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.006G010400.1.p
Common NameSb06g001050, SORBIDRAFT_06g001050
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 C3H
Protein Properties Length: 680aa    MW: 75263.2 Da    PI: 7.0929
Description C3H family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Sobic.006G010400.1.pgenomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-CCCH17.11e-051011131426
                           --TTTTT-SS-SS CS
               zf-CCCH  14 tCkyGdrCkFaHg 26 
                            CkyG +C+F+H+
  Sobic.006G010400.1.p 101 SCKYGTSCRFSHD 113
                           7***********6 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PROSITE profilePS501039.50784115IPR000571Zinc finger, CCCH-type
PROSITE profilePS501036.963128153IPR000571Zinc finger, CCCH-type
Gene3DG3DSA:3.20.20.701.5E-74323566IPR013785Aldolase-type TIM barrel
SuperFamilySSF513951.31E-65327639No hitNo description
CDDcd028011.40E-95327562No hitNo description
PfamPF012077.3E-55330597IPR001269tRNA-dihydrouridine synthase
PROSITE patternPS011360411429IPR018517tRNA-dihydrouridine synthase, conserved site
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0002943Biological ProcesstRNA dihydrouridine synthesis
GO:0055114Biological Processoxidation-reduction process
GO:0005829Cellular Componentcytosol
GO:0017150Molecular FunctiontRNA dihydrouridine synthase activity
GO:0046872Molecular Functionmetal ion binding
GO:0050660Molecular Functionflavin adenine dinucleotide binding
Sequence ? help Back to Top
Protein Sequence    Length: 680 aa     Download sequence    Send to blast
MAATAPATDP PDASPAVTED APTPARPTPA ELVARAVAPV KPAFLRPPPV REAPKEEGGG  60
GGAVVKVEKK SKRQLKRERH QEQKSTSHLC IQVGKSGNVD SCKYGTSCRF SHDINAYLSQ  120
KPADLEGTCP FTSLGQLCPY GITCRFLSTH KDTPDPQNHP EGNHERNPLS KEIQKLLWKS  180
KYKFPKASAQ IKLLGLKDGN KNKAEAANDN PDETCELNGD EKTSLSSIPV NVEPDPTLCK  240
EIDNSEGHPL VVNSVESVEP RPSKKSKVEV DETQDHGTGM HDNGAESEAV NLINGVKVSS  300
NNQSSCKVDL ITTPHLREKK IIDFREKLYL APLTTVGNLP FRRLCKTLGA DVTCGEMAMS  360
TNLLQGQASE WALLRRHPSE DLFGVQICGP YPDTVARTVE LVDNECPVDF IDINMGCPID  420
IVVNKGAGSS LLTKPMRIRS IVQAASSVTE KPLTVKVRTA FFEGRNRADS IVSDIYDWGA  480
SAITIHGRSR QQRYSKLADW DYIYQCAQKA PDYLHVIGNG DVFSFTDWNK HVSDCSKIST  540
CMIARGALIK PWLFTEIKEQ RHWDITSGER LNILKDFVRF GLEHWGSDSK GVETTRHFLL  600
EWLSYTCRYI PVGLLDVIPQ RLNWRPPSYY GRDDLETLMV SDSAADWIRI SEMLLGKVPE  660
GFTFAPKHKS NAYDRAENG*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
6ei9_A2e-2832457127266tRNA-dihydrouridine synthase B
6ei9_B2e-2832457127266tRNA-dihydrouridine synthase B
Search in ModeBase
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Sbi.169820.0callus
Functional Description ? help Back to Top
Source Description
UniProtCatalyzes the synthesis of dihydrouridine, a modified base found in the D-loop of most tRNAs. {ECO:0000250}.
Cis-element ? help Back to Top
SourceLink
PlantRegMapSobic.006G010400.1.p
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankKM3992640.0KM399264.1 Sorghum bicolor FMN-linked oxidoreductases superfamily protein mRNA, partial cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_002446053.10.0tRNA-dihydrouridine(47) synthase [NAD(P)(+)]-like
SwissprotQ7XT070.0DUS3L_ORYSJ; tRNA-dihydrouridine(47) synthase [NAD(P)(+)]-like
TrEMBLC5YBR50.0C5YBR5_SORBI; tRNA-dihydrouridine(47) synthase [NAD(P)(+)]
STRINGSb06g001050.10.0(Sorghum bicolor)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MonocotsOGMP103222527
Representative plantOGRP57511213
Publications ? help Back to Top
  1. Kikuchi S, et al.
    Collection, mapping, and annotation of over 28,000 cDNA clones from japonica rice.
    Science, 2003. 301(5631): p. 376-9
    [PMID:12869764]