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 Itr_sc000548.1_g00007.1
Organism
Ipomoea trifida
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; asterids; lamiids; Solanales; Convolvulaceae; Ipomoeeae; Ipomoea
Family MYB
Protein Properties Length: 300aa    MW: 33708 Da    PI: 4.7815
Description MYB family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Itr_sc000548.1_g00007.1genomeKazusaView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1Myb_DNA-binding521.6e-161663148
                             TSSS-HHHHHHHHHHHHHTTTT-HHHHHHHHTTTS-HHHHHHHHHHHT CS
          Myb_DNA-binding  1 rgrWTteEdellvdavkqlGggtWktIartmgkgRtlkqcksrwqkyl 48
                             +g+W++ Ed++l+  ++++G ++W++ ++  g+ R++k+c++rw +yl
  Itr_sc000548.1_g00007.1 16 KGPWSPAEDLRLISFIQKHGHPNWRALPKQAGLLRCGKSCRLRWINYL 63
                             79******************************99************97 PP
2Myb_DNA-binding574.5e-1869114148
                              TSSS-HHHHHHHHHHHHHTTTT-HHHHHHHHTTTS-HHHHHHHHHHHT CS
          Myb_DNA-binding   1 rgrWTteEdellvdavkqlGggtWktIartmgkgRtlkqcksrwqkyl 48 
                              rg++T+eE+e ++++++ lG++ W++Ia++++ gRt++++k+ w+++l
  Itr_sc000548.1_g00007.1  69 RGNFTPEEEETIIKLHNSLGNK-WSKIAAHFP-GRTDNEIKNVWNTHL 114
                              89********************.*********.************986 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:1.10.10.605.0E-24766IPR009057Homeodomain-like
PROSITE profilePS5129415.8691163IPR017930Myb domain
SuperFamilySSF466893.33E-3014110IPR009057Homeodomain-like
SMARTSM007171.5E-121565IPR001005SANT/Myb domain
PfamPF002497.4E-151663IPR001005SANT/Myb domain
CDDcd001677.79E-101863No hitNo description
PROSITE profilePS5129426.39864118IPR017930Myb domain
Gene3DG3DSA:1.10.10.603.2E-2867118IPR009057Homeodomain-like
SMARTSM007176.7E-1668116IPR001005SANT/Myb domain
PfamPF002491.1E-1669114IPR001005SANT/Myb domain
CDDcd001677.69E-1271114No hitNo description
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0009809Biological Processlignin biosynthetic process
GO:0045893Biological Processpositive regulation of transcription, DNA-templated
GO:2000652Biological Processregulation of secondary cell wall biogenesis
GO:0003677Molecular FunctionDNA binding
Sequence ? help Back to Top
Protein Sequence    Length: 300 aa     Download sequence    Send to blast
MGKGRAPCCD KSKVKKGPWS PAEDLRLISF IQKHGHPNWR ALPKQAGLLR CGKSCRLRWI  60
NYLRPDVKRG NFTPEEEETI IKLHNSLGNK WSKIAAHFPG RTDNEIKNVW NTHLKKRLTN  120
KKGKGRSNNT DDDEDDDESP QNDTVSPDTP PPKDASPTSS SSSSSTKDDH QAPPEAPPEP  180
PTPGDHDSVI DMEIWDMLDT LDDPSPQDPE IVVDDHQPAG SICGGEIEKQ VEWLRYLENE  240
LGLEDSTNNN NHAQPQKDDI DSNHNLVHLD SFDDNDDFND MVASLYFPTW PPCSPQHFGI
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
1gv2_A9e-26161184105MYB PROTO-ONCOGENE PROTEIN
1h88_C2e-251611858159MYB PROTO-ONCOGENE PROTEIN
1h89_C2e-251611858159MYB PROTO-ONCOGENE PROTEIN
1mse_C1e-25161184105C-Myb DNA-Binding Domain
1msf_C1e-25161184105C-Myb DNA-Binding Domain
Search in ModeBase
Functional Description ? help Back to Top
Source Description
UniProtTranscriptional activator that binds DNA to the AC cis-elements 5'-ACCTACC-3', 5'-ACCAACC-3' and 5'-ACCTAAC-3' of promoters and specifically activates lignin biosynthetic genes during secondary wall formation mediated by SND1. {ECO:0000269|PubMed:19122102}.
Binding Motif ? help Back to Top
Motif ID Method Source Motif file
MP00144DAPTransfer from AT1G16490Download
Motif logo
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: Slightly induced by light (PubMed:9839469). Regulated by the SND1 close homologs NST1, NST2, VND6, and VND7 and their downstream targets MYB46 and MYB83 (PubMed:19122102, PubMed:22197883). {ECO:0000269|PubMed:19122102, ECO:0000269|PubMed:22197883, ECO:0000269|PubMed:9839469}.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_019196276.11e-156PREDICTED: myb-related protein Myb4-like
RefseqXP_019196277.11e-156PREDICTED: myb-related protein Myb4-like
SwissprotQ9SA471e-78MYB58_ARATH; Transcription factor MYB58
TrEMBLA0A068UZ543e-84A0A068UZ54_COFCA; Uncharacterized protein
TrEMBLA5B1709e-84A5B170_VITVI; Uncharacterized protein
STRINGVIT_19s0085g00050.t014e-83(Vitis vinifera)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
AsteridsOGEA12242154
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT1G79180.16e-74myb domain protein 63
Publications ? help Back to Top
  1. Fernández-Pérez F,Vivar T,Pomar F,Pedreño MA,Novo-Uzal E
    Peroxidase 4 is involved in syringyl lignin formation in Arabidopsis thaliana.
    J. Plant Physiol., 2015. 175: p. 86-94
    [PMID:25506770]
  2. Noda S, et al.
    The expression of a rice secondary wall-specific cellulose synthase gene, OsCesA7, is directly regulated by a rice transcription factor, OsMYB58/63.
    Planta, 2015. 242(3): p. 589-600
    [PMID:26070439]
  3. Takeuchi M,Kegasa T,Watanabe A,Tamura M,Tsutsumi Y
    Expression analysis of transporter genes for screening candidate monolignol transporters using Arabidopsis thaliana cell suspensions during tracheary element differentiation.
    J. Plant Res., 2018. 131(2): p. 297-305
    [PMID:28921082]