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

Vradi07g23560.1

Organism

Vigna radiata

Taxonomic ID

157791

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; fabids; Fabales; Fabaceae; Papilionoideae; Phaseoleae; Vigna

Family

ARF

Protein Properties

Length: 1027aa MW: 114302 Da PI: 6.1333

Description

ARF family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Vradi07g23560.1	genome	SNU	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	B3	68.9	7.1e-22	126	220	1	90
EEEE-..-HHHHTT-EE--HHH.HTT......---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE-SSS CS B3 1 ffkvltpsdvlksgrlvlpkkfaeeh......ggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfvvFkldgrs 88 f+k+lt sd++++g +++p++ ae++ +++++ ++l+ +d++ ++W +++iyr++++r++lt+GW+ Fv+ ++L +gD+v+F + + s Vradi07g23560.1 126 FCKTLTASDTSTHGGFSVPRRAAEKIfptldySMQPPA-QELVAKDLHDNTWPFRHIYRGQPKRHLLTTGWSVFVSTKRLLAGDSVLFIRASPS 218 99***************************9545444.38*********************************************955444 PP EE CS B3 89 ef 90 ef Vradi07g23560.1 219 EF 220 44 PP
2	Auxin_resp	93.3	3.9e-31	214	279	18	83
Auxin_resp 18 rastseFvvkvekvekalkvkvsvGmRfkmafetedsserrlsGtvvgvsdldpvrWpnSkWrsLk 83 ras+seFvv+++k++ka++++vs+GmRf+m+fete+s rr++Gt++g+sdldpvrW+nS+Wr+++ Vradi07g23560.1 214 RASPSEFVVPLAKYNKAMYTQVSLGMRFRMMFETEESGVRRYMGTITGISDLDPVRWKNSQWRNIQ 279 89*************************************************************986 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SuperFamily	SSF101936	3.79E-39	116	220	IPR015300	DNA-binding pseudobarrel domain
Gene3D	G3DSA:2.40.330.10	5.2E-36	118	222	IPR015300	DNA-binding pseudobarrel domain
CDD	cd10017	1.01E-19	125	222	No hit	No description
Pfam	PF02362	7.1E-20	126	220	IPR003340	B3 DNA binding domain
SMART	SM01019	3.7E-20	126	230	IPR003340	B3 DNA binding domain
PROSITE profile	PS50863	11.871	126	228	IPR003340	B3 DNA binding domain
Pfam	PF06507	3.7E-26	214	279	IPR010525	Auxin response factor
Pfam	PF02309	6.3E-9	898	985	IPR033389	AUX/IAA domain
PROSITE profile	PS51745	26.356	899	982	IPR000270	PB1 domain
SuperFamily	SSF54277	1.18E-8	912	977	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: 1027 aa Download sequence Send to blast
MKVPSNGFLP NSGEGERKTI NSELWHACAG PLVSLPPVGS LVVYFPQGHS EQVAASMQKE 60 TEFIPSYPNL PSKLICMLHN VALHADPETD EVYAQMTLQP VNKYEKEAIL ASDMGLKQNR 120 QPTEFFCKTL TASDTSTHGG FSVPRRAAEK IFPTLDYSMQ PPAQELVAKD LHDNTWPFRH 180 IYRGQPKRHL LTTGWSVFVS TKRLLAGDSV LFIRASPSEF VVPLAKYNKA MYTQVSLGMR 240 FRMMFETEES GVRRYMGTIT GISDLDPVRW KNSQWRNIQV GWDESTAGER PSRVSIWEIE 300 PVVTPFYICP PPFFRPKFPR QPGMPEEESD MENAFKRGMP WHGEEFGLKD ASSSIFPGFS 360 LVQWMSMQPN NQLSAAQSGC FPSMFPSNTL QGNLGTEDPS KLLSFQPPVL SSPTLQLNKP 420 NLPNQINQLQ QSQQLPEPQN LPLLQQMPQQ LGQQPQKPQQ PSQHPTLMNN GVVSSNQITG 480 QFVQPPMAYG QLQQQQLLSG GIQTQQGIQS ASKNTFPLTS LPHDSQFQQQ LDQQANLLLR 540 QQQQQQTQLQ QSPLQLLQQN LPQIASQQQP PATQMLQQNS SEQQLHLQLL QKLQHQQQQI 600 LSTSTPLLQS QLLPQQNSHQ QNQQLPLPPP PVSHHQPQQL ANNVCSTEKL LNSNNFSSSS 660 LMQSQQNPMS QSQNTQKSLT TTRAPSTLTD GDAPSCSTSP STNNCQVSPP NLLKRNQQLQ 720 APLGGSLIVE PTSNLLQDLH SKPDMQNKHE LLNLKGPDQL KYKGAFTDQL EASSSGTSYC 780 LDPGNVQQNL PLSNFCMEGD AQSHPRNSLP FDTNLDDLTP DTMLLRGYDS SKDLQNLLSN 840 YGGAPRDIET ELSTADISSQ SFGVPNLPFK PGCSSDVVIN ETGVLNNSGL RGNQPPRMRT 900 YTKVQKRGSV GRCIDVTRYR GYDELRHDLA KMFGIEGQLD PQRTDWKLVY VDHENDILLV 960 GDDPWDEFVS CVQSIKILSH SEVQQMSLDG DLGGNVPIPN QACSGTDSGN AWRGQYEDNS 1020 AASFNR*

