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 GSBRNA2T00141598001
Common NameGSBRNA2T00141598001
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: 894aa    MW: 98725.6 Da    PI: 8.734
Description Trihelix family protein
Gene Model
Gene Model ID Type Source Coding Sequence
GSBRNA2T00141598001genomeGenoscopeView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1trihelix62.21.2e-19801881186
             trihelix   1 rWtkqevlaLiearremeerlrrgklkkplWeevskkmrergferspkqCkekwenlnkrykkikegekkrtsessstcpyfdqle 86 
                          +W+ +ev++ i++r e+++r++  k +++lWee+s++++++g++rsp qCk+ w +l ++y+++k+ e+++     ++++++++++
  GSBRNA2T00141598001 801 KWKPEEVKKVIRMRGELHSRFQVVKGRMALWEEISSNLSAEGINRSPGQCKSLWASLIQKYEECKADERSK-----TSWSHYEDMN 881
                          7********************************************************************95.....35999**997 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:3.60.15.109.9E-68107357IPR001279Metallo-beta-lactamase
SuperFamilySSF562812.75E-72108522IPR001279Metallo-beta-lactamase
SMARTSM008495.1E-25120317IPR001279Metallo-beta-lactamase
PfamPF127068.5E-11132267IPR001279Metallo-beta-lactamase
PfamPF075214.9E-7462494IPR011108Zn-dependent metallo-hydrolase, RNA specificity domain
PROSITE profilePS500908.107794858IPR017877Myb-like domain
Gene3DG3DSA:1.10.10.602.6E-5795860IPR009057Homeodomain-like
PfamPF138376.9E-17799882No hitNo description
CDDcd122034.38E-22800865No hitNo description
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0003677Molecular FunctionDNA binding
Sequence ? help Back to Top
Protein Sequence    Length: 894 aa     Download sequence    Send to blast
MKPATSLYGS FSSSIYFDAR RPVPTPSKMA AFSALSLSPY TFTFRQSSRV RSTISCSVTS  60
PPASSGTSSS SKAPRRRSGR LEGAGKSMED SVKRKMEQFY EGTDGPPLRV LPIGGLGEIG  120
MNCMLVGNYD RYILIDAGIM FPDYDDPGVQ KIMPDTGFIR RWKHKIEAVV ITHGHEDHIG  180
ALPWVIPALD SNTPIFASSF TMELIKKRLK EHGIFVQSRL KTFNTRRRFM AGPFEIEPIT  240
VTHSIPDCSG LVLRCADGNI LHTGDWKIDE APLDGKVFDR EALEELSKEG VTLMMSDSTN  300
VLSPGRTTSE KVVADALVRN VMAAKGRVIT TQFASNIHRL GSIKAAADLT GRKLVFVGMS  360
LRTYLEAAWK DGKAPIDPST LVKVEDIEAY SPKDLLIVTT GSQAEPRAAL NLASYGSSHA  420
FKLTKEDIIL YSAKVIPGNE SRVMKMMNRL ADIGPKIVMG KNEMLHTSGH AYRGELEEVL  480
KIVKPQHFLP IHGELLFLKE HELLGKSTGI RHTTVIKNGE MLGVSHLRNR RVLSNGFSSL  540
GRENLQLMYS DGDKAFGTAS ELCIDERLRI SSDGIIVLSM EIMRPGASEN ALKGKIRITT  600
RCMWLDKGRL LDALHKAAHA ALSSCPVNCP LSHMERTVSE VLRKIVRKYS GKRPEVIAIA  660
MENPMAVRAD EVSARMSGDP NLGSGVAALR KVVEGNNKRN RTKKTQSQED EIVDSSAGIL  720
AEEGTASSTY TEGAEDVPVR SSSEESDDFW KSFINPPSPP SPGVTENAKT EDSENSREEE  780
EEDDTSDSQT KSSTKRVRRN KWKPEEVKKV IRMRGELHSR FQVVKGRMAL WEEISSNLSA  840
EGINRSPGQC KSLWASLIQK YEECKADERS KTSWSHYEDM NNILSELDTP APK*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5a0t_A4e-8710866219560RIBONUCLEASE J
5a0t_B4e-8710866219560RIBONUCLEASE J
5a0v_A4e-8710866219560RIBONUCLEASE J
5a0v_B4e-8710866219560RIBONUCLEASE J
Search in ModeBase
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Bna.6240.0flower
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
PlantRegMapGSBRNA2T00141598001
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. 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]