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

Gorai.009G166100.1

Common Name

B456_009G166100

Organism

Gossypium raimondii

Taxonomic ID

29730

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Malvales; Malvaceae; Malvoideae; Gossypium

Family

ARF

Protein Properties

Length: 749aa MW: 81732.9 Da PI: 7.2327

Description

ARF family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Gorai.009G166100.1	genome	JGI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	B3	77.4	1.6e-24	147	248	1	99
EEEE-..-HHHHTT-EE--HHH.HTT......---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE- CS B3 1 ffkvltpsdvlksgrlvlpkkfaeeh......ggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfvvFkld 85 f+k+lt sd++++g +++p++ ae++ + +++ s++l+ +d++g +W++++iyr++++r++lt+GW+ Fv+ ++L +gD v+F Gorai.009G166100.1 147 FCKTLTASDTSTHGGFSVPRRAAEDCfppldyN-QQRPSQELVAKDLHGLEWRFRHIYRGQPRRHLLTTGWSAFVNKKKLVSGDAVLFL-- 234 99**************************963.3445679********************************************.. PP SSSEE..EEEEE-S CS B3 86 grsefelvvkvfrk 99 + +++el+++++r+ Gorai.009G166100.1 235 RGENGELRLGIRRA 248 4499999**996 PP
2	Auxin_resp	120.3	1.5e-39	273	354	1	82
Auxin_resp 1 aahaastksvFevvYnPrastseFvvkvekvekalkvkvsvGmRfkmafetedsserrlsGtvvgvsdldpvrWpnSkWrsL 82 ++ha+s+ksvF+++YnPras+seF+++v+k+ k+l++++svGmRfkm+fe+ed++e r++G+v+g+s++dpvrW++SkWr+L Gorai.009G166100.1 273 VVHAISMKSVFSIYYNPRASSSEFIIPVHKFWKSLDHSFSVGMRFKMRFESEDAAEGRYTGVVTGISEMDPVRWSGSKWRCL 354 689******************************************************************************9 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SuperFamily	SSF101936	1.57E-42	140	257	IPR015300	DNA-binding pseudobarrel domain
Gene3D	G3DSA:2.40.330.10	2.8E-40	141	251	IPR015300	DNA-binding pseudobarrel domain
CDD	cd10017	1.02E-22	145	247	No hit	No description
SMART	SM01019	1.2E-23	147	249	IPR003340	B3 DNA binding domain
PROSITE profile	PS50863	13.549	147	249	IPR003340	B3 DNA binding domain
Pfam	PF02362	1.9E-22	147	248	IPR003340	B3 DNA binding domain
Pfam	PF06507	3.7E-34	273	354	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:0009734	Biological Process	auxin-activated signaling pathway
GO:0005634	Cellular Component	nucleus
GO:0003677	Molecular Function	DNA binding

Sequence ? help Back to Top
Protein Sequence Length: 749 aa Download sequence Send to blast
MGGLIDLNTT EDEETPSSGS LSPSSSSASV LSASGSASSS PVCLELWHAC AGPLISLPKR 60 GSVVVYFPQG HLQQVSDFSG VAPAHDLPPH VFCRVVDVKL HAEGATDEVY AQVSLVPENE 120 KLKEGNIEVD GEEDAEADIK STTPHMFCKT LTASDTSTHG GFSVPRRAAE DCFPPLDYNQ 180 QRPSQELVAK DLHGLEWRFR HIYRGQPRRH LLTTGWSAFV NKKKLVSGDA VLFLRGENGE 240 LRLGIRRAAH IKNGTSFHSL CTQQLNRSNF ADVVHAISMK SVFSIYYNPR ASSSEFIIPV 300 HKFWKSLDHS FSVGMRFKMR FESEDAAEGR YTGVVTGISE MDPVRWSGSK WRCLLVRWDD 360 IDANRHNRVS PWEIEPSSSI SSSNSLLSPG SKRNRVGLPS GKPEFMVPEG IGASDFGESL 420 RFQKVLQGQE ILGFNTHHDG ANSQIMHRSE ISRRFPCSNG SGIAAIRNIG RDTLVNPDIS 480 YKGVGFEESF RFQKVLQGQE TSVSPPCRRG PTADDTRESD SPGAPDVGQL SGTRSGWSSL 540 MQSYNTHSHI GPSAQVSSPS SVLKFQHASN PFANVNPIHN LNSQEKERRV HKSSSFHAPE 600 TYGDRIPSST GGHGSRRRHL GSLDSFGPSA DTVQLGDSQP LSAQPTFRTS QELASSCKSS 660 CRLFGFSLTE GGHDAAKEDN MVQATSSLGA GAFLPRIGEQ FNTQPPAVTN TVGSSYTKGI 720 LQHCLKNYDE DATNDDRARR CMHAYSLL*

