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

Thecc1EG034194t1

Common Name

TCM_034194

Organism

Theobroma cacao

Taxonomic ID

3641

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Malvales; Malvaceae; Byttnerioideae; Theobroma

Family

ARF

Protein Properties

Length: 952aa MW: 104611 Da PI: 5.0956

Description

ARF family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Thecc1EG034194t1	genome	CGD	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	149	250	1	99
EEEE-..-HHHHTT-EE--HHH.HTT.......---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE-S CS B3 1 ffkvltpsdvlksgrlvlpkkfaeeh.......ggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfvvFkldg 86 f+k+lt sd++++g +++p++ ae+ ++++ + ++l+++d++ ++W++++iyr++++r++lt+GW+ Fv +++L++gD+v+F + Thecc1EG034194t1 149 FCKTLTASDTSTHGGFSVPRRAAEKLfppldytMQPP-T-QELVVRDLHDNTWTFRHIYRGQPKRHLLTTGWSLFVGSKRLRAGDSVLFI--R 237 99*******************999*954444.4.38********************************************..4 PP SSEE..EEEEE-S CS B3 87 rsefelvvkvfrk 99 +++ +l+v+v+r+ Thecc1EG034194t1 238 DEKSQLMVGVRRA 250 577778***97 PP
2	Auxin_resp	112.8	3.2e-37	275	358	1	83
Auxin_resp 1 aahaastksvFevvYnPrastseFvvkvekvekalk.vkvsvGmRfkmafetedsserrlsGtvvgvsdldpvrWpnSkWrsLk 83 aahaa+++s+F+++YnPra++seFv++++k++k+++ ++vsvGmRf m+fet++s +rr++Gt vg+ dldp+rWp+SkWr+L+ Thecc1EG034194t1 275 AAHAAANRSPFTIFYNPRACPSEFVIPLAKYRKSVYgTQVSVGMRFGMMFETDESGKRRYMGTLVGIGDLDPLRWPGSKWRNLQ 358 79********************************9*******************************************97 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SuperFamily	SSF101936	1.96E-46	136	278	IPR015300	DNA-binding pseudobarrel domain
Gene3D	G3DSA:2.40.330.10	1.2E-42	141	263	IPR015300	DNA-binding pseudobarrel domain
CDD	cd10017	4.33E-23	148	249	No hit	No description
Pfam	PF02362	5.4E-22	149	250	IPR003340	B3 DNA binding domain
SMART	SM01019	3.0E-25	149	251	IPR003340	B3 DNA binding domain
PROSITE profile	PS50863	13.211	149	251	IPR003340	B3 DNA binding domain
Pfam	PF06507	2.4E-32	275	358	IPR010525	Auxin response factor
Pfam	PF02309	6.5E-9	830	923	IPR033389	AUX/IAA domain
PROSITE profile	PS51745	24.401	837	921	IPR000270	PB1 domain
SuperFamily	SSF54277	5.23E-9	839	916	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:0009734	Biological Process	auxin-activated signaling pathway
GO:0009908	Biological Process	flower development
GO:0009942	Biological Process	longitudinal axis specification
GO:0010305	Biological Process	leaf vascular tissue pattern formation
GO:0048364	Biological Process	root development
GO:0048507	Biological Process	meristem development
GO:0005634	Cellular Component	nucleus
GO:0016020	Cellular Component	membrane
GO:0042802	Molecular Function	identical protein binding
GO:0044212	Molecular Function	transcription regulatory region DNA binding

