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

Kalax.0025s0071.1.p

Organism

Kalanchoe marnieriana

Taxonomic ID

80907

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; Saxifragales; Crassulaceae; Kalanchoe

Family

ARF

Protein Properties

Length: 1215aa MW: 136104 Da PI: 6.7364

Description

ARF family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Kalax.0025s0071.1.p	genome	JGI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	B3	71.1	1.4e-22	126	227	1	99
EEEE-..-HHHHTT-EE--HHH.HTT.......---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EEEEE CS B3 1 ffkvltpsdvlksgrlvlpkkfaeeh.......ggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfvvFk 83 f+k+lt sd++++g +++p++ ae++ + +++ ++lt +d++ + W++++iyr++++r++lt+GW+ Fv+ ++L +gD+v+F Kalax.0025s0071.1.p 126 FCKTLTASDTSTHGGFSVPRRAAEKIfppldfsM-QPPA-QELTARDLHDNMWTFRHIYRGQPKRHLLTTGWSVFVSTKRLFAGDSVLFI 213 99***************************954.4444.48********************************************** PP E-SSSEE..EEEEE-S CS B3 84 ldgrsefelvvkvfrk 99 +d++s+f +++++r+ Kalax.0025s0071.1.p 214 RDEKSQF--LLGIRRA 227 7766666..9999997 PP
2	Auxin_resp	118.4	6e-39	252	334	1	83
Auxin_resp 1 aahaastksvFevvYnPrastseFvvkvekvekalkvkvsvGmRfkmafetedsserrlsGtvvgvsdldpvrWpnSkWrsLk 83 aahaa+++s+F+++YnPras+ eFv++++k++ka++++ s+GmRf+m+fete+s rr++Gt++g+sdldpvrW++S+Wr+++ Kalax.0025s0071.1.p 252 AAHAAANNSPFTIFYNPRASPCEFVIPLAKYNKAMYTQASLGMRFRMMFETEESGVRRYMGTITGISDLDPVRWKGSQWRNIQ 334 79******************************************************************************986 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SuperFamily	SSF101936	7.32E-44	116	255	IPR015300	DNA-binding pseudobarrel domain
Gene3D	G3DSA:2.40.330.10	1.6E-42	119	241	IPR015300	DNA-binding pseudobarrel domain
CDD	cd10017	2.93E-20	125	226	No hit	No description
Pfam	PF02362	1.0E-20	126	227	IPR003340	B3 DNA binding domain
SMART	SM01019	2.6E-24	126	228	IPR003340	B3 DNA binding domain
PROSITE profile	PS50863	12.308	126	228	IPR003340	B3 DNA binding domain
Pfam	PF06507	5.6E-34	252	334	IPR010525	Auxin response factor
Pfam	PF02309	4.2E-9	1084	1173	IPR033389	AUX/IAA domain
PROSITE profile	PS51745	26.001	1087	1180	IPR000270	PB1 domain
SuperFamily	SSF54277	1.62E-8	1101	1165	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: 1215 aa Download sequence Send to blast
MKAPTNGFPA NSGEGERKTI NSELWHACAG PLVSLPPVGS LVVYFPQGHS EQVAASMQKE 60 TDCIPSYPNL PSKLICMLHN VTLHADPETD EVYAQMTLQP VTKYDKEALL ASDLGLKQNR 120 QPAEFFCKTL TASDTSTHGG FSVPRRAAEK IFPPLDFSMQ PPAQELTARD LHDNMWTFRH 180 IYRGQPKRHL LTTGWSVFVS TKRLFAGDSV LFIRDEKSQF LLGIRRANRQ QPALSSSVIS 240 SDSMHIGILA AAAHAAANNS PFTIFYNPRA SPCEFVIPLA KYNKAMYTQA SLGMRFRMMF 300 ETEESGVRRY MGTITGISDL DPVRWKGSQW RNIQVGWDES TAGDRPSRVS LWEIEPVVTP 360 FYLCPPPFFR PKFPKQPGFP DDESDMENTL KRGMPWLDDF GIKDAATSIF PGLSLVQWMS 420 MQQNNQFPTA QSGFFPNMMS STALHNALGT DDPTKLLSFQ NHAPSQASIQ FNKSSQQNQV 480 HHFQQPPVTW PQHHQFQQLL QYPISMQQQQ QSQLVQQQQQ QQQQQPQLVQ QQQQPQLVQQ 540 LQQQPQLVQQ QQQTLQQSSQ QLSLQQQSQQ MQLQQQQSQQ MQAQQLSPQI QQQQQQAPHL 600 QQHQPQAPHL QQHQQQALHL QQQQAPQAPH QQPQSQPQPQ PQPQPQPQPQ SRPQTQPQQH 660 QQMQSQQQPH NIVSKSLVGN GLVTGSQIPA QKPLQPVMSS VLQQQLLASN DTNQQVGSSK 720 SPYHVVSSAE MQFQHQLEPQ STFVQKPQGS QPQLQQSPPH LLQQHEVLQR PQHLSQVLQS 780 SQSHKSLVEH QLQLQMLQKL QQQQQQQSPH QAQPKQHQES QIAPVISSLQ PQLLQQLPQP 840 NQHSMFQSLS QHQQSTVSQP QQFSVTQLQI QQKALATVRA HSGLTEGEAP SCSTSPSTNY 900 CQVSPTNFLN RNGQGLAGEF GFEQANLDQE LQNKADVRVK HEQPSLRGPD AMKYRGNDHM 960 EASSSATSYC LDANNFQSNF SIPTLLDGDA QSHPRNSFSF VPNTEGLAPD TLMTTGYDSG 1020 KDLQNLLSNY DTAPRDLEAE LSTAAISSQS FGVPNMSFKP GCSGDISISD AGVIGAGMWS 1080 NQTQRMRTYT KVQKRGSVGR SIDVTRYSGY DELKHDLARM FGIEGQLDDP QRTDWKLVYV 1140 DHENDILLVG DDPWEEFVSC VQSIKILSSA EVQQMSLDGD LGNVVIPNQA CSGSDSGNAW 1200 RGNYDDTSAV SFNR*

