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_013604468.1

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: 846aa MW: 93808.7 Da PI: 5.7474

Description

ARF family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
XP_013604468.1	genome	NCBI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	B3	77.2	1.9e-24	156	257	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+ +++++ +l+++d++ ++W++++iyr++++r++lt+GW+ Fv +++L++gD+v+F +++ XP_013604468.1 156 FCKTLTASDTSTHGGFSVPRRAAEKLfppldytAQPPTQ--ELVVRDLHENTWTFRHIYRGQPKRHLLTTGWSLFVGSKRLRAGDSVLFI--RDE 246 99*******************999996444444..8********************************************..457 PP EE..EEEEE-S CS B3 89 efelvvkvfrk 99 + +l+v+v+r+ XP_013604468.1 247 KSQLMVGVRRA 257 7778***97 PP
2	Auxin_resp	108.4	7.6e-36	282	365	1	83
Auxin_resp 1 aahaastksvFevvYnPrastseFvvkvekvekalk.vkvsvGmRfkmafetedsserrlsGtvvgvsdldpvrWpnSkWrsLk 83 aaha++++++F +++nPra+++eFv+++ k++ka+ +++svGmRf m+feteds +rr++Gt+vg+sdldp+rWp+SkWr+L+ XP_013604468.1 282 AAHATANRTPFLIFFNPRACPAEFVIPLPKYRKAICgSQLSVGMRFGMMFETEDSGKRRYMGTIVGISDLDPLRWPGSKWRNLQ 365 79******************************9989******************************************97 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SuperFamily	SSF101936	1.02E-45	146	285	IPR015300	DNA-binding pseudobarrel domain
Gene3D	G3DSA:2.40.330.10	3.3E-41	149	270	IPR015300	DNA-binding pseudobarrel domain
CDD	cd10017	6.08E-23	155	256	No hit	No description
Pfam	PF02362	4.2E-22	156	257	IPR003340	B3 DNA binding domain
PROSITE profile	PS50863	13.155	156	258	IPR003340	B3 DNA binding domain
SMART	SM01019	1.1E-25	156	258	IPR003340	B3 DNA binding domain
Pfam	PF06507	1.4E-30	282	365	IPR010525	Auxin response factor
Pfam	PF02309	6.0E-9	735	826	IPR033389	AUX/IAA domain
PROSITE profile	PS51745	23.737	740	824	IPR000270	PB1 domain
SuperFamily	SSF54277	5.69E-7	754	819	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: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: 846 aa Download sequence Send to blast
MASLACGEDK MKTNGLVNGG TTTSSTSQST LLEEMKLLKD QSGTRKPVIN SMLWHACAGP 60 LVCLPQVGSL VYYFSQGHSE QVAVSTRRSA TTQVPNYPNL PSQLMCQVHN VTLHADKDSD 120 EIYAQMSLQP VHSERDVLPV PDFGLLRGSK HPSEYFCKTL TASDTSTHGG FSVPRRAAEK 180 LFPPLDYTAQ PPTQELVVRD LHENTWTFRH IYRGQPKRHL LTTGWSLFVG SKRLRAGDSV 240 LFIRDEKSQL MVGVRRANRQ QTALPSSVLS ADSMHIGVLA AAAHATANRT PFLIFFNPRA 300 CPAEFVIPLP KYRKAICGSQ LSVGMRFGMM FETEDSGKRR YMGTIVGISD LDPLRWPGSK 360 WRNLQVEWDE PGCNDKPTRV SPWDIETPES LFIFPSLTSG LKRQLHPSYF AGENDWGSLI 420 KRPLPYATFP NMASEQLMKM MMRPHNNQNA VTSLMPEMQQ NVMMGHGGLL GDVKMQQPMV 480 MNQVVQVQPD NNNPSVSNTS GQEQNLTQSI NAPTITENSS GRANHGNEEL SQKPSALSPL 540 QADPCPEQIY PPQQSDPING FSFLETEELT SQVSSFQSLA GSYKQPLMLS SNESSPIVLP 600 DSTNSFQDMW DNQLNGLKFD QFSPLMQQED LYGCQNMCMS NSTNSNILDP PPLSNTVLDD 660 FCAIKETEFH SLVGNNNSFA QDVQSQITSA SFADSQAFSR QDNSGGTGGT SSSNVDFDDT 720 SLLQQNSKGS WQKLATPRVR TYTKVQKTGS VGRSIDVTSF RDYEELKSAI ECMFGLEGLL 780 TRPQTSGWKL VYVDYESDVL LVGDDPWEEF VGCVRCIRIL SPTEVQQMSE EGRKLLNSAC 840 INDLKT

