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.004G017500.1.p
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 bHLH
Protein Properties Length: 572aa    MW: 59313.9 Da    PI: 4.2822
Description bHLH family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Sobic.004G017500.1.pgenomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1HLH39.78.7e-13311354755
                           HHHHHHHHHHHHHHHHHHCTSCC.C...TTS-STCHHHHHHHHHHHHHHH CS
                   HLH   7 erErrRRdriNsafeeLrellPk.askapskKlsKaeiLekAveYIksLq 55 
                            +ErrRR+++N+++ +Lr+l+P+ +      K++ a+iL  A++YI  Lq
  Sobic.004G017500.1.p 311 VAERRRRKKLNDRLYKLRSLVPNiS------KMDRASILGDAIDYIVGLQ 354
                           58*********************66......***************9887 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF474596.67E-18302365IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
PROSITE profilePS5088815.955304353IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
SMARTSM003536.5E-16310359IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
PfamPF000102.5E-10311354IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
CDDcd000833.21E-13311358No hitNo description
Gene3DG3DSA:4.10.280.101.1E-16311365IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0009555Biological Processpollen development
GO:0048657Biological Processanther wall tapetum cell differentiation
GO:0005634Cellular Componentnucleus
GO:0000978Molecular FunctionRNA polymerase II core promoter proximal region sequence-specific DNA binding
GO:0046983Molecular Functionprotein dimerization activity
Sequence ? help Back to Top
Protein Sequence    Length: 572 aa     Download sequence    Send to blast
MGGGGHSCVA AAGDGAGASM EAALRTLVGV DAWDYCIYWR LSPDQRFLEM TGFCCSSEFE  60
AQLSALGDLP PSIQLDSSSA GMHAEAMVSN QPIWQSSRVS ELQTSYSSEP IGSGGGPRTR  120
LLVPVAGGLV ELFAARYMAE EEQMAELVMA QCGVPGGAEA GEGGGGVHAW QPGFAWDGAA  180
DASRGMMYGG AAVPPSLGLF DAAGSVAADP FQAVVVQQAP GAGGGGGVDD AGWQYAAAAA  240
AAGSELAAVQ QEPQPPQPQP RGADSGSEGS DMQVDPEDDG DGDGDVDAQG RGGGGGGGKG  300
GGKRQQCKNL VAERRRRKKL NDRLYKLRSL VPNISKMDRA SILGDAIDYI VGLQNQVKAL  360
QDELEDPADG GAPDVLLDHP PPASLVGLEN DDSPRTSHHL PLAGSKRSRA AVQAAEEEKG  420
HDMEPQVEVR QVEANEFFLQ MLCERKPGRF VQIMDSIAAL GLEVTNVNVT SHESLVLNVF  480
RAARRDSEVA VQADRVRDSL LEVTREPYGV WSSAAPPVGV GMSGGGIVDV KLDGVDVKLD  540
GIIDGQAAPG VAVAVGEDQY GGYNHLLQYL A*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5gnj_A3e-14302363263Transcription factor MYC2
5gnj_B3e-14302363263Transcription factor MYC2
5gnj_E3e-14302363263Transcription factor MYC2
5gnj_F3e-14302363263Transcription factor MYC2
5gnj_G3e-14302363263Transcription factor MYC2
5gnj_I3e-14302363263Transcription factor MYC2
5gnj_M3e-14302363263Transcription factor MYC2
5gnj_N3e-14302363263Transcription factor MYC2
Search in ModeBase
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
1290298RGGGGGGGK
2312319ERRRRKKL
Functional Description ? help Back to Top
Source Description
UniProtTranscription factor involved in the regulation of tapetum programmed cell death (PCD) and degradation during male reproductive development. Promotes tapetal PCD. Positively regulates the expression of two tapetum-specific genes, the cysteine protease CP1 and the lipid-transfer protein C6 (PubMed:17138695). Acts upstream from and interacts with EAT1/DTD in the regulation of tapetal PCD (PubMed:23385589). Regulates the expression of genes related to aliphatic metabolism during pollen development. May play regulatory role in the lipidic metabolism involved in the formation of pollen wall (PubMed:19825565). {ECO:0000269|PubMed:17138695, ECO:0000269|PubMed:19825565, ECO:0000269|PubMed:23385589}.
