jun-Jul. 49(3-4): p. 373-85 [PMID:12036261] Kasschau KD, et al. P1/HC-Pro, a viral suppressor of RNA silencing, interferes with Arabidopsis development and miRNA unction. Dev. Cell, 2003. 4(2): p. 205-17 [PMID:12586064] Yamada K, et al. Empirical analysis of transcriptional activity in the Arabidopsis genome. Science, 2003. 302(5646): p. 842-6 [PMID:14593172] Jiao Y, et al. A genome-wide analysis of blue-light regulation of Arabidopsis transcription factor gene expression during seedling development. Plant Physiol., 2003. 133(4): p. 1480-93 [PMID:14605227] Goda H, et al. Comprehensive comparison of auxin-regulated and brassinosteroid-regulated genes in Arabidopsis. Plant Physiol., 2004. 134(4): p. 1555-73 [PMID:15047898] Chapman EJ,Prokhnevsky AI,Gopinath K,Dolja VV,Carrington JC Viral RNA silencing suppressors inhibit the microRNA pathway at an intermediate step. Genes Dev., 2004. 18(10): p. 1179-86 [PMID:15131083] Remington DL,Vision TJ,Guilfoyle TJ,Reed JW Contrasting modes of diversification in the Aux/IAA and ARF gene families. Plant Physiol., 2004. 135(3): p. 1738-52 [PMID:15247399] Souret FF,Kastenmayer JP,Green PJ AtXRN4 degrades mRNA in Arabidopsis and its substrates include selected miRNA targets. Mol. Cell, 2004. 15(2): p. 173-83 [PMID:15260969] Okushima Y, et al. Functional genomic analysis of the AUXIN RESPONSE FACTOR gene family members in Arabidopsis thaliana: unique and overlapping functions of ARF7 and ARF19. Plant Cell, 2005. 17(2): p. 444-63 [PMID:15659631] Mallory AC,Bartel DP,Bartel B MicroRNA-directed regulation of Arabidopsis AUXIN RESPONSE FACTOR17 is essential for proper development and modulates expression of early auxin response genes. Plant Cell, 2005. 17(5): p. 1360-75 [PMID:15829600] Sorin C, et al. Auxin and light control of adventitious rooting in Arabidopsis require ARGONAUTE1. Plant Cell, 2005. 17(5): p. 1343-59 [PMID:15829601] Axtell MJ,Bartel DP Antiquity of microRNAs and their targets in land plants. Plant Cell, 2005. 17(6): p. 1658-73 [PMID:15849273] Wang JW, et al. Control of root cap formation by MicroRNA-targeted auxin response factors in Arabidopsis. Plant Cell, 2005. 17(8): p. 2204-16 [PMID:16006581] Vergnolle C, et al. The cold-induced early activation of phospholipase C and D pathways determines the response of two distinct clusters of genes in Arabidopsis cell suspensions. Plant Physiol., 2005. 139(3): p. 1217-33 [PMID:16258011] Cao D,Cheng H,Wu W,Soo HM,Peng J Gibberellin mobilizes distinct DELLA-dependent transcriptomes to regulate seed germination and floral development in Arabidopsis. Plant Physiol., 2006. 142(2): p. 509-25 [PMID:16920880] Lewsey M,Robertson FC,Canto T,Palukaitis P,Carr JP Selective targeting of miRNA-regulated plant development by a viral counter-silencing protein. Plant J., 2007. 50(2): p. 240-52 [PMID:17444907] Axtell MJ,Snyder JA,Bartel DP Common functions for diverse small RNAs of land plants. Plant Cell, 2007. 19(6): p. 1750-69 [PMID:17601824] Liu PP, et al. Repression of AUXIN RESPONSE FACTOR10 by microRNA160 is critical for seed germination and post-germination stages. Plant J., 2007. 52(1): p. 133-46 [PMID:17672844] Ehrenreich IM,Purugganan MD Sequence variation of MicroRNAs and their binding sites in Arabidopsis. Plant Physiol., 2008. 146(4): p. 1974-82 [PMID:18305205] Ascencio-Ib Global analysis of Arabidopsis gene expression uncovers a complex array of changes impacting pathogen response and cell cycle during geminivirus infection. Plant Physiol., 2008. 148(1): p. 436-54 [PMID:18650403] Swaminathan K,Peterson K,Jack T The plant B3 superfamily. Trends Plant Sci., 2008. 