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

Itr_sc000912.1_g00002.1

Organism

Ipomoea trifida

Taxonomic ID

35884

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; asterids; lamiids; Solanales; Convolvulaceae; Ipomoeeae; Ipomoea

Family

ARF

Protein Properties

Length: 860aa MW: 95668.7 Da PI: 6.5117

Description

ARF family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Itr_sc000912.1_g00002.1	genome	Kazusa	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	B3	70.7	1.8e-22	156	257	1	99
EEEE-..-HHHHTT-EE--HHH.HTT......---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EE CS B3 1 ffkvltpsdvlksgrlvlpkkfaeeh......ggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfv 80 f+k+lt sd++++g +++ +++a+e+ + +++ +++l+ +d+ g +W++k+i+r++++r++l++GW+ Fv++++L +gD + Itr_sc000912.1_g00002.1 156 FCKTLTASDTSTHGGFSVLRRHADEClppldmS-QQPPNQELVAKDLLGSEWRFKHIFRGQPKRHLLQSGWSVFVSSKRLVAGDAF 240 99***************************63.4455569***************************************** PP EEEE-SSSEE..EEEEE-S CS B3 81 vFkldgrsefelvvkvfrk 99 +F + +++el+v+v+r+ Itr_sc000912.1_g00002.1 241 IFL--RGDNGELRVGVRRA 257 ..3489999***996 PP
2	Auxin_resp	121.5	6.4e-40	282	364	1	83
Auxin_resp 1 aahaastksvFevvYnPrastseFvvkvekvekalkvkvsvGmRfkmafetedsserrlsGtvvgvsdldpvrWpnSkWrsLk 83 a+ha++tk++F+v+Y+Pr+s++eF++++++++++lk+++s+GmRfkm+fe+e+++e+r++Gt+vg++d dp +Wp+SkWr+Lk Itr_sc000912.1_g00002.1 282 AWHAIQTKTMFTVYYKPRTSPAEFIIPYDQYMESLKNNYSIGMRFKMRFEGEEAPEQRFTGTIVGIEDRDPHKWPESKWRCLK 364 89*******************************************************************************96 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SuperFamily	SSF101936	2.49E-38	152	285	IPR015300	DNA-binding pseudobarrel domain
Gene3D	G3DSA:2.40.330.10	7.6E-40	152	271	IPR015300	DNA-binding pseudobarrel domain
CDD	cd10017	4.58E-20	154	256	No hit	No description
Pfam	PF02362	2.9E-20	156	257	IPR003340	B3 DNA binding domain
SMART	SM01019	3.2E-20	156	258	IPR003340	B3 DNA binding domain
PROSITE profile	PS50863	11.533	156	258	IPR003340	B3 DNA binding domain
Pfam	PF06507	9.3E-37	282	364	IPR010525	Auxin response factor
Pfam	PF02309	1.2E-11	732	826	IPR033389	AUX/IAA domain
PROSITE profile	PS51745	24.746	735	828	IPR000270	PB1 domain
SuperFamily	SSF54277	1.72E-12	736	812	No hit	No description

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: 860 aa Download sequence Send to blast
MASSEVSIRG YAEPSDGPRA GACTGLRSAA GAGNGNCIGC CDAEAALYME LWRACAGPLV 60 TVPREQDLVF YFPQGHIEQV EASTNQVADQ QMPVYGLPPK ILCRVVSVLL KAMLAEPDTD 120 EVYAQVTLIP EPNQDENAVK RESMPPPQPR FHVHSFCKTL TASDTSTHGG FSVLRRHADE 180 CLPPLDMSQQ PPNQELVAKD LLGSEWRFKH IFRGQPKRHL LQSGWSVFVS SKRLVAGDAF 240 IFLRGDNGEL RVGVRRAMRQ QGNAPSSVIS SHSMHLGVLA TAWHAIQTKT MFTVYYKPRT 300 SPAEFIIPYD QYMESLKNNY SIGMRFKMRF EGEEAPEQRF TGTIVGIEDR DPHKWPESKW 360 RCLKVRWDES STVPRPDRVS PWKIEPALSP SALNPLPVPR PKRHRSNIFP SPDSSVLTRE 420 GSCKISADPS PSTGLPRVMQ GQELPTLRGT FAESNESDSS EKPMAWEPPL DDEKIDNLSM 480 SHRHGSDKWL PLGRLESSFT DLLSGIGTQI NSPRGFCLQS GDQSAVAPSL VKQKTQHQEG 540 EFSLLGKQWS VVSSGLSLNL MDSSMKNHRE GFDATYQPLG DSRSADCEYS ALPGNKHENH 600 QANWLMQHQP MSYVQMPTHS REPMLKSTSM QQHEVMKPKD GNCKLFGIPL ITNDSATTQP 660 AMLPINAIIE SGHMHVDTNS HQTTAIELNQ RSEQTKVSKG PDSRPTGNEQ EKQFQTLRNG 720 GVRDKEGKIY SGSTRSCTKV QKQGTALGRS VDLSKFKNYD ELITKLDQLF DFNGELKSQN 780 KNWIVVYTDD EGDMMLVGDD PWQEFCGMVR KICIYTKEEV QQMNPRALNS KGDDMSSVAE 840 GLDANEVKSS ELPSASSAED

