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

PGSC0003DMP400024934

Common Name

LOC102582348

Organism

Solanum tuberosum

Taxonomic ID

4113

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; asterids; lamiids; Solanales; Solanaceae; Solanoideae; Solaneae; Solanum

Family

ARF

Protein Properties

Length: 846aa MW: 93925.3 Da PI: 6.7491

Description

ARF family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
PGSC0003DMP400024934	genome	PGSC	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	B3	73.3	2.9e-23	146	247	1	99
EEEE-..-HHHHTT-EE--HHH.HTT......---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EEEEE CS B3 1 ffkvltpsdvlksgrlvlpkkfaeeh......ggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfvvFk 83 f+k+lt sd++++g +++ +++a+e+ + ++ +++l+ +d++g++W++++i+r++++r++l++GW+ Fv++++L +gD ++F PGSC0003DMP400024934 146 FCKTLTASDTSTHGGFSVLRRHADEClpqldmS-RQPPTQELVAKDLHGNEWRFRHIFRGQPRRHLLQSGWSVFVSSKRLVAGDAFIFL 233 99**************************963.3334459******************************************** PP E-SSSEE..EEEEE-S CS B3 84 ldgrsefelvvkvfrk 99 + +++ l+v+v+r+ PGSC0003DMP400024934 234 --RGENGDLRVGVRRA 247 ..3488889**996 PP
2	Auxin_resp	119.7	2.3e-39	272	354	1	83
Auxin_resp 1 aahaastksvFevvYnPrastseFvvkvekvekalkvkvsvGmRfkmafetedsserrlsGtvvgvsdldpvrWpnSkWrsLk 83 a+ha++tk++F+v+Y+Pr+s++eF+v+++++++++k+++s+GmRfkm+fe+e+++e+r++Gt+vg++d+dp rW +SkWr+Lk PGSC0003DMP400024934 272 AWHAIQTKTMFTVYYKPRTSPTEFIVPYDHYMESVKNNYSIGMRFKMRFEGEEAPEQRFTGTIVGIEDADPQRWLESKWRCLK 354 89*******************************************************************************96 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SuperFamily	SSF101936	2.75E-40	142	275	IPR015300	DNA-binding pseudobarrel domain
Gene3D	G3DSA:2.40.330.10	2.6E-41	142	261	IPR015300	DNA-binding pseudobarrel domain
CDD	cd10017	8.21E-21	144	246	No hit	No description
PROSITE profile	PS50863	11.871	146	248	IPR003340	B3 DNA binding domain
SMART	SM01019	4.0E-22	146	248	IPR003340	B3 DNA binding domain
Pfam	PF02362	2.8E-21	146	247	IPR003340	B3 DNA binding domain
Pfam	PF06507	1.5E-36	272	354	IPR010525	Auxin response factor
Pfam	PF02309	1.8E-10	714	804	IPR033389	AUX/IAA domain
SuperFamily	SSF54277	1.67E-12	715	796	No hit	No description
PROSITE profile	PS51745	25.219	719	803	IPR000270	PB1 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: 846 aa Download sequence Send to blast
MAASEVSIQG YSEPSDGSRP VSDTVRSSSG VGRVDADTAL YTELWRSCAG PLVTVPREGE 60 LVYYFPQGHI EQVEASTNQV ADQQMPSYNL PSKILCRVVN VLLKAEPDTD EVYAQVTLMP 120 EPNQDENTVK KEPMRPPPPR FHVHSFCKTL TASDTSTHGG FSVLRRHADE CLPQLDMSRQ 180 PPTQELVAKD LHGNEWRFRH IFRGQPRRHL LQSGWSVFVS SKRLVAGDAF IFLRGENGDL 240 RVGVRRAMRQ QGNAPSSVIS SHSMHLGVLA TAWHAIQTKT MFTVYYKPRT SPTEFIVPYD 300 HYMESVKNNY SIGMRFKMRF EGEEAPEQRF TGTIVGIEDA DPQRWLESKW RCLKVRWDEN 360 SSIPRPDRVS PWKIEPALSP PALNAPPVAR PKRPRSSILP SSPDSSVLTR EGSSRVTADH 420 SQASGFPRVL QGQELSTFRG GFAESNETDL SEKPMIWQPS VNDEKNDIHS ASKRYLPDKW 480 LPLGRPESSL TDLLSGFGVP NNSSHGFCPS ADQAAFGASL VKQQTQDQEK DFSLLGKPWS 540 LLSSGLSLNL MDSGSKAPGI GGDTPYQMRG DARYSGYGEF SVLPGHRVAN QQGSWIMPQP 600 VSPYMHSREM MHKPTVVKQP EAVKPKEGNC KLFGIPLTSN VCTDPVMMRK SSLIDPASDM 660 NIGIHPHQSL ATDSDQRSEQ SKGSKVDDGI AANDHDKQFH TFHLSARDRD GKGHSSSTRS 720 CTKVHKQGTA LGRSVDLAKF NNYDELIAEL DQLFDFNGEL KARSKSWLVV YTDDEGDMML 780 VGDDPWQEFC GMVRKIFIYT KEEVQRMNPG TLNSKGEDTS SVAEGSDAKE VKNLQLPSES 840 GQAES*

