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

MDP0000886637

Organism

Malus domestica

Taxonomic ID

3750

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; fabids; Rosales; Rosaceae; Maloideae; Maleae; Malus

Family

ARF

Protein Properties

Length: 1150aa MW: 128533 Da PI: 6.8314

Description

ARF family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
MDP0000886637	genome	GDR	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	B3	69.8	3.6e-22	125	226	1	99
EEEE-..-HHHHTT-EE--HHH.HTT......---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE-SSSEE CS B3 1 ffkvltpsdvlksgrlvlpkkfaeeh......ggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfvvFkldgrsef 90 f+k+lt sd++++g +++p++ ae++ +++++ ++l+ +d++ W++++iyr++++r++lt+GW+ Fv+ ++L +gD+v+F ++++ MDP0000886637 125 FCKTLTASDTSTHGGFSVPRRAAEKIlppldfSMQPPA-QELVAKDLHDSAWTFRHIYRGQPKRHLLTTGWSVFVSNKRLFAGDSVLFI--RDEKS 217 99***************************9445444.38**********************************************..45677 PP ..EEEEE-S CS B3 91 elvvkvfrk 99 +l+++++r+ MDP0000886637 218 QLLLGIRRA 226 789999986 PP
2	Auxin_resp	124.4	7.8e-41	251	333	1	83
Auxin_resp 1 aahaastksvFevvYnPrastseFvvkvekvekalkvkvsvGmRfkmafetedsserrlsGtvvgvsdldpvrWpnSkWrsLk 83 aahaa+++s+F+++YnPras+seFvv+++k++ka++++vs+GmRf+m+fete+s rr++Gtv+g+sdldpvrW++S+Wr+L+ MDP0000886637 251 AAHAAANNSPFTIFYNPRASPSEFVVPLAKYNKAMYTQVSLGMRFRMMFETEESGVRRYMGTVTGISDLDPVRWKGSQWRNLQ 333 79*******************************************************************************97 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SuperFamily	SSF101936	4.71E-43	115	254	IPR015300	DNA-binding pseudobarrel domain
Gene3D	G3DSA:2.40.330.10	1.3E-40	117	240	IPR015300	DNA-binding pseudobarrel domain
CDD	cd10017	4.48E-19	124	225	No hit	No description
SMART	SM01019	5.7E-20	125	227	IPR003340	B3 DNA binding domain
Pfam	PF02362	1.9E-20	125	226	IPR003340	B3 DNA binding domain
PROSITE profile	PS50863	12.097	125	227	IPR003340	B3 DNA binding domain
Pfam	PF06507	7.9E-36	251	333	IPR010525	Auxin response factor
Pfam	PF02309	2.6E-9	1033	1123	IPR033389	AUX/IAA domain
PROSITE profile	PS51745	24.865	1037	1130	IPR000270	PB1 domain
SuperFamily	SSF54277	2.22E-8	1039	1115	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:0009725	Biological Process	response to hormone
GO:0005634	Cellular Component	nucleus
GO:0003677	Molecular Function	DNA binding
GO:0005515	Molecular Function	protein binding

Sequence ? help Back to Top
Protein Sequence Length: 1150 aa Download sequence Send to blast
MQILDDLLIF RYPGEQKRIN SELWHACAGP LVSLPPVGSL VVYFPQGHSE QVAASMQKET 60 DLIPNYTNLP SKLICMLHNV TLHADTETDE VYAQMTLQPV NKYEKEALLA SDMGLKQSRQ 120 PAEFFCKTLT ASDTSTHGGF SVPRRAAEKI LPPLDFSMQP PAQELVAKDL HDSAWTFRHI 180 YRGQPKRHLL TTGWSVFVSN KRLFAGDSVL FIRDEKSQLL LGIRRAHRQQ PALSSSVISS 240 DSMHIGILAA AAHAAANNSP FTIFYNPRAS PSEFVVPLAK YNKAMYTQVS LGMRFRMMFE 300 TEESGVRRYM GTVTGISDLD PVRWKGSQWR NLQVGWDEST AGDRPSRVSI WEIEPVITPF 360 YICPPPFFRP KFPKQPGMPD DESDIDNAFR RAMPWLGDEF GMKNSPSSFF PGLSLVQWMN 420 MQQNNQFSAA QSGFFPSMVP PTGLQNNLGT DDPSKLLSFQ APVLSSLGLQ SNKSAPQNHA 480 SQMQQPNVTW AQQQQLQQLM HNPMNQQQQS NPQQQQLQQL LNSSVNQHQQ NHPPQQQLQQ 540 LLNSSANQHQ QNHPQQQQQL LQTPTNQQLH NFSHQQQQRE PQQQQEXQNL LQHQQLHQQQ 600 PQRHQQQQLS QPNPVNNGSV APNQVPGQNS QQPVMFSQHQ QQQLLTGNTQ QAVPSSSKNS 660 FQLPTGQQNS QLQQQQLEPQ PSLLQRQQQA AQLQSPPHQL LQQSVSQKVQ QQPQVQQSSP 720 QGISEQQLQL QLLQKFQQQQ QPQLLSSSSS LLQPQLLQQQ LARQQNQQLQ QLPMTQHHQQ 780 QLSGNXFSTD KLLNNFAAPS MMQSQHMPSI QPQNQHKPLT AIRSHSGLTE GDGPSCSTSP 840 STNCQMSPSN FLNRNQQGMA MLLGDSVAEP AHNLVQELQS KSDVWVKHEP PSSKGPDHIK 900 YKGTITDQLE ASSSGTSYCL DTSTIHQNYA LPTFCLDGDV QSNPRSSLPF SANIDGLAPD 960 TLLSREYDSQ KDLQNLLSNY GGTPRDIETE LSTAAISSQS FGAPNIPFKA GCSSDIPITD 1020 AGVLGNGSWA NQAQRMRTYT KVQKRGSVGR CIDVNRYKGY DELRXALARM FGIEGQLEEP 1080 HRTDWKLVYV DHENEILLVG DDPWEEFVSC VQSIKILSSV EVQQMSLDGD LGNIPVPNQA 1140 SSGTASGNA*

