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 XP_009114317.1
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 HD-ZIP
Protein Properties Length: 825aa    MW: 91888.2 Da    PI: 5.2749
Description HD-ZIP family protein
Gene Model
Gene Model ID Type Source Coding Sequence
XP_009114317.1genomeNCBIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1Homeobox63.92.3e-20113168156
                     TT--SS--HHHHHHHHHHHHHSSS--HHHHHHHHHHCTS-HHHHHHHHHHHHHHHH CS
        Homeobox   1 rrkRttftkeqleeLeelFeknrypsaeereeLAkklgLterqVkvWFqNrRakek 56 
                     +++ +++t+ q++e+e+lF++n++p  ++r++L+++lgL+ rqVk+WFqNrR+++k
  XP_009114317.1 113 KKRYHRHTDRQIQEMEALFKENPHPEDKQRQRLSHELGLKPRQVKFWFQNRRTQMK 168
                     688899***********************************************998 PP
2START147.41.3e-463255512206
                     HHHHHHHHHHHHHHHC-TT-EEEE........EXCCTTEEEEEEESSS..............SCEEEEEEEECCSCHHHHHHHHHCCCGGCT-TT CS
           START   2 laeeaaqelvkkalaeepgWvkss........esengdevlqkfeeskv.............dsgealrasgvvdmvlallveellddkeqWdet 75 
                     +a ++ qel k+ + eep+Wv             +n++e+++                    ++ ea++a +vv+m++ +lv+ +l+   +W+e+
  XP_009114317.1 325 FAVSCVQELTKMCDTEEPLWVNKKsdkiggetLCLNEEEYMR------LfpwpmeknnnngdFRREASKANAVVIMNSITLVNAFLNAD-KWSEM 412
                     67899****************999555554443345555555......155555677889999**************************.***** PP

                     -S....EEEEEEEECTT.....EEEEEEEEXXTTXX-SSX.EEEEEEEEEEE..TTS-EEEEEEEEE-TTS--.-TTSEE-EESSEEEEEEEECT CS
           START  76 la....kaetlevissg.....galqlmvaelqalsplvp.RdfvfvRyirq.lgagdwvivdvSvdseqkppesssvvRaellpSgiliepksn 159
                     +     +++t++ issg     g l lm+aelq+lsplvp R+ +f+Ry +q ++ g w+ivd  +ds  ++++ +++    + pSg++i++++n
  XP_009114317.1 413 FCsivaRVKTVQIISSGvsgasGSLMLMYAELQVLSPLVPtREAYFLRYVEQnSENGNWAIVDFPIDSFHDQNSPHEYK---RKPSGCIIQDMPN 504
                     *99999*************************************************************999998445555...5************ PP

                     CEEEEEEEE-EE--SSXXHHHHHHHHHHHHHHHHHHHHHHTXXXXXX CS
           START 160 ghskvtwvehvdlkgrlphwllrslvksglaegaktwvatlqrqcek 206
                     g+skv wvehv++ +r++h+ +   vksg+a+ga++wv  l+rqce+
  XP_009114317.1 505 GYSKVKWVEHVEVVERHVHETFAEYVKSGMAFGASRWVDVLERQCER 551
                     *********************************************97 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF466891.11E-19104171IPR009057Homeodomain-like
Gene3DG3DSA:1.10.10.604.5E-21107176IPR009057Homeodomain-like
PROSITE profilePS5007117.702110170IPR001356Homeobox domain
SMARTSM003893.8E-18111174IPR001356Homeobox domain
CDDcd000866.94E-19113171No hitNo description
PfamPF000467.2E-18113168IPR001356Homeobox domain
PROSITE patternPS000270145168IPR017970Homeobox, conserved site
PROSITE profilePS5084841.829315554IPR002913START domain
SuperFamilySSF559611.79E-28316553No hitNo description
CDDcd088754.01E-101319550No hitNo description
SMARTSM002341.2E-26324551IPR002913START domain
PfamPF018525.1E-39325551IPR002913START domain
SuperFamilySSF559613.71E-13581802No hitNo description
