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

Cotton_A_01955_BGI-A2_v1.0

Common Name

F383_35574

Organism

Gossypium arboreum

Taxonomic ID

29729

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: 869aa MW: 96723.7 Da PI: 6.7189

Description

ARF family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Cotton_A_01955_BGI-A2_v1.0	genome	BGI	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	163	264	1	99
EEEE-..-HHHHTT-EE--HHH.HTT......---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT CS B3 1 ffkvltpsdvlksgrlvlpkkfaeeh......ggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkeg 77 f+k+lt sd++++g +++ +++a+e+ ++++++ ++l+ +d++g++W++++i+r++++r++l++GW+ Fv++++L +g Cotton_A_01955_BGI-A2_v1.0 163 FCKTLTASDTSTHGGFSVLRRHADEClppldmSLQPPT-QELVSKDLHGNEWRFRHIFRGQPRRHLLQSGWSVFVSSKKLVAG 244 99***************************9777666.49999*********************************** PP -EEEEEE-SSSEE..EEEEE-S CS B3 78 DfvvFkldgrsefelvvkvfrk 99 D ++F + +++el+v+v+r+ Cotton_A_01955_BGI-A2_v1.0 245 DAFIFL--RGENGELRVGVRRA 264 **..449999***985 PP
2	Auxin_resp	119.1	3.5e-39	289	371	1	83
Auxin_resp 1 aahaastksvFevvYnPrastseFvvkvekvekalkvkvsvGmRfkmafetedsserrlsGtvvgvsdldpvrWpnSkWrsLk 83 a+ha +t+++F+v+Y+Pr+s++eF+v+++++++++k+++s+GmRfkm+fe+e+++e+r++Gt+vg++d+dp rW++SkWr+Lk Cotton_A_01955_BGI-A2_v1.0 289 AWHAYTTRTIFTVYYKPRTSPAEFIVPFNQYMESVKNNYSIGMRFKMRFEGEEAPEQRFTGTIVGIEDADPKRWQGSKWRCLK 371 79*******************************************************************************96 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SuperFamily	SSF101936	1.26E-39	153	292	IPR015300	DNA-binding pseudobarrel domain
Gene3D	G3DSA:2.40.330.10	6.4E-40	159	278	IPR015300	DNA-binding pseudobarrel domain
CDD	cd10017	1.51E-20	161	263	No hit	No description
Pfam	PF02362	4.0E-21	163	264	IPR003340	B3 DNA binding domain
SMART	SM01019	2.8E-21	163	265	IPR003340	B3 DNA binding domain
PROSITE profile	PS50863	11.646	163	265	IPR003340	B3 DNA binding domain
Pfam	PF06507	4.0E-36	289	371	IPR010525	Auxin response factor
Pfam	PF02309	7.4E-6	721	770	IPR033389	AUX/IAA domain
SuperFamily	SSF54277	6.38E-13	728	814	No hit	No description
PROSITE profile	PS51745	24.292	734	818	IPR000270	PB1 domain
Pfam	PF02309	6.7E-7	780	819	IPR033389	AUX/IAA domain

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
GO:0005515	Molecular Function	protein binding

