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 Carubv10025165m
Organism
Capsella rubella
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae; Capsella
Family MYB_related
Protein Properties Length: 421aa    MW: 47296.7 Da    PI: 9.503
Description MYB_related family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Carubv10025165mgenomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1Myb_DNA-binding22.33e-07132174346
                      SS-HHHHHHHHHHHHHTTTT-HHHHHHHHTTTS-HHHHHHHHHH CS
  Myb_DNA-binding   3 rWTteEdellvdavkqlGggtWktIartmgkgRtlkqcksrwqk 46 
                       WT+eE ++l + ++ +  + +  Ia +++  Rt +++k+r+++
  Carubv10025165m 132 VWTKEETDQLFEFCQNFDLR-FVVIADRFPVSRTVEELKDRYYS 174
                      6*******************.*********************97 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PfamPF162824.0E-30105179IPR032563DAMP1, SANT/Myb-like domain
SMARTSM007173.6E-8129178IPR001005SANT/Myb domain
SuperFamilySSF466898.97E-7129181IPR009057Homeodomain-like
Gene3DG3DSA:1.10.10.602.3E-6132177IPR009057Homeodomain-like
CDDcd116583.59E-19133175No hitNo description
PfamPF054991.6E-6322391IPR008468DNA methyltransferase 1-associated 1
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0045892Biological Processnegative regulation of transcription, DNA-templated
GO:0005634Cellular Componentnucleus
GO:0003677Molecular FunctionDNA binding
Sequence ? help Back to Top
Protein Sequence    Length: 421 aa     Download sequence    Send to blast
MGGTDAKDIL GLPKTPLSLT QEKRSRPQKE SHRKPDGISR EVYALTGGVA PLMPSIDVAH  60
LKRRPPADEK VAWQWLPFTS SARKDDLQLY HWARVVNNVP PTGDYSFAKY NKSVDILKYT  120
DEEYENHLTD PVWTKEETDQ LFEFCQNFDL RFVVIADRFP VSRTVEELKD RYYSVTRALL  180
RARAQSPADV ANHPLMKEPY DITRDRERKR ALSVVLSQSR HQEKKDAEIL AEAKRITEMR  240
LAARRAEEPD VSANENAGLD KADGIVSGRS ISPSSNSQLP ATAVAPSTLT MADYASTLAS  300
LRMLHVYLRT YGLEQMVQAA SSAVGLRTIK RVEQTLQDLG VNLKPKVPTK TVCDEHLELR  360
KEILTLLNLQ KQLQYKESEG SSHREGLYAA MPDTPKGPGR QADTPSPAHK RPRKMKASDL  420
*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
3hm5_A8e-19104184488DNA methyltransferase 1-associated protein 1
4iej_A8e-19104184488DNA methyltransferase 1-associated protein 1
Search in ModeBase
Functional Description ? help Back to Top
Source Description
UniProtComponent of the SWR1 complex which mediates the ATP-dependent exchange of histone H2A for the H2A variant HZT1 leading to transcriptional regulation of selected genes by chromatin remodeling. Component of the NuA4 histone acetyltransferase complex which is involved in transcriptional activation of selected genes principally by acetylation of nucleosomal histone H4 and H2A. {ECO:0000305|Ref.5}.
Cis-element ? help Back to Top
SourceLink
PlantRegMapCarubv10025165m
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAB4935950.0AB493595.1 Arabidopsis thaliana At2g47210 mRNA for hypothetical protein, partial cds, clone: RAAt2g47210.
GenBankAY0640240.0AY064024.1 Arabidopsis thaliana unknown protein (At2g47210) mRNA, complete cds.
GenBankAY0966100.0AY096610.1 Arabidopsis thaliana unknown protein (At2g47210) mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_006293545.20.0SWR1-complex protein 4
SwissprotQ8VZL60.0SWC4_ARATH; SWR1-complex protein 4
TrEMBLR0HR490.0R0HR49_9BRAS; Uncharacterized protein (Fragment)
STRINGCagra.6400s0005.1.p0.0(Capsella grandiflora)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM85432435
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT2G47210.10.0MYB_related family protein
Publications ? help Back to Top
  1. Gómez-Zambrano Á, et al.
    Arabidopsis SWC4 Binds DNA and Recruits the SWR1 Complex to Modulate Histone H2A.Z Deposition at Key Regulatory Genes.
    Mol Plant, 2018. 11(6): p. 815-832
    [PMID:29604400]