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_013629533.1
Organism
Brassica oleracea
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 Trihelix
Protein Properties Length: 904aa    MW: 99904.9 Da    PI: 8.7327
Description Trihelix family protein
Gene Model
Gene Model ID Type Source Coding Sequence
XP_013629533.1genomeNCBIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1trihelix62.21.2e-19812892186
        trihelix   1 rWtkqevlaLiearremeerlrrgklkkplWeevskkmrergferspkqCkekwenlnkrykkikegekkrtsessstcpyfdqle 86 
                     +W+ +ev++ i++r e+++r++  k +++lWee+s++++++g++rsp qCk+ w +l ++y+++k+ e+++     ++++++++++
  XP_013629533.1 812 KWKPEEVKKVIRMRGELHSRFQVVKGRMALWEEISSNLSAEGINRSPGQCKSLWASLIQKYEECKADERSK-----TSWSHYEDMN 892
                     7********************************************************************95.....35999**997 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:3.60.15.101.0E-67110360IPR001279Metallo-beta-lactamase
SuperFamilySSF562812.97E-72111525IPR001279Metallo-beta-lactamase
SMARTSM008495.1E-25123320IPR001279Metallo-beta-lactamase
PfamPF127068.6E-11135270IPR001279Metallo-beta-lactamase
PfamPF075214.9E-7465497IPR011108Zn-dependent metallo-hydrolase, RNA specificity domain
PROSITE profilePS500908.107805869IPR017877Myb-like domain
Gene3DG3DSA:1.10.10.602.6E-5806871IPR009057Homeodomain-like
PfamPF138377.0E-17810893No hitNo description
CDDcd122035.28E-22811876No hitNo description
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0009658Biological Processchloroplast organization
GO:0009942Biological Processlongitudinal axis specification
GO:0060918Biological Processauxin transport
GO:0009507Cellular Componentchloroplast
GO:0003677Molecular FunctionDNA binding
Sequence ? help Back to Top
Protein Sequence    Length: 904 aa     Download sequence    Send to blast
MKPAASLHGS FSYPSSSIYF DARRPVTTPS KMAAFSALSL SPYTFTFRQS SRVRSTISCS  60
VTSPPASSGT SSSSKAPRRR SGRLEGAGKS MEDSVKRKME QFYEGTDGPP LRVLPIGGLG  120
EIGMNCMLVG NYDRYILIDA GIMFPDYDDP GVQKIMPDTG FIRRWKHKIE AVVITHGHED  180
HIGALPWVIP ALDSNTPIFA SSFTMELIKK RLKEHGIFVQ SRLKTFNTRR RFMAGPFEIE  240
PITVTHSIPD CSGLVLRCAD GNILHTGDWK IDEAPLDGKV FDREALEELS KEGVTLMMSD  300
STNVLSPGRT TSEKVVADAL VRNVMAAKGR VITTQFASNI HRLGSIKAAA DLTGRKLVFV  360
GMSLRTYLEA AWKDGKAPID PSSLVKVEDI EAYSPKDLLI VTTGSQAEPR AALNLASYGS  420
SHAFKLTKED IILYSAKVIP GNESRVMKMM NRLADIGPKI VMGKNEMLHT SGHAYRGELE  480
EVLKIVKPQH FLPIHGELLF LKEHELLGKS TGIRHTTVIK NGEMLGVSHL RNRRVLSNGF  540
SSLGRENLQL MYSDGDKAFG TASELCIDER LRISSDGIIV LSMEIMRPGA SENALKGKIR  600
ITTRCMWLDK GRLLDALHKA AHAALSSCPV NCPLSHMERT VSEVLRKIVR KYSGKRPEVI  660
AIAMENPMAV RADEVNARMS GDPNLGSGVA ALRKVVEGNN KRNRTKKTQS QEDEIIDSSA  720
GLLAEEGTAS STYTEGAEDV PVRSSSEESD DFWKSFINPP SPPSPGVTEN VDKLTDAEAK  780
TEDSENSREE KEDDDTSDSQ TKSSTKRVRR NKWKPEEVKK VIRMRGELHS RFQVVKGRMA  840
LWEEISSNLS AEGINRSPGQ CKSLWASLIQ KYEECKADER SKTSWSHYED MNNILSELDT  900
PAPK
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5a0t_A4e-8711166519560RIBONUCLEASE J
5a0t_B4e-8711166519560RIBONUCLEASE J
5a0v_A4e-8711166519560RIBONUCLEASE J
5a0v_B4e-8711166519560RIBONUCLEASE J
Search in ModeBase
Expression -- Description ? help Back to Top
Source Description
UniprotDEVELOPMENTAL STAGE: During the early stages of embryo development, first observed at the transition stage. In the heart and torpedo stages, predominantly present in the upper part of embryos. In seedlings, strongly expressed in shoot meristems, hypocotyls, in the vascular bundles of cotyledons, and in the veins of mature leaves. In reproductive organs, detected in inflorescences, especially in sepals, filaments, and stigmas, as well as in mature siliques and seeds. {ECO:0000269|PubMed:25871650}.
UniprotTISSUE SPECIFICITY: Moslty expressed in inflorescences, seedlings, leaves, flowers and flower buds, and, to a lower extent, in stems, siliques and roots. {ECO:0000269|PubMed:25871650}.
Functional Description ? help Back to Top
Source Description
UniProtEssential protein required during embryogenesis, especially in initiating and maintaining the organization of shoot apical meristems (SAMs), cotyledons, and hypocotyls (PubMed:15266054, PubMed:25871650). Involved in auxin-mediated pathways during embryogenesis (PubMed:25871650). RNase that has both endonuclease and 5'-3' exonuclease activities. Involved in RNA surveillance to prevent overaccumulation of antisense RNA (PubMed:22033332). Probably involved in maturation of rRNA and in some organisms also mRNA maturation and/or decay (By similarity). {ECO:0000250|UniProtKB:Q72JJ7, ECO:0000269|PubMed:15266054, ECO:0000269|PubMed:22033332, ECO:0000269|PubMed:25871650}.
Cis-element ? help Back to Top
SourceLink
PlantRegMapXP_013629533.1
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: By light. {ECO:0000269|PubMed:25871650}.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAK2212720.0AK221272.1 Arabidopsis thaliana mRNA for putative protein, complete cds, clone: RAFL24-15-P14.
GenBankBT0042100.0BT004210.1 Arabidopsis thaliana clone RAFL16-01-C03 (R50172) unknown protein (At5g63420) mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_013629533.10.0PREDICTED: ribonuclease J
SwissprotQ84W560.0RNJ_ARATH; Ribonuclease J
TrEMBLA0A0D3BFF60.0A0A0D3BFF6_BRAOL; Uncharacterized protein
STRINGBo3g103450.10.0(Brassica oleracea)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM95392634
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT5G63420.10.0Trihelix family protein
Publications ? help Back to Top
  1. Bryant N,Lloyd J,Sweeney C,Myouga F,Meinke D
    Identification of nuclear genes encoding chloroplast-localized proteins required for embryo development in Arabidopsis.
    Plant Physiol., 2011. 155(4): p. 1678-89
    [PMID:21139083]
  2. Halpert M,Liveanu V,Glaser F,Schuster G
    The Arabidopsis chloroplast RNase J displays both exo- and robust endonucleolytic activities.
    Plant Mol. Biol., 2019. 99(1-2): p. 17-29
    [PMID:30511330]