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 GSBRNA2T00073135001
Common NameGSBRNA2T00073135001
Organism
Brassica napus
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: 1150aa    MW: 126907 Da    PI: 9.2364
Description Trihelix family protein
Gene Model
Gene Model ID Type Source Coding Sequence
GSBRNA2T00073135001genomeGenoscopeView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1trihelix61.81.6e-19811891186
             trihelix   1 rWtkqevlaLiearremeerlrrgklkkplWeevskkmrergferspkqCkekwenlnkrykkikegekkrtsessstcpyfdqle 86 
                          +W+ +ev++ i++r e+++r++  k +++lWee+s++++++g++rsp qCk+ w +l ++y+++k+ e+++     ++++++++++
  GSBRNA2T00073135001 811 KWKPEEVKKVIRMRGELHSRFQVVKGRMALWEEISSNLSAEGINRSPGQCKSLWASLIQKYEECKADERSK-----TSWSHYEDMN 891
                          7********************************************************************95.....35999**997 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:3.60.15.101.6E-67111361IPR001279Metallo-beta-lactamase
SuperFamilySSF562815.05E-72112526IPR001279Metallo-beta-lactamase
SMARTSM008495.1E-25124321IPR001279Metallo-beta-lactamase
PfamPF127061.2E-10136271IPR001279Metallo-beta-lactamase
PfamPF075216.5E-7466498IPR011108Zn-dependent metallo-hydrolase, RNA specificity domain
PROSITE profilePS500908.107804868IPR017877Myb-like domain
Gene3DG3DSA:1.10.10.603.5E-5805870IPR009057Homeodomain-like
PfamPF138379.5E-17809892No hitNo description
CDDcd122033.56E-22810875No hitNo description
Gene3DG3DSA:3.30.1200.102.6E-2510491145IPR003746Protein of unknown function DUF167
SuperFamilySSF697861.57E-1710501136IPR003746Protein of unknown function DUF167
HamapMF_0063414.53810571145IPR003746Protein of unknown function DUF167
SMARTSM011528.3E-1710571133IPR003746Protein of unknown function DUF167
PfamPF025941.4E-1610611131IPR003746Protein of unknown function DUF167
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: 1150 aa     Download sequence    Send to blast
MKPAASLHGY PSSPIYFDAR RPVPTPPSKM AAFSALSLSP YSFTFRQSSP VRSTVSCSVT  60
SPPASSGTSS SSSSNKTPRR RSGRLEGAGK SMEDSVKRKM EQFYEGTDGP PLRVLPIGGL  120
GEIGMNCMLV GNYDRYILID AGIMFPDYDD PGVQKIMPDT GFIRRWKHKI EAVVITHGHE  180
DHIGALPWVI PALDSNTPIF ASSFTMELIK KRLKEHGIFV QSRLKTFNTR RRFMAGPFEI  240
EPITVTHSIP DCSGLVLRCA DGNILHTGDW KIDEAPLDGK VFDREALEEL SKEGVTLMMS  300
DSTNVLSPGR TTSEKVVADA LVRNVMAAKG RVITTQFASN IHRLGSIKAA ADLTGRKLVF  360
VGMSLRTYLE AAWKDGKAPI DPSSLVKVED IEAYSPKDLL IVTTGSQAEP RAALNLASYG  420
SSHAFKLTKE DIILYSAKVI PGNESRVMKM MNRLADIGPK IVMGKNEMLH TSGHAYRGEL  480
EEVLKIVKPQ HFLPIHGELL FLKEHELLGK STGIRHTTVI KNGEMLGVSH LRNRRVLSNG  540
FSSLGRENLQ LMYNDGDKAF GTASELCIDE RLRISSDGII VLSMEIMRPG ASENTLKGKI  600
RITTRCMWLD KGRLLDALHK AAHAALSSCP VNCPLSHMER TVSEVLRKIV RKYSGKRPEV  660
IAIAMENPMA VRADEVSARM SGDPNLGSGV AALRKVVEGN NKRNRTKKAP SQEEAGEIID  720
SSAGLLGEVE TASSSYTEGA EDVPVRSSSE ESDDFWKSFI NPSSPPSPDE TKNVDKSPDA  780
EDSESSSEEE DDDNTSDSQT KSSTKRVRRN KWKPEEVKKV IRMRGELHSR FQVVKGRMAL  840
WEEISSNLSA EGINRSPGQC KSLWASLIQK YEECKADERS KTSWSHYEDM NNILSELDTP  900
APKKKKALSQ IGGEFGKIEE ERCRRERRIR TRARTRRRKD PTLISSFTTA STVVLMSSSL  960
KMPKRKTDRS SVLDKKKHLA RLNVSEGGKV LLKRGEGKLE RQFRMNCIGC ELFVCYRADE  1020
SLETAAFVYI VDGALSAVAA ETNPQDAPVP PCISQLDGGL VQVAIEVEDR AQRSAITRVN  1080
ADDVRVTIAA PAARGEANNE LLEFMGRVLG LRLSQMTLQR GWNSKSKLLV VEDLSARQVY  1140
EKLLEAVVS*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5a0t_A4e-8511266619560RIBONUCLEASE J
5a0t_B4e-8511266619560RIBONUCLEASE J
5a0v_A4e-8511266619560RIBONUCLEASE J
5a0v_B4e-8511266619560RIBONUCLEASE J
Search in ModeBase
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
1927937RIRTRARTRRR
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Bna.86280.0microspore-derived embryo| seed
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
PlantRegMapGSBRNA2T00073135001
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_009150395.10.0PREDICTED: uncharacterized protein LOC103873754
RefseqXP_013642983.10.0uncharacterized protein LOC106347909
SwissprotQ84W560.0RNJ_ARATH; Ribonuclease J
TrEMBLA0A078HV120.0A0A078HV12_BRANA; BnaA06g22690D 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. Chalhoub B, et al.
    Plant genetics. Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome.
    Science, 2014. 345(6199): p. 950-3
    [PMID:25146293]
  3. 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]