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

Kalax.0316s0030.1.p

Organism

Kalanchoe marnieriana

Taxonomic ID

80907

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; Saxifragales; Crassulaceae; Kalanchoe

Family

ARF

Protein Properties

Length: 674aa MW: 72778.9 Da PI: 7.6014

Description

ARF family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Kalax.0316s0030.1.p	genome	JGI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	B3	73.7	2.2e-23	171	272	1	99
EEEE-..-HHHHTT-EE--HHH.HTT.......---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EEEEE CS B3 1 ffkvltpsdvlksgrlvlpkkfaeeh.......ggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfvvFk 83 f+k+lt sd++++g +++p++ ae++ + ++ s++++ +d++g++W++++iyr++++r++lt+GW+ Fv+ +++ +gD v+F Kalax.0316s0030.1.p 171 FCKTLTASDTSTHGGFSVPRRAAEDCfppldytQ--QRPSQEIVAKDLHGQEWRFRHIYRGQPRRHLLTTGWSAFVNMKKIASGDAVLFL 258 99**************************9743..345679********************************************** PP E-SSSEE..EEEEE-S CS B3 84 ldgrsefelvvkvfrk 99 + ++ l+++++r+ Kalax.0316s0030.1.p 259 RG--GDGVLRLGIRRA 272 43..677789999986 PP
2	Auxin_resp	93.2	4.3e-31	299	377	3	82
Auxin_resp 3 haastksvFevvYnPrastseFvvkvekvekalkvkvsvGmRfkmafetedsserrlsGtvvgvsdldpvrWpnSkWrsL 82 ++++ s+F+v+YnPr s F+++v k++++l++++svG Rfkm++e+ed++errl+G+++g+sdldp +Wp+S+W++L Kalax.0316s0030.1.p 299 NSITAPSAFSVCYNPRGNLSPFIIPVCKFSRSLDHSLSVGVRFKMRVEGEDAAERRLTGVITGMSDLDP-KWPGSRWKCL 377 6788899************************************************************.*******9 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Gene3D	G3DSA:2.40.330.10	7.9E-40	161	276	IPR015300	DNA-binding pseudobarrel domain
SuperFamily	SSF101936	4.58E-40	168	277	IPR015300	DNA-binding pseudobarrel domain
CDD	cd10017	3.70E-22	169	271	No hit	No description
SMART	SM01019	5.0E-22	171	273	IPR003340	B3 DNA binding domain
PROSITE profile	PS50863	13.324	171	273	IPR003340	B3 DNA binding domain
Pfam	PF02362	1.6E-21	171	272	IPR003340	B3 DNA binding domain
Pfam	PF06507	4.2E-26	299	377	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: 674 aa Download sequence Send to blast
MGGFNFIDLN DVGGGEGVEE DEAAPSVATT LSSSAGSASS SSVSSASAST APLPTAGGAL 60 SSSVCLELWH ACAGRLISLP KRGSCVVYFP QGHLELLPER PSSTFNLPPH VFCRVIDVKL 120 QAEVDTDEVF ALVSLIPDSQ IEQRWRDGMI EDNGDEDGSE AAAKHITPHM FCKTLTASDT 180 STHGGFSVPR RAAEDCFPPL DYTQQRPSQE IVAKDLHGQE WRFRHIYRGQ PRRHLLTTGW 240 SAFVNMKKIA SGDAVLFLRG GDGVLRLGIR RAAQVKSVSP FPASCGQQFN LSNFSALVNS 300 ITAPSAFSVC YNPRGNLSPF IIPVCKFSRS LDHSLSVGVR FKMRVEGEDA AERRLTGVIT 360 GMSDLDPKWP GSRWKCLSVR WDGVHGNQQS SRLSPWEIEP CGSLSGCHMT SPGLKRTRSS 420 FPAANLDYPA NGVRSPEFRE PSRSQKVLQG QEIDRFSFYG MQSQHPSELM RCFPGTDRSG 480 TAMMRNGVGI AQMIPSAPFN HSGFGESFRF HKVLQGQEKY PGPTFMAPSA NLTRDSGGGF 540 GILDGVRVAS LQGAPPGLMY PPSNFHQQVN GVVNPHQAGE MSNVPATHPL HPPSPYARIF 600 GRDLMASLSH PGQALAHDQL GASRHPIMIR PAMYATNQDS AATEANASCR LFGFSLREGA 660 RATTNGDDPV HFI*

