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

WALNUT_00015008-RA

Organism

Juglans regia

Taxonomic ID

51240

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; fabids; Fagales; Juglandaceae; Juglans

Family

ARF

Protein Properties

Length: 850aa MW: 94811.9 Da PI: 6.7688

Description

ARF family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
WALNUT_00015008-RA	genome	JHU	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	B3	73	3.7e-23	150	251	1	99
EEEE-..-HHHHTT-EE--HHH.HTT.......---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE CS B3 1 ffkvltpsdvlksgrlvlpkkfaeeh.......ggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfvvFkl 84 f+k+lt sd++++g +++ +++a+e+ ++ +++l +d++g++W++++i+r++++r++l++GW+ Fv++++L +gD ++F WALNUT_00015008-RA 150 FCKTLTASDTSTHGGFSVLRRHADEClppldmsR--QPPTQDLAAKDLHGNEWRFRHIFRGQPRRHLLQSGWSVFVSSKRLVAGDAFIFL- 237 99***************************743..334459********************************************. PP -SSSEE..EEEEE-S CS B3 85 dgrsefelvvkvfrk 99 + +++el+v+v+r+ WALNUT_00015008-RA 238 -RGENGELRVGVRRA 251 .449999***996 PP
2	Auxin_resp	121.1	8.5e-40	276	358	1	83
Auxin_resp 1 aahaastksvFevvYnPrastseFvvkvekvekalkvkvsvGmRfkmafetedsserrlsGtvvgvsdldpvrWpnSkWrsLk 83 a+ha+stk++F+v+Y+Pr+s++eF+v+++++++++k+++s+GmRfkm+fe+e+++e+r++Gt+vgv+d+d rWpnSkWr+Lk WALNUT_00015008-RA 276 AWHAISTKTMFTVYYKPRTSPTEFIVPYDQYMESIKKNYSIGMRFKMRFESEEAPEQRFTGTIVGVEDADAKRWPNSKWRCLK 358 89*******************************************************************************96 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SuperFamily	SSF101936	9.94E-40	146	279	IPR015300	DNA-binding pseudobarrel domain
Gene3D	G3DSA:2.40.330.10	7.1E-41	147	265	IPR015300	DNA-binding pseudobarrel domain
CDD	cd10017	1.04E-20	148	250	No hit	No description
SMART	SM01019	6.6E-22	150	252	IPR003340	B3 DNA binding domain
PROSITE profile	PS50863	11.73	150	252	IPR003340	B3 DNA binding domain
Pfam	PF02362	5.2E-21	150	251	IPR003340	B3 DNA binding domain
Pfam	PF06507	3.6E-37	276	358	IPR010525	Auxin response factor
Pfam	PF02309	3.0E-5	709	761	IPR033389	AUX/IAA domain
SuperFamily	SSF54277	3.04E-11	723	802	No hit	No description
PROSITE profile	PS51745	24	725	809	IPR000270	PB1 domain
Pfam	PF02309	4.0E-7	766	810	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: 850 aa Download sequence Send to blast
MTASEVSTKG SSGYSDQTDV RNSTEGQKGH SKFSGTSKDA ETALYTELWH ACAGPLVTVP 60 REDERVFYFP QGHIEQVEAS TNQLADQQMP LYDLPAKILC RVINVQLKAE ADTDEVFAQV 120 TLIPEANQDE NAVEKIPPPP PLPKFHVHSF CKTLTASDTS THGGFSVLRR HADECLPPLD 180 MSRQPPTQDL AAKDLHGNEW RFRHIFRGQP RRHLLQSGWS VFVSSKRLVA GDAFIFLRGE 240 NGELRVGVRR AMRQQDNVPS SVISSHSMHL GVLATAWHAI STKTMFTVYY KPRTSPTEFI 300 VPYDQYMESI KKNYSIGMRF KMRFESEEAP EQRFTGTIVG VEDADAKRWP NSKWRCLKVR 360 WDETSTMPRP ERVSPWKVEP ALAPTLNPLP MPRAKRPRSN MVSSSPDSSV LTREGSSKAT 420 LDPSPASVFL RVLPGQEFST LRGNFLDSNE SDTAEKSVVW PPLVEDEKID VSASRRHGSE 480 NWMSRGRQEP TYTDLLSGFG ASSGSSHGTC APLVDQAAAA VNFPRKQSLE QEGKFNLLAS 540 PWSLMPSNLS LNLSDTSLKD PVQGGDVAYQ APGNARHDAI TEYSMIHSHR VEHPRGNWLM 600 PSPASCQFEN SAHSKEPMQK PVLVQQCEAV KPKDGKYKLF GIPLICNPAT PERAAPRRGM 660 MNEPTGHILD TSHVAQTLDS DQKSEQSRGS KSADNPLPVI EKMLVQRREQ RSREVQGKVL 720 NSSTRSCTKV HKQGIALGRS VDLTKFNSYE ELIAELDQLF EFGGELLASE KNWLIVYTDD 780 EGDMMLVGDD PWAEFCGMVR KIFIYTREEV QKMNPGTLNL KAGENQLAGE AEDAKELNLK 840 SFVVTTPEKC

