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 Carubv10025876m
Common NameCARUB_v10025876mg
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: 844aa    MW: 92336 Da    PI: 5.9286
Description HD-ZIP family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Carubv10025876mgenomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1Homeobox56.45e-182583357
                     --SS--HHHHHHHHHHHHHSSS--HHHHHHHHHHC....TS-HHHHHHHHHHHHHHHHC CS
         Homeobox  3 kRttftkeqleeLeelFeknrypsaeereeLAkkl....gLterqVkvWFqNrRakekk 57
                     k  ++t+eq+e+Le++++++++ps  +r++L +++    +++ +q+kvWFqNrR ++k+
  Carubv10025876m 25 KYVRYTAEQVEALERVYAECPKPSSLRRQQLIRECsilaNIEPKQIKVWFQNRRCRDKQ 83
                     56789***************************************************996 PP
2START153.71.6e-481613662202
                      HHHHHHHHHHHHHHHC-TT-EEEEEXCCTTEEEEEEESSS.SCEEEEEEEECCSCHHHHHHHHHCCCGGCT-TT-SEEEEEEEECTT..EEEEE CS
            START   2 laeeaaqelvkkalaeepgWvkssesengdevlqkfeeskvdsgealrasgvvdmvlallveellddkeqWdetlakaetlevissg..galql 93 
                      +aee+++e+++ka+ ++  Wv+++ +++g++++ +f+ s+ +sg a+ra+g+v  +++   +e+l+d++ W +++++ e+      g  g+++l
  Carubv10025876m 161 IAEETLAEFLSKATGTAVDWVQMPGMKPGPDSVGIFAISQRCSGVAARACGLVSLEPM-KIAEILKDRPSWFRDCRSLEVFTMFPAGngGTIEL 253
                      7899******************************************************.7777777777***********999999999***** PP

                      EEEXXTTXX-SSX.EEEEEEEEEEE.TTS-EEEEEEEEE-TTS--....-TTSEE-EESSEEEEEEEECTCEEEEEEEE-EE--SSXXHHHHHH CS
            START  94 mvaelqalsplvp.RdfvfvRyirqlgagdwvivdvSvdseqkppe...sssvvRaellpSgiliepksnghskvtwvehvdlkgrlphwllrs 183
                       +++++a+++l+p Rdf+++Ry+ +l  g++v++++S++     p+    s++vRae+l Sg+li+p+++g+s +++v+h +l++++++ +lr+
  Carubv10025876m 254 VYMQTYAPTTLAPaRDFWTLRYTTSLDNGSFVVCERSLSGSGAGPNaasASQFVRAEMLSSGYLIRPCDGGGSIIHIVDHLNLEAWSVPDVLRP 347
                      ***************************************999999989999******************************************* PP

                      HHHHHHHHHHHHHHHHTXX CS
            START 184 lvksglaegaktwvatlqr 202
                      l++s+ + ++k++ ++l++
  Carubv10025876m 348 LYESSKVVAQKMTISALRY 366
                      *************999987 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PROSITE profilePS5007115.3052084IPR001356Homeobox domain
SuperFamilySSF466891.11E-162187IPR009057Homeodomain-like
SMARTSM003892.0E-162288IPR001356Homeobox domain
CDDcd000866.23E-162585No hitNo description
PfamPF000461.3E-152683IPR001356Homeobox domain
Gene3DG3DSA:1.10.10.603.0E-182780IPR009057Homeodomain-like
CDDcd146863.26E-677116No hitNo description
Gene3DG3DSA:1.20.5.1706.1E-481130No hitNo description
PROSITE profilePS5084827.323151379IPR002913START domain
CDDcd088751.64E-67155371No hitNo description
Gene3DG3DSA:3.30.530.201.3E-19160365IPR023393START-like domain
SuperFamilySSF559617.28E-35160372No hitNo description
SMARTSM002341.8E-38160370IPR002913START domain
PfamPF018523.2E-46161367IPR002913START domain
PfamPF086703.1E-49695842IPR013978MEKHLA
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0009855Biological Processdetermination of bilateral symmetry
GO:0009944Biological Processpolarity specification of adaxial/abaxial axis
GO:0009956Biological Processradial pattern formation
GO:0010014Biological Processmeristem initiation
GO:0010051Biological Processxylem and phloem pattern formation
GO:0010089Biological Processxylem development
GO:0030154Biological Processcell differentiation
GO:0005634Cellular Componentnucleus
GO:0008289Molecular Functionlipid binding
GO:0044212Molecular Functiontranscription regulatory region DNA binding
Sequence ? help Back to Top
Protein Sequence    Length: 844 aa     Download sequence    Send to blast
