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

HL.SW.v1.0.G029043.1

Organism

Humulus lupulus

Taxonomic ID

3486

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; fabids; Rosales; Cannabaceae; Humulus

Family

ARF

Protein Properties

Length: 1126aa MW: 125650 Da PI: 6.4787

Description

ARF family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
HL.SW.v1.0.G029043.1	genome	HOPBASE	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	B3	72.7	4.7e-23	123	224	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++ +++++ ++l+ +d++ ++W++++iyr++++r++lt+GW+ Fv+ ++L +gD+v+F HL.SW.v1.0.G029043.1 123 FCKTLTASDTSTHGGFSVPRRAAEKIfppldySMQPPA-QELVARDLHDNTWTFRHIYRGQPKRHLLTTGWSVFVSTKRLFAGDSVLFI 210 99***************************9545444.38********************************************** PP E-SSSEE..EEEEE-S CS B3 84 ldgrsefelvvkvfrk 99 ++++ +l+++++r+ HL.SW.v1.0.G029043.1 211 --RDEKSQLLLGIRRA 224 ..45677789999997 PP
2	Auxin_resp	122.3	3.5e-40	249	331	1	83
Auxin_resp 1 aahaastksvFevvYnPrastseFvvkvekvekalkvkvsvGmRfkmafetedsserrlsGtvvgvsdldpvrWpnSkWrsLk 83 aahaa+++s+F+++YnPras+seFv++++k++ka++++vs+GmRf+m+fete+s rr++Gtv+g+sdldp+rW+ S+Wr+L+ HL.SW.v1.0.G029043.1 249 AAHAAANTSPFTIFYNPRASPSEFVIPLAKYNKAMYTQVSLGMRFRMMFETEESGVRRYMGTVTGISDLDPLRWKSSQWRNLQ 331 79*******************************************************************************97 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SuperFamily	SSF101936	1.96E-44	113	252	IPR015300	DNA-binding pseudobarrel domain
Gene3D	G3DSA:2.40.330.10	3.0E-42	115	238	IPR015300	DNA-binding pseudobarrel domain
CDD	cd10017	3.99E-20	122	223	No hit	No description
Pfam	PF02362	7.2E-21	123	224	IPR003340	B3 DNA binding domain
PROSITE profile	PS50863	12.323	123	225	IPR003340	B3 DNA binding domain
SMART	SM01019	1.6E-23	123	225	IPR003340	B3 DNA binding domain
Pfam	PF06507	8.5E-35	249	331	IPR010525	Auxin response factor
Pfam	PF02309	1.7E-8	995	1084	IPR033389	AUX/IAA domain
PROSITE profile	PS51745	25.492	998	1091	IPR000270	PB1 domain
SuperFamily	SSF54277	1.42E-8	1011	1076	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: 1126 aa Download sequence Send to blast
MKAPPNGFLA TAGEGERKSI NSELWHACAG PLVSLPPVGS LVVYFPQGHS EQVAASMQKE 60 TDFIPNYPNL PSKLICMLHN VTLHADLETD EVYAQMTLQP HDREALLASD MGLKQNRQPS 120 EFFCKTLTAS DTSTHGGFSV PRRAAEKIFP PLDYSMQPPA QELVARDLHD NTWTFRHIYR 180 GQPKRHLLTT GWSVFVSTKR LFAGDSVLFI RDEKSQLLLG IRRATRQQPA LSSSVISSDS 240 MHIGILAAAA HAAANTSPFT IFYNPRASPS EFVIPLAKYN KAMYTQVSLG MRFRMMFETE 300 ESGVRRYMGT VTGISDLDPL RWKSSQWRNL QVGWDESTAG ERPSRVSIWE VEPVVTPFYI 360 CPPPFFRPKF LKQPGMPDDE SDMENAFKRA MPWLGDDFGM KDTSSTIFPG LSLVQWMNMQ 420 QNNQLSAAQS GFFPPMVSSS GMPNNLGTDD PSKLLSFQAP VMSGTNVPLS KATPSNQMQQ 480 PPVTWPQQQQ QQQQQLQQQQ QQQLHQLLQT PANQQQQNYS QQQLQQLLQS PPNQQLQNHS 540 QNQQLPQQRQ QHQEPPQHQQ LQQQQSNQQQ ICQSLVNNGV GSTNQIPNQS LQQPVMFSQH 600 QQQQLVTGNA QSQQSGYSSK NSVQLTSLPM DSQFQQQMEL QSNLFQKQQQ PTHLQQNQLQ 660 FLQHNLPQRT QQQSQSQQLS QQGLSEQQSQ LQLIQRLQQQ QQQQLLSPSS SHLQSQLLQQ 720 QGNQQNQQLQ SLPLSQHQQP LNSNGFSTEK LLNINNFSTS TLTQSQQIPT SQPQSQHKPL 780 VAIRANSGLT DGDAPSCSTS PSTNNCQISP SNLLNRNQHG QAMLIGDPVV EPANNLLQEL 840 QSKTDVRIKH EFPGSKGPDQ LKYKGSIPDH LEASSSGTSY LDASTIQQTF PLPTFCLDGD 900 VQSNHRNNLS FGANIDGLTP DTLLSREYDS QKDLQNLLSN CGGAPRDIET ELSTAAISSQ 960 SFGVPNMSFK PGCSSDVAIT DAGVLSNGLW ASQAQRMRTY TKVQKRGSVG RCIDVTRYKG 1020 YDELRHDLAR MFGIEGQLED PQRTDWKLVY VDHENDILLV GDDPWQEFVS CVQSIKILSS 1080 VEVQQMSLDG DLGQVPVPNQ ACSGTDSGNA WRGQYEDTSA ASFNR*

