PlantTFDB
PlantRegMap/PlantTFDB v5.0
Plant Transcription Factor Database
Home  TFext  BLAST  Prediction  Download  Help  About  Links  PlantRegMap
(e.g., LFY)
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID XP_009115534.1
Organism
Brassica rapa
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Brassiceae; Brassica
Family TALE
Protein Properties Length: 328aa    MW: 36821.5 Da    PI: 4.6475
Description TALE family protein
Gene Model
Gene Model ID Type Source Coding Sequence
XP_009115534.1genomeNCBIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1Homeobox26.11.5e-082713052155
                     HSSS--HHHHHHHHHHCTS-HHHHHHHHHHHHHHH CS
        Homeobox  21 knrypsaeereeLAkklgLterqVkvWFqNrRake 55 
                     k +yp++ ++  LA+ +gL+++q+ +WF N+R ++
  XP_009115534.1 271 KWPYPTEGDKIALADATGLDQKQINNWFINQRKRH 305
                     569*****************************885 PP
2ELK30.11.1e-10225246122
             ELK   1 ELKhqLlrKYsgyLgsLkqEFs 22 
                     +LK++LlrK++++++sLk EFs
  XP_009115534.1 225 DLKDRLLRKFGSRISSLKLEFS 246
                     69*******************8 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SMARTSM012554.6E-2284128IPR005540KNOX1
PfamPF037901.5E-2186127IPR005540KNOX1
SMARTSM012563.1E-25136187IPR005541KNOX2
PfamPF037916.2E-25140186IPR005541KNOX2
SMARTSM011886.3E-5225246IPR005539ELK domain
PROSITE profilePS512139.83225245IPR005539ELK domain
PfamPF037892.6E-7225246IPR005539ELK domain
PROSITE profilePS5007112.374245308IPR001356Homeobox domain
SuperFamilySSF466891.63E-19246321IPR009057Homeodomain-like
SMARTSM003891.0E-12247312IPR001356Homeobox domain
Gene3DG3DSA:1.10.10.609.8E-28250309IPR009057Homeodomain-like
CDDcd000861.17E-11257309No hitNo description
PfamPF059202.9E-17265304IPR008422Homeobox KN domain
PROSITE patternPS000270283306IPR017970Homeobox, conserved site
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006355Biological Processregulation of transcription, DNA-templated
GO:0010073Biological Processmeristem maintenance
GO:0005634Cellular Componentnucleus
GO:0043565Molecular Functionsequence-specific DNA binding
Sequence ? help Back to Top
Protein Sequence    Length: 328 aa     Download sequence    Send to blast
MDGMYGFHPT DGDYSDKAVL MMSPDNLMFP SDYQTLLCSS AGDNRVSDVF GSDELLSAAA  60
SALSSEAASI APEIPRNDDK VSLGVIKGKI ACHPLYPRLL QAYIDCQKVG APPEIACLLE  120
EIQRESHVHK QNVVPLSSSF GADPELDEFM ETYCDILVKY KSDLARPFDE ATTFLNKIEM  180
QLRNLCTGVE SDRGLSEDGA VSSDEELNGG DEILQDGKQI CEDRDLKDRL LRKFGSRISS  240
LKLEFSKKKK KGKLPKEARQ ALLDWWNVHY KWPYPTEGDK IALADATGLD QKQINNWFIN  300
QRKRHWKPSE NMPFAMMDDS SGSFFTEE
Expression -- Description ? help Back to Top
Source Description
UniprotDEVELOPMENTAL STAGE: First detected in torpedo stage embryos at the boundaries between the presumptive SAM and the cotyledons. Later expressed between the cotyledons and the meristem, and between the cotyledons. In seedlings, localised in stipules and at the boundaries between the SAM and the emerging primordia. Expressed at the site of lateral roots. {ECO:0000269|PubMed:16798887}.
UniprotTISSUE SPECIFICITY: Expressed predominantly in shoot apices of seedlings, and, to a lower extent, in rosette leaves. {ECO:0000269|PubMed:11311158}.
Functional Description ? help Back to Top
Source Description
UniProtPlays a role in meristem function. Contributes to the shoot apical meristem (SAM) maintenance and organ separation by controlling boundary establishment in embryo in a CUC1, CUC2 and STM-dependent manner. Involved in maintaining cells in an undifferentiated, meristematic state. Probably binds to the DNA sequence 5'-TGAC-3'. {ECO:0000269|PubMed:16798887}.
Cis-element ? help Back to Top
SourceLink
PlantRegMapXP_009115534.1
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: Seems to be repressed by AS2 and AS1 but induced by STM, CUC1 and CUC2. {ECO:0000269|PubMed:11311158, ECO:0000269|PubMed:16798887}.
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_009115534.10.0PREDICTED: homeobox protein knotted-1-like 6 isoform X1
SwissprotQ84JS60.0KNAT6_ARATH; Homeobox protein knotted-1-like 6
TrEMBLA0A3P5YKR30.0A0A3P5YKR3_BRACM; Uncharacterized protein
TrEMBLM4E7360.0M4E736_BRARP; Uncharacterized protein
STRINGBra024591.1-P0.0(Brassica rapa)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM8352785
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT1G23380.10.0KNOTTED1-like homeobox gene 6
Publications ? help Back to Top
  1. 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]
  2. Khan M, et al.
    Repression of Lateral Organ Boundary Genes by PENNYWISE and POUND-FOOLISH Is Essential for Meristem Maintenance and Flowering in Arabidopsis.
    Plant Physiol., 2015. 169(3): p. 2166-86
    [PMID:26417006]