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

DCAR_011930

Organism

Daucus carota

Taxonomic ID

4039

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; asterids; campanulids; Apiales; Apiineae; Apiaceae; Apioideae; Scandiceae; Daucinae; Daucus

Family

ARF

Protein Properties

Length: 1112aa MW: 124010 Da PI: 6.3979

Description

ARF family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
DCAR_011930	genome	ARS-USDA	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	B3	72.2	6.6e-23	115	216	1	99
EEEE-..-HHHHTT-EE--HHH.HTT.......---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE-SSSEE. CS B3 1 ffkvltpsdvlksgrlvlpkkfaeeh.......ggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfvvFkldgrsefe 91 f+k+lt sd++++g +++p++ ae++ ++++++ +++ +d++ ++W++++i+r++++r++lt+GW+ Fv++++L +gD+v+F ++++ + DCAR_011930 115 FCKTLTASDTSTHGGFSVPRRAAEKIfppldftMQPPAQ--EIVARDLHDQTWTFRHIFRGQPKRHLLTTGWSVFVSSKRLFAGDSVLFI--RDEKSQ 208 99***************************96555544..8**********************************************..456777 PP .EEEEE-S CS B3 92 lvvkvfrk 99 l+++++r+ DCAR_011930 209 LLLGIRRA 216 89999997 PP
2	Auxin_resp	118.3	6.3e-39	241	323	1	83
Auxin_resp 1 aahaastksvFevvYnPrastseFvvkvekvekalkvkvsvGmRfkmafetedsserrlsGtvvgvsdldpvrWpnSkWrsLk 83 aahaa+++s+F+++YnPras++eFv++++k++ka++ +vs+GmRf+m+fete+s rr++Gt++g+sdld rW+ S+Wr+L+ DCAR_011930 241 AAHAAANNSPFTIFYNPRASPAEFVIPLAKYNKAMYAQVSLGMRFRMMFETEESGVRRYMGTITGISDLDAARWKSSQWRNLQ 323 79*******************************************************************************97 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SuperFamily	SSF101936	1.1E-43	104	244	IPR015300	DNA-binding pseudobarrel domain
Gene3D	G3DSA:2.40.330.10	1.1E-41	107	230	IPR015300	DNA-binding pseudobarrel domain
CDD	cd10017	9.38E-21	114	215	No hit	No description
PROSITE profile	PS50863	12.562	115	217	IPR003340	B3 DNA binding domain
SMART	SM01019	5.6E-24	115	217	IPR003340	B3 DNA binding domain
Pfam	PF02362	6.3E-21	115	216	IPR003340	B3 DNA binding domain
Pfam	PF06507	2.1E-34	241	323	IPR010525	Auxin response factor
Pfam	PF02309	1.1E-8	981	1070	IPR033389	AUX/IAA domain
PROSITE profile	PS51745	25.592	984	1077	IPR000270	PB1 domain
SuperFamily	SSF54277	4.71E-9	997	1062	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:0009723	Biological Process	response to ethylene
GO:0009733	Biological Process	response to auxin
GO:0010311	Biological Process	lateral root formation
GO:0048366	Biological Process	leaf development
GO:0005634	Cellular Component	nucleus
GO:0043565	Molecular Function	sequence-specific DNA binding
GO:0046983	Molecular Function	protein dimerization activity

Sequence ? help Back to Top
Protein Sequence Length: 1112 aa Download sequence Send to blast
MEAGERKAIN SELWHACAGP LVSLPPVGSL VVYFPQGHSE QVAASMQKET DGIPSYPNLP 60 SKLVCMLHNV TLQADAETDE VYAQMTLQPV NKYDQDALLI SDMGLKQSRQ PAEFFCKTLT 120 ASDTSTHGGF SVPRRAAEKI FPPLDFTMQP PAQEIVARDL HDQTWTFRHI FRGQPKRHLL 180 TTGWSVFVSS KRLFAGDSVL FIRDEKSQLL LGIRRANRQQ PALSSSVISS DSMHIGILAA 240 AAHAAANNSP FTIFYNPRAS PAEFVIPLAK YNKAMYAQVS LGMRFRMMFE TEESGVRRYM 300 GTITGISDLD AARWKSSQWR NLQVGWDEST AGERPSRVSI WDIEPVVTPF YICPPPFFRP 360 KFPRQAGLPD DESDMENAFK RGMPWLDDYG MKDASNSILP GLSLVQWMSM QQNQRFPGTQ 420 PASFSPVVSS TALQSGLGTD DPSKLLNFQA PALSIPNLQF NKANQQNQPG GQMQQSSLAW 480 HQQQQMQQLL QTSANQQQQQ QQQQQQQQSH QHSQQQQQQQ QQQQSNQPQQ QHQQKQSIQQ 540 SQPLQLPQQQ QQPLVQVQQP IQQVQQPRPQ QLHQQQQILQ SSLVNSGGVS SNQIPIQSSM 600 LPINYSQLQQ QQLLAGNTQL QQTNPINSRN SIQMTSLPQD LQFQQSMEQM SRPQQQQHPQ 660 LQQAQMQLLQ QSLSQRPQMQ HTLQQSLSEQ QLQLLQKLQQ QQQQQLPTPV SPRLEPQLPL 720 QQQAFQQNRQ SQQMPMSQQQ LSGNSFSTSM LLPSAQFPMN QLLSQHKPLG INRAHSGITE 780 GDAPSCSTSP STNNCQVAPS SFLNKNQQGS GGFLDETVVG PATNSIQELQ SRPDIRMKHE 840 IMNPKGPDQP KYKGIASDQL EASSSATSYC LDVGGLQNFS LPGFTLDSDV QSHVKSNLPF 900 AVNMDGLTPD ALLSRGFDSQ NVLSNYGGTP RDIETELSTA IDSQSFGVPN MSFKPGCSND 960 VDIAMNETGV VSSGLWGNQT QRMRTYTKVQ KRGSVGRTID VTRYKGYDDL RHDLARMFGI 1020 EGQLQDPQRN EWKLVYVDNE NDILLVGDDP WEEFLGCVQS IKILSSAEVQ QMSLDGDLGN 1080 VAVLNQTCSG SDSGNAWKGQ YDDNSAASFN R*

