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

XP_015895934.1

Organism

Ziziphus jujuba

Taxonomic ID

326968

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; fabids; Rosales; Rhamnaceae; Paliureae; Ziziphus

Family

ARF

Protein Properties

Length: 820aa MW: 92131.8 Da PI: 7.315

Description

ARF family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
XP_015895934.1	genome	NCBI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	B3	74.1	1.7e-23	139	240	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 +++ k++a+e+ ++k++ s++l+ +d++g++W++++i+r++++r++l++GW+ Fv++++L +gD ++F + +++ XP_015895934.1 139 FCKTLTASDTSTHGGFSVLKRHADEClpqldMSKQPPSQELVARDLHGNRWRFRHIFRGHPKRHLLQSGWSLFVSSKKLVAGDAFIFL--RGETG 231 99**************************955556678*********************************************..34899 PP ..EEEEE-S CS B3 91 elvvkvfrk 99 l+v+v+r+ XP_015895934.1 232 DLRVGVRRA 240 99**996 PP
2	Auxin_resp	116.6	2.1e-38	265	347	1	83
Auxin_resp 1 aahaastksvFevvYnPrastseFvvkvekvekalkvkvsvGmRfkmafetedsserrlsGtvvgvsdldpvrWpnSkWrsLk 83 a+ha+st+++F+v+Y+Pr+s++eF+v+++++++++k+++ +GmRfkm+fe+e+++e+r+sGtv+gv+d+d vrWp+S+Wr+Lk XP_015895934.1 265 AWHAVSTGTMFTVYYKPRTSPAEFIVPFDEYMESVKNSYPIGMRFKMRFEGEEAPEQRFSGTVIGVEDSDHVRWPGSQWRCLK 347 89*******************************************************************************96 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Gene3D	G3DSA:2.40.330.10	1.3E-39	132	254	IPR015300	DNA-binding pseudobarrel domain
SuperFamily	SSF101936	1.96E-39	133	268	IPR015300	DNA-binding pseudobarrel domain
CDD	cd10017	3.85E-20	137	239	No hit	No description
Pfam	PF02362	4.5E-21	139	240	IPR003340	B3 DNA binding domain
SMART	SM01019	2.5E-20	139	241	IPR003340	B3 DNA binding domain
PROSITE profile	PS50863	11.674	139	241	IPR003340	B3 DNA binding domain
Pfam	PF06507	8.2E-36	265	347	IPR010525	Auxin response factor
SuperFamily	SSF54277	9.81E-11	694	773	No hit	No description
PROSITE profile	PS51745	19.98	696	789	IPR000270	PB1 domain
Pfam	PF02309	2.1E-8	698	777	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: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: 820 aa Download sequence Send to blast
MEYNTVNHTD ARDGVLRASS AFPLADHDDA LYKELWHACA GPLVTVPRQG QLVFYFPQGH 60 IEQVEASTNQ VVDQQMPAYD PPTKILCRVI NVHLKAEPDT DEVYAQVILL PEPKQDEKSV 120 VKEALLPSPP PPRPRVHSFC KTLTASDTST HGGFSVLKRH ADECLPQLDM SKQPPSQELV 180 ARDLHGNRWR FRHIFRGHPK RHLLQSGWSL FVSSKKLVAG DAFIFLRGET GDLRVGVRRA 240 MRQFSNVPSS VISSHSMHIG VLATAWHAVS TGTMFTVYYK PRTSPAEFIV PFDEYMESVK 300 NSYPIGMRFK MRFEGEEAPE QRFSGTVIGV EDSDHVRWPG SQWRCLKVHW DETSPVHRPE 360 KISPWKVEPA LAHAPNSLLV SQMKRPRVNI SSSSNSSRHA TEGSSKINRE TTAQNQVSRA 420 LQGQEIRTLR RTFANNENSD TAQNLTVWAS SQGTDQTGTP FGKRIFGPED RVTQVRFGMP 480 CTNQSSHSRA AQESFRVGWP LVDRNPVNAN QFWKQGSGQE KIFHLSSSPV SMMRLIPSSD 540 LTESSSIKLP VAEVNDSDGM HEHEVKQQPG HWLLPRSSAE NSCHPMSLNL ENLHRQHDEK 600 AKGNGNCKLF GISLVSNPAV TNLDVLHTNS KHRPQGQIDV ASEHYQDMES ERLLEHEKCS 660 KFAVTATGGS ERQKPFPVSK QFSVDIPVKL PGGSTRRSIK VHKQGATLGR SVDLSKFNGY 720 DEMIAELDQI FEFNGELSSP EKKWMVVFTD DEGDMMLVGD DPWQEFRHIV RKICIYTPKE 780 VKKMDLQTSN KKLEEISAMA DQNMGSEEDQ ILDHPSAASP

