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 LOC_Os04g38770.1
Common NameB1358B12.2
Organism
Oryza sativa subsp. japonica
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; Liliopsida; Petrosaviidae; commelinids; Poales; Poaceae; BOP clade; Oryzoideae; Oryzeae; Oryzinae; Oryza; Oryza sativa
Family M-type_MADS
Protein Properties Length: 100aa    MW: 11297 Da    PI: 10.0427
Description M-type_MADS family protein
Gene Model
Gene Model ID Type Source Coding Sequence
LOC_Os04g38770.1genomeMSUView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1SRF-TF91.54.2e-291059251
                      ---SHHHHHHHHHHHHHHHHHHHHHHHHHHT-EEEEEEE-TTSEEEEEE- CS
            SRF-TF  2 rienksnrqvtfskRrngilKKAeELSvLCdaevaviifsstgklyeyss 51
                      ri+n++ rqvtfskRrngi+KKA+EL +LCdaev ++ifsstg+lyey+s
  LOC_Os04g38770.1 10 RIDNSTSRQVTFSKRRNGIFKKAKELAILCDAEVGLVIFSSTGRLYEYAS 59
                      8***********************************************86 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PROSITE profilePS5006631.805161IPR002100Transcription factor, MADS-box
SMARTSM004321.7E-39160IPR002100Transcription factor, MADS-box
SuperFamilySSF554551.44E-33285IPR002100Transcription factor, MADS-box
CDDcd002651.84E-43277No hitNo description
PROSITE patternPS003500357IPR002100Transcription factor, MADS-box
PRINTSPR004048.2E-29323IPR002100Transcription factor, MADS-box
PfamPF003192.8E-261057IPR002100Transcription factor, MADS-box
PRINTSPR004048.2E-292338IPR002100Transcription factor, MADS-box
PRINTSPR004048.2E-293859IPR002100Transcription factor, MADS-box
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006355Biological Processregulation of transcription, DNA-templated
GO:0005634Cellular Componentnucleus
GO:0003677Molecular FunctionDNA binding
GO:0046983Molecular Functionprotein dimerization activity
Sequence ? help Back to Top
Protein Sequence    Length: 100 aa     Download sequence    Send to blast
MGRGKIVIRR IDNSTSRQVT FSKRRNGIFK KAKELAILCD AEVGLVIFSS TGRLYEYAST  60
SMKSVIDRYG RAKEEQQHVA NPNSELKEFC SVFIYITEN*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5f28_A7e-23188186MEF2C
5f28_B7e-23188186MEF2C
5f28_C7e-23188186MEF2C
5f28_D7e-23188186MEF2C
Search in ModeBase
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Os.581291e-147callus| flower| leaf| root| seed| stem
Expression -- Microarray ? help Back to Top
Source ID
Expression AtlasQ6MWF2
Expression -- Description ? help Back to Top
Source Description
UniprotTISSUE SPECIFICITY: Ubiquitous. {ECO:0000269|PubMed:14701936}.
Functional Description ? help Back to Top
Source Description
UniProtProbable transcription factor.
Cis-element ? help Back to Top
SourceLink
PlantRegMapLOC_Os04g38770.1
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Phenotype -- Mutation ? help Back to Top
Source ID
RiceGEOs04g38770
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAK2436697e-97AK243669.1 Oryza sativa Japonica Group cDNA, clone: J100089N11, full insert sequence.
GenBankAL6064607e-97AL606460.3 Oryza sativa genomic DNA, chromosome 4, BAC clone: OSJNBa0072F16, complete sequence.
GenBankAP0149607e-97AP014960.1 Oryza sativa Japonica Group DNA, chromosome 4, cultivar: Nipponbare, complete sequence.
GenBankBX8426057e-97BX842605.1 Oryza sativa genomic DNA, chromosome 4, BAC clone: B1358B12, complete sequence.
GenBankCP0126127e-97CP012612.1 Oryza sativa Indica Group cultivar RP Bio-226 chromosome 4 sequence.
GenBankCR8552037e-97CR855203.1 Oryza sativa genomic DNA, chromosome 4, BAC clone: H0219H12, complete sequence.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_015636306.16e-57MADS-box transcription factor 27-like
SwissprotQ6EP496e-54MAD27_ORYSJ; MADS-box transcription factor 27
TrEMBLI1PLY11e-66I1PLY1_ORYGL; Uncharacterized protein
TrEMBLQ6MWF21e-66Q6MWF2_ORYSJ; B1358B12.2 protein
STRINGORGLA04G0120000.12e-67(Oryza glaberrima)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MonocotsOGMP12938398
Representative plantOGRP1617761
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT4G37940.11e-46AGAMOUS-like 21
Publications ? help Back to Top
  1. Puig J, et al.
    Analysis of the expression of the AGL17-like clade of MADS-box transcription factors in rice.
    Gene Expr. Patterns, 2013 Jun-Jul. 13(5-6): p. 160-70
    [PMID:23466806]
  2. Yu C, et al.
    The effects of fluctuations in the nutrient supply on the expression of five members of the AGL17 clade of MADS-box genes in rice.
    PLoS ONE, 2014. 9(8): p. e105597
    [PMID:25140876]