Sequence ? help Back to Top
Protein Sequence Length: 869 aa Download sequence Send to blast
MTTSEISIKG NCVNGRGDSF SSGYTEPRDT RNTMEGQNGH SARTAAVRET VDPERALYTE 60 LWHACAGPLV TVPREGERVF YFPQGHIEQV EASTHQVSEQ QMPVYDLPPK ILCRVINVQL 120 KAEPDTDEVF AQVTLLPEHT QDENMVDKEP PILEPPRFQV HSFCKTLTAS DTSTHGGFSV 180 LRRHADECLP PLDMSLQPPT QELVSKDLHG NEWRFRHIFR GQPRRHLLQS GWSVFVSSKK 240 LVAGDAFIFL RGENGELRVG VRRALRQQGN VPSSVISSHS MHLGVLATAW HAYTTRTIFT 300 VYYKPRTSPA EFIVPFNQYM ESVKNNYSIG MRFKMRFEGE EAPEQRFTGT IVGIEDADPK 360 RWQGSKWRCL KVRWDETSTI PRPERVSPWK IEHALSPPAL NPLPMPRPKR PRTNAVSSSP 420 DSSVLTREGS SKVTVDPLPA SSFSRVLQGQ EFSTLRGTFA ESNDSDTADR SVMWPPSIDD 480 EKIDVAHGER KFGSENWMPS RRHEPTYTDL LSGFGSNADT SRGYYPSVVD QTSVAGNSGK 540 KQLLDQEGKL GAWSLLPSGL SLKLSDSSTD PPLQGSDVPY QARGNGRFCG FGDYPILEGR 600 RIECTRGNWL MPPPSTSCYD NSVHSRDLMP KTSLVQEHKN GKSREGNCKL FGIPLISISS 660 ASGPAVSHIS AFAKPVGHMQ AALHQIHALK SDKRSENSNA SQMAEDVSAF NEQEKMGQPH 720 AREFQSKPST ASTRSCTKVL MQGTALGRSV DLTKFNNYDE LIAELDQLFE FGGELMAPQK 780 NWLVVYTDDE GDMMLVGDDP WQEFCAMVRK IGIYTREEVQ KMKPGSLGSK FEDIPVPSEG 840 TVAKEVNCPS ASSAKNCSGF LMETWGVAW

Sequence ? help Back to Top

Protein Sequence Length: 869 aa Download sequence Send to blast

MTTSEISIKG NCVNGRGDSF SSGYTEPRDT RNTMEGQNGH SARTAAVRET VDPERALYTE  60
LWHACAGPLV TVPREGERVF YFPQGHIEQV EASTHQVSEQ QMPVYDLPPK ILCRVINVQL  120
KAEPDTDEVF AQVTLLPEHT QDENMVDKEP PILEPPRFQV HSFCKTLTAS DTSTHGGFSV  180
LRRHADECLP PLDMSLQPPT QELVSKDLHG NEWRFRHIFR GQPRRHLLQS GWSVFVSSKK  240
LVAGDAFIFL RGENGELRVG VRRALRQQGN VPSSVISSHS MHLGVLATAW HAYTTRTIFT  300
VYYKPRTSPA EFIVPFNQYM ESVKNNYSIG MRFKMRFEGE EAPEQRFTGT IVGIEDADPK  360
RWQGSKWRCL KVRWDETSTI PRPERVSPWK IEHALSPPAL NPLPMPRPKR PRTNAVSSSP  420
DSSVLTREGS SKVTVDPLPA SSFSRVLQGQ EFSTLRGTFA ESNDSDTADR SVMWPPSIDD  480
EKIDVAHGER KFGSENWMPS RRHEPTYTDL LSGFGSNADT SRGYYPSVVD QTSVAGNSGK  540
KQLLDQEGKL GAWSLLPSGL SLKLSDSSTD PPLQGSDVPY QARGNGRFCG FGDYPILEGR  600
RIECTRGNWL MPPPSTSCYD NSVHSRDLMP KTSLVQEHKN GKSREGNCKL FGIPLISISS  660
ASGPAVSHIS AFAKPVGHMQ AALHQIHALK SDKRSENSNA SQMAEDVSAF NEQEKMGQPH  720
AREFQSKPST ASTRSCTKVL MQGTALGRSV DLTKFNNYDE LIAELDQLFE FGGELMAPQK  780
NWLVVYTDDE GDMMLVGDDP WQEFCAMVRK IGIYTREEVQ KMKPGSLGSK FEDIPVPSEG  840
TVAKEVNCPS ASSAKNCSGF LMETWGVAW

