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

Lsa007568

Organism

Lactuca sativa

Taxonomic ID

4236

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; asterids; campanulids; Asterales; Asteraceae; Cichorioideae; Cichorieae; Lactucinae; Lactuca

Family

ARF

Protein Properties

Length: 596aa MW: 65522.7 Da PI: 7.6737

Description

ARF family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
gnl\|UG\|Lsa#S58694429	PU_ref	Unigene	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	B3	75.1	8.1e-24	165	266	1	99
EEEE-..-HHHHTT-EE--HHH.HTT......---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE-SSSEE..EE CS B3 1 ffkvltpsdvlksgrlvlpkkfaeeh......ggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfvvFkldgrsefelvv 94 f+k+lt sd++++g +++p++ ae++ + +++ s++l+ +d++g +W++++iyr++++r++lt+GW+ Fv+ ++L gD v+F + +++ l++ Lsa007568 165 FCKTLTASDTSTHGGFSVPRRAAEDCfppldyK-QQRPSQELVAKDLHGTEWKFRHIYRGQPRRHLLTTGWSAFVNKKKLVCGDAVLFL--RGDDGVLRL 261 99**************************963.3445679**********************************************..347888999 PP EEE-S CS B3 95 kvfrk 99 +++r+ Lsa007568 262 GIRRA 266 99987 PP
2	Auxin_resp	108.3	8.2e-36	289	370	1	82
Auxin_resp 1 aahaastksvFevvYnPrastseFvvkvekvekalkvkvsvGmRfkmafetedsserrlsGtvvgvsdldpvrWpnSkWrsL 82 +++++s ++vF+v+YnPr ++se +v++++++k+l+v +s+GmRfkm++eteds +r +Gtv+gvsd+dp +Wp+SkWr+L Lsa007568 289 VVNSISRRTVFNVYYNPRGGSSECIVPYNQFLKSLSVTFSPGMRFKMRLETEDSGDQRSMGTVTGVSDIDPAKWPGSKWRCL 370 67899****************************************************************************9 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Gene3D	G3DSA:2.40.330.10	9.1E-41	157	270	IPR015300	DNA-binding pseudobarrel domain
SuperFamily	SSF101936	8.76E-42	159	267	IPR015300	DNA-binding pseudobarrel domain
CDD	cd10017	2.58E-23	163	265	No hit	No description
Pfam	PF02362	5.1E-22	165	266	IPR003340	B3 DNA binding domain
SMART	SM01019	2.2E-22	165	267	IPR003340	B3 DNA binding domain
PROSITE profile	PS50863	13.112	165	267	IPR003340	B3 DNA binding domain
Pfam	PF06507	4.9E-31	290	370	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: 596 aa Download sequence Send to blast
MCGLIDLNTV NDDDTDEVST SSSSSNASGS ITVPAPAPPP VSSGSGSDST PVVCCLELWH 60 ACAGPLISLP KKGNAVVYCP QGHLEQLQSS GDCPTSGDCN LPPHVFCCVL DVKLHAEAGT 120 DDVYAQVSLI QDPQLEQKWR EGGRKVESAE DDNGVAEKST TPHMFCKTLT ASDTSTHGGF 180 SVPRRAAEDC FPPLDYKQQR PSQELVAKDL HGTEWKFRHI YRGQPRRHLL TTGWSAFVNK 240 KKLVCGDAVL FLRGDDGVLR LGIRRATQAK VASSLPTFCS LQMNDFANVV NSISRRTVFN 300 VYYNPRGGSS ECIVPYNQFL KSLSVTFSPG MRFKMRLETE DSGDQRSMGT VTGVSDIDPA 360 KWPGSKWRCL TVRWDSVEVP RQNRVSPWEI ERLGPVSEIG SFVSPISKRT RTGFPVLKDR 420 TTSDLGESIR FHKVLQGQEI YGFYPSNNTR NQTSVGFGES LRFNRVLQGQ EITSNGNLWS 480 QPSRAFSSSS PSSVLRFPQA IGRVPDGYPV HYVDNVKAFN DQSRQVFVSP MKKLPEEPVS 540 TAKNSCRLFG FSLTEGMEAS RCPNEDLVHA KGPLGSCTNE RVYPWCRSND GCVQGL

Sequence ? help Back to Top

Protein Sequence Length: 596 aa Download sequence Send to blast

MCGLIDLNTV NDDDTDEVST SSSSSNASGS ITVPAPAPPP VSSGSGSDST PVVCCLELWH  60
ACAGPLISLP KKGNAVVYCP QGHLEQLQSS GDCPTSGDCN LPPHVFCCVL DVKLHAEAGT  120
DDVYAQVSLI QDPQLEQKWR EGGRKVESAE DDNGVAEKST TPHMFCKTLT ASDTSTHGGF  180
SVPRRAAEDC FPPLDYKQQR PSQELVAKDL HGTEWKFRHI YRGQPRRHLL TTGWSAFVNK  240
KKLVCGDAVL FLRGDDGVLR LGIRRATQAK VASSLPTFCS LQMNDFANVV NSISRRTVFN  300
VYYNPRGGSS ECIVPYNQFL KSLSVTFSPG MRFKMRLETE DSGDQRSMGT VTGVSDIDPA  360
KWPGSKWRCL TVRWDSVEVP RQNRVSPWEI ERLGPVSEIG SFVSPISKRT RTGFPVLKDR  420
TTSDLGESIR FHKVLQGQEI YGFYPSNNTR NQTSVGFGES LRFNRVLQGQ EITSNGNLWS  480
QPSRAFSSSS PSSVLRFPQA IGRVPDGYPV HYVDNVKAFN DQSRQVFVSP MKKLPEEPVS  540
TAKNSCRLFG FSLTEGMEAS RCPNEDLVHA KGPLGSCTNE RVYPWCRSND GCVQGL

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
4ldv_A	1e-111	42	398	7	360	Auxin response factor 1
4ldw_A	1e-111	42	398	7	360	Auxin response factor 1
4ldw_B	1e-111	42	398	7	360	Auxin response factor 1
4ldy_A	1e-111	42	398	7	360	Auxin response factor 1
4ldy_B	1e-111	42	398	7	360	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. Involved in the establishment or elaboration of tissue patterning during gynoecial development. {ECO:0000269\|PubMed:10952886, ECO:0000269\|PubMed:12036261}.