Sequence ? help Back to Top

Protein Sequence Length: 846 aa Download sequence Send to blast

MAASEVSIQG YSEPSDGSRP VSDTVRSSSG VGRVDADTAL YTELWRSCAG PLVTVPREGE  60
LVYYFPQGHI EQVEASTNQV ADQQMPSYNL PSKILCRVVN VLLKAEPDTD EVYAQVTLMP  120
EPNQDENTVK KEPMRPPPPR FHVHSFCKTL TASDTSTHGG FSVLRRHADE CLPQLDMSRQ  180
PPTQELVAKD LHGNEWRFRH IFRGQPRRHL LQSGWSVFVS SKRLVAGDAF IFLRGENGDL  240
RVGVRRAMRQ QGNAPSSVIS SHSMHLGVLA TAWHAIQTKT MFTVYYKPRT SPTEFIVPYD  300
HYMESVKNNY SIGMRFKMRF EGEEAPEQRF TGTIVGIEDA DPQRWLESKW RCLKVRWDEN  360
SSIPRPDRVS PWKIEPALSP PALNAPPVAR PKRPRSSILP SSPDSSVLTR EGSSRVTADH  420
SQASGFPRVL QGQELSTFRG GFAESNETDL SEKPMIWQPS VNDEKNDIHS ASKRYLPDKW  480
LPLGRPESSL TDLLSGFGVP NNSSHGFCPS ADQAAFGASL VKQQTQDQEK DFSLLGKPWS  540
LLSSGLSLNL MDSGSKAPGI GGDTPYQMRG DARYSGYGEF SVLPGHRVAN QQGSWIMPQP  600
VSPYMHSREM MHKPTVVKQP EAVKPKEGNC KLFGIPLTSN VCTDPVMMRK SSLIDPASDM  660
NIGIHPHQSL ATDSDQRSEQ SKGSKVDDGI AANDHDKQFH TFHLSARDRD GKGHSSSTRS  720
CTKVHKQGTA LGRSVDLAKF NNYDELIAEL DQLFDFNGEL KARSKSWLVV YTDDEGDMML  780
VGDDPWQEFC GMVRKIFIYT KEEVQRMNPG TLNSKGEDTS SVAEGSDAKE VKNLQLPSES  840
GQAES*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
4ldv_A	1e-175	27	376	7	354	Auxin response factor 1
4ldw_A	1e-175	27	376	7	354	Auxin response factor 1
4ldw_B	1e-175	27	376	7	354	Auxin response factor 1
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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	PGSC0003DMP400024934

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 -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	DQ340255	0.0	DQ340255.1 Lycopersicon esculentum auxin response factor 2 (ARF2) mRNA, complete cds.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_006341482.1	0.0	PREDICTED: auxin response factor 2-like
Swissprot	Q2LAJ3	0.0	ARF2A_SOLLC; Auxin response factor 2A
TrEMBL	M1B469	0.0	M1B469_SOLTU; Auxin response factor
STRING	PGSC0003DMT400036765	0.0	(Solanum tuberosum)

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

Link Out ? help Back to Top
Phytozome	PGSC0003DMP400024934
Entrez Gene	102582348

Publications ? help Back to Top
Xu X, et al. Genome sequence and analysis of the tuber crop potato. Nature, 2011. 475(7355): p. 189-95 [PMID:21743474] 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]