PlantTFDB - Plant Transcription Factor Database @ CBI, PKU

PlantRegMap/PlantTFDB v5.0

Plant Transcription Factor Database

Previous version: v3.0 v4.0

Transcription Factor Information

Basic Information | Signature Domain | Sequence |

Basic Information? help Back to Top

TF ID

Zosma59g00400.1

Common Name

ZOSMA_59G00400

Organism

Zostera marina

Taxonomic ID

29655

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; Liliopsida; Alismatales; Zosteraceae; Zostera

Family

ARF

Protein Properties

Length: 1131aa MW: 126826 Da PI: 6.5787

Description

ARF family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Zosma59g00400.1	genome	JGI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	B3	71.6	9.7e-23	126	227	1	99
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++++ yr++++r++lt+GW+ Fv+ ++L +gD+v+F + ++ Zosma59g00400.1 126 FCKTLTASDTSTHGGFSVPRRAAEKIfppldfSMQPPA-QELVAKDLHDATWTFRHVYRGQPKRHLLTTGWSVFVSTKRLLAGDSVLFIR--DE 216 99***************************9445444.38**********************************************4..46 PP EE..EEEEE-S CS B3 89 efelvvkvfrk 99 + +l+++++r+ Zosma59g00400.1 217 TSQLLLGIRRA 227 66679999997 PP
2	Auxin_resp	123.5	1.4e-40	252	334	1	83
Auxin_resp 1 aahaastksvFevvYnPrastseFvvkvekvekalkvkvsvGmRfkmafetedsserrlsGtvvgvsdldpvrWpnSkWrsLk 83 aahaa+++s+F+++YnPras+seFvv+++k++ka+++++s+GmRf+m fete+s rr++Gt++g+sdldp+rW+nS+Wr+L+ Zosma59g00400.1 252 AAHAAANNSTFTIFYNPRASPSEFVVPLAKYNKAMYTQLSLGMRFRMLFETEESGVRRYMGTITGISDLDPIRWKNSQWRNLQ 334 79*******************************************************************************97 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SuperFamily	SSF101936	4.32E-44	114	255	IPR015300	DNA-binding pseudobarrel domain
Gene3D	G3DSA:2.40.330.10	2.4E-41	117	240	IPR015300	DNA-binding pseudobarrel domain
CDD	cd10017	3.61E-20	125	226	No hit	No description
PROSITE profile	PS50863	12.435	126	228	IPR003340	B3 DNA binding domain
SMART	SM01019	3.8E-23	126	228	IPR003340	B3 DNA binding domain
Pfam	PF02362	6.7E-21	126	227	IPR003340	B3 DNA binding domain
Pfam	PF06507	2.1E-35	252	334	IPR010525	Auxin response factor
Pfam	PF02309	1.3E-8	1000	1088	IPR033389	AUX/IAA domain
PROSITE profile	PS51745	25.183	1002	1086	IPR000270	PB1 domain
SuperFamily	SSF54277	6.28E-8	1017	1080	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:0009734	Biological Process	auxin-activated signaling pathway
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: 1131 aa Download sequence Send to blast
MKAPGNGIAP DVGDGEKKNI NSELWHACAG PLVSLPPVGS LVVYFPQGHS EQVAATMHKE 60 TDTVPNYTSL PSKLICVLHT VTLHADAETD EVFAQMTLQP VNKYDKESLM ASNIGVKQNK 120 QPTEFFCKTL TASDTSTHGG FSVPRRAAEK IFPPLDFSMQ PPAQELVAKD LHDATWTFRH 180 VYRGQPKRHL LTTGWSVFVS TKRLLAGDSV LFIRDETSQL LLGIRRANRQ QPSLSSSVLS 240 SESMHIGVLA AAAHAAANNS TFTIFYNPRA SPSEFVVPLA KYNKAMYTQL SLGMRFRMLF 300 ETEESGVRRY MGTITGISDL DPIRWKNSQW RNLQIGWDES TAGERQSRVS IWEIEPVATP 360 YYICPPPFFR PKLPKHPGDE SEPDSSFNRE LPWLGEEIGL KDAQNPLYHG LNLVQWMNMQ 420 RSSQLMTSAS QSPYFPSMMP PTMQNNIVTD DPSKMLNFQT STLPMSSSHL NIPKTNQIQQ 480 FDGFQQTHLS WPQQQQLLLL QQQIPVHPPQ QQIPVHPTQP QISVHLPQQY IQQASGLSQQ 540 QLQQQQQQVA MLPQLHQKQQ QPNICTQQMV QHQQNQQQTE PLQHMRQQQH ELPMQQQSQQ 600 QQIRPSIISP VIADQQQRQP QHFVGQSSPQ QYQSPRAQQQ IQQQSILPQN SGVHQMAHSS 660 NHNLQTSTPQ NMQFQQQIEL QQGLSLRQQQ VTPCQPQLQF QLLQKMQQQQ MLSQMTPYVQ 720 SQLLQQNVGV GAQQNAGVGV QQIAGVQQNP KLPQQQVNGT TLSHSQKELQ SYPNHIDWQI 780 KSGLPITEPS SLANTDLPSC SNSPFNNNQV CSMSLLNNRN SGSAIFSEER EVQTPNNSIV 840 QDINCKSDTR VKHEFHSTKD HDNLTYRNSM VDQLEASSSA NSFCMDRSGE ENYLLPPICL 900 EGEVQPGPRN SIPFGSHVSE LRPDTLLSRG FDAGKDLQNL LSGYGNQKDI ETEISTAGIS 960 SQSFGASDMP FKPGCSNDAV LNDNGVLNRG SWVTTNQPQR MRTYTKVQKR GSVGRSIDVT 1020 RYKGYDELRH DLACMFGING QLEDPHRSEW KLVYVDHEND ILLVGDDPWE EFVGCVQSIK 1080 ILSAAEVQQM SLDGDLGSLP PQQNQAGSGS DNVNLWRGNY DNNSASSFDR *