Sequence ? help Back to Top

Protein Sequence Length: 749 aa Download sequence Send to blast

MGGLIDLNTT EDEETPSSGS LSPSSSSASV LSASGSASSS PVCLELWHAC AGPLISLPKR  60
GSVVVYFPQG HLQQVSDFSG VAPAHDLPPH VFCRVVDVKL HAEGATDEVY AQVSLVPENE  120
KLKEGNIEVD GEEDAEADIK STTPHMFCKT LTASDTSTHG GFSVPRRAAE DCFPPLDYNQ  180
QRPSQELVAK DLHGLEWRFR HIYRGQPRRH LLTTGWSAFV NKKKLVSGDA VLFLRGENGE  240
LRLGIRRAAH IKNGTSFHSL CTQQLNRSNF ADVVHAISMK SVFSIYYNPR ASSSEFIIPV  300
HKFWKSLDHS FSVGMRFKMR FESEDAAEGR YTGVVTGISE MDPVRWSGSK WRCLLVRWDD  360
IDANRHNRVS PWEIEPSSSI SSSNSLLSPG SKRNRVGLPS GKPEFMVPEG IGASDFGESL  420
RFQKVLQGQE ILGFNTHHDG ANSQIMHRSE ISRRFPCSNG SGIAAIRNIG RDTLVNPDIS  480
YKGVGFEESF RFQKVLQGQE TSVSPPCRRG PTADDTRESD SPGAPDVGQL SGTRSGWSSL  540
MQSYNTHSHI GPSAQVSSPS SVLKFQHASN PFANVNPIHN LNSQEKERRV HKSSSFHAPE  600
TYGDRIPSST GGHGSRRRHL GSLDSFGPSA DTVQLGDSQP LSAQPTFRTS QELASSCKSS  660
CRLFGFSLTE GGHDAAKEDN MVQATSSLGA GAFLPRIGEQ FNTQPPAVTN TVGSSYTKGI  720
LQHCLKNYDE DATNDDRARR CMHAYSLL*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
4ldy_A	1e-119	35	383	12	361	Auxin response factor 1
4ldy_B	1e-119	35	383	12	361	Auxin response factor 1
Search in ModeBase

Expression -- Description ? help Back to Top
Source	Description
Uniprot	DEVELOPMENTAL STAGE: Detected during gynoecium development.
Uniprot	TISSUE SPECIFICITY: Expressed in the whole plant. {ECO:0000269\|PubMed:10476078, ECO:0000269\|PubMed:9409666}.

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_012444770.1	0.0	PREDICTED: auxin response factor 3 isoform X5
Swissprot	O23661	0.0	ARFC_ARATH; Auxin response factor 3
TrEMBL	A0A0D2TL70	0.0	A0A0D2TL70_GOSRA; Auxin response factor
STRING	Gorai.009G166100.1	0.0	(Gossypium raimondii)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM4924	28	49

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT2G33860.1	0.0	ARF family protein

Link Out ? help Back to Top
Phytozome	Gorai.009G166100.1

Publications ? help Back to Top
Paterson AH, et al. Repeated polyploidization of Gossypium genomes and the evolution of spinnable cotton fibres. Nature, 2012. 492(7429): p. 423-7 [PMID:23257886] 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]