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 Carubv10008304m
Common NameCARUB_v10008304mg
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: 841aa    MW: 92336.8 Da    PI: 6.5054
Description HD-ZIP family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Carubv10008304mgenomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1Homeobox58.98.6e-192078357
                     --SS--HHHHHHHHHHHHHSSS--HHHHHHHHHHC....TS-HHHHHHHHHHHHHHHHC CS
         Homeobox  3 kRttftkeqleeLeelFeknrypsaeereeLAkkl....gLterqVkvWFqNrRakekk 57
                     k  ++t+eq+e+Le++++++++ps  +r++L +++    +++ rq+kvWFqNrR +ek+
  Carubv10008304m 20 KYVRYTPEQVEALERVYAECPKPSSLRRQQLIRECpilcNIEPRQIKVWFQNRRCREKQ 78
                     5678*****************************************************97 PP
2START172.23.4e-541693772205
                      HHHHHHHHHHHHHHHC-TT-EEEEEXCCTTEEEEEEESSS.SCEEEEEEEECCSCHHHHHHHHHCCCGGCT-TT-SEEEEEEEECTT..EEEEE CS
            START   2 laeeaaqelvkkalaeepgWvkssesengdevlqkfeeskvdsgealrasgvvdmvlallveellddkeqWdetlakaetlevissg..galql 93 
                      +aee+++e++ ka  ++  Wv++  +++g++++ +++ s+++sg a+ra+g+v  +++  v+e+l+d++ W ++++++etl+vi +g  g+++l
  Carubv10008304m 169 IAEETLAEFLCKARGTAVDWVQMIGMKPGPDSIGIVAVSRNCSGIAARACGLVSLEPM-KVAEILKDRPSWFRDCRSVETLNVIPTGngGTIEL 261
                      7899******************************************************.8888888888************************* PP

                      EEEXXTTXX-SSX.EEEEEEEEEEE.TTS-EEEEEEEEE-TTS--....-TTSEE-EESSEEEEEEEECTCEEEEEEEE-EE--SSXXHHHHHH CS
            START  94 mvaelqalsplvp.RdfvfvRyirqlgagdwvivdvSvdseqkppe...sssvvRaellpSgiliepksnghskvtwvehvdlkgrlphwllrs 183
                       +++ +a+++l++ Rdf+++Ry+ +l++g++v++++S++s +  p+   sss+vRa++l Sg+li+p+++g+s + +v+hvdl+ ++++++lr+
  Carubv10008304m 262 VNTQIYAPTTLAAaRDFWTLRYSTTLEDGSYVVCERSLTSATGGPNgpmSSSFVRAKMLSSGFLIRPCDGGGSIIQIVDHVDLDVSSVPEVLRP 355
                      *********************************************99*********************************************** PP

                      HHHHHHHHHHHHHHHHTXXXXX CS
            START 184 lvksglaegaktwvatlqrqce 205
                      l++s+ + ++k++va+l++ ++
  Carubv10008304m 356 LYESSKILAQKMTVAALRHVRQ 377
                      *****************98765 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PROSITE profilePS5007115.4511579IPR001356Homeobox domain
SMARTSM003894.2E-161783IPR001356Homeobox domain
SuperFamilySSF466891.41E-161981IPR009057Homeodomain-like
CDDcd000865.82E-172080No hitNo description
PfamPF000462.5E-162178IPR001356Homeobox domain
Gene3DG3DSA:1.10.10.608.0E-192278IPR009057Homeodomain-like
CDDcd146863.21E-672111No hitNo description
PROSITE profilePS5084826.074159387IPR002913START domain
CDDcd088753.41E-69163379No hitNo description
Gene3DG3DSA:3.30.530.204.1E-20168373IPR023393START-like domain
SMARTSM002341.1E-51168378IPR002913START domain
SuperFamilySSF559619.06E-35168380No hitNo description
PfamPF018522.2E-51169377IPR002913START domain
PfamPF086702.6E-49693839IPR013978MEKHLA
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0009855Biological Processdetermination of bilateral symmetry
GO:0009880Biological Processembryonic pattern specification
GO:0009944Biological Processpolarity specification of adaxial/abaxial axis
GO:0010072Biological Processprimary shoot apical meristem specification
GO:0080060Biological Processintegument development
GO:0005634Cellular Componentnucleus
