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

KHN39439.1

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: 868aa MW: 96627.2 Da PI: 5.2058

Description

ARF family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
KHN39439.1	genome	TCUHK	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	B3	31.2	3.9e-10	115	186	1	67
EEEE-..-HHHHTT-EE--HHH.HTT......---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHH CS B3 1 ffkvltpsdvlksgrlvlpkkfaeeh......ggkkeesktltledesgrsWevkliyrkksgryvltkGWke 67 f+k+lt sd++++g +++p++ ae+ +++++ ++l+++d++ ++W++++iyr+ ++r l+ G ++ KHN39439.1 115 FCKTLTASDTSTHGGFSVPRRAAEKLfppldyTIQPPT-QELVVRDLHDNTWTFRHIYRGVDERSQLRVGVRR 186 99*******************999*9555555.49***************999998888888776 PP
2	Auxin_resp	114.3	1.1e-37	212	295	1	83
Auxin_resp 1 aahaastksvFevvYnPrastseFvvkvekvekalk.vkvsvGmRfkmafetedsserrlsGtvvgvsdldpvrWpnSkWrsLk 83 aahaa+++s+F+++YnPra++seFv++++k++k++ ++vsvGmRf m+fete+s +rr++Gt+vg+sd+dp+rWp+SkWr+++ KHN39439.1 212 AAHAAANRSPFTIFYNPRACPSEFVIPLAKYRKSVFgTQVSVGMRFGMMFETEESGKRRYMGTIVGISDVDPLRWPGSKWRNIQ 295 79******************************988******************************************986 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SuperFamily	SSF101936	1.23E-31	104	215	IPR015300	DNA-binding pseudobarrel domain
Gene3D	G3DSA:2.40.330.10	1.2E-19	108	186	IPR015300	DNA-binding pseudobarrel domain
CDD	cd10017	1.96E-10	114	183	No hit	No description
SMART	SM01019	0.0037	115	202	IPR003340	B3 DNA binding domain
Pfam	PF02362	5.9E-8	115	186	IPR003340	B3 DNA binding domain
Pfam	PF06507	1.1E-32	212	295	IPR010525	Auxin response factor
PROSITE profile	PS51745	23.555	762	846	IPR000270	PB1 domain
SuperFamily	SSF54277	7.55E-8	764	841	No hit	No description
Pfam	PF02309	1.3E-7	808	849	IPR033389	AUX/IAA domain

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
GO:0005515	Molecular Function	protein binding

Sequence ? help Back to Top
Protein Sequence Length: 868 aa Download sequence Send to blast
MMASMEEKIK IGGGMIVGAQ TLAAEMKLLK EMQEHSGVRK TLNSELWHAC ARPLVSLPQV 60 GSLVFYFPQG HSEQADKETD EIYAQMTLQP LNSEREVFPI SDFGHKHSKH PSEFFCKTLT 120 ASDTSTHGGF SVPRRAAEKL FPPLDYTIQP PTQELVVRDL HDNTWTFRHI YRGVDERSQL 180 RVGVRRVNRQ QTTLPSSVLS ADSMHIGVLA AAAHAAANRS PFTIFYNPRA CPSEFVIPLA 240 KYRKSVFGTQ VSVGMRFGMM FETEESGKRR YMGTIVGISD VDPLRWPGSK WRNIQVEWDE 300 PGCGDKQNRV SVWEIETPES LFIFPSLTSG LKRPLPSGLL ENEWGTLLRR PFIRVPENGT 360 MELSNSIPNL YSEHMMRMLL KPQLINNNGA FLSAMQQESA ATRGPLQEMK TTLAAENQMP 420 LKNLHPHSIP DQPNALNMQS LLKNDQPEKL HPLGKIDNHL SSGIVIDKPK SESEVLPDHV 480 IDYPSMEGCN IEKVAANPVN QQGLANQLPF HNQNQSPLLP QSSPWPMPPQ IESSMPHPQM 540 IDMVQADSAM VNGLFPQLDI NEWMSYASSQ PFAGQNRPTG PLSDLQEHTS LQPQVVNPPL 600 PSMNNEVWDH YVKNLKFLSQ ADQLTSICQP GLYGLNGIPS SNNLRDLSAE SNNQSEICVN 660 VDASNSVGTT VVDPSTSSTI LDEFCTMKDR EFQNPQDCMV GNLSSSQDVQ SQITSASLTE 720 SHAFPLRDIP DNSGGTSSSH VDFDESSFLQ NNSWQQVPAP IRTYTKVQKA GSVGRSIDVT 780 TFKNYEELIR AIECMFGLDG LLNDTKCSGW KLVYVDYESD VLLVGDDPWE EFVGCVRCIR 840 ILSPSEVQQM SEEGMKLLNS GALQGMNV

