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

335174

Common Name

ARALYDRAFT_335174

Organism

Arabidopsis lyrata

Taxonomic ID

81972

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis

Family

ARF

Protein Properties

Length: 1097aa MW: 121472 Da PI: 6.7102

Description

ARF family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
335174	genome	JGI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	B3	67.5	1.9e-21	126	217	1	87
EEEE-..-HHHHTT-EE--HHH.HTT.......---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE-SS CS B3 1 ffkvltpsdvlksgrlvlpkkfaeeh.......ggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfvvFkldgr 87 f+k+lt sd++++g +++p++ ae++ + +++ ++++ +d++ +W++++iyr++++r++lt+GW+ Fv+ ++L +gD+v+F ++g 335174 126 FCKTLTASDTSTHGGFSVPRRAAEKIfppldfsM-QPPA-QEIVAKDLHDTTWTFRHIYRGQPKRHLLTTGWSVFVSTKRLFAGDSVLFVRIGL 217 99***************************954.4444.48*********************************************97764 PP
2	Auxin_resp	118.5	5.6e-39	266	348	1	83
Auxin_resp 1 aahaastksvFevvYnPrastseFvvkvekvekalkvkvsvGmRfkmafetedsserrlsGtvvgvsdldpvrWpnSkWrsLk 83 aaha +++s+F++++nPras+seF+v+++k++kal+ +vs+GmRf+m+feted+ rr++Gtv+g+sdldpvrW++S+Wr+L+ 335174 266 AAHANANSSPFTIFFNPRASPSEFIVPLAKYNKALYAQVSLGMRFRMMFETEDCGVRRYMGTVTGISDLDPVRWKGSQWRNLQ 348 799******************************************************************************97 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SuperFamily	SSF101936	6.15E-41	116	269	IPR015300	DNA-binding pseudobarrel domain
Gene3D	G3DSA:2.40.330.10	1.3E-38	120	255	IPR015300	DNA-binding pseudobarrel domain
CDD	cd10017	5.37E-20	125	219	No hit	No description
Pfam	PF02362	1.2E-19	126	217	IPR003340	B3 DNA binding domain
PROSITE profile	PS50863	11.35	126	242	IPR003340	B3 DNA binding domain
SMART	SM01019	1.1E-19	126	242	IPR003340	B3 DNA binding domain
Pfam	PF06507	7.5E-34	266	348	IPR010525	Auxin response factor
Pfam	PF02309	2.8E-9	966	1054	IPR033389	AUX/IAA domain
PROSITE profile	PS51745	24.801	968	1061	IPR000270	PB1 domain
SuperFamily	SSF54277	1.63E-8	982	1046	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:0009723	Biological Process	response to ethylene
GO:0009734	Biological Process	auxin-activated signaling pathway
GO:0010311	Biological Process	lateral root formation
GO:0048366	Biological Process	leaf development
GO:0005634	Cellular Component	nucleus
GO:0043565	Molecular Function	sequence-specific DNA binding
GO:0046983	Molecular Function	protein dimerization activity

Sequence ? help Back to Top
Protein Sequence Length: 1097 aa Download sequence Send to blast
MKAPSNGFLP TSNEGEKKPI NSQLWHACAG PLVSLPPVGS LVVYFPQGHS EQVAASMQKQ 60 TDFIPNYPNL PSKLICLLHS VTLHADTETD EVYAQMTLQP VNKYDREALL ASDMGLKLNR 120 QPTEFFCKTL TASDTSTHGG FSVPRRAAEK IFPPLDFSMQ PPAQEIVAKD LHDTTWTFRH 180 IYRGQPKRHL LTTGWSVFVS TKRLFAGDSV LFVRIGLSSS HKGTWVCRDE KSQLMLGIRR 240 ANRQTPTLSS SVISSDSMHI GILAAAAHAN ANSSPFTIFF NPRASPSEFI VPLAKYNKAL 300 YAQVSLGMRF RMMFETEDCG VRRYMGTVTG ISDLDPVRWK GSQWRNLQVG WDESTAGDRP 360 SRVSIWEIEP VITPFYICPP PFFRPKYPRQ PGMPDDELDM ENAFKRAMPW MGEDFGMKDA 420 QSSMFPGLSL VQWMSMQQNN PLSGSATPQL PSALSSYNLP NNFASNDPSK LLNFQSPNLS 480 SANSQFNKSN TVNHISQQMQ AQPAMVKSLQ QQQQQQQQQL QQQQQQQLQI SHQQLQQQGN 540 YSNGASAVAN QVSCQNPNQP TGFSQSQLQQ QSMLPSGAKM IHQNINSVGN KGSSQMTSFV 600 QEMQFQQQLE LHNSSQLLRN QQEQSSLHSS QQNLSQNPQQ LQMQQQSSKP SPSQQLQLQL 660 LQKLQQQQQQ QSVPPVSSSL QPQLSVLQQT QSHQLQQLLS SQNQQPLAHG NNSFSASTFM 720 QPPQIQVSHQ QQEQMNNKNL VAAGQSHSGH TDGEAPSCST SPSANHTGHD NVSPTNFLSR 780 NQQQGQAASV SASDSVFDRA SNPVQEHYTK TESRFNQGMV NLKSGGEQFR FKGAVTDQID 840 VSTAGATYCP DVVGPAQQQQ TFPLPSFGFD GDCQSHHPRN NLAFPGNLEA VTSDVLYSQK 900 DFQNLVPNYG NAPRDIETEL SSAAISSQSF GIPSIPFKSG CSNEVGGIND SGIMNGGGLW 960 PNQTQRMRTY TKVQKRGSVG RSIDVTRYSG YDELRHDLAR MFGIEGQLED PLTSDWKLVY 1020 TDHENDILLV GDDPWEEFVN CVQNIKILSS VEVQQMSLDG DLAAIPITNQ ACSETDSGNA 1080 WKVHYEDTSA AASFNR*

