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

AT4G30080.1

Common Name

ARF16, F6G3.110

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: 670aa MW: 73978.8 Da PI: 7.3381

Description

auxin response factor 16

Gene Model

Gene Model ID	Type	Source	Coding Sequence
AT4G30080.1	genome	TAIR	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	B3	77.3	1.7e-24	120	221	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+ + +++ AT4G30080.1 120 FAKTLTQSDANNGGGFSVPRYCAETIfprldynAEPPVQ--TILAKDVHGDVWKFRHIYRGTPRRHLLTTGWSNFVNQKKLVAGDSIVFM--RAENGD 213 89**************************985444444..8999*****************************************..448899 PP .EEEEE-S CS B3 92 lvvkvfrk 99 l+v+++r+ AT4G30080.1 214 LCVGIRRA 221 9**997 PP
2	Auxin_resp	113.7	1.7e-37	279	362	1	83
Auxin_resp 1 aahaastksvFevvYnPrastseFvvkvekvekalkvkvsvGmRfkmafetedsserrl.sGtvvgvsdldpvrWpnSkWrsLk 83 aa+ a ++ +FevvY+PrastseF+vk+ + ++a++++++ GmRfkmafetedss++++ +Gtv++v+ +dp+rWpnS+Wr+L+ AT4G30080.1 279 AATLAISGRPFEVVYYPRASTSEFCVKALDARAAMRIPWCSGMRFKMAFETEDSSRISWfMGTVSAVNVSDPIRWPNSPWRLLQ 362 67788899**************************************************************************97 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Gene3D	G3DSA:2.40.330.10	5.5E-39	112	227	IPR015300	DNA-binding pseudobarrel domain
SuperFamily	SSF101936	7.72E-30	115	223	IPR015300	DNA-binding pseudobarrel domain
CDD	cd10017	2.25E-22	118	220	No hit	No description
SMART	SM01019	7.1E-23	120	222	IPR003340	B3 DNA binding domain
PROSITE profile	PS50863	13.352	120	222	IPR003340	B3 DNA binding domain
Pfam	PF02362	1.8E-22	120	221	IPR003340	B3 DNA binding domain
Pfam	PF06507	2.7E-31	279	362	IPR010525	Auxin response factor
PROSITE profile	PS51745	18.27	584	664	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:0009733	Biological Process	response to auxin
GO:0009734	Biological Process	auxin-activated signaling pathway
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: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:0020038	anatomy	petiole
PO:0020100	anatomy	hypocotyl
PO:0020130	anatomy	central root cap
PO:0020131	anatomy	lateral root cap
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: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:0007611	developmental stage	petal differentiation and expansion stage
PO:0007616	developmental stage	flowering stage

Sequence ? help Back to Top
Protein Sequence Length: 670 aa Download sequence Send to blast
MINVMNPMKG GTEKGLDPQL WHACAGGMVR MPPMNSKVFY FPQGHAENAY DCVDFGNLPI 60 PPMVLCRVLA IKYMADAESD EVFAKLRLIP LKDDEYVDHE YGDGEDSNGF ESNSEKTPSF 120 AKTLTQSDAN NGGGFSVPRY CAETIFPRLD YNAEPPVQTI LAKDVHGDVW KFRHIYRGTP 180 RRHLLTTGWS NFVNQKKLVA GDSIVFMRAE NGDLCVGIRR AKRGGIGNGP EYSAGWNPIG 240 GSCGYSSLLR EDESNSLRRS NCSLADRKGK VTAESVIEAA TLAISGRPFE VVYYPRASTS 300 EFCVKALDAR AAMRIPWCSG MRFKMAFETE DSSRISWFMG TVSAVNVSDP IRWPNSPWRL 360 LQVAWDEPDL LQNVKRVNPW LVELVSNVHP IPLTSFSPPR KKMRLPQHPD YNNLINSIPV 420 PSFPSNPLIR SSPLSSVLDN VPVGLQGARH NAHQYYGLSS SDLHHYYLNR PPPPPPPSSL 480 QLSPSLGLRN IDTKNEKGFC FLTMGTTPCN DTKSKKSHIV LFGKLILPEE QLSEKGSTDT 540 ANIEKTQISS GGSNQNGVAG REFSSSDEGS PCSKKVHDAS GLETGHCKVF MESDDVGRTL 600 DLSVLGSYEE LSRKLSDMFG IKKSEMLSSV LYRDASGAIK YAGNEPFSEF LKTARRLTIL 660 TEQGSESVVV

Sequence ? help Back to Top

Protein Sequence Length: 670 aa Download sequence Send to blast

MINVMNPMKG GTEKGLDPQL WHACAGGMVR MPPMNSKVFY FPQGHAENAY DCVDFGNLPI  60
PPMVLCRVLA IKYMADAESD EVFAKLRLIP LKDDEYVDHE YGDGEDSNGF ESNSEKTPSF  120
AKTLTQSDAN NGGGFSVPRY CAETIFPRLD YNAEPPVQTI LAKDVHGDVW KFRHIYRGTP  180
RRHLLTTGWS NFVNQKKLVA GDSIVFMRAE NGDLCVGIRR AKRGGIGNGP EYSAGWNPIG  240
GSCGYSSLLR EDESNSLRRS NCSLADRKGK VTAESVIEAA TLAISGRPFE VVYYPRASTS  300
EFCVKALDAR AAMRIPWCSG MRFKMAFETE DSSRISWFMG TVSAVNVSDP IRWPNSPWRL  360
LQVAWDEPDL LQNVKRVNPW LVELVSNVHP IPLTSFSPPR KKMRLPQHPD YNNLINSIPV  420
PSFPSNPLIR SSPLSSVLDN VPVGLQGARH NAHQYYGLSS SDLHHYYLNR PPPPPPPSSL  480
QLSPSLGLRN IDTKNEKGFC FLTMGTTPCN DTKSKKSHIV LFGKLILPEE QLSEKGSTDT  540
ANIEKTQISS GGSNQNGVAG REFSSSDEGS PCSKKVHDAS GLETGHCKVF MESDDVGRTL  600
DLSVLGSYEE LSRKLSDMFG IKKSEMLSSV LYRDASGAIK YAGNEPFSEF LKTARRLTIL  660
TEQGSESVVV