13(12): p. 647-55 [PMID:18986826] Nonogaki H Repression of transcription factors by microRNA during seed germination and postgerminaiton: Another level of molecular repression in seeds. Plant Signal Behav, 2008. 3(1): p. 65-7 [PMID:19704775] Gutierrez L, et al. Phenotypic plasticity of adventitious rooting in Arabidopsis is controlled by complex regulation of AUXIN RESPONSE FACTOR transcripts and microRNA abundance. Plant Cell, 2009. 21(10): p. 3119-32 [PMID:19820192] Liu X, et al. The role of floral organs in carpels, an Arabidopsis loss-of-function mutation in MicroRNA160a, in organogenesis and the mechanism regulating its expression. Plant J., 2010. 62(3): p. 416-28 [PMID:20136729] Ding Z,Friml J Auxin regulates distal stem cell differentiation in Arabidopsis roots. Proc. Natl. Acad. Sci. U.S.A., 2010. 107(26): p. 12046-51 [PMID:20543136] Varaud E, et al. AUXIN RESPONSE FACTOR8 regulates Arabidopsis petal growth by interacting with the bHLH transcription factor BIGPETALp. Plant Cell, 2011. 23(3): p. 973-83 [PMID:21421811] Vernoux T, et al. The auxin signalling network translates dynamic input into robust patterning at the shoot apex. Mol. Syst. Biol., 2011. 7: p. 508 [PMID:21734647] Li JF,Bush J,Xiong Y,Li L,McCormack M Large-scale protein-protein interaction analysis in Arabidopsis mesophyll protoplasts by split firefly luciferase complementation. PLoS ONE, 2011. 6(11): p. e27364 [PMID:22096563] Qiao M, et al. Proper regeneration from in vitro cultured Arabidopsis thaliana requires the microRNA-directed action of an auxin response factor. Plant J., 2012. 71(1): p. 14-22 [PMID:22335436] Qiao M,Xiang F A set of Arabidopsis thaliana miRNAs involve shoot regeneration in vitro. Plant Signal Behav, 2013. 8(3): p. e23479 [PMID:23333958] Liu X, et al. Auxin controls seed dormancy through stimulation of abscisic acid signaling by inducing ARF-mediated ABI3 activation in Arabidopsis. Proc. Natl. Acad. Sci. U.S.A., 2013. 110(38): p. 15485-90 [PMID:23986496] Yang ZB, et al. TAA1-regulated local auxin biosynthesis in the root-apex transition zone mediates the aluminum-induced inhibition of root growth in Arabidopsis. Plant Cell, 2014. 26(7): p. 2889-904 [PMID:25052716] Bennett T,van den Toorn A,Willemsen V,Scheres B Precise control of plant stem cell activity through parallel regulatory inputs. Development, 2014. 141(21): p. 4055-64 [PMID:25256342] Piya S,Shrestha SK,Binder B,Stewart CN,Hewezi T Protein-protein interaction and gene co-expression maps of ARFs and Aux/IAAs in Arabidopsis. Front Plant Sci, 2014. 5: p. 744 [PMID:25566309] Jin J, et al. An Arabidopsis Transcriptional Regulatory Map Reveals Distinct Functional and Evolutionary Features of Novel Transcription Factors. Mol. Biol. Evol., 2015. 32(7): p. 1767-73 [PMID:25750178] Ye Y, et al. Germostatin resistance locus 1 encodes a PHD finger protein involved in auxin-mediated seed dormancy and germination. Plant J., 2016. 85(1): p. 3-15 [PMID:26611158] Nguyen TC,Obermeier C,Friedt W,Abrams SR,Snowdon RJ Disruption of Germination and Seedling Development in Brassica napus by Mutations Causing Severe Seed Hormonal Imbalance. Front Plant Sci, 2016. 7: p. 322 [PMID:27014334] Liu Z, et al. Repression of callus initiation by the miRNA-directed interaction of auxin-cytokinin in Arabidopsis thaliana. Plant J., 2016. 87(4): p. 391-402 [PMID:27189514] 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] Wójcik AM,Nodine MD,Gaj MD miR160 and miR166/165 Contribute to the LEC2-Mediated Auxin Response Involved in the Somatic Embryogenesis Induction in Arabidopsis. Front Plant Sci, 2017. 8: p. 2024 [PMID:29321785] Lin JS, et al. MicroRNA160 Modulates Plant Development and Heat Shock Protein Gene Expression to Mediate Heat Tolerance in Arabidopsis. Front Plant Sci, 2018. 9: p. 68 [PMID:29449855]