GO:0003677Molecular FunctionDNA binding
GO:0008289Molecular Functionlipid binding
Sequence ? help Back to Top
Protein Sequence    Length: 841 aa     Download sequence    Send to blast
MMAHSMDDRD SPDKGFDSGK YVRYTPEQVE ALERVYAECP KPSSLRRQQL IRECPILCNI  60
EPRQIKVWFQ NRRCREKQRK ESARLQTVNR KLSAMNKLLM EENDRLQKQV SHLVYENGFM  120
KHRIHTASGT TTDNSCESVV VSGQQRQQQN PTHQHPQRDA NNPANLLSIA EETLAEFLCK  180
ARGTAVDWVQ MIGMKPGPDS IGIVAVSRNC SGIAARACGL VSLEPMKVAE ILKDRPSWFR  240
DCRSVETLNV IPTGNGGTIE LVNTQIYAPT TLAAARDFWT LRYSTTLEDG SYVVCERSLT  300
SATGGPNGPM SSSFVRAKML SSGFLIRPCD GGGSIIQIVD HVDLDVSSVP EVLRPLYESS  360
KILAQKMTVA ALRHVRQIAQ ETSGEVQYSG GRQPAVLRTF SQRLCRGFND AVNGFADDGW  420
SPMSSDGAED ITIMINSSSA KFAGSQYGSS FLPSFGSGVL CAKASMLLQN VPPLVLIRFL  480
REHRAEWADY GVDAYSAASL RATPFAVPCV RTGGFPSNQV ILPLAQTLEH EEFLEVVRLG  540
GHAYSPEDMG LSRDMYLLQL CSGVDENVVG GCAQLVFAPI DESFADDAPL LPSGFRVIPL  600
EQKTNPNDHQ SASRTRDLAS SLDGSTKTDS ETNSRLVLTI AFQFTFDNHS RDNVATMARQ  660
YVRNVVGSIQ RVALAITPRP GSMQLPTSPE ALTLVRWITR SYSTHTGADL FGSDSQSCGG  720
DTLLKLLWNH SDAILCCSLK TNASPVFTFA NQAGLDMLET TLVALQDIML DKTLDDSGRK  780
ALCSEFAKIM QQGYANLPAG ICMSSMGRPV SYEQATVWKV VDDNESNHCL AFILVNWSFV  840
*
Functional Description ? help Back to Top
Source Description
UniProtProbable transcription factor involved in the determination of adaxial-abaxial polarity in ovule primordium. Specifies adaxial leaf fates. Binds to the DNA sequence 5'-GTAAT[GC]ATTAC-3'. {ECO:0000269|PubMed:11395776, ECO:0000269|PubMed:15598805, ECO:0000269|PubMed:17900520, ECO:0000269|PubMed:9747806}.
Binding Motif ? help Back to Top
Motif ID Method Source Motif file
MP00170DAPTransfer from AT1G30490Download
Motif logo
Cis-element ? help Back to Top
SourceLink
PlantRegMapCarubv10008304m
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: By auxin. Repressed by miR165 and miR166. {ECO:0000269|PubMed:14999284, ECO:0000269|PubMed:16033795, ECO:0000269|PubMed:17237362}.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieveRetrieve
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAJ4409670.0AJ440967.1 Arabidopsis thaliana mRNA for homeodomain-leucine zipper protein (hb9 gene).
GenBankAK2265700.0AK226570.1 Arabidopsis thaliana mRNA for HD-Zip protein, complete cds, clone: RAFL07-12-P11.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_006306764.10.0homeobox-leucine zipper protein ATHB-9
SwissprotO042920.0ATBH9_ARATH; Homeobox-leucine zipper protein ATHB-9
TrEMBLR0GUM60.0R0GUM6_9BRAS; Uncharacterized protein
STRINGCagra.1508s0156.1.p0.0(Capsella grandiflora)
STRINGXP_006306764.10.0(Capsella rubella)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM42562653
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT1G30490.10.0HD-ZIP family protein
Publications ? help Back to Top
  1. Jia X, et al.
    Functional plasticity of miR165/166 in plant development revealed by small tandem target mimic.
    Plant Sci., 2015. 233: p. 11-21
    [PMID:25711809]
  2. Yamada T,Sasaki Y,Hashimoto K,Nakajima K,Gasser CS
    CORONA, PHABULOSA and PHAVOLUTA collaborate with BELL1 to confine WUSCHEL expression to the nucellus in Arabidopsis ovules.
    Development, 2016. 143(3): p. 422-6
    [PMID:26700684]
  3. Wójcik AM,Nodine MD,Gaj MD
    miR160 and miR166/165 Contribute to the LEC2-Mediated Auxin Response Involved in the Somatic Embryogenesis Induction in Arabidopsis.
    Front Plant Sci, 2017. 8: p. 2024
    [PMID:29321785]