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 Carubv10000300m
Common NameCARUB_v10000300mg
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 HD-ZIP
Protein Properties Length: 746aa    MW: 81432 Da    PI: 5.7591
Description HD-ZIP family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Carubv10000300mgenomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1Homeobox61.21.6e-1962117156
                      TT--SS--HHHHHHHHHHHHHSSS--HHHHHHHHHHCTS-HHHHHHHHHHHHHHHH CS
         Homeobox   1 rrkRttftkeqleeLeelFeknrypsaeereeLAkklgLterqVkvWFqNrRakek 56 
                      +++ +++t+ q++eLe++F+++++p+ ++r+eL++ l+L+  qVk+WFqN+R+++k
  Carubv10000300m  62 KKRYHRHTQRQIQELESFFKECPHPDDKQRKELSRDLNLEPLQVKFWFQNKRTQMK 117
                      688999***********************************************998 PP
2START221.52.7e-692524721206
                      HHHHHHHHHHHHHHHHC-TT-EEEE...EXCCTTEEEEEEESSS......SCEEEEEEEECCSCHHHHHHHHHCCCGGCT-TT-S....EEEEE CS
            START   1 elaeeaaqelvkkalaeepgWvkss...esengdevlqkfeeskv.....dsgealrasgvvdmvlallveellddkeqWdetla....kaetl 82 
                      ela +a++elv++a+a++p+Wv+     e++n++e+ ++f+++ +      ++ea+r+s+vv+m++ +lve+l+d++ qW+  +     +a tl
  Carubv10000300m 252 ELAVAAMEELVRMAQAGDPLWVSTDnsiEILNEEEYFRTFPRGIGpkplgLRSEASRESAVVIMNHINLVEILMDVN-QWSCIFSgivsRALTL 344
                      57899******************99999**************999********************************.**************** PP

                      EEECTT......EEEEEEEEXXTTXX-SSX.EEEEEEEEEEE.TTS-EEEEEEEEE-TTS--.-TTSEE-EESSEEEEEEEECTCEEEEEEEE- CS
            START  83 evissg......galqlmvaelqalsplvp.RdfvfvRyirqlgagdwvivdvSvdseqkppesssvvRaellpSgiliepksnghskvtwveh 169
                      ev+s+g      galq+m+ae+q++splvp R+ +fvRy++q+++g+w++vdvS+ds ++ +   ++ R +++pSg+li++++ng+skvtw+eh
  Carubv10000300m 345 EVLSTGvagnynGALQVMTAEFQVPSPLVPtRENYFVRYCKQHSDGSWAVVDVSLDSLRPST---PILRTRRRPSGCLIQELPNGYSKVTWIEH 435
                      ***********************************************************976...7**************************** PP

                      EE--SSXXHHHHHHHHHHHHHHHHHHHHHHTXXXXXX CS
            START 170 vdlkgrlphwllrslvksglaegaktwvatlqrqcek 206
                      +++++r++h+++++lv+sgla+gak+wvatl+rqce+
  Carubv10000300m 436 MEVDDRSVHNMYKPLVHSGLAFGAKRWVATLERQCER 472
                      ***********************************97 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:1.10.10.605.2E-2342117IPR009057Homeodomain-like
SuperFamilySSF466891.09E-1851119IPR009057Homeodomain-like
PROSITE profilePS5007116.95759119IPR001356Homeobox domain
SMARTSM003891.0E-1760123IPR001356Homeobox domain
CDDcd000863.60E-1862120No hitNo description
PfamPF000463.7E-1762117IPR001356Homeobox domain
PROSITE patternPS00027094117IPR017970Homeobox, conserved site
PROSITE profilePS5084845.48243475IPR002913START domain
SuperFamilySSF559612.75E-36245474No hitNo description
CDDcd088759.15E-127247471No hitNo description
SMARTSM002342.0E-77252472IPR002913START domain
PfamPF018521.6E-58253472IPR002913START domain