MEMAVANHHD RSSDSMNRHL DSSGKYVRYT AEQVEALERV YAECPKPSSL RRQQLIRECS  60
ILANIEPKQI KVWFQNRRCR DKQRKEASRL QSVNRKLSAM NKLLMEENDR LQKQVSQLVC  120
ENGYMKQQLT TVVTDASCDS AVTTPQHSLR DANSPAGLLS IAEETLAEFL SKATGTAVDW  180
VQMPGMKPGP DSVGIFAISQ RCSGVAARAC GLVSLEPMKI AEILKDRPSW FRDCRSLEVF  240
TMFPAGNGGT IELVYMQTYA PTTLAPARDF WTLRYTTSLD NGSFVVCERS LSGSGAGPNA  300
ASASQFVRAE MLSSGYLIRP CDGGGSIIHI VDHLNLEAWS VPDVLRPLYE SSKVVAQKMT  360
ISALRYIRQL AQESNGEVVY GLGRQPAVLR TFSQRLSRGF NDAVNGFGDD GWSTMHCDGA  420
EDIIVAINST KHLNNISNSL SFLGGVLCAK ASMLLQNVPP AVLIRFLREH RSEWADFNVD  480
AYSAATLKAG TFAYPGMRPT RFTGSQIIMP LGHTIEHEEM LEVVRLEGHS LAQEDAFMSR  540
DVHLLQICTG IDENAVGACS ELIFAPINEM FPDDAPLVPS GFRVIPVDAK TGDAQDLLTA  600
NHRTLDLTSS LEVGPSPENA SGNSTSSSSS SRCILTIAFQ FPFENNLQEN VAGMACQYVR  660
SVISSVQRVA MAISPSGISP SLGSKLSPGS PEAVTLAQWI SQSYNHHLGS ELLTIDSLGS  720
NDSVLKLLWD HQDAILCCSL KPQPVFMFAN QAGLDMLETT LVALQDITLE KIFDESGRKA  780
LCSDFAKLMQ QGFACLPSGI CVSTMGRHVS YEQAVAWKVF AASEDNNNNL HCLAFSFVNW  840
SFV*
Functional Description ? help Back to Top
Source Description
UniProtProbable transcription factor involved in the regulation of interfascicular fiber (cortical cells) and secondary xylem differentiation in the inflorescence stems. Required for lateral shoot meristems (LSMs) and flower meristems (FMs) initiation. May be involved in the determination of vascular patterning and organ polarity (PubMed:10559440, PubMed:11169198, PubMed:11402186, PubMed:15111711, PubMed:15598805, PubMed:7555701). Directly regulates the expression of AGO10, ZPR1, ZPR2, ZPR3 and ZPR4 (PubMed:22781836). Required to regulate adaxial-abaxial polarity and leaf axial patterning (PubMed:20807212). {ECO:0000269|PubMed:10559440, ECO:0000269|PubMed:11169198, ECO:0000269|PubMed:11402186, ECO:0000269|PubMed:15111711, ECO:0000269|PubMed:15598805, ECO:0000269|PubMed:20807212, ECO:0000269|PubMed:22781836, ECO:0000269|PubMed:7555701}.
Cis-element ? help Back to Top
SourceLink
PlantRegMapCarubv10025876m
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: By auxin. Repressed by ZPR and miR165. Induced by DOF5.1 (PubMed:20807212). {ECO:0000269|PubMed:15111711, ECO:0000269|PubMed:17237362, ECO:0000269|PubMed:20807212}.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAF1889940.0AF188994.1 Arabidopsis thaliana homeodomain-leucine zipper protein interfascicular fiberless 1 (IFL1) mRNA, complete cds.
GenBankAF2335920.0AF233592.1 Arabidopsis thaliana REVOLUTA mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_006280004.10.0homeobox-leucine zipper protein REVOLUTA
SwissprotQ9SE430.0REV_ARATH; Homeobox-leucine zipper protein REVOLUTA
TrEMBLR0EUU00.0R0EUU0_9BRAS; Uncharacterized protein
STRINGXP_006280004.10.0(Capsella rubella)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM47792754
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT5G60690.10.0HD-ZIP family protein
Publications ? help Back to Top
  1. Lian H,Li X,Liu Z,He Y
    HYL1 is required for establishment of stamen architecture with four microsporangia in Arabidopsis.
    J. Exp. Bot., 2013. 64(11): p. 3397-410
    [PMID:23918970]
  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]
  3. Baima S, et al.
    Negative feedback regulation of auxin signaling by ATHB8/ACL5-BUD2 transcription module.
    Mol Plant, 2014. 7(6): p. 1006-1025
    [PMID:24777988]
  4. 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]
  5. Roodbarkelari F,Du F,Truernit E,Laux T
    ZLL/AGO10 maintains shoot meristem stem cells during Arabidopsis embryogenesis by down-regulating ARF2-mediated auxin response.
    BMC Biol., 2015. 13: p. 74
    [PMID:26358077]
  6. Shi B, et al.
    Two-Step Regulation of a Meristematic Cell Population Acting in Shoot Branching in Arabidopsis.
    PLoS Genet., 2016. 12(7): p. e1006168
    [PMID:27398935]