Sequence ? help Back to Top
Protein Sequence Length: 952 aa Download sequence Send to blast
MGSVVEEKIK PGALVNGGPQ ATLLEEMKLL KEMQDQSGAR KAIHSELWHA CAGPLVSLPQ 60 VGSLVYYFPQ GHSEQVAVST KRMATSQIPN YPNLPSQLMC QVHNVTLHAD RDTDEIYAQM 120 SLQPVNSEKD VFPIPDFGLK SSKHPNEFFC KTLTASDTST HGGFSVPRRA AEKLFPPLDY 180 TMQPPTQELV VRDLHDNTWT FRHIYRGQPK RHLLTTGWSL FVGSKRLRAG DSVLFIRDEK 240 SQLMVGVRRA NRQQTTLPSS VLSADSMHIG VLAAAAHAAA NRSPFTIFYN PRACPSEFVI 300 PLAKYRKSVY GTQVSVGMRF GMMFETDESG KRRYMGTLVG IGDLDPLRWP GSKWRNLQVE 360 WDEPGCNDKP NRVSAWEIET PESLFIFPSL TSGLKRPLHP GILGAESEWG SLIKRPLLQF 420 PENGNGNLPY SISNLCSEQL MKMMLKPQLV NHPGVFASTL QQISAVKGSP LEEMKNLQST 480 SNQKPQLIQS ENLFVENQNL TQLVPDQPDP INSNLPKINA NGNLHPPANK FESQTQARSS 540 NEKLKLESEH STDQLSQLTS TSECNEEKLA ANAASPSTIL NQLSFPNQNQ IPFPLQNNPW 600 PIQSQLESSA LQAHQMQVPQ ADITTLSSFL PFLDPDEWTS HLSACQPLAG IYRSPGPVPV 660 VGLQDSSAVF TEATDPSLTT GGQDTWDHQL NNCRILSHVD QLTSIPQQDS YNLSSGGVRD 720 LSDDSNNQSG IYSCLNIDVS NGGSTVIDPS VSSAILDEFC SLKDADFQNP SDCLVGNFSS 780 SQDVQSQITS ASLADSQAFS RQELPDSSGG TSSSNVDFDE SGLLQNNSWQ QMAPRVRTYT 840 KVQKAGSVGR SLDVTSFKNY DELISAIECM FGLKGLLNDP RGSGWKLVYV DYENDVLLVG 900 DDPWEEFVGC VRCIRILSPT EVQQMSEEGM KLLNSATVQG INGTNSEGCN A*

Sequence ? help Back to Top

Protein Sequence Length: 952 aa Download sequence Send to blast

MGSVVEEKIK PGALVNGGPQ ATLLEEMKLL KEMQDQSGAR KAIHSELWHA CAGPLVSLPQ  60
VGSLVYYFPQ GHSEQVAVST KRMATSQIPN YPNLPSQLMC QVHNVTLHAD RDTDEIYAQM  120
SLQPVNSEKD VFPIPDFGLK SSKHPNEFFC KTLTASDTST HGGFSVPRRA AEKLFPPLDY  180
TMQPPTQELV VRDLHDNTWT FRHIYRGQPK RHLLTTGWSL FVGSKRLRAG DSVLFIRDEK  240
SQLMVGVRRA NRQQTTLPSS VLSADSMHIG VLAAAAHAAA NRSPFTIFYN PRACPSEFVI  300
PLAKYRKSVY GTQVSVGMRF GMMFETDESG KRRYMGTLVG IGDLDPLRWP GSKWRNLQVE  360
WDEPGCNDKP NRVSAWEIET PESLFIFPSL TSGLKRPLHP GILGAESEWG SLIKRPLLQF  420
PENGNGNLPY SISNLCSEQL MKMMLKPQLV NHPGVFASTL QQISAVKGSP LEEMKNLQST  480
SNQKPQLIQS ENLFVENQNL TQLVPDQPDP INSNLPKINA NGNLHPPANK FESQTQARSS  540
NEKLKLESEH STDQLSQLTS TSECNEEKLA ANAASPSTIL NQLSFPNQNQ IPFPLQNNPW  600
PIQSQLESSA LQAHQMQVPQ ADITTLSSFL PFLDPDEWTS HLSACQPLAG IYRSPGPVPV  660
VGLQDSSAVF TEATDPSLTT GGQDTWDHQL NNCRILSHVD QLTSIPQQDS YNLSSGGVRD  720
LSDDSNNQSG IYSCLNIDVS NGGSTVIDPS VSSAILDEFC SLKDADFQNP SDCLVGNFSS  780
SQDVQSQITS ASLADSQAFS RQELPDSSGG TSSSNVDFDE SGLLQNNSWQ QMAPRVRTYT  840
KVQKAGSVGR SLDVTSFKNY DELISAIECM FGLKGLLNDP RGSGWKLVYV DYENDVLLVG  900
DDPWEEFVGC VRCIRILSPT EVQQMSEEGM KLLNSATVQG INGTNSEGCN A*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
4ldu_A	0.0	3	383	6	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}.

Binding Motif ? help Back to Top
Motif ID	Method	Source	Motif file
MP00153	DAP	Transfer from AT1G19850	Download

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

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_017981253.1	0.0	PREDICTED: auxin response factor 5
Swissprot	P93024	0.0	ARFE_ARATH; Auxin response factor 5
TrEMBL	A0A061FD42	0.0	A0A061FD42_THECC; Auxin response factor
STRING	EOY14976	0.0	(Theobroma cacao)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM5808	27	46

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

Link Out ? help Back to Top
Phytozome	Thecc1EG034194t1
Entrez Gene	18591522

Publications ? help Back to Top
Motamayor JC, et al. The genome sequence of the most widely cultivated cacao type and its use to identify candidate genes regulating pod color. Genome Biol., 2013. 14(6): p. r53 [PMID:23731509] 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] 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]