Sequence ? help Back to Top

Protein Sequence Length: 868 aa Download sequence Send to blast

MMASMEEKIK IGGGMIVGAQ TLAAEMKLLK EMQEHSGVRK TLNSELWHAC ARPLVSLPQV  60
GSLVFYFPQG HSEQADKETD EIYAQMTLQP LNSEREVFPI SDFGHKHSKH PSEFFCKTLT  120
ASDTSTHGGF SVPRRAAEKL FPPLDYTIQP PTQELVVRDL HDNTWTFRHI YRGVDERSQL  180
RVGVRRVNRQ QTTLPSSVLS ADSMHIGVLA AAAHAAANRS PFTIFYNPRA CPSEFVIPLA  240
KYRKSVFGTQ VSVGMRFGMM FETEESGKRR YMGTIVGISD VDPLRWPGSK WRNIQVEWDE  300
PGCGDKQNRV SVWEIETPES LFIFPSLTSG LKRPLPSGLL ENEWGTLLRR PFIRVPENGT  360
MELSNSIPNL YSEHMMRMLL KPQLINNNGA FLSAMQQESA ATRGPLQEMK TTLAAENQMP  420
LKNLHPHSIP DQPNALNMQS LLKNDQPEKL HPLGKIDNHL SSGIVIDKPK SESEVLPDHV  480
IDYPSMEGCN IEKVAANPVN QQGLANQLPF HNQNQSPLLP QSSPWPMPPQ IESSMPHPQM  540
IDMVQADSAM VNGLFPQLDI NEWMSYASSQ PFAGQNRPTG PLSDLQEHTS LQPQVVNPPL  600
PSMNNEVWDH YVKNLKFLSQ ADQLTSICQP GLYGLNGIPS SNNLRDLSAE SNNQSEICVN  660
VDASNSVGTT VVDPSTSSTI LDEFCTMKDR EFQNPQDCMV GNLSSSQDVQ SQITSASLTE  720
SHAFPLRDIP DNSGGTSSSH VDFDESSFLQ NNSWQQVPAP IRTYTKVQKA GSVGRSIDVT  780
TFKNYEELIR AIECMFGLDG LLNDTKCSGW KLVYVDYESD VLLVGDDPWE EFVGCVRCIR  840
ILSPSEVQQM SEEGMKLLNS GALQGMNV

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
4ldu_A	1e-161	21	320	32	392	Auxin response factor 5
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). Seems to act as transcriptional activator. Formation of heterodimers with Aux/IAA proteins may alter their ability to modulate early auxin response genes expression. Mediates embryo axis formation and vascular tissues differentiation. Functionally redundant with ARF7. May be necessary to counteract AMP1 activity. {ECO:0000269\|PubMed:12036261, ECO:0000269\|PubMed:14973283, ECO:0000269\|PubMed:17553903}.

Cis-element ? help Back to Top
Source	Link
PlantRegMap	KHN39439.1

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	AP015036	0.0	AP015036.1 Vigna angularis var. angularis DNA, chromosome 3, almost complete sequence, cultivar: Shumari.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_028201013.1	0.0	auxin response factor 5-like
Swissprot	P93024	0.0	ARFE_ARATH; Auxin response factor 5
TrEMBL	A0A445H8Z3	0.0	A0A445H8Z3_GLYSO; Auxin response factor
STRING	GLYMA14G40540.1	0.0	(Glycine max)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Fabids	OGEF8991	32	41

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT1G19850.1	0.0	ARF family protein