Sequence ? help Back to Top

Protein Sequence Length: 850 aa Download sequence Send to blast

MTASEVSTKG SSGYSDQTDV RNSTEGQKGH SKFSGTSKDA ETALYTELWH ACAGPLVTVP  60
REDERVFYFP QGHIEQVEAS TNQLADQQMP LYDLPAKILC RVINVQLKAE ADTDEVFAQV  120
TLIPEANQDE NAVEKIPPPP PLPKFHVHSF CKTLTASDTS THGGFSVLRR HADECLPPLD  180
MSRQPPTQDL AAKDLHGNEW RFRHIFRGQP RRHLLQSGWS VFVSSKRLVA GDAFIFLRGE  240
NGELRVGVRR AMRQQDNVPS SVISSHSMHL GVLATAWHAI STKTMFTVYY KPRTSPTEFI  300
VPYDQYMESI KKNYSIGMRF KMRFESEEAP EQRFTGTIVG VEDADAKRWP NSKWRCLKVR  360
WDETSTMPRP ERVSPWKVEP ALAPTLNPLP MPRAKRPRSN MVSSSPDSSV LTREGSSKAT  420
LDPSPASVFL RVLPGQEFST LRGNFLDSNE SDTAEKSVVW PPLVEDEKID VSASRRHGSE  480
NWMSRGRQEP TYTDLLSGFG ASSGSSHGTC APLVDQAAAA VNFPRKQSLE QEGKFNLLAS  540
PWSLMPSNLS LNLSDTSLKD PVQGGDVAYQ APGNARHDAI TEYSMIHSHR VEHPRGNWLM  600
PSPASCQFEN SAHSKEPMQK PVLVQQCEAV KPKDGKYKLF GIPLICNPAT PERAAPRRGM  660
MNEPTGHILD TSHVAQTLDS DQKSEQSRGS KSADNPLPVI EKMLVQRREQ RSREVQGKVL  720
NSSTRSCTKV HKQGIALGRS VDLTKFNSYE ELIAELDQLF EFGGELLASE KNWLIVYTDD  780
EGDMMLVGDD PWAEFCGMVR KIFIYTREEV QKMNPGTLNL KAGENQLAGE AEDAKELNLK  840
SFVVTTPEKC

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
4ldv_A	1e-174	43	380	18	354	Auxin response factor 1
4ldw_A	1e-174	43	380	18	354	Auxin response factor 1
4ldw_B	1e-174	43	380	18	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}.

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_018836630.1	0.0	PREDICTED: auxin response factor 2-like
Refseq	XP_018836638.1	0.0	PREDICTED: auxin response factor 2-like
Refseq	XP_018836647.1	0.0	PREDICTED: auxin response factor 2-like
Swissprot	Q2LAJ3	0.0	ARF2A_SOLLC; Auxin response factor 2A
TrEMBL	A0A2I4FYC5	0.0	A0A2I4FYC5_JUGRE; Auxin response factor
STRING	VIT_17s0000g00320.t01	0.0	(Vitis vinifera)

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]