PlantTFDB - Plant Transcription Factor Database @ CBI, PKU

PlantRegMap/PlantTFDB v5.0

Plant Transcription Factor Database

Previous version: v3.0 v4.0

Transcription Factor Information

Basic Information | Signature Domain | Sequence |

Basic Information? help Back to Top

TF ID

XP_013586634.1

Organism

Brassica oleracea

Taxonomic ID

3712

Taxonomic Lineage

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

Family

ARF

Protein Properties

Length: 1042aa MW: 115582 Da PI: 6.653

Description

ARF family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
XP_013586634.1	genome	NCBI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	B3	72.8	4.1e-23	126	227	1	99
EEEE-..-HHHHTT-EE--HHH.HTT.......---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE-SSS CS B3 1 ffkvltpsdvlksgrlvlpkkfaeeh.......ggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfvvFkldgrs 88 f+k+lt sd++++g +++p++ ae++ + +++ ++++ +d++ +W++++iyr++++r++lt+GW+ Fv+ ++L +gD+v+F +++ XP_013586634.1 126 FCKTLTASDTSTHGGFSVPRRAAEKIfppldfsM-QPPA-QEIVAKDLHDTTWTFRHIYRGQPKRHLLTTGWSVFVSTKRLFAGDSVLFV--RDE 216 99***************************954.4444.48**********************************************..456 PP EE..EEEEE-S CS B3 89 efelvvkvfrk 99 + +l+++++r+ XP_013586634.1 217 KSQLTLGIRRA 227 77789999997 PP
2	Auxin_resp	118.6	5.1e-39	252	334	1	83
Auxin_resp 1 aahaastksvFevvYnPrastseFvvkvekvekalkvkvsvGmRfkmafetedsserrlsGtvvgvsdldpvrWpnSkWrsLk 83 aaha +++s+F++++nPras+seFvv+++k++kal+ +vs+GmRf+m+feted+ rr++Gtv+g+sdldpvrW++S+Wr+L+ XP_013586634.1 252 AAHANANSSPFTIFFNPRASPSEFVVPLAKYNKALYAQVSLGMRFRMMFETEDCGVRRYMGTVTGISDLDPVRWKGSQWRNLQ 334 799******************************************************************************97 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SuperFamily	SSF101936	3.79E-44	116	255	IPR015300	DNA-binding pseudobarrel domain
Gene3D	G3DSA:2.40.330.10	1.0E-41	120	241	IPR015300	DNA-binding pseudobarrel domain
CDD	cd10017	9.25E-21	125	226	No hit	No description
SMART	SM01019	4.3E-24	126	228	IPR003340	B3 DNA binding domain
Pfam	PF02362	2.0E-21	126	227	IPR003340	B3 DNA binding domain
PROSITE profile	PS50863	12.492	126	228	IPR003340	B3 DNA binding domain
Pfam	PF06507	7.2E-34	252	334	IPR010525	Auxin response factor
Pfam	PF02309	9.2E-10	912	1000	IPR033389	AUX/IAA domain
PROSITE profile	PS51745	25.365	914	1007	IPR000270	PB1 domain
SuperFamily	SSF54277	3.09E-8	928	992	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:0009733	Biological Process	response to auxin
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: 1042 aa Download sequence Send to blast
MKAPSNGFHP NPTEGEKKAI NSQLWHACAG PLVSLPPVGS LVVYFPQGHS EQVAASMQKQ 60 TDFIPNYPNL PSKLICLLHS VTLHADTETD EVYAQMTLQP VNKYDREALL ASDMGLKINR 120 QPTEFFCKTL TASDTSTHGG FSVPRRAAEK IFPPLDFSMQ PPAQEIVAKD LHDTTWTFRH 180 IYRGQPKRHL LTTGWSVFVS TKRLFAGDSV LFVRDEKSQL TLGIRRANRQ TPTLSSSVIS 240 SDSMHIGILA AAAHANANSS PFTIFFNPRA SPSEFVVPLA KYNKALYAQV SLGMRFRMMF 300 ETEDCGVRRY MGTVTGISDL DPVRWKGSQW RNLQVGWDES TAGDRPSRVS IWEIEPVITP 360 FYICPPPFFR PKYPRQPGMP DDELDMENAF KRAMPWMGEE FGMKDAQSSM FPGLSLVQWM 420 SMQQNNPLSA GAAAATTHLP SSYNLPNNFS PNDHSKLLNF QSPNLSPAIT QFNKPNMVSH 480 ISQQMQAQPA MVQSQQQQQQ QLQQQVQMSH QQLQQQHHQH QQQGGYNSGS VNNGVSVVSN 540 QVSCQNQSAG FTQSKMTHQN MVSAGNKGSS QMTAQELQFQ QQLELHNSTQ LLRNQQEQSS 600 MHSLQQNPQQ LQMQQQQSSK PSPSQQFQLQ LLQKLQQQQQ STPPPVSSSL QPQLSSLQQT 660 QSHQLQQLLS SQNQQPLPQS NNNSFMQPPQ IQASHHQQQG YMNNNKPIVR SQSGHIDGEA 720 PSCSTSPSAN NTGHDNVSPT NFLSRNQQQG QGVSVPASDP VQQGMVNLKS AGEQFKFKAA 780 VTDQIDVTTA GTTYCPDVVV GPGQQQQQTF PLPSFGFDGD LQQSQHPRNS LAFAGNIEAV 840 NPDALYSQKD FQNLVVPNYG NAPRDIETEL SSASQSFGIP SIPFKSGGSN EIGGINDSGI 900 MNGGIWPNQA QRMRTYTKVQ KRGSVGRSID VTRYSGYEEL RNDLARMFGI EGQLEDPQIS 960 DWKLVYTDHE NDILLVGDDP WEEFVNCVQN IKILSSAEVQ QMSLDGDLAA IPTTNQACSE 1020 TDSGNAWKVH YEDTSAAASF NR

