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_009150395.1
Organism
Brassica rapa
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: 907aa    MW: 100034 Da    PI: 8.5061
Description Trihelix family protein
Gene Model
Gene Model ID Type Source Coding Sequence
XP_009150395.1genomeNCBIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1trihelix62.11.3e-19815895186
        trihelix   1 rWtkqevlaLiearremeerlrrgklkkplWeevskkmrergferspkqCkekwenlnkrykkikegekkrtsessstcpyfdqle 86 
                     +W+ +ev++ i++r e+++r++  k +++lWee+s++++++g++rsp qCk+ w +l ++y+++k+ e+++     ++++++++++
  XP_009150395.1 815 KWKPEEVKKVIRMRGELHSRFQVVKGRMALWEEISSNLSAEGINRSPGQCKSLWASLIQKYEECKADERSK-----TSWSHYEDMN 895
                     7********************************************************************95.....35999*9996 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-67112362IPR001279Metallo-beta-lactamase
SuperFamilySSF562812.97E-72113527IPR001279Metallo-beta-lactamase
SMARTSM008495.1E-25125322IPR001279Metallo-beta-lactamase
PfamPF127068.7E-11137272IPR001279Metallo-beta-lactamase
PfamPF075215.0E-7467499IPR011108Zn-dependent metallo-hydrolase, RNA specificity domain
PROSITE profilePS500908.107808872IPR017877Myb-like domain
Gene3DG3DSA:1.10.10.602.6E-5809874IPR009057Homeodomain-like
PfamPF138374.6E-17813897No hitNo description
CDDcd122033.54E-22814879No 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: 907 aa     Download sequence    Send to blast
MKPAASLHGY PSSPIYFDAR RPVPTPPSKM AAFSALSLSP YSFTFRQSSP VRSTVSCSVT  60
SPPASSGTSS SSSSSNKTPR RRSGRLEGAG KSMEDSVKRK MEQFYEGTDG PPLRVLPIGG  120
LGEIGMNCML VGNYDRYILI DAGIMFPDYD DPGVQKIMPD TGFIRRWKHK IEAVVITHGH  180
EDHIGALPWV IPALDSNTPI FASSFTMELI KKRLKEHGIF VQSRLKTFNT RRRFMAGPFE  240
IEPITVTHSI PDCSGLVLRC ADGNILHTGD WKIDEAPLDG KVFDREALEE LSKEGVTLMM  300
SDSTNVLSPG RTTSEKVVAD ALVRNVMAAK GRVITTQFAS NIHRLGSIKA AADLTGRKLV  360
FVGMSLRTYL EAAWKDGKAP IDPSSLVKVE DIEAYSPKDL LIVTTGSQAE PRAALNLASY  420
GSSHAFKLTK EDIILYSAKV IPGNESRVMK MMNRLADIGP KIVMGKNEML HTSGHAYRGE  480
LEEVLKIVKP QHFLPIHGEL LFLKEHELLG KSTGIRHTTV IKNGEMLGVS HLRNRRVLSN  540
GFSSLGRENL QLMYSDGDKA FGTASELCID ERLRISSDGI IVLSMEIMRP GASENTLKGK  600
IRITTRCMWL DKGRLLDALH KAAHAALSSC PVNCPLSHME RTVSEVLRKI VRKYSGKRPE  660
VIAIAMENPM AVRADEVSAR MSGDPNLGSG VAALRKVVEG NHKRNRTKKA PSQEEAGEII  720
DSAGLLAEEG TASSTYTEGA EDVPVRSSSE ESDDFWKSFI NPSSPPSPDE TKNVDKSPDA  780
ETKTEDSESS REEEDDDNTS DSQTKSSTKR VRRNKWKPEE VKKVIRMRGE LHSRFQVVKG  840
RMALWEEISS NLSAEGINRS PGQCKSLWAS LIQKYEECKA DERSKTSWSH YEDMNSILSE  900
LDTPAPK
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5a0t_A8e-8711366719560RIBONUCLEASE J
5a0t_B8e-8711366719560RIBONUCLEASE J
5a0v_A8e-8711366719560RIBONUCLEASE J
5a0v_B8e-8711366719560RIBONUCLEASE J
Search in ModeBase
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Bra.49770.0flower| leaf| root
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_009150395.1
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_009150395.10.0PREDICTED: uncharacterized protein LOC103873754
RefseqXP_013642983.10.0uncharacterized protein LOC106347909
SwissprotQ84W560.0RNJ_ARATH; Ribonuclease J
TrEMBLM4FC130.0M4FC13_BRARP; Uncharacterized protein
STRINGBra038629.1-P0.0(Brassica rapa)
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]