Sequence ? help Back to Top

Protein Sequence Length: 820 aa Download sequence Send to blast

MEYNTVNHTD ARDGVLRASS AFPLADHDDA LYKELWHACA GPLVTVPRQG QLVFYFPQGH  60
IEQVEASTNQ VVDQQMPAYD PPTKILCRVI NVHLKAEPDT DEVYAQVILL PEPKQDEKSV  120
VKEALLPSPP PPRPRVHSFC KTLTASDTST HGGFSVLKRH ADECLPQLDM SKQPPSQELV  180
ARDLHGNRWR FRHIFRGHPK RHLLQSGWSL FVSSKKLVAG DAFIFLRGET GDLRVGVRRA  240
MRQFSNVPSS VISSHSMHIG VLATAWHAVS TGTMFTVYYK PRTSPAEFIV PFDEYMESVK  300
NSYPIGMRFK MRFEGEEAPE QRFSGTVIGV EDSDHVRWPG SQWRCLKVHW DETSPVHRPE  360
KISPWKVEPA LAHAPNSLLV SQMKRPRVNI SSSSNSSRHA TEGSSKINRE TTAQNQVSRA  420
LQGQEIRTLR RTFANNENSD TAQNLTVWAS SQGTDQTGTP FGKRIFGPED RVTQVRFGMP  480
CTNQSSHSRA AQESFRVGWP LVDRNPVNAN QFWKQGSGQE KIFHLSSSPV SMMRLIPSSD  540
LTESSSIKLP VAEVNDSDGM HEHEVKQQPG HWLLPRSSAE NSCHPMSLNL ENLHRQHDEK  600
AKGNGNCKLF GISLVSNPAV TNLDVLHTNS KHRPQGQIDV ASEHYQDMES ERLLEHEKCS  660
KFAVTATGGS ERQKPFPVSK QFSVDIPVKL PGGSTRRSIK VHKQGATLGR SVDLSKFNGY  720
DEMIAELDQI FEFNGELSSP EKKWMVVFTD DEGDMMLVGD DPWQEFRHIV RKICIYTPKE  780
VKKMDLQTSN KKLEEISAMA DQNMGSEEDQ ILDHPSAASP

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
4ldv_A	1e-169	19	369	7	354	Auxin response factor 1
4ldw_A	1e-169	19	369	7	354	Auxin response factor 1
4ldw_B	1e-169	19	369	7	354	Auxin response factor 1
4ldx_A	1e-169	19	369	7	354	Auxin response factor 1
4ldx_B	1e-169	19	369	7	354	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) (By similarity). Could act as transcriptional activator or repressor (PubMed:26959229, PubMed:26716451, PubMed:27645097, PubMed:28167023). Involved in the control of fruit ripening process (PubMed:26959229, PubMed:26716451, PubMed:28167023). Regulates expression of a number of ripening regulators, transcription factors, and ethylene biosynthesis and signaling components (PubMed:26959229, PubMed:26716451). May act as a transcriptional repressor of auxin-responsive genes (PubMed:26716451). Regulates vegetative growth, lateral root formation and flower organ senescence, possibly partially by regulating gene expression of auxin and ethylene response factor (ERF) genes (PubMed:28167023). Plays a negative role in axillary shoot meristem formation (PubMed:27645097). {ECO:0000255\|RuleBase:RU004561, ECO:0000269\|PubMed:26716451, ECO:0000269\|PubMed:26959229, ECO:0000269\|PubMed:27645097, ECO:0000269\|PubMed:28167023}.

Cis-element ? help Back to Top
Source	Link
PlantRegMap	XP_015895934.1

Regulation -- Description ? help Back to Top
Source	Description
UniProt	INDUCTION: By tomato fruit ripening. Expression in tomato fruits is up-regulated by exogenous application of ethylene and down-regulated by inhibition of ethylene receptors with 1-methylcyclopropene (1-MCP) (PubMed:26959229, PubMed:26716451). Up-regulated by plant hormone abscisic acid (ABA) in tomato fruits (PubMed:26959229). Expression is not up-regulated by plant hormone auxin in tomato fruits (PubMed:26716451). Up-regulated by auxin and gibberellic acid (GA), and down-regulated by ethylene in seedlings (PubMed:28167023). Down-regulated during decapitation-induced axillary shoot development and by excision of immature leaves. Down-regulation is inhibited by the application of auxin on the cut surface (PubMed:27645097). {ECO:0000269\|PubMed:26716451, ECO:0000269\|PubMed:26959229, ECO:0000269\|PubMed:27645097, ECO:0000269\|PubMed:28167023}.

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_015895934.1	0.0	auxin response factor 2A-like
Swissprot	Q2LAJ3	0.0	ARF2A_SOLLC; Auxin response factor 2A
TrEMBL	A0A2P5F1Y5	0.0	A0A2P5F1Y5_TREOI; Auxin response factor
STRING	XP_010100039.1	0.0	(Morus notabilis)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Fabids	OGEF3281	33	66

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
Tomato Genome Consortium The tomato genome sequence provides insights into fleshy fruit evolution. Nature, 2012. 485(7400): p. 635-41 [PMID:22660326] Breitel DA, et al. AUXIN RESPONSE FACTOR 2 Intersects Hormonal Signals in the Regulation of Tomato Fruit Ripening. PLoS Genet., 2016. 12(3): p. e1005903 [PMID:26959229] Xu T, et al. SlARF2a plays a negative role in mediating axillary shoot formation. Sci Rep, 2016. 6: p. 33728 [PMID:27645097] Ren Z,Liu R,Gu W,Dong X The Solanum lycopersicum auxin response factor SlARF2 participates in regulating lateral root formation and flower organ senescence. Plant Sci., 2017. 256: p. 103-111 [PMID:28167023]