Sequence ? help Back to Top

Protein Sequence Length: 1097 aa Download sequence Send to blast

MKAPSNGFLP TSNEGEKKPI NSQLWHACAG PLVSLPPVGS LVVYFPQGHS EQVAASMQKQ  60
TDFIPNYPNL PSKLICLLHS VTLHADTETD EVYAQMTLQP VNKYDREALL ASDMGLKLNR  120
QPTEFFCKTL TASDTSTHGG FSVPRRAAEK IFPPLDFSMQ PPAQEIVAKD LHDTTWTFRH  180
IYRGQPKRHL LTTGWSVFVS TKRLFAGDSV LFVRIGLSSS HKGTWVCRDE KSQLMLGIRR  240
ANRQTPTLSS SVISSDSMHI GILAAAAHAN ANSSPFTIFF NPRASPSEFI VPLAKYNKAL  300
YAQVSLGMRF RMMFETEDCG VRRYMGTVTG ISDLDPVRWK GSQWRNLQVG WDESTAGDRP  360
SRVSIWEIEP VITPFYICPP PFFRPKYPRQ PGMPDDELDM ENAFKRAMPW MGEDFGMKDA  420
QSSMFPGLSL VQWMSMQQNN PLSGSATPQL PSALSSYNLP NNFASNDPSK LLNFQSPNLS  480
SANSQFNKSN TVNHISQQMQ AQPAMVKSLQ QQQQQQQQQL QQQQQQQLQI SHQQLQQQGN  540
YSNGASAVAN QVSCQNPNQP TGFSQSQLQQ QSMLPSGAKM IHQNINSVGN KGSSQMTSFV  600
QEMQFQQQLE LHNSSQLLRN QQEQSSLHSS QQNLSQNPQQ LQMQQQSSKP SPSQQLQLQL  660
LQKLQQQQQQ QSVPPVSSSL QPQLSVLQQT QSHQLQQLLS SQNQQPLAHG NNSFSASTFM  720
QPPQIQVSHQ QQEQMNNKNL VAAGQSHSGH TDGEAPSCST SPSANHTGHD NVSPTNFLSR  780
NQQQGQAASV SASDSVFDRA SNPVQEHYTK TESRFNQGMV NLKSGGEQFR FKGAVTDQID  840
VSTAGATYCP DVVGPAQQQQ TFPLPSFGFD GDCQSHHPRN NLAFPGNLEA VTSDVLYSQK  900
DFQNLVPNYG NAPRDIETEL SSAAISSQSF GIPSIPFKSG CSNEVGGIND SGIMNGGGLW  960
PNQTQRMRTY TKVQKRGSVG RSIDVTRYSG YDELRHDLAR MFGIEGQLED PLTSDWKLVY  1020
TDHENDILLV GDDPWEEFVN CVQNIKILSS VEVQQMSLDG DLAAIPITNQ ACSETDSGNA  1080
WKVHYEDTSA AASFNR*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
4ldu_A	1e-168	15	369	45	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). 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}.

Cis-element ? help Back to Top
Source	Link
PlantRegMap	335174

Regulation -- Description ? help Back to Top
Source	Description
UniProt	INDUCTION: By auxin and ethylene. {ECO:0000269\|PubMed:16461383}.

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	ATU53672	0.0	U53672.2 Arabidopsis thaliana early auxin-induced IAA22 mRNA, complete cds.
GenBank	AY669794	0.0	AY669794.1 Arabidopsis thaliana clone C105352 ARF19 (At1g19220) mRNA, complete cds.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_020870042.1	0.0	auxin response factor 19
Swissprot	Q8RYC8	0.0	ARFS_ARATH; Auxin response factor 19
TrEMBL	D7KHB3	0.0	D7KHB3_ARALL; Auxin response factor
STRING	fgenesh1_pg.C_scaffold_1001739	0.0	(Arabidopsis lyrata)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM2629	26	65

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

Link Out ? help Back to Top
Phytozome	335174
Entrez Gene	9329096

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]