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 Sobic.004G070200.1.p
Common NameSb04g005900, SORBIDRAFT_04g005900
Organism
Sorghum bicolor
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; Liliopsida; Petrosaviidae; commelinids; Poales; Poaceae; PACMAD clade; Panicoideae; Andropogonodae; Andropogoneae; Sorghinae; Sorghum
Family Trihelix
Protein Properties Length: 881aa    MW: 96845.5 Da    PI: 9.2193
Description Trihelix family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Sobic.004G070200.1.pgenomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1trihelix67.62.5e-21787867186
              trihelix   1 rWtkqevlaLiearremeerlrrgklkkplWeevskkmrergferspkqCkekwenlnkrykkikegekkrtsessstcpyfdqle 86 
                           +W+ +e++ Li++r em+e++++ k ++ lWee+s+ m  +g++r+p qCk+ w +l ++y++ k+ +++      +t+pyf+ ++
  Sobic.004G070200.1.p 787 KWKPEEIKSLIQMRGEMNEKFQSVKGRMVLWEEISDTMLNQGISRTPAQCKSLWTSLVQKYEESKKDMES-----MKTWPYFSAMD 867
                           7****************************************************************99998.....479*******8 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:3.60.15.108.1E-6785335IPR001279Metallo-beta-lactamase
SuperFamilySSF562814.55E-7386500IPR001279Metallo-beta-lactamase
SMARTSM008491.5E-2498295IPR001279Metallo-beta-lactamase
PfamPF127062.4E-10110245IPR001279Metallo-beta-lactamase
PfamPF075211.8E-7443472IPR011108Zn-dependent metallo-hydrolase, RNA specificity domain
PROSITE profilePS500907.863780844IPR017877Myb-like domain
Gene3DG3DSA:1.10.10.602.5E-5783846IPR009057Homeodomain-like
PfamPF138375.5E-18786869No hitNo description
CDDcd122036.16E-22786851No 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: 881 aa     Download sequence    Send to blast
MVALASLSSL CPCGIARRRA ASASSSVAVS ISCCAVATPS SSGKGPQESR TPRRRLRKTE  60
GATKSLEDSV KRKMEQFYEG VDGPPLRVLP IGGLGEIGMN CMLVGNYDRY ILIDAGVMFP  120
DYDEFGVQKI IPDTTFIKKW SHKIEAVIIT HGHEDHIGAL PWVIPALDST TPIFASSFTM  180
ELIKKRLKEF GIFLSSRLKV LRIKKRFQAG PFEVEPIRVT HSIPDCCGLV LRCGDGIIFH  240
TGDWKIDESP VDGKIFDRQA LEELSKEGVT LMMSDSTNVL SPGRSISESV VAGSLLRHIS  300
EAKGRVITTQ FASNIHRIGS IKAAADLTGR KMVFVGMSLR TYLEAAFKDG KAPMDPSTLV  360
KAEDMDAYAP KDLLVVTTGS QGEPRAALNL ASYGGSHALK LSKEDVLLYS AKVIPGNETR  420
VMKMMNRLTD LGPKIIMGKD SGLHTSGHAY REELEEVLRI VKPQHFLPVH GELLFLKEHE  480
LLGRSTGIRH TTVIKNGEML GVSHLRSRRV LSNGFVSLGK EDLQLMYSDG DKAFGTSTDL  540
CIDERLRIAS DGIIFVSMEI FRPQKEHGLA QSGLKGKFKI TTRCLWLDNG RLLDALYKAA  600
HAALSSCPVN CPLSHMERMV AEILRKMVRK YSGKRPDVIA VATENTTAGF PEHLDAKSSG  660
NFGPSSTTSH LSRSPATSLE GSYKTHPDNP EVDAEVLCHT ETPPKAVRTT PDDATTSSNG  720
EAFFSSDLHQ PKTLEHFWES FKSPTAVKIA RIVNGGNKQN LSKIGIMGKD SSIQSAPAPV  780
KSSKKNKWKP EEIKSLIQMR GEMNEKFQSV KGRMVLWEEI SDTMLNQGIS RTPAQCKSLW  840
TSLVQKYEES KKDMESMKTW PYFSAMDRIL SQQGEMATKG *
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
3bk1_A1e-838664517562Metal dependent hydrolase
3bk2_A1e-838664517562Metal dependent hydrolase
Search in ModeBase
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
15257RRRLRK
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Sbi.187360.0leaf
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
PlantRegMapSobic.004G070200.1.p
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 -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_021315488.10.0uncharacterized protein LOC8079424 isoform X1
SwissprotQ84W560.0RNJ_ARATH; Ribonuclease J
TrEMBLC5XWZ40.0C5XWZ4_SORBI; Uncharacterized protein
STRINGSb04g005900.10.0(Sorghum bicolor)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MonocotsOGMP49963542
Representative plantOGRP30821521
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]