Cis-element ? help Back to Top
SourceLink
PlantRegMapSobic.004G017500.1.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
GenBankBT0343260.0BT034326.1 Zea mays full-length cDNA clone ZM_BFc0007A07 mRNA, complete cds.
GenBankBT0427910.0BT042791.1 Zea mays full-length cDNA clone ZM_BFc0041J08 mRNA, complete cds.
GenBankBT0630100.0BT063010.2 Zea mays full-length cDNA clone ZM_BFc0017C04 mRNA, complete cds.
GenBankBT0631180.0BT063118.1 Zea mays full-length cDNA clone ZM_BFc0027J15 mRNA, complete cds.
GenBankBT0657170.0BT065717.1 Zea mays full-length cDNA clone ZM_BFc0042K04 mRNA, complete cds.
GenBankBT0677850.0BT067785.1 Zea mays full-length cDNA clone ZM_BFc0159F07 mRNA, complete cds.
GenBankBT0688360.0BT068836.1 Zea mays full-length cDNA clone ZM_BFc0079O03 mRNA, complete cds.
GenBankBT0880900.0BT088090.1 Zea mays full-length cDNA clone ZM_BFc0009P17 mRNA, complete cds.
GenBankBT0882990.0BT088299.1 Zea mays full-length cDNA clone ZM_BFc0123M15 mRNA, complete cds.
GenBankEU9729610.0EU972961.1 Zea mays clone 390787 mRNA sequence.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_002453206.20.0transcription factor TDR
SwissprotQ6YUS31e-168TDR_ORYSJ; Transcription factor TDR
TrEMBLA0A194YNA40.0A0A194YNA4_SORBI; Uncharacterized protein
STRINGSb04g001650.10.0(Sorghum bicolor)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MonocotsOGMP55303449
Representative plantOGRP37041323
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT2G16910.15e-52bHLH family protein
Publications ? help Back to Top
  1. Endo M, et al.
    High temperatures cause male sterility in rice plants with transcriptional alterations during pollen development.
    Plant Cell Physiol., 2009. 50(11): p. 1911-22
    [PMID:19808807]
  2. Xu J,Wu M,He C
    [Identification and functional analysis of Tdrxoo, the member of TonB-dependent-receptor family proteins in Xanthomonas oryzae pv. oryzae].
    Wei Sheng Wu Xue Bao, 2010. 50(2): p. 155-61
    [PMID:20387456]
  3. Liu Z,Bao W,Liang W,Yin J,Zhang D
    Identification of gamyb-4 and analysis of the regulatory role of GAMYB in rice anther development.
    J Integr Plant Biol, 2010. 52(7): p. 670-8
    [PMID:20590996]
  4. Zhang D, et al.
    OsC6, encoding a lipid transfer protein, is required for postmeiotic anther development in rice.
    Plant Physiol., 2010. 154(1): p. 149-62
    [PMID:20610705]
  5. Senapati PK,Behera S
    Experimental investigation on an entrained flow type biomass gasification system using coconut coir dust as powdery biomass feedstock.
    Bioresour. Technol., 2012. 117: p. 99-106
    [PMID:22613886]
  6. Zhang SR,Dong DM,Zheng WG,Zhao XD,Wang JH
    [Laser-induced fluorescence spectroscopy characterization of farmland soil moisture content].
    Guang Pu Xue Yu Guang Pu Fen Xi, 2012. 32(10): p. 2623-7
    [PMID:23285852]
  7. Li L, et al.
    An anther development F-box (ADF) protein regulated by tapetum degeneration retardation (TDR) controls rice anther development.
    Planta, 2015. 241(1): p. 157-66
    [PMID:25236969]
  8. Yi J, et al.
    Defective Tapetum Cell Death 1 (DTC1) Regulates ROS Levels by Binding to Metallothionein during Tapetum Degeneration.
    Plant Physiol., 2016. 170(3): p. 1611-23
    [PMID:26697896]