Sequence ? help Back to Top

Protein Sequence Length: 1215 aa Download sequence Send to blast

MKAPTNGFPA NSGEGERKTI NSELWHACAG PLVSLPPVGS LVVYFPQGHS EQVAASMQKE  60
TDCIPSYPNL PSKLICMLHN VTLHADPETD EVYAQMTLQP VTKYDKEALL ASDLGLKQNR  120
QPAEFFCKTL TASDTSTHGG FSVPRRAAEK IFPPLDFSMQ PPAQELTARD LHDNMWTFRH  180
IYRGQPKRHL LTTGWSVFVS TKRLFAGDSV LFIRDEKSQF LLGIRRANRQ QPALSSSVIS  240
SDSMHIGILA AAAHAAANNS PFTIFYNPRA SPCEFVIPLA KYNKAMYTQA SLGMRFRMMF  300
ETEESGVRRY MGTITGISDL DPVRWKGSQW RNIQVGWDES TAGDRPSRVS LWEIEPVVTP  360
FYLCPPPFFR PKFPKQPGFP DDESDMENTL KRGMPWLDDF GIKDAATSIF PGLSLVQWMS  420
MQQNNQFPTA QSGFFPNMMS STALHNALGT DDPTKLLSFQ NHAPSQASIQ FNKSSQQNQV  480
HHFQQPPVTW PQHHQFQQLL QYPISMQQQQ QSQLVQQQQQ QQQQQPQLVQ QQQQPQLVQQ  540
LQQQPQLVQQ QQQTLQQSSQ QLSLQQQSQQ MQLQQQQSQQ MQAQQLSPQI QQQQQQAPHL  600
QQHQPQAPHL QQHQQQALHL QQQQAPQAPH QQPQSQPQPQ PQPQPQPQPQ SRPQTQPQQH  660
QQMQSQQQPH NIVSKSLVGN GLVTGSQIPA QKPLQPVMSS VLQQQLLASN DTNQQVGSSK  720
SPYHVVSSAE MQFQHQLEPQ STFVQKPQGS QPQLQQSPPH LLQQHEVLQR PQHLSQVLQS  780
SQSHKSLVEH QLQLQMLQKL QQQQQQQSPH QAQPKQHQES QIAPVISSLQ PQLLQQLPQP  840
NQHSMFQSLS QHQQSTVSQP QQFSVTQLQI QQKALATVRA HSGLTEGEAP SCSTSPSTNY  900
CQVSPTNFLN RNGQGLAGEF GFEQANLDQE LQNKADVRVK HEQPSLRGPD AMKYRGNDHM  960
EASSSATSYC LDANNFQSNF SIPTLLDGDA QSHPRNSFSF VPNTEGLAPD TLMTTGYDSG  1020
KDLQNLLSNY DTAPRDLEAE LSTAAISSQS FGVPNMSFKP GCSGDISISD AGVIGAGMWS  1080
NQTQRMRTYT KVQKRGSVGR SIDVTRYSGY DELKHDLARM FGIEGQLDDP QRTDWKLVYV  1140
DHENDILLVG DDPWEEFVSC VQSIKILSSA EVQQMSLDGD LGNVVIPNQA CSGSDSGNAW  1200
RGNYDDTSAV SFNR*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
4ldu_A	1e-171	15	355	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}.

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
Swissprot	Q8RYC8	0.0	ARFS_ARATH; Auxin response factor 19
TrEMBL	A0A2P5EGE2	0.0	A0A2P5EGE2_TREOI; Auxin response factor
TrEMBL	W9QR34	0.0	W9QR34_9ROSA; Auxin response factor
STRING	XP_010089663.1	0.0	(Morus notabilis)

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	Kalax.0025s0071.1.p

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]