Sequence ? help Back to Top

Protein Sequence Length: 1027 aa Download sequence Send to blast

MKVPSNGFLP NSGEGERKTI NSELWHACAG PLVSLPPVGS LVVYFPQGHS EQVAASMQKE  60
TEFIPSYPNL PSKLICMLHN VALHADPETD EVYAQMTLQP VNKYEKEAIL ASDMGLKQNR  120
QPTEFFCKTL TASDTSTHGG FSVPRRAAEK IFPTLDYSMQ PPAQELVAKD LHDNTWPFRH  180
IYRGQPKRHL LTTGWSVFVS TKRLLAGDSV LFIRASPSEF VVPLAKYNKA MYTQVSLGMR  240
FRMMFETEES GVRRYMGTIT GISDLDPVRW KNSQWRNIQV GWDESTAGER PSRVSIWEIE  300
PVVTPFYICP PPFFRPKFPR QPGMPEEESD MENAFKRGMP WHGEEFGLKD ASSSIFPGFS  360
LVQWMSMQPN NQLSAAQSGC FPSMFPSNTL QGNLGTEDPS KLLSFQPPVL SSPTLQLNKP  420
NLPNQINQLQ QSQQLPEPQN LPLLQQMPQQ LGQQPQKPQQ PSQHPTLMNN GVVSSNQITG  480
QFVQPPMAYG QLQQQQLLSG GIQTQQGIQS ASKNTFPLTS LPHDSQFQQQ LDQQANLLLR  540
QQQQQQTQLQ QSPLQLLQQN LPQIASQQQP PATQMLQQNS SEQQLHLQLL QKLQHQQQQI  600
LSTSTPLLQS QLLPQQNSHQ QNQQLPLPPP PVSHHQPQQL ANNVCSTEKL LNSNNFSSSS  660
LMQSQQNPMS QSQNTQKSLT TTRAPSTLTD GDAPSCSTSP STNNCQVSPP NLLKRNQQLQ  720
APLGGSLIVE PTSNLLQDLH SKPDMQNKHE LLNLKGPDQL KYKGAFTDQL EASSSGTSYC  780
LDPGNVQQNL PLSNFCMEGD AQSHPRNSLP FDTNLDDLTP DTMLLRGYDS SKDLQNLLSN  840
YGGAPRDIET ELSTADISSQ SFGVPNLPFK PGCSSDVVIN ETGVLNNSGL RGNQPPRMRT  900
YTKVQKRGSV GRCIDVTRYR GYDELRHDLA KMFGIEGQLD PQRTDWKLVY VDHENDILLV  960
GDDPWDEFVS CVQSIKILSH SEVQQMSLDG DLGGNVPIPN QACSGTDSGN AWRGQYEDNS  1020
AASFNR*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
4ldu_A	1e-123	15	300	45	388	Auxin response factor 5
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. Involved in ethylene responses. Regulates lateral root formation through direct regulation of LBD16 and/or LBD29. Functionally redundant with ARF7. {ECO:0000269\|PubMed:12036261, ECO:0000269\|PubMed:16461383, ECO:0000269\|PubMed:17259263}.