Sequence ? help Back to Top

Protein Sequence Length: 860 aa Download sequence Send to blast

MASSEVSIRG YAEPSDGPRA GACTGLRSAA GAGNGNCIGC CDAEAALYME LWRACAGPLV  60
TVPREQDLVF YFPQGHIEQV EASTNQVADQ QMPVYGLPPK ILCRVVSVLL KAMLAEPDTD  120
EVYAQVTLIP EPNQDENAVK RESMPPPQPR FHVHSFCKTL TASDTSTHGG FSVLRRHADE  180
CLPPLDMSQQ PPNQELVAKD LLGSEWRFKH IFRGQPKRHL LQSGWSVFVS SKRLVAGDAF  240
IFLRGDNGEL RVGVRRAMRQ QGNAPSSVIS SHSMHLGVLA TAWHAIQTKT MFTVYYKPRT  300
SPAEFIIPYD QYMESLKNNY SIGMRFKMRF EGEEAPEQRF TGTIVGIEDR DPHKWPESKW  360
RCLKVRWDES STVPRPDRVS PWKIEPALSP SALNPLPVPR PKRHRSNIFP SPDSSVLTRE  420
GSCKISADPS PSTGLPRVMQ GQELPTLRGT FAESNESDSS EKPMAWEPPL DDEKIDNLSM  480
SHRHGSDKWL PLGRLESSFT DLLSGIGTQI NSPRGFCLQS GDQSAVAPSL VKQKTQHQEG  540
EFSLLGKQWS VVSSGLSLNL MDSSMKNHRE GFDATYQPLG DSRSADCEYS ALPGNKHENH  600
QANWLMQHQP MSYVQMPTHS REPMLKSTSM QQHEVMKPKD GNCKLFGIPL ITNDSATTQP  660
AMLPINAIIE SGHMHVDTNS HQTTAIELNQ RSEQTKVSKG PDSRPTGNEQ EKQFQTLRNG  720
GVRDKEGKIY SGSTRSCTKV QKQGTALGRS VDLSKFKNYD ELITKLDQLF DFNGELKSQN  780
KNWIVVYTDD EGDMMLVGDD PWQEFCGMVR KICIYTKEEV QQMNPRALNS KGDDMSSVAE  840
GLDANEVKSS ELPSASSAED

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
4ldv_A	1e-165	46	386	18	354	Auxin response factor 1
4ldw_A	1e-165	46	386	18	354	Auxin response factor 1
4ldw_B	1e-165	46	386	18	354	Auxin response factor 1
4ldx_A	1e-165	46	386	18	354	Auxin response factor 1
4ldx_B	1e-165	46	386	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}.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_019167437.1	0.0	PREDICTED: auxin response factor 2-like isoform X1
Swissprot	Q2LAJ3	0.0	ARF2A_SOLLC; Auxin response factor 2A
TrEMBL	A0A1J6IK53	0.0	A0A1J6IK53_NICAT; Auxin response factor
STRING	XP_009769542.1	0.0	(Nicotiana sylvestris)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Asterids	OGEA2618	24	44

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]