Gene3DG3DSA:3.30.530.202.0E-7351472IPR023393START-like domain
SuperFamilySSF559616.73E-26491730No hitNo description
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006355Biological Processregulation of transcription, DNA-templated
GO:0009845Biological Processseed germination
GO:0009913Biological Processepidermal cell differentiation
GO:0048497Biological Processmaintenance of floral organ identity
GO:0048825Biological Processcotyledon development
GO:0005634Cellular Componentnucleus
GO:0008289Molecular Functionlipid binding
GO:0043565Molecular Functionsequence-specific DNA binding
Sequence ? help Back to Top
Protein Sequence    Length: 746 aa     Download sequence    Send to blast
MYHPNMFESH HMFDMTPKST SDNDLGITGS REDDFETKSG AEVTTENPGE ELQDPNQRPN  60
KKKRYHRHTQ RQIQELESFF KECPHPDDKQ RKELSRDLNL EPLQVKFWFQ NKRTQMKAQS  120
ERHENQILKS DNDKLRAENN RYKEALSNAT CPNCGGPAAI GEMSFDEQHL RIENARLREE  180
IDRISAIAAK YVGKPLGTSF APLAIHAPSR SLDLEVGNFG NQTGFGGDMY GTGDILRSVS  240
IPSETDKPII VELAVAAMEE LVRMAQAGDP LWVSTDNSIE ILNEEEYFRT FPRGIGPKPL  300
GLRSEASRES AVVIMNHINL VEILMDVNQW SCIFSGIVSR ALTLEVLSTG VAGNYNGALQ  360
VMTAEFQVPS PLVPTRENYF VRYCKQHSDG SWAVVDVSLD SLRPSTPILR TRRRPSGCLI  420
QELPNGYSKV TWIEHMEVDD RSVHNMYKPL VHSGLAFGAK RWVATLERQC ERLASSMANN  480
IPGDLSVITS PEGRKSMLKL AERMVMSFCS GVGASTAHAW TTMSTTGSDD VRVMTRKSMD  540
DPGRPPGIVL SAATSFWIPV APKRVFDFLR DENSRKEWDI LSNGGMVQEM AHIANGREPG  600
NCVSLLRVNS GNSSQSNMLI LQESCTDASG SYVIYAPVDI VAMNVVLSGG DPDYVALLPS  660
GFAILPDGSV GGGDGNHQEV VSSTSAGSCG GSLLTVAFQI LVDSVPTAKL SLGSVATVNS  720
LIKCTVERIK AAVACDAGGG GGGGA*
Functional Description ? help Back to Top
Source Description
UniProtProbable transcription factor that binds to the L1 box DNA sequence 5'-TAAATG[CT]A-3'. Plays a role in maintaining the identity of L1 cells, possibly by interacting with their L1 box or other target-gene promoters. Functionally redundant to ATML1. {ECO:0000269|PubMed:12505995}.
Cis-element ? help Back to Top
SourceLink
PlantRegMapCarubv10000300m
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAF4245600.0AF424560.1 Arabidopsis thaliana AT4g04890/T1J1_3 mRNA, complete cds.
GenBankAY0625750.0AY062575.1 Arabidopsis thaliana Unknown protein (At4g04890; T1J1.3) mRNA, complete cds.
GenBankBT0001440.0BT000144.1 Arabidopsis thaliana Unknown protein (At4g04890) mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_023636874.10.0homeobox-leucine zipper protein PROTODERMAL FACTOR 2
RefseqXP_023636875.10.0homeobox-leucine zipper protein PROTODERMAL FACTOR 2
SwissprotQ93V990.0PDF2_ARATH; Homeobox-leucine zipper protein PROTODERMAL FACTOR 2
TrEMBLR0FD460.0R0FD46_9BRAS; Uncharacterized protein
STRINGXP_006287129.10.0(Capsella rubella)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM49128149
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT4G04890.10.0protodermal factor 2
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. Ding Y, et al.
    Four distinct types of dehydration stress memory genes in Arabidopsis thaliana.
    BMC Plant Biol., 2013. 13: p. 229
    [PMID:24377444]