Sequence ? help Back to Top

Protein Sequence Length: 846 aa Download sequence Send to blast

MASLACGEDK MKTNGLVNGG TTTSSTSQST LLEEMKLLKD QSGTRKPVIN SMLWHACAGP  60
LVCLPQVGSL VYYFSQGHSE QVAVSTRRSA TTQVPNYPNL PSQLMCQVHN VTLHADKDSD  120
EIYAQMSLQP VHSERDVLPV PDFGLLRGSK HPSEYFCKTL TASDTSTHGG FSVPRRAAEK  180
LFPPLDYTAQ PPTQELVVRD LHENTWTFRH IYRGQPKRHL LTTGWSLFVG SKRLRAGDSV  240
LFIRDEKSQL MVGVRRANRQ QTALPSSVLS ADSMHIGVLA AAAHATANRT PFLIFFNPRA  300
CPAEFVIPLP KYRKAICGSQ LSVGMRFGMM FETEDSGKRR YMGTIVGISD LDPLRWPGSK  360
WRNLQVEWDE PGCNDKPTRV SPWDIETPES LFIFPSLTSG LKRQLHPSYF AGENDWGSLI  420
KRPLPYATFP NMASEQLMKM MMRPHNNQNA VTSLMPEMQQ NVMMGHGGLL GDVKMQQPMV  480
MNQVVQVQPD NNNPSVSNTS GQEQNLTQSI NAPTITENSS GRANHGNEEL SQKPSALSPL  540
QADPCPEQIY PPQQSDPING FSFLETEELT SQVSSFQSLA GSYKQPLMLS SNESSPIVLP  600
DSTNSFQDMW DNQLNGLKFD QFSPLMQQED LYGCQNMCMS NSTNSNILDP PPLSNTVLDD  660
FCAIKETEFH SLVGNNNSFA QDVQSQITSA SFADSQAFSR QDNSGGTGGT SSSNVDFDDT  720
SLLQQNSKGS WQKLATPRVR TYTKVQKTGS VGRSIDVTSF RDYEELKSAI ECMFGLEGLL  780
TRPQTSGWKL VYVDYESDVL LVGDDPWEEF VGCVRCIRIL SPTEVQQMSE EGRKLLNSAC  840
INDLKT

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
4ldu_A	0.0	1	390	2	392	Auxin response factor 5
Search in ModeBase

Expression -- Description ? help Back to Top
Source	Description
Uniprot	DEVELOPMENTAL STAGE: In early embryo and during organ development.
Uniprot	TISSUE SPECIFICITY: Expressed in the whole plant with a lower expression in leaves. Detected in embryo axis, provascular tissues, procambium and some differentiated vascular regions of mature organs. {ECO:0000269\|PubMed:10476078}.

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). Seems to act as transcriptional activator. Formation of heterodimers with Aux/IAA proteins may alter their ability to modulate early auxin response genes expression. Mediates embryo axis formation and vascular tissues differentiation. Functionally redundant with ARF7. May be necessary to counteract AMP1 activity. {ECO:0000269\|PubMed:12036261, ECO:0000269\|PubMed:14973283, ECO:0000269\|PubMed:17553903}.

Cis-element ? help Back to Top
Source	Link
PlantRegMap	XP_013604468.1

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	JN979466	0.0	JN979466.1 Brassica rapa subsp. pekinensis auxin response factor 5-2 (ARF5-2) mRNA, complete cds.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_013604468.1	0.0	PREDICTED: auxin response factor 5-like
Swissprot	P93024	0.0	ARFE_ARATH; Auxin response factor 5
TrEMBL	A0A0D3DQG9	0.0	A0A0D3DQG9_BRAOL; Auxin response factor
STRING	Bo8g069820.1	0.0	(Brassica oleracea)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM5808	27	46

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT1G19850.1	0.0	ARF family protein