Sequence ? help Back to Top

Protein Sequence Length: 1112 aa Download sequence Send to blast

MEAGERKAIN SELWHACAGP LVSLPPVGSL VVYFPQGHSE QVAASMQKET DGIPSYPNLP  60
SKLVCMLHNV TLQADAETDE VYAQMTLQPV NKYDQDALLI SDMGLKQSRQ PAEFFCKTLT  120
ASDTSTHGGF SVPRRAAEKI FPPLDFTMQP PAQEIVARDL HDQTWTFRHI FRGQPKRHLL  180
TTGWSVFVSS KRLFAGDSVL FIRDEKSQLL LGIRRANRQQ PALSSSVISS DSMHIGILAA  240
AAHAAANNSP FTIFYNPRAS PAEFVIPLAK YNKAMYAQVS LGMRFRMMFE TEESGVRRYM  300
GTITGISDLD AARWKSSQWR NLQVGWDEST AGERPSRVSI WDIEPVVTPF YICPPPFFRP  360
KFPRQAGLPD DESDMENAFK RGMPWLDDYG MKDASNSILP GLSLVQWMSM QQNQRFPGTQ  420
PASFSPVVSS TALQSGLGTD DPSKLLNFQA PALSIPNLQF NKANQQNQPG GQMQQSSLAW  480
HQQQQMQQLL QTSANQQQQQ QQQQQQQQSH QHSQQQQQQQ QQQQSNQPQQ QHQQKQSIQQ  540
SQPLQLPQQQ QQPLVQVQQP IQQVQQPRPQ QLHQQQQILQ SSLVNSGGVS SNQIPIQSSM  600
LPINYSQLQQ QQLLAGNTQL QQTNPINSRN SIQMTSLPQD LQFQQSMEQM SRPQQQQHPQ  660
LQQAQMQLLQ QSLSQRPQMQ HTLQQSLSEQ QLQLLQKLQQ QQQQQLPTPV SPRLEPQLPL  720
QQQAFQQNRQ SQQMPMSQQQ LSGNSFSTSM LLPSAQFPMN QLLSQHKPLG INRAHSGITE  780
GDAPSCSTSP STNNCQVAPS SFLNKNQQGS GGFLDETVVG PATNSIQELQ SRPDIRMKHE  840
IMNPKGPDQP KYKGIASDQL EASSSATSYC LDVGGLQNFS LPGFTLDSDV QSHVKSNLPF  900
AVNMDGLTPD ALLSRGFDSQ NVLSNYGGTP RDIETELSTA IDSQSFGVPN MSFKPGCSND  960
VDIAMNETGV VSSGLWGNQT QRMRTYTKVQ KRGSVGRTID VTRYKGYDDL RHDLARMFGI  1020
EGQLQDPQRN EWKLVYVDNE NDILLVGDDP WEEFLGCVQS IKILSSAEVQ QMSLDGDLGN  1080
VAVLNQTCSG SDSGNAWKGQ YDDNSAASFN R*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
4ldu_A	1e-173	2	344	43	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}.

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 -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_017241749.1	0.0	PREDICTED: auxin response factor 19-like
Swissprot	Q8RYC8	0.0	ARFS_ARATH; Auxin response factor 19
TrEMBL	A0A166C1W5	0.0	A0A166C1W5_DAUCS; Auxin response factor
STRING	PGSC0003DMT400035592	0.0	(Solanum tuberosum)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Asterids	OGEA1302	24	65

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT1G19220.1	0.0	auxin response factor 19

Link Out ? help Back to Top
Phytozome	DCAR_011930

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]