Sequence ? help Back to Top

Protein Sequence Length: 1150 aa Download sequence Send to blast

MQILDDLLIF RYPGEQKRIN SELWHACAGP LVSLPPVGSL VVYFPQGHSE QVAASMQKET  60
DLIPNYTNLP SKLICMLHNV TLHADTETDE VYAQMTLQPV NKYEKEALLA SDMGLKQSRQ  120
PAEFFCKTLT ASDTSTHGGF SVPRRAAEKI LPPLDFSMQP PAQELVAKDL HDSAWTFRHI  180
YRGQPKRHLL TTGWSVFVSN KRLFAGDSVL FIRDEKSQLL LGIRRAHRQQ PALSSSVISS  240
DSMHIGILAA AAHAAANNSP FTIFYNPRAS PSEFVVPLAK YNKAMYTQVS LGMRFRMMFE  300
TEESGVRRYM GTVTGISDLD PVRWKGSQWR NLQVGWDEST AGDRPSRVSI WEIEPVITPF  360
YICPPPFFRP KFPKQPGMPD DESDIDNAFR RAMPWLGDEF GMKNSPSSFF PGLSLVQWMN  420
MQQNNQFSAA QSGFFPSMVP PTGLQNNLGT DDPSKLLSFQ APVLSSLGLQ SNKSAPQNHA  480
SQMQQPNVTW AQQQQLQQLM HNPMNQQQQS NPQQQQLQQL LNSSVNQHQQ NHPPQQQLQQ  540
LLNSSANQHQ QNHPQQQQQL LQTPTNQQLH NFSHQQQQRE PQQQQEXQNL LQHQQLHQQQ  600
PQRHQQQQLS QPNPVNNGSV APNQVPGQNS QQPVMFSQHQ QQQLLTGNTQ QAVPSSSKNS  660
FQLPTGQQNS QLQQQQLEPQ PSLLQRQQQA AQLQSPPHQL LQQSVSQKVQ QQPQVQQSSP  720
QGISEQQLQL QLLQKFQQQQ QPQLLSSSSS LLQPQLLQQQ LARQQNQQLQ QLPMTQHHQQ  780
QLSGNXFSTD KLLNNFAAPS MMQSQHMPSI QPQNQHKPLT AIRSHSGLTE GDGPSCSTSP  840
STNCQMSPSN FLNRNQQGMA MLLGDSVAEP AHNLVQELQS KSDVWVKHEP PSSKGPDHIK  900
YKGTITDQLE ASSSGTSYCL DTSTIHQNYA LPTFCLDGDV QSNPRSSLPF SANIDGLAPD  960
TLLSREYDSQ KDLQNLLSNY GGTPRDIETE LSTAAISSQS FGAPNIPFKA GCSSDIPITD  1020
AGVLGNGSWA NQAQRMRTYT KVQKRGSVGR CIDVNRYKGY DELRXALARM FGIEGQLEEP  1080
HRTDWKLVYV DHENEILLVG DDPWEEFVSC VQSIKILSSV EVQQMSLDGD LGNIPVPNQA  1140
SSGTASGNA*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
4ldu_A	1e-171	19	354	51	388	Auxin response factor 5
Search in ModeBase

Expression -- UniGene ? help Back to Top
UniGene ID	E-value	Expressed in
Mdo.24725	0.0	leaf

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_008388980.2	0.0	auxin response factor 7-like
Refseq	XP_028945055.1	0.0	auxin response factor 7-like
Swissprot	Q8RYC8	0.0	ARFS_ARATH; Auxin response factor 19
TrEMBL	A0A498KLI9	0.0	A0A498KLI9_MALDO; Auxin response factor
STRING	XP_008388980.1	0.0	(Malus domestica)

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

Link Out ? help Back to Top
Phytozome	MDP0000886637

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]