PlantTFDB
PlantRegMap/PlantTFDB v5.0
Plant Transcription Factor Database
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(e.g., LFY)
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID PSME_00021251-RA
Organism
Pseudotsuga menziesii
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Acrogymnospermae; Pinidae; Pinales; Pinaceae; Pseudotsuga
Family B3
Protein Properties Length: 283aa    MW: 31391.7 Da    PI: 6.6217
Description B3 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
PSME_00021251-RAgenomePRSView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B372.74.4e-23137238199
                       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++      ++++ s++l+ +d++g +W++++iyr++++r++lt+GW+ Fv+ ++L +gD ++F   +++
  PSME_00021251-RA 137 FCKTLTVSDTSIHGGFSVPRRAAEDCfppldYKQERPSQELVAKDLHGVVWKFRHIYRGQPRRHLLTTGWSVFVSHKRLVSGDAILFL--RDE 227
                       99****************************8444556789************************************************..557 PP

                       EE..EEEEE-S CS
                B3  89 efelvvkvfrk 99 
                       ++ l+++++r+
  PSME_00021251-RA 228 NGDLRLGIRRA 238
                       88889999986 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF1019364.32E-44130266IPR015300DNA-binding pseudobarrel domain
Gene3DG3DSA:2.40.330.102.9E-40133252IPR015300DNA-binding pseudobarrel domain
CDDcd100171.07E-22135237No hitNo description
SMARTSM010192.4E-22137239IPR003340B3 DNA binding domain
PfamPF023624.3E-21137238IPR003340B3 DNA binding domain
PROSITE profilePS5086312.689137239IPR003340B3 DNA binding domain
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0003677Molecular FunctionDNA binding
Sequence ? help Back to Top
Protein Sequence    Length: 283 aa     Download sequence    Send to blast
MEIADLVSGD GFKPLPAENG GNGEMAEPIC SELWHASAGP LTSLPAKGSY VVYFPQGHME  60
QVAASLNQDT EQQMPSYNIP TQIFCRVLCV KLHADQETDE VYAQLTLVPV PEPTAKSLEE  120
KEEEHVHTSG TCTPHMFCKT LTVSDTSIHG GFSVPRRAAE DCFPPLDYKQ ERPSQELVAK  180
DLHGVVWKFR HIYRGQPRRH LLTTGWSVFV SHKRLVSGDA ILFLRDENGD LRLGIRRAAQ  240
QPCVIPSSVL SSQSMHLGLL AAAAHAVATK SMFHIFYNPR YTQ
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4ldv_A1e-1102328313270Auxin response factor 1
4ldw_A1e-1102328313270Auxin response factor 1
4ldw_B1e-1102328313270Auxin response factor 1
Search in ModeBase
Functional Description ? help Back to Top
Source Description
UniProtAuxin 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. {ECO:0000269|PubMed:12036261}.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_009592534.11e-115PREDICTED: auxin response factor 4-like
RefseqXP_020526715.11e-114auxin response factor 4 isoform X4
SwissprotQ9ZTX91e-107ARFD_ARATH; Auxin response factor 4
TrEMBLD4HTT81e-128D4HTT8_GINBI; Auxin response factor
STRINGAquca_027_00067.11e-113(Aquilegia coerulea)
STRINGXP_009592534.11e-114(Nicotiana tomentosiformis)
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT5G60450.11e-106auxin response factor 4
Publications ? help Back to Top
  1. Ozerova LV,Krasnikova MS,Troitsky AV,Solovyev AG,Morozov SY
    TAS3 Genes for small ta-siARF RNAs in plants belonging to subtribe Senecioninae: occurrence of prematurely terminated RNA precursors.
    Mol. Gen. Mikrobiol. Virusol., 2013.
    [PMID:24003511]
  2. Machida C,Nakagawa A,Kojima S,Takahashi H,Machida Y
    The complex of ASYMMETRIC LEAVES (AS) proteins plays a central role in antagonistic interactions of genes for leaf polarity specification in Arabidopsis.
    Wiley Interdiscip Rev Dev Biol, 2015 Nov-Dec. 4(6): p. 655-71
    [PMID:26108442]
  3. Pashkovskiy PP,Kartashov AV,Zlobin IE,Pogosyan SI,Kuznetsov VV
    Blue light alters miR167 expression and microRNA-targeted auxin response factor genes in Arabidopsis thaliana plants.
    Plant Physiol. Biochem., 2016. 104: p. 146-54
    [PMID:27031426]
  4. Matsumura Y, et al.
    A genetic link between epigenetic repressor AS1-AS2 and a putative small subunit processome in leaf polarity establishment of Arabidopsis.
    Biol Open, 2016. 5(7): p. 942-54
    [PMID:27334696]
  5. Guan C, et al.
    Spatial Auxin Signaling Controls Leaf Flattening in Arabidopsis.
    Curr. Biol., 2017. 27(19): p. 2940-2950.e4
    [PMID:28943086]
  6. Liu Z, et al.
    ARF2-ARF4 and ARF5 are Essential for Female and Male Gametophyte Development in Arabidopsis.
    Plant Cell Physiol., 2018. 59(1): p. 179-189
    [PMID:29145642]