Publications ? help Back to Top
Chen MK,Wilson RL,Palme K,Ditengou FA,Shpak ED ERECTA family genes regulate auxin transport in the shoot apical meristem and forming leaf primordia. Plant Physiol., 2013. 162(4): p. 1978-91 [PMID:23821653] 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] Huang JB, et al. ROP3 GTPase contributes to polar auxin transport and auxin responses and is important for embryogenesis and seedling growth in Arabidopsis. Plant Cell, 2014. 26(9): p. 3501-18 [PMID:25217509] Qi J, et al. Auxin depletion from leaf primordia contributes to organ patterning. Proc. Natl. Acad. Sci. U.S.A., 2014. 111(52): p. 18769-74 [PMID:25512543] Crawford BC, et al. Plant development. Genetic control of distal stem cell fate within root and embryonic meristems. Science, 2015. 347(6222): p. 655-9 [PMID:25612610] Zhang Y, et al. Regulation of oncogene expression in T-DNA-transformed host plant cells. PLoS Pathog., 2015. 11(1): p. e1004620 [PMID:25615824] Robert HS, et al. Plant embryogenesis requires AUX/LAX-mediated auxin influx. Development, 2015. 142(4): p. 702-11 [PMID:25617434] Krogan NT,Berleth T The identification and characterization of specific ARF-Aux/IAA regulatory modules in plant growth and development. Plant Signal Behav, 2015. 10(4): p. e992748 [PMID:25830553] Ckurshumova W,Berleth T Overcoming recalcitrance - Auxin response factor functions in plant regeneration. Plant Signal Behav, 2015. 10(7): p. e993293 [PMID:26098229] Wendrich JR, et al. A set of domain-specific markers in the Arabidopsis embryo. Plant Reprod, 2015. 28(3-4): p. 153-60 [PMID:26216537] Wu MF, et al. Auxin-regulated chromatin switch directs acquisition of flower primordium founder fate. Elife, 2015. 4: p. e09269 [PMID:26460543] Yamaguchi N,Jeong CW,Nole-Wilson S,Krizek BA,Wagner D AINTEGUMENTA and AINTEGUMENTA-LIKE6/PLETHORA3 Induce LEAFY Expression in Response to Auxin to Promote the Onset of Flower Formation in Arabidopsis. Plant Physiol., 2016. 170(1): p. 283-93 [PMID:26537561] Müller CJ, et al. PHABULOSA Mediates an Auxin Signaling Loop to Regulate Vascular Patterning in Arabidopsis. Plant Physiol., 2016. 170(2): p. 956-70 [PMID:26637548] Herud O,Weijers D,Lau S,Jürgens G Auxin responsiveness of the MONOPTEROS-BODENLOS module in primary root initiation critically depends on the nuclear import kinetics of the Aux/IAA inhibitor BODENLOS. Plant J., 2016. 85(2): p. 269-77 [PMID:26714008] Luo S, et al. Constitutive Expression of OsIAA9 Affects Starch Granules Accumulation and Root Gravitropic Response in Arabidopsis. Front Plant Sci, 2015. 6: p. 1156 [PMID:26734051] 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] Krogan NT,Marcos D,Weiner AI,Berleth T The auxin response factor MONOPTEROS controls meristem function and organogenesis in both the shoot and root through the direct regulation of PIN genes. New Phytol., 2016. 212(1): p. 42-50 [PMID:27441727] Fendrych M,Leung J,Friml J TIR1/AFB-Aux/IAA auxin perception mediates rapid cell wall acidification and growth of Arabidopsis hypocotyls. Elife, 2018. [PMID:27627746] Matthes M,Torres-Ruiz RA Boronic acid treatment phenocopies monopteros by affecting PIN1 membrane stability and polar auxin transport in Arabidopsis thaliana embryos. Development, 2016. 143(21): p. 4053-4062 [PMID:27697905] Bhatia N, et al. Auxin Acts through MONOPTEROS to Regulate Plant Cell Polarity and Pattern Phyllotaxis. Curr. Biol., 2016. 26(23): p. 3202-3208 [PMID:27818174] 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] Möller BK, et al. Auxin response cell-autonomously controls ground tissue initiation in the early Arabidopsis embryo. Proc. Natl. Acad. Sci. U.S.A., 2017. 114(12): p. E2533-E2539 [PMID:28265057] Carey NS,Krogan NT The role of AUXIN RESPONSE FACTORs in the development and differential growth of inflorescence stems. Plant Signal Behav, 2017. 12(4): p. e1307492 [PMID:28340328] Guan C, et al. Spatial Auxin Signaling Controls Leaf Flattening in Arabidopsis. Curr. Biol., 2017. 27(19): p. 2940-2950.e4 [PMID:28943086] Gaillochet C, et al. Control of plant cell fate transitions by transcriptional and hormonal signals. Elife, 2018. [PMID:29058667] Zheng K, et al. Involvement of PACLOBUTRAZOL RESISTANCE6/KIDARI, an Atypical bHLH Transcription Factor, in Auxin Responses in Arabidopsis. Front Plant Sci, 2017. 8: p. 1813 [PMID:29114256] 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]