PlantRegMap/PlantTFDB v5.0
Plant Transcription
Factor Database
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Transcription Factor Information
Basic Information? help Back to Top | |||||||||
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TF ID | Solyc03g118290.2.1 | ||||||||
Common Name | ARF2 | ||||||||
Organism | |||||||||
Taxonomic ID | |||||||||
Taxonomic Lineage |
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; asterids; lamiids; Solanales; Solanaceae; Solanoideae; Solaneae; Solanum; Lycopersicon
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Family | ARF | ||||||||
Protein Properties | Length: 847aa MW: 94013.6 Da PI: 6.7504 | ||||||||
Description | ARF family protein | ||||||||
Gene Model |
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Signature Domain? help Back to Top | |||||||
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No. | Domain | Score | E-value | Start | End | HMM Start | HMM End |
1 | B3 | 74.9 | 9.6e-24 | 146 | 247 | 1 | 99 |
EEEE-..-HHHHTT-EE--HHH.HTT......---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE- CS B3 1 ffkvltpsdvlksgrlvlpkkfaeeh......ggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfvvFkld 85 f+k+lt sd++++g +++ +++a+e+ + ++ +++l+ +d++g++W++++i+r++++r++l++GW+ Fv++++L +gD ++F Solyc03g118290.2.1 146 FCKTLTASDTSTHGGFSVLRRHADEClpqldmS-RQPPTQELVAKDLHGNEWRFRHIFRGQPRRHLLQSGWSVFVSSKRLVAGDAFIFL-- 233 99****************************963.3334459************************************************.. PP SSSEE..EEEEE-S CS B3 86 grsefelvvkvfrk 99 + +++el+v+v+r+ Solyc03g118290.2.1 234 RGENGELRVGVRRA 247 449999*****996 PP | |||||||
2 | Auxin_resp | 120.6 | 1.2e-39 | 272 | 354 | 1 | 83 |
Auxin_resp 1 aahaastksvFevvYnPrastseFvvkvekvekalkvkvsvGmRfkmafetedsserrlsGtvvgvsdldpvrWpnSkWrsLk 83 a+ha++tk++F+v+Y+Pr+s++eF+v+++++++++k+++s+GmRfkm+fe+e+++e+r++Gt+vg++d+dp rW +SkWr+Lk Solyc03g118290.2.1 272 AWHAIQTKTMFTVYYKPRTSPAEFIVPYDHYMESVKNNYSIGMRFKMRFEGEEAPEQRFTGTIVGIEDADPQRWLESKWRCLK 354 89*******************************************************************************96 PP |
Protein Features ? help Back to Top | ||||||
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Database | Entry ID | E-value | Start | End | InterPro ID | Description |
Gene3D | G3DSA:2.40.330.10 | 2.5E-41 | 142 | 261 | IPR015300 | DNA-binding pseudobarrel domain |
SuperFamily | SSF101936 | 3.01E-40 | 142 | 275 | IPR015300 | DNA-binding pseudobarrel domain |
CDD | cd10017 | 2.61E-21 | 144 | 246 | No hit | No description |
PROSITE profile | PS50863 | 12.012 | 146 | 248 | IPR003340 | B3 DNA binding domain |
Pfam | PF02362 | 1.1E-21 | 146 | 247 | IPR003340 | B3 DNA binding domain |
SMART | SM01019 | 1.4E-22 | 146 | 248 | IPR003340 | B3 DNA binding domain |
Pfam | PF06507 | 1.2E-36 | 272 | 354 | IPR010525 | Auxin response factor |
Pfam | PF02309 | 1.5E-10 | 712 | 805 | IPR033389 | AUX/IAA domain |
SuperFamily | SSF54277 | 1.72E-12 | 717 | 797 | No hit | No description |
PROSITE profile | PS51745 | 25.219 | 720 | 804 | IPR000270 | PB1 domain |
Gene Ontology ? help Back to Top | ||||||
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GO Term | GO Category | GO Description | ||||
GO:0008285 | Biological Process | negative regulation of cell proliferation | ||||
GO:0009734 | Biological Process | auxin-activated signaling pathway | ||||
GO:0009737 | Biological Process | response to abscisic acid | ||||
GO:0009911 | Biological Process | positive regulation of flower development | ||||
GO:0010047 | Biological Process | fruit dehiscence | ||||
GO:0010150 | Biological Process | leaf senescence | ||||
GO:0010227 | Biological Process | floral organ abscission | ||||
GO:0045892 | Biological Process | negative regulation of transcription, DNA-templated | ||||
GO:0048481 | Biological Process | plant ovule development | ||||
GO:0005634 | Cellular Component | nucleus | ||||
GO:0005515 | Molecular Function | protein binding | ||||
GO:0043565 | Molecular Function | sequence-specific DNA binding |