Sequence ? help Back to Top

Protein Sequence Length: 1126 aa Download sequence Send to blast

MKAPPNGFLA TAGEGERKSI NSELWHACAG PLVSLPPVGS LVVYFPQGHS EQVAASMQKE  60
TDFIPNYPNL PSKLICMLHN VTLHADLETD EVYAQMTLQP HDREALLASD MGLKQNRQPS  120
EFFCKTLTAS DTSTHGGFSV PRRAAEKIFP PLDYSMQPPA QELVARDLHD NTWTFRHIYR  180
GQPKRHLLTT GWSVFVSTKR LFAGDSVLFI RDEKSQLLLG IRRATRQQPA LSSSVISSDS  240
MHIGILAAAA HAAANTSPFT IFYNPRASPS EFVIPLAKYN KAMYTQVSLG MRFRMMFETE  300
ESGVRRYMGT VTGISDLDPL RWKSSQWRNL QVGWDESTAG ERPSRVSIWE VEPVVTPFYI  360
CPPPFFRPKF LKQPGMPDDE SDMENAFKRA MPWLGDDFGM KDTSSTIFPG LSLVQWMNMQ  420
QNNQLSAAQS GFFPPMVSSS GMPNNLGTDD PSKLLSFQAP VMSGTNVPLS KATPSNQMQQ  480
PPVTWPQQQQ QQQQQLQQQQ QQQLHQLLQT PANQQQQNYS QQQLQQLLQS PPNQQLQNHS  540
QNQQLPQQRQ QHQEPPQHQQ LQQQQSNQQQ ICQSLVNNGV GSTNQIPNQS LQQPVMFSQH  600
QQQQLVTGNA QSQQSGYSSK NSVQLTSLPM DSQFQQQMEL QSNLFQKQQQ PTHLQQNQLQ  660
FLQHNLPQRT QQQSQSQQLS QQGLSEQQSQ LQLIQRLQQQ QQQQLLSPSS SHLQSQLLQQ  720
QGNQQNQQLQ SLPLSQHQQP LNSNGFSTEK LLNINNFSTS TLTQSQQIPT SQPQSQHKPL  780
VAIRANSGLT DGDAPSCSTS PSTNNCQISP SNLLNRNQHG QAMLIGDPVV EPANNLLQEL  840
QSKTDVRIKH EFPGSKGPDQ LKYKGSIPDH LEASSSGTSY LDASTIQQTF PLPTFCLDGD  900
VQSNHRNNLS FGANIDGLTP DTLLSREYDS QKDLQNLLSN CGGAPRDIET ELSTAAISSQ  960
SFGVPNMSFK PGCSSDVAIT DAGVLSNGLW ASQAQRMRTY TKVQKRGSVG RCIDVTRYKG  1020
YDELRHDLAR MFGIEGQLED PQRTDWKLVY VDHENDILLV GDDPWQEFVS CVQSIKILSS  1080
VEVQQMSLDG DLGQVPVPNQ ACSGTDSGNA WRGQYEDTSA ASFNR*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
4ldu_A	1e-173	15	352	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
Refseq	XP_003609970.1	0.0	auxin response factor 19 isoform X1
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
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]