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

Cla016872

Organism

Citrullus lanatus

Taxonomic ID

3654

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; fabids; Cucurbitales; Cucurbitaceae; Benincaseae; Citrullus

Family

ARF

Protein Properties

Length: 1110aa MW: 123483 Da PI: 6.4436

Description

ARF family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Cla016872	genome	ICuGI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	B3	73.1	3.5e-23	126	227	1	99
EEEE-..-HHHHTT-EE--HHH.HTT......---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE-SSSEE..EE CS B3 1 ffkvltpsdvlksgrlvlpkkfaeeh......ggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfvvFkldgrsefelvv 94 f+k+lt sd++++g +++p++ ae++ +++++ ++l+ +d++ +sW++++iyr++++r++lt+GW+ Fv+ ++L +gD+v+F ++++ +l++ Cla016872 126 FCKTLTASDTSTHGGFSVPRRAAEKIfppldySMQPPA-QELVARDLHDNSWTFRHIYRGQPKRHLLTTGWSVFVSTKRLFAGDSVLFI--RDEKSQLLL 222 99***************************9545444.38**********************************************..456777899 PP EEE-S CS B3 95 kvfrk 99 +++r+ Cla016872 223 GIRRA 227 99997 PP
2	Auxin_resp	124.6	6.9e-41	252	334	1	83
Auxin_resp 1 aahaastksvFevvYnPrastseFvvkvekvekalkvkvsvGmRfkmafetedsserrlsGtvvgvsdldpvrWpnSkWrsLk 83 aahaa+++s+F+++YnPras+seFv++++k++ka++++vs+GmRf+m+fete+s rr++Gt++g+sd+d+vrW+nS+Wr+L+ Cla016872 252 AAHAAANNSPFTIFYNPRASPSEFVIPLAKYNKAMYTQVSLGMRFRMMFETEESGVRRYMGTITGISDMDSVRWKNSQWRNLQ 334 79*******************************************************************************97 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SuperFamily	SSF101936	2.75E-44	116	255	IPR015300	DNA-binding pseudobarrel domain
Gene3D	G3DSA:2.40.330.10	3.7E-42	118	241	IPR015300	DNA-binding pseudobarrel domain
CDD	cd10017	5.32E-20	125	226	No hit	No description
SMART	SM01019	2.5E-24	126	228	IPR003340	B3 DNA binding domain
PROSITE profile	PS50863	12.407	126	228	IPR003340	B3 DNA binding domain
Pfam	PF02362	4.3E-21	126	227	IPR003340	B3 DNA binding domain
Pfam	PF06507	4.5E-36	252	334	IPR010525	Auxin response factor
Pfam	PF02309	2.4E-9	980	1069	IPR033389	AUX/IAA domain
PROSITE profile	PS51745	25.792	983	1076	IPR000270	PB1 domain
SuperFamily	SSF54277	1.81E-8	996	1061	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: 1110 aa Download sequence Send to blast
MKAPPNGFLA NSGEGERKNI NSELWHACAG PLVSLPPVGS LVVYFPQGHS EQVAASMNKE 60 TDFIPNYPNL PSKLICMLHN VTLHADPETD EVYAQMTLQP VNKYEKEALL ASDIGLKQSR 120 QPAEFFCKTL TASDTSTHGG FSVPRRAAEK IFPPLDYSMQ PPAQELVARD LHDNSWTFRH 180 IYRGQPKRHL LTTGWSVFVS TKRLFAGDSV LFIRDEKSQL LLGIRRANRQ QPALSSSVIS 240 SDSMHIGILA SAAHAAANNS PFTIFYNPRA SPSEFVIPLA KYNKAMYTQV SLGMRFRMMF 300 ETEESGVRRY MGTITGISDM DSVRWKNSQW RNLQVGWDES AAGERPNRVS IWEVEPVVTP 360 FYICPPPFFR PKFPKQPGMP DDESDIENAF KRAMPWFGDD FGMKDTPSSI FPGLSLVQWM 420 SMQHNNQFPA AQSGILPSMV PSALHGTLTN EDPSKLLSFQ APVLSSPNLQ FSKATQQNQA 480 GQLPPTAWSQ QQQLQQLLQV PASQQLQQQQ LPPQQELQQQ QQLQQQQLQQ LPQQQQLQSQ 540 QPQRQQQTSQ SVLLNNSVTA ANHLPNPSLQ QPLVYSQLQQ QQLLAGNIQS HQTSQPSNKN 600 SFQTTLSEET QFQPQIEQQP SLLPRHQQPT QFQQAPLQLL QQSLSQRAQQ QPQVQQFSQP 660 IPTEQQLQLQ LLQKLQQQQQ QQQQQQPLLS PASPLLPPQL LQQQHVHQQN QQMPPLPLPN 720 QQQFSTSGGS FQTEKLNSNG FASLGLMQSQ QVPITQSHNQ FKPTTAIRAY SGLTDGDAPS 780 CSTSPSTNNC AVSVSNLLNK NQQGAATLGG DSVVEPATNP TQELQSKPDL RIKHEFPNSK 840 GLDQLKYKGT VPDQLEASSS GTSYCLDAGT IQQTLPLPTC LDNDVQSHPR NNIPFSNSID 900 GLTPDTLLSR GYDSQKDLQN LLSNYGGGVP RDIETELSTA AISSQSFGVP NLPFKPGCSN 960 DVNVNEAGAL SSGLWANHSQ RMRTYTKVQK RGSVGRCIDV TRYKGYEELR HDLARMFGIE 1020 GQLEDPQRTD WKLVYVDHEN DILLVGDDPW EEFVSCVQSI KILSSAEVQQ MSLDGNLGHI 1080 QAPNQACSGT DSGNAWRGQY DDNSAASFNR

