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

Lsa004622

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: 824aa MW: 90626.8 Da PI: 6.7326

Description

ARF family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
PUT-187a-Lactuca_sativa-51908	PU_ref	plantGDB	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	B3	68.7	8.1e-22	134	235	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++ +++++ ++l+ +d++ W++++iyr++++r++lt+GW+ Fv+ ++L +gD+v+F ++++++l++ Lsa004622 134 FCKTLTASDTSTHGGFSVPRRAAEKIfppldfSMQPPA-QELVARDLHDTLWTFRHIYRGQPKRHLLTTGWSLFVSGKRLFAGDSVLFI--RDEKQQLLL 230 99***************************9445444.38********************************************..5688889 PP EEE-S CS B3 95 kvfrk 99 +++r+ Lsa004622 231 GIRRA 235 **997 PP
2	Auxin_resp	119.7	2.4e-39	260	343	1	83
Auxin_resp 1 aahaastksvFevvYnPrastseFvvkvekvekalk.vkvsvGmRfkmafetedsserrlsGtvvgvsdldpvrWpnSkWrsLk 83 aahaa+++s+F+v+YnPras+seFv++++k+ ka+ +++s+GmRf+m+fete+s +rr++Gt++g+sdldp+rW+nS+Wr+L+ Lsa004622 260 AAHAAANNSPFTVFYNPRASPSEFVIPLAKYYKAVCsNQISLGMRFRMMFETEESGTRRYMGTITGISDLDPIRWKNSQWRNLQ 343 79****************************998669******************************************97 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SuperFamily	SSF101936	6.41E-44	124	263	IPR015300	DNA-binding pseudobarrel domain
Gene3D	G3DSA:2.40.330.10	1.0E-40	128	249	IPR015300	DNA-binding pseudobarrel domain
CDD	cd10017	2.56E-18	133	225	No hit	No description
SMART	SM01019	1.1E-21	134	236	IPR003340	B3 DNA binding domain
Pfam	PF02362	6.6E-20	134	235	IPR003340	B3 DNA binding domain
PROSITE profile	PS50863	11.773	134	236	IPR003340	B3 DNA binding domain
Pfam	PF06507	1.2E-34	260	343	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: 824 aa Download sequence Send to blast
MKTPANASGS TLTTENPGEA GEKKTIINPE LWQTCAGPLV NLPAAGTHVV YFPQGHSEQV 60 AASMKKDVDS QIPNYPNLQS KLLCVLHSVT LHADPETDEV YAQMTLQPVP SFDKEALLRS 120 DLSTKINKPQ TQFFCKTLTA SDTSTHGGFS VPRRAAEKIF PPLDFSMQPP AQELVARDLH 180 DTLWTFRHIY RGQPKRHLLT TGWSLFVSGK RLFAGDSVLF IRDEKQQLLL GIRRANRQPT 240 NLSSSVLSSD SMHIGILAAA AHAAANNSPF TVFYNPRASP SEFVIPLAKY YKAVCSNQIS 300 LGMRFRMMFE TEESGTRRYM GTITGISDLD PIRWKNSQWR NLQVGWDEST GGERRTRVSV 360 WEIEPVTAPF FICPTPPFYR PKRPRQPGMP DDESADLDNI FKRSMPWLGE DMSTKDPGLS 420 LVQWMNMQQN SSPNYLNPLS GSIPGSIFSG SDLSRQLGAP PPPPPQILTH GASMVQPPQQ 480 LTDPNQSQQM FRQNLINQNQ NQNQNQIQNH HLYRNLQSPQ TQFHDTQQLQ IPDNQISIQL 540 LQKLHQQQQS LLAQQSVSLP QQQDEQKPLI DVHVPVPQSF SRSMSTSQTM DAHTPPLSKN 600 NSQPNLRFSG HKFSGPNQIS TGGGGQSGIT DDIPSCSTSP STNNFQTMVT GVETLSTNVN 660 FGKVSPPVNA VNIPKGQNPS FLAPITYLNN IGGPQMDFLD SSSSATSICA PQSDLHPQPL 720 RTTIQDDSRA DIPFGGGNMV GMPSMIVDPL TTKGMVGSSK DFESNVSPGG MILYENNNNP 780 SKDAQPELSS SMVSQSFGVP DMAFNPIDST LNDSGLLNTG VWAP

