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

Lsa004567

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: 731aa MW: 81822.3 Da PI: 6.9513

Description

ARF family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
PUT-187a-Lactuca_sativa-44562	PU_ref	plantGDB	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	B3	74.1	1.6e-23	160	261	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 +++ +++a+e+ + ++ +++l+ +d++g +W++++i+r++++r++l++GW+ Fv++++L +gD ++F + +++el+v Lsa004567 160 FCKTLTASDTSTHGGFSVLRRHADEClpqldmS-RQPPTQELVAKDLHGTEWRFRHIFRGQPRRHLLQSGWSVFVSSKRLVAGDAFIFL--RGENGELRV 256 99**************************963.3334459********************************************..449999* PP EEE-S CS B3 95 kvfrk 99 +v+r+ Lsa004567 257 GVRRA 261 **996 PP
2	Auxin_resp	119.3	3e-39	286	368	1	83
Auxin_resp 1 aahaastksvFevvYnPrastseFvvkvekvekalkvkvsvGmRfkmafetedsserrlsGtvvgvsdldpvrWpnSkWrsLk 83 a+ha++t+++F+v+Y+Pr+s++eF+v+++++++++k+++s+GmRfkm+fe+e+++e+r++Gt+vg++++dp rWp+SkWrsLk Lsa004567 286 AWHAIQTGTIFTVYYKPRTSPTEFIVPYDQYMESIKNNYSIGMRFKMRFEGEEAPEQRFTGTIVGIEESDPKRWPESKWRSLK 368 89*******************************************************************************96 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SuperFamily	SSF101936	1.57E-40	156	289	IPR015300	DNA-binding pseudobarrel domain
Gene3D	G3DSA:2.40.330.10	1.2E-41	156	275	IPR015300	DNA-binding pseudobarrel domain
CDD	cd10017	4.74E-21	158	260	No hit	No description
Pfam	PF02362	2.1E-21	160	261	IPR003340	B3 DNA binding domain
SMART	SM01019	4.2E-22	160	262	IPR003340	B3 DNA binding domain
PROSITE profile	PS50863	11.942	160	262	IPR003340	B3 DNA binding domain
Pfam	PF06507	2.3E-36	286	368	IPR010525	Auxin response factor
Pfam	PF02309	8.8E-11	579	688	IPR033389	AUX/IAA domain
SuperFamily	SSF54277	8.83E-12	605	683	No hit	No description
PROSITE profile	PS51745	24.055	606	690	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:0009725	Biological Process	response to hormone
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: 731 aa Download sequence Send to blast
MTSSEVSSKG NNSMRGDRDT FSLSGFSDKN DAVGDSRAVT AVSGAGKAEA DMALYKELWR 60 ACAGPLVTVP RENELVFYFP QGHIEQVEAS TNQVAEQQMP MYNLPSKILC RVVNVQLKAE 120 QDTDEVFAQI TLMPEADQDE NAVKKEPPPP PQSRFQVHSF CKTLTASDTS THGGFSVLRR 180 HADECLPQLD MSRQPPTQEL VAKDLHGTEW RFRHIFRGQP RRHLLQSGWS VFVSSKRLVA 240 GDAFIFLRGE NGELRVGVRR AMRQQPNVPS SVISSHSMHL GVLATAWHAI QTGTIFTVYY 300 KPRTSPTEFI VPYDQYMESI KNNYSIGMRF KMRFEGEEAP EQRFTGTIVG IEESDPKRWP 360 ESKWRSLKVR WDETSTVPRP DRVSPWKIEP ALTPPAITPL PVNKQKRHRS SILSTSPDSS 420 VLTREGSSKM ATADPSRVEL STLRPPFTEI NDSDSCDALS VSRCLPFGRP TESSFTDLLS 480 GFGSHNNSTE FSNPWSKMPS NMPLNLLGSS MKGVDIPFQS YPIHRNPKWM MPPPLPSYLH 540 IPSHSTDVIP KTPLVQNEVK KPQDGSCKIF GVPLAGNTVA SPGKDREKQY SNPQPQVKVQ 600 GGVSTRSCTK VHKQGIALGR SLDLTKFNNY DELIAELDEL FEFNGELKTR NRSWLVVYTD 660 DEGDMMLVGD DPWQEFCGMV RKIFIYTREE VQRMNLGALN SRGDDTSSVA EGMDARDTRI 720 NLLSSSSPED V