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006355Biological Processregulation of transcription, DNA-templated
GO:0048497Biological Processmaintenance of floral organ identity
GO:0008289Molecular Functionlipid binding
GO:0043565Molecular Functionsequence-specific DNA binding
Sequence ? help Back to Top
Protein Sequence    Length: 825 aa     Download sequence    Send to blast
MLTIGEESVM TSDNRFASPP PPASSSPATI QNPNFNFIPF NSFSSIIPKE EHGMMSMSMM  60
MMMGDEAVEE MMENGSMGGS FGSGSEQAED PKSGTEFDVN ELRDDEQPPP AKKKRYHRHT  120
DRQIQEMEAL FKENPHPEDK QRQRLSHELG LKPRQVKFWF QNRRTQMKAQ QDRAENVMLR  180
ADNDNLKLEN SQLQAELRCL SCPSCGGPTV LGDIPFNELH IENCRLREEL DRLCCIASRY  240
TDRPMQPMPP SQPLINPASE LPHHQPSLEL DISAYAGNYP DHPCSDLMSL PPQDSACFFP  300
TQTINNSSNN NMLLADEEKV MAMEFAVSCV QELTKMCDTE EPLWVNKKSD KIGGETLCLN  360
EEEYMRLFPW PMEKNNNNGD FRREASKANA VVIMNSITLV NAFLNADKWS EMFCSIVARV  420
KTVQIISSGV SGASGSLMLM YAELQVLSPL VPTREAYFLR YVEQNSENGN WAIVDFPIDS  480
FHDQNSPHEY KRKPSGCIIQ DMPNGYSKVK WVEHVEVVER HVHETFAEYV KSGMAFGASR  540
WVDVLERQCE RMASLMARNI TDLGVIRSAE ARRNMMRLSQ RMMKTFCVNI STSYGQSWTA  600
LSETAKDTVR ITTRKVCEPG QPTGVVLVAV STTWLPFSHF KVFDLLRDQH HHSLLEVLFS  660
GNSSHEVAHI ANGSHPGNCI SLLRVNVASN SWHNVELMLQ ESCIDNSGGL IVYSTVGVDS  720
IQHVMNGEDP SNVPVLPLGF SVVPVNPPGE VEGISVNSIP PPSCLLTVGI QVLASNVPTA  780
KPNLSTVTTI NNHLCSIVNQ ITSVLSSTIS PTIASSAAAA KQDVI
Expression -- Description ? help Back to Top
Source Description
UniprotTISSUE SPECIFICITY: Expressed in shoot apical meristem (SAM) with higher levels in L1 cells and the epidermal layer of young leaves. Expressed in the L1 of apical inflorescence meristems, early flower primordia, carpel and stamen filament epidermis, ovule primordia, nucellus and chalaze. {ECO:0000269|PubMed:16778018}.
Functional Description ? help Back to Top
Source Description
UniProtProbable transcription factor. {ECO:0000250}.
Cis-element ? help Back to Top
SourceLink
PlantRegMapXP_009114317.1
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAB0133941e-144AB013394.1 Arabidopsis thaliana genomic DNA, chromosome 5, P1 clone:MQD22.
GenBankCP0026881e-144CP002688.1 Arabidopsis thaliana chromosome 5 sequence.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_009114317.10.0PREDICTED: homeobox-leucine zipper protein HDG5
RefseqXP_009114318.10.0PREDICTED: homeobox-leucine zipper protein HDG5
RefseqXP_009114319.10.0PREDICTED: homeobox-leucine zipper protein HDG5
RefseqXP_009114320.10.0PREDICTED: homeobox-leucine zipper protein HDG5
RefseqXP_018510071.10.0PREDICTED: homeobox-leucine zipper protein HDG5
SwissprotQ9FJS20.0HDG5_ARATH; Homeobox-leucine zipper protein HDG5
TrEMBLM4DLY80.0M4DLY8_BRARP; Uncharacterized protein
STRINGBra017519.1-P0.0(Brassica rapa)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM43562548
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT5G46880.10.0homeobox-7
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. Lung SC, et al.
    Arabidopsis ACYL-COA-BINDING PROTEIN1 interacts with STEROL C4-METHYL OXIDASE1-2 to modulate gene expression of homeodomain-leucine zipper IV transcription factors.
    New Phytol., 2018. 218(1): p. 183-200
    [PMID:29288621]