Sequence ? help Back to Top

Protein Sequence Length: 1042 aa Download sequence Send to blast

MKAPSNGFHP NPTEGEKKAI NSQLWHACAG PLVSLPPVGS LVVYFPQGHS EQVAASMQKQ  60
TDFIPNYPNL PSKLICLLHS VTLHADTETD EVYAQMTLQP VNKYDREALL ASDMGLKINR  120
QPTEFFCKTL TASDTSTHGG FSVPRRAAEK IFPPLDFSMQ PPAQEIVAKD LHDTTWTFRH  180
IYRGQPKRHL LTTGWSVFVS TKRLFAGDSV LFVRDEKSQL TLGIRRANRQ TPTLSSSVIS  240
SDSMHIGILA AAAHANANSS PFTIFFNPRA SPSEFVVPLA KYNKALYAQV SLGMRFRMMF  300
ETEDCGVRRY MGTVTGISDL DPVRWKGSQW RNLQVGWDES TAGDRPSRVS IWEIEPVITP  360
FYICPPPFFR PKYPRQPGMP DDELDMENAF KRAMPWMGEE FGMKDAQSSM FPGLSLVQWM  420
SMQQNNPLSA GAAAATTHLP SSYNLPNNFS PNDHSKLLNF QSPNLSPAIT QFNKPNMVSH  480
ISQQMQAQPA MVQSQQQQQQ QLQQQVQMSH QQLQQQHHQH QQQGGYNSGS VNNGVSVVSN  540
QVSCQNQSAG FTQSKMTHQN MVSAGNKGSS QMTAQELQFQ QQLELHNSTQ LLRNQQEQSS  600
MHSLQQNPQQ LQMQQQQSSK PSPSQQFQLQ LLQKLQQQQQ STPPPVSSSL QPQLSSLQQT  660
QSHQLQQLLS SQNQQPLPQS NNNSFMQPPQ IQASHHQQQG YMNNNKPIVR SQSGHIDGEA  720
PSCSTSPSAN NTGHDNVSPT NFLSRNQQQG QGVSVPASDP VQQGMVNLKS AGEQFKFKAA  780
VTDQIDVTTA GTTYCPDVVV GPGQQQQQTF PLPSFGFDGD LQQSQHPRNS LAFAGNIEAV  840
NPDALYSQKD FQNLVVPNYG NAPRDIETEL SSASQSFGIP SIPFKSGGSN EIGGINDSGI  900
MNGGIWPNQA QRMRTYTKVQ KRGSVGRSID VTRYSGYEEL RNDLARMFGI EGQLEDPQIS  960
DWKLVYTDHE NDILLVGDDP WEEFVNCVQN IKILSSAEVQ QMSLDGDLAA IPTTNQACSE  1020
TDSGNAWKVH YEDTSAAASF NR

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
4ldu_A	1e-171	16	355	47	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	XP_013586634.1

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	JN979484	0.0	JN979484.1 Brassica rapa subsp. pekinensis auxin response factor 19-2 (ARF19-2) mRNA, complete cds.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_013586634.1	0.0	PREDICTED: auxin response factor 19 isoform X2
Swissprot	Q8RYC8	0.0	ARFS_ARATH; Auxin response factor 19
TrEMBL	A0A0D3CBG4	0.0	A0A0D3CBG4_BRAOL; Auxin response factor
STRING	Bo5g027250.1	0.0	(Brassica oleracea)

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]