Sequence ? help Back to Top

Protein Sequence Length: 1110 aa Download sequence Send to blast

MKAPPNGFLA NSGEGERKNI NSELWHACAG PLVSLPPVGS LVVYFPQGHS EQVAASMNKE  60
TDFIPNYPNL PSKLICMLHN VTLHADPETD EVYAQMTLQP VNKYEKEALL ASDIGLKQSR  120
QPAEFFCKTL TASDTSTHGG FSVPRRAAEK IFPPLDYSMQ PPAQELVARD LHDNSWTFRH  180
IYRGQPKRHL LTTGWSVFVS TKRLFAGDSV LFIRDEKSQL LLGIRRANRQ QPALSSSVIS  240
SDSMHIGILA SAAHAAANNS PFTIFYNPRA SPSEFVIPLA KYNKAMYTQV SLGMRFRMMF  300
ETEESGVRRY MGTITGISDM DSVRWKNSQW RNLQVGWDES AAGERPNRVS IWEVEPVVTP  360
FYICPPPFFR PKFPKQPGMP DDESDIENAF KRAMPWFGDD FGMKDTPSSI FPGLSLVQWM  420
SMQHNNQFPA AQSGILPSMV PSALHGTLTN EDPSKLLSFQ APVLSSPNLQ FSKATQQNQA  480
GQLPPTAWSQ QQQLQQLLQV PASQQLQQQQ LPPQQELQQQ QQLQQQQLQQ LPQQQQLQSQ  540
QPQRQQQTSQ SVLLNNSVTA ANHLPNPSLQ QPLVYSQLQQ QQLLAGNIQS HQTSQPSNKN  600
SFQTTLSEET QFQPQIEQQP SLLPRHQQPT QFQQAPLQLL QQSLSQRAQQ QPQVQQFSQP  660
IPTEQQLQLQ LLQKLQQQQQ QQQQQQPLLS PASPLLPPQL LQQQHVHQQN QQMPPLPLPN  720
QQQFSTSGGS FQTEKLNSNG FASLGLMQSQ QVPITQSHNQ FKPTTAIRAY SGLTDGDAPS  780
CSTSPSTNNC AVSVSNLLNK NQQGAATLGG DSVVEPATNP TQELQSKPDL RIKHEFPNSK  840
GLDQLKYKGT VPDQLEASSS GTSYCLDAGT IQQTLPLPTC LDNDVQSHPR NNIPFSNSID  900
GLTPDTLLSR GYDSQKDLQN LLSNYGGGVP RDIETELSTA AISSQSFGVP NLPFKPGCSN  960
DVNVNEAGAL SSGLWANHSQ RMRTYTKVQK RGSVGRCIDV TRYKGYEELR HDLARMFGIE  1020
GQLEDPQRTD WKLVYVDHEN DILLVGDDPW EEFVSCVQSI KILSSAEVQQ MSLDGNLGHI  1080
QAPNQACSGT DSGNAWRGQY DDNSAASFNR

3D Structure ? help Back to Top

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

Annotation -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	KU323418	0.0	KU323418.1 UNVERIFIED: Trichosanthes dioica clone TdARF_26 auxin response factor 19-like mRNA, partial sequence.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_022975315.1	0.0	auxin response factor 19-like isoform X1
Refseq	XP_022975316.1	0.0	auxin response factor 19-like isoform X1
Swissprot	Q8RYC8	0.0	ARFS_ARATH; Auxin response factor 19
TrEMBL	A0A1S3CBQ4	0.0	A0A1S3CBQ4_CUCME; Auxin response factor
STRING	XP_008460034.1	0.0	(Cucumis melo)

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
AT1G19220.1	0.0	auxin response factor 19

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]