Publications ? help Back to Top
Chen MK,Wilson RL,Palme K,Ditengou FA,Shpak ED ERECTA family genes regulate auxin transport in the shoot apical meristem and forming leaf primordia. Plant Physiol., 2013. 162(4): p. 1978-91 [PMID:23821653] Huang JB, et al. ROP3 GTPase contributes to polar auxin transport and auxin responses and is important for embryogenesis and seedling growth in Arabidopsis. Plant Cell, 2014. 26(9): p. 3501-18 [PMID:25217509] Qi J, et al. Auxin depletion from leaf primordia contributes to organ patterning. Proc. Natl. Acad. Sci. U.S.A., 2014. 111(52): p. 18769-74 [PMID:25512543] Crawford BC, et al. Plant development. Genetic control of distal stem cell fate within root and embryonic meristems. Science, 2015. 347(6222): p. 655-9 [PMID:25612610] Zhang Y, et al. Regulation of oncogene expression in T-DNA-transformed host plant cells. PLoS Pathog., 2015. 11(1): p. e1004620 [PMID:25615824] Robert HS, et al. Plant embryogenesis requires AUX/LAX-mediated auxin influx. Development, 2015. 142(4): p. 702-11 [PMID:25617434] Krogan NT,Berleth T The identification and characterization of specific ARF-Aux/IAA regulatory modules in plant growth and development. Plant Signal Behav, 2015. 10(4): p. e992748 [PMID:25830553] Ckurshumova W,Berleth T Overcoming recalcitrance - Auxin response factor functions in plant regeneration. Plant Signal Behav, 2015. 10(7): p. e993293 [PMID:26098229] Wendrich JR, et al. A set of domain-specific markers in the Arabidopsis embryo. Plant Reprod, 2015. 28(3-4): p. 153-60 [PMID:26216537] Wu MF, et al. Auxin-regulated chromatin switch directs acquisition of flower primordium founder fate. Elife, 2015. 4: p. e09269 [PMID:26460543] Yamaguchi N,Jeong CW,Nole-Wilson S,Krizek BA,Wagner D AINTEGUMENTA and AINTEGUMENTA-LIKE6/PLETHORA3 Induce LEAFY Expression in Response to Auxin to Promote the Onset of Flower Formation in Arabidopsis. Plant Physiol., 2016. 170(1): p. 283-93 [PMID:26537561] Müller CJ, et al. PHABULOSA Mediates an Auxin Signaling Loop to Regulate Vascular Patterning in Arabidopsis. Plant Physiol., 2016. 170(2): p. 956-70 [PMID:26637548] Herud O,Weijers D,Lau S,Jürgens G Auxin responsiveness of the MONOPTEROS-BODENLOS module in primary root initiation critically depends on the nuclear import kinetics of the Aux/IAA inhibitor BODENLOS. Plant J., 2016. 85(2): p. 269-77 [PMID:26714008] Luo S, et al. Constitutive Expression of OsIAA9 Affects Starch Granules Accumulation and Root Gravitropic Response in Arabidopsis. Front Plant Sci, 2015. 6: p. 1156 [PMID:26734051] 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] Krogan NT,Marcos D,Weiner AI,Berleth T The auxin response factor MONOPTEROS controls meristem function and organogenesis in both the shoot and root through the direct regulation of PIN genes. New Phytol., 2016. 212(1): p. 42-50 [PMID:27441727] Fendrych M,Leung J,Friml J TIR1/AFB-Aux/IAA auxin perception mediates rapid cell wall acidification and growth of Arabidopsis hypocotyls. Elife, 2018. [PMID:27627746] Matthes M,Torres-Ruiz RA Boronic acid treatment phenocopies monopteros by affecting PIN1 membrane stability and polar auxin transport in Arabidopsis thaliana embryos. Development, 2016. 143(21): p. 4053-4062 [PMID:27697905] Bhatia N, et al. Auxin Acts through MONOPTEROS to Regulate Plant Cell Polarity and Pattern Phyllotaxis. Curr. Biol., 2016. 26(23): p. 3202-3208 [PMID:27818174] 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] Möller BK, et al. Auxin response cell-autonomously controls ground tissue initiation in the early Arabidopsis embryo. Proc. Natl. Acad. Sci. U.S.A., 2017. 114(12): p. E2533-E2539 [PMID:28265057] Carey NS,Krogan NT The role of AUXIN RESPONSE FACTORs in the development and differential growth of inflorescence stems. Plant Signal Behav, 2017. 12(4): p. e1307492 [PMID:28340328] Guan C, et al. Spatial Auxin Signaling Controls Leaf Flattening in Arabidopsis. Curr. Biol., 2017. 27(19): p. 2940-2950.e4 [PMID:28943086] Gaillochet C, et al. Control of plant cell fate transitions by transcriptional and hormonal signals. Elife, 2018. [PMID:29058667] Zheng K, et al. Involvement of PACLOBUTRAZOL RESISTANCE6/KIDARI, an Atypical bHLH Transcription Factor, in Auxin Responses in Arabidopsis. Front Plant Sci, 2017. 8: p. 1813 [PMID:29114256] Liu Z, et al. ARF2-ARF4 and ARF5 are Essential for Female and Male Gametophyte Development in Arabidopsis. Plant Cell Physiol., 2018. 59(1): p. 179-189 [PMID:29145642]