Sequence ? help Back to Top |
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Protein Sequence Length: 847 aa Download sequence Send to blast |
MAASEVSIQG YSEPSDGSRP VSETGRSSSG VGIVDADTAL YTELWRSCAG PLVTVPREGE 60 LVYYFPQGHI EQVEASTNQV ADQQMPLYNL PSKILCRVVN VLLKAEPDTD EVYAQVTLMP 120 EPNQDENAVK KEPMRPPPPR FHVHSFCKTL TASDTSTHGG FSVLRRHADE CLPQLDMSRQ 180 PPTQELVAKD LHGNEWRFRH IFRGQPRRHL LQSGWSVFVS SKRLVAGDAF IFLRGENGEL 240 RVGVRRAMRQ QGNAPSSVIS SHSMHLGVLA TAWHAIQTKT MFTVYYKPRT SPAEFIVPYD 300 HYMESVKNNY SIGMRFKMRF EGEEAPEQRF TGTIVGIEDA DPQRWLESKW RCLKVRWDEN 360 SSIPRPDRVS PWKIEPALSP PALNVPPVAR PKRPRSSILP TSPDSSVLTR EGSSRATADH 420 SQASGFPRVL QGQELSTFRG GFAEINETDL SEKPMIWQTS VNDEKNDIHS ASKRYLPDKW 480 LPLGRPESSL TDLLSGFGSS HGFCLPSADQ AAFGARLVKQ QTQDQEKDFS LLGKPWSLLS 540 SGLSLNLMDS GSKAPGIGGD TPYQMRGDAR YSGYGEFSVL PGHRVANQQG SWIMPQPVSP 600 YMQLSSHSRE MMHKPSVVKQ PEAVKPKEGN YKLFGIPLTS NVCTDAVMMR KSSLIDPASD 660 MNIGIHPHQS LATDSDQRSE QSKGSKVDDG VAANDHDKQF HTFHLAARDK DGKGHSSSTR 720 SCTKVHKQGT ALGRSVDLAK FNNYDELIAE LDQLFDFNGE LKARSKSWLV VYTDDEGDMM 780 LVGDDPWQEF CGMVRKIFIY TKEEVQRMNP GTLNSKGEDT SSVAEGSDAK EVKNLQLPSE 840 SGQAES* |
3D Structure ? help Back to Top | ||||||
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PDB ID | Evalue | Query Start | Query End | Hit Start | Hit End | Description |
4ldv_A | 1e-174 | 21 | 376 | 1 | 354 | Auxin response factor 1 |
4ldw_A | 1e-174 | 21 | 376 | 1 | 354 | Auxin response factor 1 |
4ldw_B | 1e-174 | 21 | 376 | 1 | 354 | Auxin response factor 1 |
4ldx_A | 1e-174 | 21 | 376 | 1 | 354 | Auxin response factor 1 |
4ldx_B | 1e-174 | 21 | 376 | 1 | 354 | Auxin response factor 1 |
Search in ModeBase |
Expression -- UniGene ? help Back to Top | ||||||
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UniGene ID | E-value | Expressed in | ||||
Les.20300 | 0.0 | callus| flower| fruit| leaf| stem |
Expression -- Description ? help Back to Top | ||||||
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Source | Description | |||||
Uniprot | DEVELOPMENTAL STAGE: Expression increases at the orange (Or) and red (R) fruit stages. Expression is increased with ethylene at mature green (MG) stage, but only after six days post-treatment. Expression is increased three days post-treatment with plant hormone abscisic acid (ABA) at the Or stage, but not at the MG or breaker (Br) stages. No change in expression level up to six days post-treatment with ABA at the MG fruit stage (PubMed:26959229). Expressed during floral development (PubMed:21735233, PubMed:28167023, PubMed:27645097). During bud-anthesis stages flowers exhibit dynamic expression pattern in sepal, stamen, ovary and petal (PubMed:28167023). Expressed during ovary development with the highest expression on the third day after the flower fully opened (PubMed:21735233). During seed germination, expressed in the cotyledon. Expressed strongly in the pollen grain. Expressed in the developing fruits, in which mainly expressed in the vascular tissues and seeds. During growth, strongly expressed in leaf, where mainly expressed in the trichome and in the root tip and lateral root formation sites. Expressed in the vascular tissue and the epicycle of the root. Also expressed in branch (PubMed:27645097). {ECO:0000269|PubMed:21735233, ECO:0000269|PubMed:26959229, ECO:0000269|PubMed:27645097, ECO:0000269|PubMed:28167023}. | |||||
Uniprot | TISSUE SPECIFICITY: Expressed in root, leaf and flower (PubMed:26716451, PubMed:27645097, PubMed:28167023, PubMed:21735233). Expressed in flower buds about three days before opening including ovary, petal and sepal with the highest in stamen (PubMed:21735233). Expressed in stem (PubMed:26716451, PubMed:28167023, PubMed:21735233). Expressed in fruit (PubMed:26716451, PubMed:27645097, PubMed:28167023). Expressed in seeds (PubMed:27645097). {ECO:0000269|PubMed:21735233, ECO:0000269|PubMed:26716451, ECO:0000269|PubMed:27645097, ECO:0000269|PubMed:28167023}. |
