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 Cagra.4849s0002.1.p
Organism
Capsella grandiflora
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 HD-ZIP
Protein Properties Length: 725aa    MW: 81427.2 Da    PI: 6.641
Description HD-ZIP family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Cagra.4849s0002.1.pgenomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1Homeobox62.18.7e-202580156
                         TT--SS--HHHHHHHHHHHHHSSS--HHHHHHHHHHCTS-HHHHHHHHHHHHHHHH CS
             Homeobox  1 rrkRttftkeqleeLeelFeknrypsaeereeLAkklgLterqVkvWFqNrRakek 56
                         +r+ +++t++q+++Le++F+++++p+  +r++L+++l+L+ +q+k+WFqN+R++ k
  Cagra.4849s0002.1.p 25 KRNYHRHTSHQIQRLEAYFKECPHPDDLQRRQLSEELNLKPKQIKFWFQNKRTQAK 80
                         688999***********************************************988 PP
2START105.58.8e-342414642206
                          HHHHHHHHHHHHHHHC-TT-EEEE.......EXCCTTEEEEEEESSS...SCEEEEEEEECCSCHHHHHHHHHCCCGGCT-TT-S..... CS
                START   2 laeeaaqelvkkalaeepgWvkss.......esengdevlqkfeeskv..dsgealrasgvvdmvlallveellddkeqWdetla..... 77 
                          +ae+a +e++++++ ee +W+kss       + +n++++  k+   kv   + e +++++vv m++  lv  +ld+  +W + ++     
  Cagra.4849s0002.1.p 241 MAEKAVAEVMTLIQIEESMWKKSSidgrlviDPSNYEKCFAKINHFKVpsGRPESSKEVVVVQMDARILVDMFLDTE-KWARLFPtivne 329
                          68999**************************************777777767788************9999999999.****99999996 PP

                          ..EEEEEEEECTT..EEEEEEEEXXTTXX-SSX.EEEEEEEEEEE.TTS-EEEEEEEEE-TTS--.-TTSEE-EESSEEEEEEEECTCEE CS
                START  78 ..kaetlevissg..galqlmvaelqalsplvp.RdfvfvRyirqlgagdwvivdvSvdseqkppesssvvRaellpSgiliepksnghs 162
                             + +l+ +++g   +  +++ ++  lsplvp R+f ++R+++q+++ +w+i+dvS + ++    +s v  ++++pSg li+ +++g s
  Cagra.4849s0002.1.p 330 skTIYVLDSVDQGrkIFSRVIYEQMHILSPLVPaREFIILRSCQQMEENVWMIADVSCNIPNVEF-ESTVPLCNKRPSGVLIQALPDGFS 418
                          66666666667778755567788888888****************************99998877.899********************* PP

                          EEEEEE-EE--SSXX.HHHHHHH.HHHHHHHHHHHHHHHTXXXXXX CS
                START 163 kvtwvehvdlkgrlp.hwllrsl.vksglaegaktwvatlqrqcek 206
                          kvtwvehv++++++  h l+r l +  gl  ga++w+  l+r ce+
  Cagra.4849s0002.1.p 419 KVTWVEHVEVNDKMRpHRLYRDLfLYGGLGYGARRWTVILERMCER 464
                          ************9955*****97257789***************96 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF466891.25E-18881IPR009057Homeodomain-like
Gene3DG3DSA:1.10.10.608.5E-20982IPR009057Homeodomain-like
PROSITE profilePS5007116.7952282IPR001356Homeobox domain
SMARTSM003891.4E-182486IPR001356Homeobox domain
PfamPF000462.4E-172580IPR001356Homeobox domain
CDDcd000865.23E-182583No hitNo description
PROSITE patternPS0002705780IPR017970Homeobox, conserved site
PROSITE profilePS5084841.535231467IPR002913START domain
SuperFamilySSF559611.28E-26232439No hitNo description
CDDcd088753.15E-83237463No hitNo description
Gene3DG3DSA:3.30.530.204.4E-9240428IPR023393START-like domain
SMARTSM002344.6E-20240464IPR002913START domain
PfamPF018521.7E-28241464IPR002913START domain
SuperFamilySSF559611.58E-7487693No hitNo description
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006355Biological Processregulation of transcription, DNA-templated
GO:0008289Molecular Functionlipid binding
GO:0043565Molecular Functionsequence-specific DNA binding
Sequence ? help Back to Top
Protein Sequence    Length: 725 aa     Download sequence    Send to blast
MDSSRDDSSS DERGTSPDTN NNHDKRNYHR HTSHQIQRLE AYFKECPHPD DLQRRQLSEE  60
LNLKPKQIKF WFQNKRTQAK SHSEKADNAA LRADNMKIRR ENEAMEEALN NAVCPPCSGR  120
GFGSAEKLRH IQKLRAENTL LKKEYERLSS YIAQHGGHPL PSVDAFTSLH GPSTYGSTST  180
NRRASYGSSS NHLHQPSSSS LRGPYSRENI SMTAPPQSPK QLPLHHFPPL SQMDRMVMFE  240
MAEKAVAEVM TLIQIEESMW KKSSIDGRLV IDPSNYEKCF AKINHFKVPS GRPESSKEVV  300
VVQMDARILV DMFLDTEKWA RLFPTIVNES KTIYVLDSVD QGRKIFSRVI YEQMHILSPL  360
VPAREFIILR SCQQMEENVW MIADVSCNIP NVEFESTVPL CNKRPSGVLI QALPDGFSKV  420
TWVEHVEVND KMRPHRLYRD LFLYGGLGYG ARRWTVILER MCERLYLSSV SDLSNDDYAG  480
VVQTMEGRRS VMSLGERMSK NFAWMINMVQ KLDFSQQSET NNSGVRISVR TNDAAGEPPG  540
LIVCAGSSLS LPLPPLQVYD FLRNLEVRHQ WDVLCQGNPV TEVARFITGT DTKNNVNFLE  600
PSSGGEKKNE LMILQDSFID ALGGMVVYAP MDLETAASAI SGQIDSSTIP ILPSGFIISC  660
DGRPPSADEQ DSGSSSTLLT VAFQILVSDP RYSTNINIEE SATTVNTLIS STVQRIKSML  720
NCES*
Functional Description ? help Back to Top
Source Description
UniProtProbable transcription factor that binds to the DNA sequence 5'-GCATTAAATGCGCA-3'. {ECO:0000269|PubMed:16778018}.
Cis-element ? help Back to Top
SourceLink
PlantRegMapCagra.4849s0002.1.p
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankCP0026841e-84CP002684.1 Arabidopsis thaliana chromosome 1 sequence.
GenBankF21H21e-84AC007894.2 Arabidopsis thaliana chromosome 1 BAC F21H2 sequence, complete sequence.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_006286655.10.0homeobox-leucine zipper protein HDG9
SwissprotQ9FFI00.0HDG9_ARATH; Homeobox-leucine zipper protein HDG9
TrEMBLR0H7P30.0R0H7P3_9BRAS; Uncharacterized protein
STRINGCagra.4849s0002.1.p0.0(Capsella grandiflora)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM84681531
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT5G17320.10.0homeodomain GLABROUS 9
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]