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
4ldv_A	1e-178	56	392	18	353	Auxin response factor 1
4ldw_A	1e-178	56	392	18	353	Auxin response factor 1
4ldw_B	1e-178	56	392	18	353	Auxin response factor 1
4ldx_A	1e-178	56	392	18	353	Auxin response factor 1
4ldx_B	1e-178	56	392	18	353	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. Promotes flowering, stamen development, floral organ abscission and fruit dehiscence. Functions independently of ethylene and cytokinin response pathways. May act as a repressor of cell division and organ growth. {ECO:0000269\|PubMed:12036261, ECO:0000269\|PubMed:15960614, ECO:0000269\|PubMed:16176952, ECO:0000269\|PubMed:16339187}.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_017637282.1	0.0	PREDICTED: auxin response factor 2-like
Swissprot	Q94JM3	0.0	ARFB_ARATH; Auxin response factor 2
TrEMBL	A0A0B0N6Z7	0.0	A0A0B0N6Z7_GOSAR; Auxin response factor
STRING	Gorai.007G044900.1	0.0	(Gossypium raimondii)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM5348	26	47

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT5G62000.3	0.0	auxin response factor 2

Publications ? help Back to Top
Chao WS,Doğramaci M,Foley ME,Horvath DP,Anderson JV Selection and validation of endogenous reference genes for qRT-PCR analysis in leafy spurge (Euphorbia esula). PLoS ONE, 2012. 7(8): p. e42839 [PMID:22916167] 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] Li C, et al. Ectopic expression of a maize hybrid down-regulated gene ZmARF25 decreases organ size by affecting cellular proliferation in Arabidopsis. PLoS ONE, 2014. 9(4): p. e94830 [PMID:24756087] Lyons R, et al. Fusarium oxysporum triggers tissue-specific transcriptional reprogramming in Arabidopsis thaliana. PLoS ONE, 2015. 10(4): p. e0121902 [PMID:25849296] Roodbarkelari F,Du F,Truernit E,Laux T ZLL/AGO10 maintains shoot meristem stem cells during Arabidopsis embryogenesis by down-regulating ARF2-mediated auxin response. BMC Biol., 2015. 13: p. 74 [PMID:26358077] Meng LS,Wang ZB,Yao SQ,Liu A The ARF2-ANT-COR15A gene cascade regulates ABA-signaling-mediated resistance of large seeds to drought in Arabidopsis. J. Cell. Sci., 2015. 128(21): p. 3922-32 [PMID:26395398] Zhao S,Zhang ML,Ma TL,Wang Y Phosphorylation of ARF2 Relieves Its Repression of Transcription of the K+ Transporter Gene HAK5 in Response to Low Potassium Stress. Plant Cell, 2016. 28(12): p. 3005-3019 [PMID:27895227] Promchuea S,Zhu Y,Chen Z,Zhang J,Gong Z ARF2 coordinates with PLETHORAs and PINs to orchestrate ABA-mediated root meristem activity in Arabidopsis . J Integr Plant Biol, 2017. 59(1): p. 30-43 [PMID:28074634] 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] Sanz-Fernández M, et al. Screening Arabidopsis mutants in genes useful for phytoremediation. J. Hazard. Mater., 2017. 335: p. 143-151 [PMID:28441590] Zhang M,Hu X,Zhu M,Xu M,Wang L Transcription factors NF-YA2 and NF-YA10 regulate leaf growth via auxin signaling in Arabidopsis. Sci Rep, 2017. 7(1): p. 1395 [PMID:28469131] Guan C, et al. Spatial Auxin Signaling Controls Leaf Flattening in Arabidopsis. Curr. Biol., 2017. 27(19): p. 2940-2950.e4 [PMID:28943086] 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] Sarkar Das S, et al. Expression dynamics of miRNAs and their targets in seed germination conditions reveals miRNA-ta-siRNA crosstalk as regulator of seed germination. Sci Rep, 2018. 8(1): p. 1233 [PMID:29352229]