Sequence ? help Back to Top

Protein Sequence Length: 674 aa Download sequence Send to blast

MGGFNFIDLN DVGGGEGVEE DEAAPSVATT LSSSAGSASS SSVSSASAST APLPTAGGAL  60
SSSVCLELWH ACAGRLISLP KRGSCVVYFP QGHLELLPER PSSTFNLPPH VFCRVIDVKL  120
QAEVDTDEVF ALVSLIPDSQ IEQRWRDGMI EDNGDEDGSE AAAKHITPHM FCKTLTASDT  180
STHGGFSVPR RAAEDCFPPL DYTQQRPSQE IVAKDLHGQE WRFRHIYRGQ PRRHLLTTGW  240
SAFVNMKKIA SGDAVLFLRG GDGVLRLGIR RAAQVKSVSP FPASCGQQFN LSNFSALVNS  300
ITAPSAFSVC YNPRGNLSPF IIPVCKFSRS LDHSLSVGVR FKMRVEGEDA AERRLTGVIT  360
GMSDLDPKWP GSRWKCLSVR WDGVHGNQQS SRLSPWEIEP CGSLSGCHMT SPGLKRTRSS  420
FPAANLDYPA NGVRSPEFRE PSRSQKVLQG QEIDRFSFYG MQSQHPSELM RCFPGTDRSG  480
TAMMRNGVGI AQMIPSAPFN HSGFGESFRF HKVLQGQEKY PGPTFMAPSA NLTRDSGGGF  540
GILDGVRVAS LQGAPPGLMY PPSNFHQQVN GVVNPHQAGE MSNVPATHPL HPPSPYARIF  600
GRDLMASLSH PGQALAHDQL GASRHPIMIR PAMYATNQDS AATEANASCR LFGFSLREGA  660
RATTNGDDPV HFI*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
4ldy_A	1e-108	57	405	12	359	Auxin response factor 1
4ldy_B	1e-108	57	405	12	359	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). 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 the establishment or elaboration of tissue patterning during gynoecial development. {ECO:0000269\|PubMed:10952886, ECO:0000269\|PubMed:12036261}.

Regulation -- Description ? help Back to Top
Source	Description
UniProt	INDUCTION: Negatively regulated by AHL21/GIK. {ECO:0000269\|PubMed:19956801}.

Regulation -- PlantRegMap ? help Back to Top
Source	Upstream Regulator	Target Gene
PlantRegMap	Retrieve	-

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_010655464.1	0.0	PREDICTED: auxin response factor 3
Refseq	XP_019078171.1	0.0	PREDICTED: auxin response factor 3
Swissprot	O23661	1e-180	ARFC_ARATH; Auxin response factor 3
TrEMBL	F6HM45	0.0	F6HM45_VITVI; Auxin response factor
STRING	VIT_10s0003g00420.t01	0.0	(Vitis vinifera)

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT2G33860.1	1e-180	ARF family protein