Sequence ? help Back to Top

Protein Sequence Length: 824 aa Download sequence Send to blast

MKTPANASGS TLTTENPGEA GEKKTIINPE LWQTCAGPLV NLPAAGTHVV YFPQGHSEQV  60
AASMKKDVDS QIPNYPNLQS KLLCVLHSVT LHADPETDEV YAQMTLQPVP SFDKEALLRS  120
DLSTKINKPQ TQFFCKTLTA SDTSTHGGFS VPRRAAEKIF PPLDFSMQPP AQELVARDLH  180
DTLWTFRHIY RGQPKRHLLT TGWSLFVSGK RLFAGDSVLF IRDEKQQLLL GIRRANRQPT  240
NLSSSVLSSD SMHIGILAAA AHAAANNSPF TVFYNPRASP SEFVIPLAKY YKAVCSNQIS  300
LGMRFRMMFE TEESGTRRYM GTITGISDLD PIRWKNSQWR NLQVGWDEST GGERRTRVSV  360
WEIEPVTAPF FICPTPPFYR PKRPRQPGMP DDESADLDNI FKRSMPWLGE DMSTKDPGLS  420
LVQWMNMQQN SSPNYLNPLS GSIPGSIFSG SDLSRQLGAP PPPPPQILTH GASMVQPPQQ  480
LTDPNQSQQM FRQNLINQNQ NQNQNQIQNH HLYRNLQSPQ TQFHDTQQLQ IPDNQISIQL  540
LQKLHQQQQS LLAQQSVSLP QQQDEQKPLI DVHVPVPQSF SRSMSTSQTM DAHTPPLSKN  600
NSQPNLRFSG HKFSGPNQIS TGGGGQSGIT DDIPSCSTSP STNNFQTMVT GVETLSTNVN  660
FGKVSPPVNA VNIPKGQNPS FLAPITYLNN IGGPQMDFLD SSSSATSICA PQSDLHPQPL  720
RTTIQDDSRA DIPFGGGNMV GMPSMIVDPL TTKGMVGSSK DFESNVSPGG MILYENNNNP  780
SKDAQPELSS SMVSQSFGVP DMAFNPIDST LNDSGLLNTG VWAP

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
4ldu_A	1e-170	19	364	43	388	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).
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 ethylene responses. Regulates lateral root formation through direct regulation of LBD16 and/or LBD29. Functionally redundant with ARF7. {ECO:0000269\|PubMed:12036261, ECO:0000269\|PubMed:16461383, ECO:0000269\|PubMed:17259263}.

Regulation -- Description ? help Back to Top
Source	Description
UniProt	INDUCTION: By auxin and ethylene. {ECO:0000269\|PubMed:16461383}.
UniProt	INDUCTION: Down-regulated by auxin under light condition. {ECO:0000269\|PubMed:17408882}.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_023739623.1	0.0	auxin response factor 19-like
Swissprot	Q6Z2W3	0.0	ARFE_ORYSJ; Auxin response factor 5
Swissprot	Q8RYC8	0.0	ARFS_ARATH; Auxin response factor 19
TrEMBL	A0A2J6K2M3	0.0	A0A2J6K2M3_LACSA; Auxin response factor
STRING	XP_010106948.1	0.0	(Morus notabilis)

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT1G19220.1	0.0	auxin response factor 19

Publications ? help Back to Top
Duarte JM, et al. Expression pattern shifts following duplication indicative of subfunctionalization and neofunctionalization in regulatory genes of Arabidopsis. Mol. Biol. Evol., 2006. 23(2): p. 469-78 [PMID:16280546] Perilli S, et al. RETINOBLASTOMA-RELATED protein stimulates cell differentiation in the Arabidopsis root meristem by interacting with cytokinin signaling. Plant Cell, 2013. 25(11): p. 4469-78 [PMID:24285791] Sun Y, et al. Manipulation of Auxin Response Factor 19 affects seed size in the woody perennial Jatropha curcas. Sci Rep, 2017. 7: p. 40844 [PMID:28102350] 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] Olmo R, et al. Molecular Transducers from Roots Are Triggered in Arabidopsis Leaves by Root-Knot Nematodes for Successful Feeding Site Formation: A Conserved Post-Embryogenic De novo Organogenesis Program? Front Plant Sci, 2017. 8: p. 875 [PMID:28603536] Lee K,Seo PJ High-temperature promotion of callus formation requires the BIN2-ARF-LBD axis in Arabidopsis. Planta, 2017. 246(4): p. 797-802 [PMID:28766014] Ayala-Rodríguez JÁ,Barrera-Ortiz S,Ruiz-Herrera LF,López-Bucio J Folic acid orchestrates root development linking cell elongation with auxin response and acts independently of the TARGET OF RAPAMYCIN signaling in Arabidopsis thaliana. Plant Sci., 2017. 264: p. 168-178 [PMID:28969797] Nakamura M, et al. Auxin and ROP GTPase Signaling of Polar Nuclear Migration in Root Epidermal Hair Cells. Plant Physiol., 2018. 176(1): p. 378-391 [PMID:29084900] Hong L, et al. Alternative polyadenylation is involved in auxin-based plant growth and development. Plant J., 2018. 93(2): p. 246-258 [PMID:29155478] Lee K,Park OS,Seo PJ Arabidopsis ATXR2 deposits H3K36me3 at the promoters of LBD genes to facilitate cellular dedifferentiation. Sci Signal, 2018. [PMID:29184030] Kimura T, et al. Asymmetric Auxin Distribution is Not Required to Establish Root Phototropism in Arabidopsis. Plant Cell Physiol., 2018. 59(4): p. 823-835 [PMID:29401292] Schoenaers S, et al. The Auxin-Regulated CrRLK1L Kinase ERULUS Controls Cell Wall Composition during Root Hair Tip Growth. Curr. Biol., 2018. 28(5): p. 722-732.e6 [PMID:29478854] Huang KL, et al. The ARF7 and ARF19 Transcription Factors Positively Regulate PHOSPHATE STARVATION RESPONSE1 in Arabidopsis Roots. Plant Physiol., 2018. 178(1): p. 413-427 [PMID:30026290]