PlantTFDB - Plant Transcription Factor Database @ CBI, PKU

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; fabids; Malpighiales; Euphorbiaceae; Crotonoideae; Jatropheae; Jatropha

Family

Protein Properties

Length: 282aa MW: 31273.2 Da PI: 7.3773

Description

B3 family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Jcr4S09185.10	genome	Kazusa	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	B3	77.5	1.5e-24	156	257	1	99
EEEE-..-HHHHTT-EE--HHH.HTT......---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE-SSSEE CS B3 1 ffkvltpsdvlksgrlvlpkkfaeeh......ggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfvvFkldgrsef 90 f+k+lt sd++++g +++ +++a+e+ + + + +++l+ +d++g++W++++i+r++++r++l++GW+ Fv++++L +gD ++F + +++ Jcr4S09185.10 156 FCKTLTASDTSTHGGFSVLRRHADEClppldmSRQ-PPTQELVAKDLHGNEWRFRHIFRGQPRRHLLQSGWSVFVSSKRLVAGDAFIFL--RGENG 248 99***************************7333.34459********************************************..44999 PP ..EEEEE-S CS B3 91 elvvkvfrk 99 el+v+v+r+ Jcr4S09185.10 249 ELRVGVRRA 257 9***996 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SuperFamily	SSF101936	9.55E-41	152	280	IPR015300	DNA-binding pseudobarrel domain
Gene3D	G3DSA:2.40.330.10	1.8E-42	152	271	IPR015300	DNA-binding pseudobarrel domain
CDD	cd10017	2.08E-23	154	256	No hit	No description
Pfam	PF02362	1.7E-22	156	257	IPR003340	B3 DNA binding domain
SMART	SM01019	2.0E-23	156	258	IPR003340	B3 DNA binding domain
PROSITE profile	PS50863	12.012	156	258	IPR003340	B3 DNA binding domain

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0003677	Molecular Function	DNA binding

Sequence ? help Back to Top
Protein Sequence Length: 282 aa Download sequence Send to blast
MDSSEISIKG NSGNVRGESF SPGYSEPNAV EGQKGHCRRQ ASARDAETAL YTELWHACAG 60 PLVTVPREGE RVFYFPQGHI EQVEASTNQV ADRQMPVYDL PSKILCSVIN VLLKAEPDTD 120 EVYAQVTLVP EAKQDENAVE KESPKPPPPR FHVHSFCKTL TASDTSTHGG FSVLRRHADE 180 CLPPLDMSRQ PPTQELVAKD LHGNEWRFRH IFRGQPRRHL LQSGWSVFVS SKRLVAGDAF 240 IFLRGENGEL RVGVRRAMRQ QGNVPSSVIS SHSMHLGVLA TA

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
4ldv_A	1e-130	49	282	18	250	Auxin response factor 1
4ldw_A	1e-130	49	282	18	250	Auxin response factor 1
4ldw_B	1e-130	49	282	18	250	Auxin response factor 1
4ldx_A	1e-130	49	282	18	250	Auxin response factor 1
4ldx_B	1e-130	49	282	18	250	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}.

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	KF022004	0.0	KF022004.1 Jatropha curcas auxin response factor (ARF) mRNA, partial cds.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_012090599.1	0.0	auxin response factor 2
Swissprot	Q94JM3	1e-167	ARFB_ARATH; Auxin response factor 2
TrEMBL	A0A067JF52	0.0	A0A067JF52_JATCU; Auxin response factor
STRING	cassava4.1_001542m	1e-177	(Manihot esculenta)

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT5G62000.3	1e-169	auxin response factor 2

Link Out ? help Back to Top
Entrez Gene	105648728

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] Zhang L, et al. Global analysis of gene expression profiles in physic nut (Jatropha curcas L.) seedlings exposed to salt stress. PLoS ONE, 2014. 9(5): p. e97878 [PMID:24837971] 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]