Sequence ? help Back to Top

Protein Sequence Length: 1131 aa Download sequence Send to blast

MKAPGNGIAP DVGDGEKKNI NSELWHACAG PLVSLPPVGS LVVYFPQGHS EQVAATMHKE  60
TDTVPNYTSL PSKLICVLHT VTLHADAETD EVFAQMTLQP VNKYDKESLM ASNIGVKQNK  120
QPTEFFCKTL TASDTSTHGG FSVPRRAAEK IFPPLDFSMQ PPAQELVAKD LHDATWTFRH  180
VYRGQPKRHL LTTGWSVFVS TKRLLAGDSV LFIRDETSQL LLGIRRANRQ QPSLSSSVLS  240
SESMHIGVLA AAAHAAANNS TFTIFYNPRA SPSEFVVPLA KYNKAMYTQL SLGMRFRMLF  300
ETEESGVRRY MGTITGISDL DPIRWKNSQW RNLQIGWDES TAGERQSRVS IWEIEPVATP  360
YYICPPPFFR PKLPKHPGDE SEPDSSFNRE LPWLGEEIGL KDAQNPLYHG LNLVQWMNMQ  420
RSSQLMTSAS QSPYFPSMMP PTMQNNIVTD DPSKMLNFQT STLPMSSSHL NIPKTNQIQQ  480
FDGFQQTHLS WPQQQQLLLL QQQIPVHPPQ QQIPVHPTQP QISVHLPQQY IQQASGLSQQ  540
QLQQQQQQVA MLPQLHQKQQ QPNICTQQMV QHQQNQQQTE PLQHMRQQQH ELPMQQQSQQ  600
QQIRPSIISP VIADQQQRQP QHFVGQSSPQ QYQSPRAQQQ IQQQSILPQN SGVHQMAHSS  660
NHNLQTSTPQ NMQFQQQIEL QQGLSLRQQQ VTPCQPQLQF QLLQKMQQQQ MLSQMTPYVQ  720
SQLLQQNVGV GAQQNAGVGV QQIAGVQQNP KLPQQQVNGT TLSHSQKELQ SYPNHIDWQI  780
KSGLPITEPS SLANTDLPSC SNSPFNNNQV CSMSLLNNRN SGSAIFSEER EVQTPNNSIV  840
QDINCKSDTR VKHEFHSTKD HDNLTYRNSM VDQLEASSSA NSFCMDRSGE ENYLLPPICL  900
EGEVQPGPRN SIPFGSHVSE LRPDTLLSRG FDAGKDLQNL LSGYGNQKDI ETEISTAGIS  960
SQSFGASDMP FKPGCSNDAV LNDNGVLNRG SWVTTNQPQR MRTYTKVQKR GSVGRSIDVT  1020
RYKGYDELRH DLACMFGING QLEDPHRSEW KLVYVDHEND ILLVGDDPWE EFVGCVQSIK  1080
ILSAAEVQQM SLDGDLGSLP PQQNQAGSGS DNVNLWRGNY DNNSASSFDR *

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
4ldu_A	1e-163	16	355	47	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	A0A0K9NWY3	0.0	A0A0K9NWY3_ZOSMR; Auxin response factor

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Monocots	OGMP9045	33	38

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	Zosma59g00400.1

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]