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
4ldu_A	5e-77	2	383	37	388	Auxin response factor 5
Search in ModeBase

Expression -- UniGene ? help Back to Top
UniGene ID	E-value	Expressed in
At.3365	0.0	root\| silique

Expression -- Microarray ? help Back to Top
Source	ID	E-value
GEO	145349425	0.0
Genevisible	253662_at	0.0
Expression Atlas	AT4G30080	-
AtGenExpress	AT4G30080	-
ATTED-II	AT4G30080	-

Functional Description ? help Back to Top
Source	Description
TAIR	Involved in root cap cell differentiation. Gene expression is regulated by mir160.Located in the nucleus.
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
ARF10 and ARF16 control root cap formation in root. Auxin and micro RNA 160(miR160) regulate the expression of ARF10 and ARF16 genes independently. [ARF16] [PMID: 16006581] 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] Auxin recruits AUXIN RESPONSE FACTOR 10 and AUXIN RESPONSE FACTOR 16 to control the expression of ABI3 during seed germination. [PMID: 23986496]

Binding Motif ? help Back to Top
Motif ID	Method	Source	Motif file
MP00461	DAP	27203113	Download

Cis-element ? help Back to Top
Source	Link
PlantRegMap	AT4G30080.1

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 -- Hormone ? help Back to Top
Source	Hormone
AHD	auxin

Interaction ? help Back to Top
Source	Intact With
IntAct	Search Q93YR9

Phenotype -- Mutation ? help Back to Top
Source	ID
T-DNA Express	AT4G30080

Annotation -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	AY059792	0.0	AY059792.1 Arabidopsis thaliana putative transcription factor (At4g30080) mRNA, complete cds.
GenBank	AY091198	0.0	AY091198.1 Arabidopsis thaliana putative transcription factor (At4g30080) mRNA, complete cds.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	NP_567841.1	0.0	auxin response factor 16
Swissprot	Q93YR9	0.0	ARFP_ARATH; Auxin response factor 16
TrEMBL	D7MC88	0.0	D7MC88_ARALL; Auxin response factor
STRING	AT4G30080.1	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	AT4G30080.1
Entrez Gene	829131
iHOP	AT4G30080
wikigenes	AT4G30080

Publications ? help Back to Top
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] Yamada K, et al. Empirical analysis of transcriptional activity in the Arabidopsis genome. Science, 2003. 302(5646): p. 842-6 [PMID:14593172] 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] Tepperman JM, et al. Expression profiling of phyB mutant demonstrates substantial contribution of other phytochromes to red-light-regulated gene expression during seedling de-etiolation. Plant J., 2004. 38(5): p. 725-39 [PMID:15144375] 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] Nemhauser JL,Mockler TC,Chory J Interdependency of brassinosteroid and auxin signaling in Arabidopsis. PLoS Biol., 2004. 2(9): p. E258 [PMID:15328536] 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] Weijers D, et al. Developmental specificity of auxin response by pairs of ARF and Aux/IAA transcriptional regulators. EMBO J., 2005. 24(10): p. 1874-85 [PMID:15889151] 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] Vanneste S, et al. Cell cycle progression in the pericycle is not sufficient for SOLITARY ROOT/IAA14-mediated lateral root initiation in Arabidopsis thaliana. Plant Cell, 2005. 17(11): p. 3035-50 [PMID:16243906] Nemhauser JL,Hong F,Chory J Different plant hormones regulate similar processes through largely nonoverlapping transcriptional responses. Cell, 2006. 126(3): p. 467-75 [PMID:16901781] 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] Ehrenreich IM,Purugganan MD Sequence variation of MicroRNAs and their binding sites in Arabidopsis. Plant Physiol., 2008. 146(4): p. 1974-82 [PMID:18305205] Swaminathan K,Peterson K,Jack T The plant B3 superfamily. Trends Plant Sci., 2008. 13(12): p. 647-55 [PMID:18986826] 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] 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] Liu Z,Jia L,Wang H,He Y HYL1 regulates the balance between adaxial and abaxial identity for leaf flattening via miRNA-mediated pathways. J. Exp. Bot., 2011. 62(12): p. 4367-81 [PMID:21610018] 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] Arabidopsis Interactome Mapping Consortium Evidence for network evolution in an Arabidopsis interactome map. Science, 2011. 333(6042): p. 601-7 [PMID:21798944] 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] We Convergent targeting of a common host protein-network by pathogen effectors from three kingdoms of life. Cell Host Microbe, 2014. 16(3): p. 364-75 [PMID:25211078] 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] 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] Zhang GZ, et al. Ectopic expression of UGT75D1, a glycosyltransferase preferring indole-3-butyric acid, modulates cotyledon development and stress tolerance in seed germination of Arabidopsis thaliana. Plant Mol. Biol., 2016. 90(1-2): p. 77-93 [PMID:26496910] 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] 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]