Functional Description ? help Back to Top | ||||||
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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) (By similarity). Could act as transcriptional activator or repressor (PubMed:26959229, PubMed:26716451, PubMed:27645097, PubMed:28167023). Involved in the control of fruit ripening process (PubMed:26959229, PubMed:26716451, PubMed:28167023). Regulates expression of a number of ripening regulators, transcription factors, and ethylene biosynthesis and signaling components (PubMed:26959229, PubMed:26716451). May act as a transcriptional repressor of auxin-responsive genes (PubMed:26716451). Regulates vegetative growth, lateral root formation and flower organ senescence, possibly partially by regulating gene expression of auxin and ethylene response factor (ERF) genes (PubMed:28167023). Plays a negative role in axillary shoot meristem formation (PubMed:27645097). {ECO:0000255|RuleBase:RU004561, ECO:0000269|PubMed:26716451, ECO:0000269|PubMed:26959229, ECO:0000269|PubMed:27645097, ECO:0000269|PubMed:28167023}. |
Function -- GeneRIF ? help Back to Top | ||||||
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Binding Motif ? help Back to Top | |||
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Motif ID | Method | Source | Motif file |
MP00574 | DAP | Transfer from AT5G62000 | Download |
Cis-element ? help Back to Top | |
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Source | Link |
PlantRegMap | Solyc03g118290.2.1 |
Regulation -- Description ? help Back to Top | ||||||
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Source | Description | |||||
UniProt | INDUCTION: By tomato fruit ripening. Expression in tomato fruits is up-regulated by exogenous application of ethylene and down-regulated by inhibition of ethylene receptors with 1-methylcyclopropene (1-MCP) (PubMed:26959229, PubMed:26716451). Up-regulated by plant hormone abscisic acid (ABA) in tomato fruits (PubMed:26959229). Expression is not up-regulated by plant hormone auxin in tomato fruits (PubMed:26716451). Up-regulated by auxin and gibberellic acid (GA), and down-regulated by ethylene in seedlings (PubMed:28167023). Down-regulated during decapitation-induced axillary shoot development and by excision of immature leaves. Down-regulation is inhibited by the application of auxin on the cut surface (PubMed:27645097). {ECO:0000269|PubMed:26716451, ECO:0000269|PubMed:26959229, ECO:0000269|PubMed:27645097, ECO:0000269|PubMed:28167023}. |
Regulation -- PlantRegMap ? help Back to Top | ||||||
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Source | Upstream Regulator | Target Gene | ||||
PlantRegMap | Retrieve | Retrieve |
Annotation -- Nucleotide ? help Back to Top | ||||||
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Source | Hit ID | E-value | Description | |||
GenBank | DQ340255 | 0.0 | Lycopersicon esculentum auxin response factor 2 (ARF2) mRNA, complete cds |
Annotation -- Protein ? help Back to Top | |||||||
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Source | Hit ID | E-value | Description | ||||
Refseq | NP_001233765.1 | 0.0 | auxin response factor 2A | ||||
Swissprot | Q2LAJ3 | 0.0 | ARF2A_SOLLC; Auxin response factor 2A | ||||
TrEMBL | M1B469 | 0.0 | M1B469_SOLTU; Auxin response factor | ||||
STRING | Solyc03g118290.2.1 | 0.0 | (Solanum lycopersicum) |
Orthologous Group ? help Back to Top | |||
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Lineage | Orthologous Group ID | Taxa Number | Gene Number |
Asterids | OGEA2618 | 24 | 44 | Representative plant | OGRP550 | 15 | 82 |
Best hit in Arabidopsis thaliana ? help Back to Top | ||||||
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Hit ID | E-value | Description | ||||
AT5G62000.3 | 0.0 | auxin response factor 2 |
Link Out ? help Back to Top | |
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Phytozome | Solyc03g118290.2.1 |
Entrez Gene | 778240 |