Cis-element ? help Back to Top
Source	Link
PlantRegMap	Vradi07g23560.1

Regulation -- Description ? help Back to Top
Source	Description
UniProt	INDUCTION: By auxin and ethylene. {ECO:0000269\|PubMed:16461383}.

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	AP015034	0.0	AP015034.1 Vigna angularis var. angularis DNA, chromosome 1, almost complete sequence, cultivar: Shumari.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_027329332.1	0.0	auxin response factor 19-like isoform X2
Swissprot	Q8RYC8	0.0	ARFS_ARATH; Auxin response factor 19
TrEMBL	G7JS69	0.0	G7JS69_MEDTR; Auxin response factor
STRING	AES92167	0.0	(Medicago truncatula)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Fabids	OGEF4918	33	52

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT5G20730.2	0.0	ARF family protein

Publications ? help Back to Top
Duarte JM, et al. Expression pattern shifts following duplication indicative of subfunctionalization and neofunctionalization in regulatory genes of Arabidopsis. Mol. Biol. Evol., 2006. 23(2): p. 469-78 [PMID:16280546] Perilli S, et al. RETINOBLASTOMA-RELATED protein stimulates cell differentiation in the Arabidopsis root meristem by interacting with cytokinin signaling. Plant Cell, 2013. 25(11): p. 4469-78 [PMID:24285791] Sun Y, et al. Manipulation of Auxin Response Factor 19 affects seed size in the woody perennial Jatropha curcas. Sci Rep, 2017. 7: p. 40844 [PMID:28102350] 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] Olmo R, et al. Molecular Transducers from Roots Are Triggered in Arabidopsis Leaves by Root-Knot Nematodes for Successful Feeding Site Formation: A Conserved Post-Embryogenic De novo Organogenesis Program? Front Plant Sci, 2017. 8: p. 875 [PMID:28603536] Lee K,Seo PJ High-temperature promotion of callus formation requires the BIN2-ARF-LBD axis in Arabidopsis. Planta, 2017. 246(4): p. 797-802 [PMID:28766014] Ayala-Rodríguez JÁ,Barrera-Ortiz S,Ruiz-Herrera LF,López-Bucio J Folic acid orchestrates root development linking cell elongation with auxin response and acts independently of the TARGET OF RAPAMYCIN signaling in Arabidopsis thaliana. Plant Sci., 2017. 264: p. 168-178 [PMID:28969797] Nakamura M, et al. Auxin and ROP GTPase Signaling of Polar Nuclear Migration in Root Epidermal Hair Cells. Plant Physiol., 2018. 176(1): p. 378-391 [PMID:29084900] Hong L, et al. Alternative polyadenylation is involved in auxin-based plant growth and development. Plant J., 2018. 93(2): p. 246-258 [PMID:29155478] Lee K,Park OS,Seo PJ Arabidopsis ATXR2 deposits H3K36me3 at the promoters of LBD genes to facilitate cellular dedifferentiation. Sci Signal, 2018. [PMID:29184030] Kimura T, et al. Asymmetric Auxin Distribution is Not Required to Establish Root Phototropism in Arabidopsis. Plant Cell Physiol., 2018. 59(4): p. 823-835 [PMID:29401292] Schoenaers S, et al. The Auxin-Regulated CrRLK1L Kinase ERULUS Controls Cell Wall Composition during Root Hair Tip Growth. Curr. Biol., 2018. 28(5): p. 722-732.e6 [PMID:29478854] Huang KL, et al. The ARF7 and ARF19 Transcription Factors Positively Regulate PHOSPHATE STARVATION RESPONSE1 in Arabidopsis Roots. Plant Physiol., 2018. 178(1): p. 413-427 [PMID:30026290]