Link Out ? help Back to Top
Phytozome	Kalax.0316s0030.1.p

Publications ? help Back to Top
Ozerova LV,Krasnikova MS,Troitsky AV,Solovyev AG,Morozov SY TAS3 Genes for small ta-siARF RNAs in plants belonging to subtribe Senecioninae: occurrence of prematurely terminated RNA precursors. Mol. Gen. Mikrobiol. Virusol., 2013. [PMID:24003511] Thoma R,Chandler JW Polarity in the early floral meristem of Arabidopsis. Plant Signal Behav, 2015. 10(4): p. e992733 [PMID:25806573] Lora J,Hormaza JI,Herrero M Transition from two to one integument in Prunus species: expression pattern of INNER NO OUTER (INO), ABERRANT TESTA SHAPE (ATS) and ETTIN (ETT). New Phytol., 2015. 208(2): p. 584-95 [PMID:25991552] Machida C,Nakagawa A,Kojima S,Takahashi H,Machida Y The complex of ASYMMETRIC LEAVES (AS) proteins plays a central role in antagonistic interactions of genes for leaf polarity specification in Arabidopsis. Wiley Interdiscip Rev Dev Biol, 2015 Nov-Dec. 4(6): p. 655-71 [PMID:26108442] Cabrera J, et al. Differentially expressed small RNAs in Arabidopsis galls formed by Meloidogyne javanica: a functional role for miR390 and its TAS3-derived tasiRNAs. New Phytol., 2016. 209(4): p. 1625-40 [PMID:26542733] Husbands AY,Benkovics AH,Nogueira FT,Lodha M,Timmermans MC The ASYMMETRIC LEAVES Complex Employs Multiple Modes of Regulation to Affect Adaxial-Abaxial Patterning and Leaf Complexity. Plant Cell, 2015. 27(12): p. 3321-35 [PMID:26589551] 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] Matsumura Y, et al. A genetic link between epigenetic repressor AS1-AS2 and a putative small subunit processome in leaf polarity establishment of Arabidopsis. Biol Open, 2016. 5(7): p. 942-54 [PMID:27334696] Simonini S, et al. A noncanonical auxin-sensing mechanism is required for organ morphogenesis in Arabidopsis. Genes Dev., 2016. 30(20): p. 2286-2296 [PMID:27898393] Pfannebecker KC,Lange M,Rupp O,Becker A An Evolutionary Framework for Carpel Developmental Control Genes. Mol. Biol. Evol., 2017. 34(2): p. 330-348 [PMID:28049761] 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] Su Z, et al. The THO Complex Non-Cell-Autonomously Represses Female Germline Specification through the TAS3-ARF3 Module. Curr. Biol., 2017. 27(11): p. 1597-1609.e2 [PMID:28552357] Simonini S,Bencivenga S,Trick M,Østergaard L Auxin-Induced Modulation of ETTIN Activity Orchestrates Gene Expression in Arabidopsis. Plant Cell, 2017. 29(8): p. 1864-1882 [PMID:28804059] Guan C, et al. Spatial Auxin Signaling Controls Leaf Flattening in Arabidopsis. Curr. Biol., 2017. 27(19): p. 2940-2950.e4 [PMID:28943086] Simonini S, et al. Corrigendum: A noncanonical auxin-sensing mechanism is required for organ morphogenesis in Arabidopsis. Genes Dev., 2017. 31(17): p. 1821 [PMID:28982764] Zhang K, et al. AUXIN RESPONSE FACTOR3 Regulates Floral Meristem Determinacy by Repressing Cytokinin Biosynthesis and Signaling. Plant Cell, 2018. 30(2): p. 324-346 [PMID:29371438] Vial-Pradel S, et al. Arabidopsis Zinc-Finger-Like Protein ASYMMETRIC LEAVES2 (AS2) and Two Nucleolar Proteins Maintain Gene Body DNA Methylation in the Leaf Polarity Gene ETTIN (ARF3). Plant Cell Physiol., 2018. 59(7): p. 1385-1397 [PMID:29415182] Simonini S,Stephenson P,Østergaard L A molecular framework controlling style morphology in Brassicaceae. Development, 2018. [PMID:29440299] Andres-Robin A, et al. Evidence for the Regulation of Gynoecium Morphogenesis by ETTIN via Cell Wall Dynamics. Plant Physiol., 2018. 178(3): p. 1222-1232 [PMID:30237208] Hablak SG Features inheritance of root system Arabidopsis thaliana (L.) Heynh. the interaction of genes CTR1 AND ALF3, NPH4 and IAR2. Tsitol. Genet., 2019. [PMID:30484609]