Sequence ? help Back to Top

Protein Sequence Length: 731 aa Download sequence Send to blast

MTSSEVSSKG NNSMRGDRDT FSLSGFSDKN DAVGDSRAVT AVSGAGKAEA DMALYKELWR  60
ACAGPLVTVP RENELVFYFP QGHIEQVEAS TNQVAEQQMP MYNLPSKILC RVVNVQLKAE  120
QDTDEVFAQI TLMPEADQDE NAVKKEPPPP PQSRFQVHSF CKTLTASDTS THGGFSVLRR  180
HADECLPQLD MSRQPPTQEL VAKDLHGTEW RFRHIFRGQP RRHLLQSGWS VFVSSKRLVA  240
GDAFIFLRGE NGELRVGVRR AMRQQPNVPS SVISSHSMHL GVLATAWHAI QTGTIFTVYY  300
KPRTSPTEFI VPYDQYMESI KNNYSIGMRF KMRFEGEEAP EQRFTGTIVG IEESDPKRWP  360
ESKWRSLKVR WDETSTVPRP DRVSPWKIEP ALTPPAITPL PVNKQKRHRS SILSTSPDSS  420
VLTREGSSKM ATADPSRVEL STLRPPFTEI NDSDSCDALS VSRCLPFGRP TESSFTDLLS  480
GFGSHNNSTE FSNPWSKMPS NMPLNLLGSS MKGVDIPFQS YPIHRNPKWM MPPPLPSYLH  540
IPSHSTDVIP KTPLVQNEVK KPQDGSCKIF GVPLAGNTVA SPGKDREKQY SNPQPQVKVQ  600
GGVSTRSCTK VHKQGIALGR SLDLTKFNNY DELIAELDEL FEFNGELKTR NRSWLVVYTD  660
DEGDMMLVGD DPWQEFCGMV RKIFIYTREE VQRMNLGALN SRGDDTSSVA EGMDARDTRI  720
NLLSSSSPED V

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
4ldv_A	1e-179	53	390	18	354	Auxin response factor 1
4ldw_A	1e-179	53	390	18	354	Auxin response factor 1
4ldw_B	1e-179	53	390	18	354	Auxin response factor 1
4ldx_A	1e-179	53	390	18	354	Auxin response factor 1
4ldx_B	1e-179	53	390	18	354	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) (By similarity). Could act as transcriptional activator or repressor (PubMed:26959229, PubMed:26716451, PubMed:27645097, PubMed:28167023). Involved in the control of fruit ripening process (PubMed:26959229, PubMed:26716451, PubMed:28167023). Regulates expression of a number of ripening regulators, transcription factors, and ethylene biosynthesis and signaling components (PubMed:26959229, PubMed:26716451). May act as a transcriptional repressor of auxin-responsive genes (PubMed:26716451). Regulates vegetative growth, lateral root formation and flower organ senescence, possibly partially by regulating gene expression of auxin and ethylene response factor (ERF) genes (PubMed:28167023). Plays a negative role in axillary shoot meristem formation (PubMed:27645097). {ECO:0000255\|RuleBase:RU004561, ECO:0000269\|PubMed:26716451, ECO:0000269\|PubMed:26959229, ECO:0000269\|PubMed:27645097, ECO:0000269\|PubMed:28167023}.

Regulation -- Description ? help Back to Top
Source	Description
UniProt	INDUCTION: By tomato fruit ripening. Expression in tomato fruits is up-regulated by exogenous application of ethylene and down-regulated by inhibition of ethylene receptors with 1-methylcyclopropene (1-MCP) (PubMed:26959229, PubMed:26716451). Up-regulated by plant hormone abscisic acid (ABA) in tomato fruits (PubMed:26959229). Expression is not up-regulated by plant hormone auxin in tomato fruits (PubMed:26716451). Up-regulated by auxin and gibberellic acid (GA), and down-regulated by ethylene in seedlings (PubMed:28167023). Down-regulated during decapitation-induced axillary shoot development and by excision of immature leaves. Down-regulation is inhibited by the application of auxin on the cut surface (PubMed:27645097). {ECO:0000269\|PubMed:26716451, ECO:0000269\|PubMed:26959229, ECO:0000269\|PubMed:27645097, ECO:0000269\|PubMed:28167023}.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_023771555.1	0.0	auxin response factor 2A-like
Swissprot	Q2LAJ3	0.0	ARF2A_SOLLC; Auxin response factor 2A
TrEMBL	A0A2J6KWP1	0.0	A0A2J6KWP1_LACSA; Auxin response factor
STRING	VIT_17s0000g00320.t01	0.0	(Vitis vinifera)

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT5G62000.3	0.0	auxin response factor 2

Publications ? help Back to Top
Tomato Genome Consortium The tomato genome sequence provides insights into fleshy fruit evolution. Nature, 2012. 485(7400): p. 635-41 [PMID:22660326] Breitel DA, et al. AUXIN RESPONSE FACTOR 2 Intersects Hormonal Signals in the Regulation of Tomato Fruit Ripening. PLoS Genet., 2016. 12(3): p. e1005903 [PMID:26959229] Xu T, et al. SlARF2a plays a negative role in mediating axillary shoot formation. Sci Rep, 2016. 6: p. 33728 [PMID:27645097] Ren Z,Liu R,Gu W,Dong X The Solanum lycopersicum auxin response factor SlARF2 participates in regulating lateral root formation and flower organ senescence. Plant Sci., 2017. 256: p. 103-111 [PMID:28167023]