Regulation -- Description ? help Back to Top
Source	Description
UniProt	INDUCTION: Negatively regulated by AHL21/GIK. {ECO:0000269\|PubMed:19956801}.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_023736755.1	0.0	auxin response factor 3-like
Swissprot	O23661	1e-173	ARFC_ARATH; Auxin response factor 3
TrEMBL	A0A2J6K983	0.0	A0A2J6K983_LACSA; Auxin response factor
STRING	Migut.M01096.1.p	0.0	(Erythranthe guttata)

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT2G33860.1	1e-171	ARF family protein

Publications ? help Back to Top
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] Thoma R,Chandler JW Polarity in the early floral meristem of Arabidopsis. Plant Signal Behav, 2015. 10(4): p. e992733 [PMID:25806573] Lora J,Hormaza JI,Herrero M Transition from two to one integument in Prunus species: expression pattern of INNER NO OUTER (INO), ABERRANT TESTA SHAPE (ATS) and ETTIN (ETT). New Phytol., 2015. 208(2): p. 584-95 [PMID:25991552] Machida C,Nakagawa A,Kojima S,Takahashi H,Machida Y The complex of ASYMMETRIC LEAVES (AS) proteins plays a central role in antagonistic interactions of genes for leaf polarity specification in Arabidopsis. Wiley Interdiscip Rev Dev Biol, 2015 Nov-Dec. 4(6): p. 655-71 [PMID:26108442] Cabrera J, et al. Differentially expressed small RNAs in Arabidopsis galls formed by Meloidogyne javanica: a functional role for miR390 and its TAS3-derived tasiRNAs. New Phytol., 2016. 209(4): p. 1625-40 [PMID:26542733] Husbands AY,Benkovics AH,Nogueira FT,Lodha M,Timmermans MC The ASYMMETRIC LEAVES Complex Employs Multiple Modes of Regulation to Affect Adaxial-Abaxial Patterning and Leaf Complexity. Plant Cell, 2015. 27(12): p. 3321-35 [PMID:26589551] 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] Matsumura Y, et al. A genetic link between epigenetic repressor AS1-AS2 and a putative small subunit processome in leaf polarity establishment of Arabidopsis. Biol Open, 2016. 5(7): p. 942-54 [PMID:27334696] Simonini S, et al. A noncanonical auxin-sensing mechanism is required for organ morphogenesis in Arabidopsis. Genes Dev., 2016. 30(20): p. 2286-2296 [PMID:27898393] Pfannebecker KC,Lange M,Rupp O,Becker A An Evolutionary Framework for Carpel Developmental Control Genes. Mol. Biol. Evol., 2017. 34(2): p. 330-348 [PMID:28049761] 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] Su Z, et al. The THO Complex Non-Cell-Autonomously Represses Female Germline Specification through the TAS3-ARF3 Module. Curr. Biol., 2017. 27(11): p. 1597-1609.e2 [PMID:28552357] Simonini S,Bencivenga S,Trick M,Østergaard L Auxin-Induced Modulation of ETTIN Activity Orchestrates Gene Expression in Arabidopsis. Plant Cell, 2017. 29(8): p. 1864-1882 [PMID:28804059] Guan C, et al. Spatial Auxin Signaling Controls Leaf Flattening in Arabidopsis. Curr. Biol., 2017. 27(19): p. 2940-2950.e4 [PMID:28943086] Simonini S, et al. Corrigendum: A noncanonical auxin-sensing mechanism is required for organ morphogenesis in Arabidopsis. Genes Dev., 2017. 31(17): p. 1821 [PMID:28982764] Zhang K, et al. AUXIN RESPONSE FACTOR3 Regulates Floral Meristem Determinacy by Repressing Cytokinin Biosynthesis and Signaling. Plant Cell, 2018. 30(2): p. 324-346 [PMID:29371438] Vial-Pradel S, et al. Arabidopsis Zinc-Finger-Like Protein ASYMMETRIC LEAVES2 (AS2) and Two Nucleolar Proteins Maintain Gene Body DNA Methylation in the Leaf Polarity Gene ETTIN (ARF3). Plant Cell Physiol., 2018. 59(7): p. 1385-1397 [PMID:29415182] Simonini S,Stephenson P,Østergaard L A molecular framework controlling style morphology in Brassicaceae. Development, 2018. [PMID:29440299] Andres-Robin A, et al. Evidence for the Regulation of Gynoecium Morphogenesis by ETTIN via Cell Wall Dynamics. Plant Physiol., 2018. 178(3): p. 1222-1232 [PMID:30237208] Hablak SG Features inheritance of root system Arabidopsis thaliana (L.) Heynh. the interaction of genes CTR1 AND ALF3, NPH4 and IAR2. Tsitol. Genet., 2019. [PMID:30484609]