PlantTFDB
PlantRegMap/PlantTFDB v5.0
Plant Transcription Factor Database
Previous version: v3.0 v4.0
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID Neem_42214_a_1
Organism
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Sapindales; Meliaceae; Azadirachta
Family M-type_MADS
Protein Properties Length: 65aa    MW: 7545.86 Da    PI: 10.938
Description M-type_MADS family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Neem_42214_a_1genomeNGDView Nucleic Acid
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1SRF-TF104.14.7e-33959151
                    S---SHHHHHHHHHHHHHHHHHHHHHHHHHHT-EEEEEEE-TTSEEEEEE- CS
          SRF-TF  1 krienksnrqvtfskRrngilKKAeELSvLCdaevaviifsstgklyeyss 51
                    krienk+nrqvtf+kRrng+lKKA+ELSvLCdaeva+iifs++gklye++s
  Neem_42214_a_1  9 KRIENKINRQVTFAKRRNGLLKKAYELSVLCDAEVALIIFSNRGKLYEFCS 59
                    79***********************************************96 PP

Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PROSITE profilePS5006633.557161IPR002100Transcription factor, MADS-box
SMARTSM004321.3E-41160IPR002100Transcription factor, MADS-box
CDDcd002653.65E-38264No hitNo description
SuperFamilySSF554552.75E-31263IPR002100Transcription factor, MADS-box
PRINTSPR004046.9E-34323IPR002100Transcription factor, MADS-box
PROSITE patternPS003500357IPR002100Transcription factor, MADS-box
PfamPF003191.1E-271057IPR002100Transcription factor, MADS-box
PRINTSPR004046.9E-342338IPR002100Transcription factor, MADS-box
PRINTSPR004046.9E-343859IPR002100Transcription factor, MADS-box
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0003677Molecular FunctionDNA binding
GO:0046983Molecular Functionprotein dimerization activity
Sequence ? help Back to Top
Protein Sequence    Length: 65 aa     Download sequence    Send to blast
MGRGRVELKR IENKINRQVT FAKRRNGLLK KAYELSVLCD AEVALIIFSN RGKLYEFCST  60
NRKQA
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5f28_A4e-21161161MEF2C
5f28_B4e-21161161MEF2C
5f28_C4e-21161161MEF2C
5f28_D4e-21161161MEF2C
6byy_A3e-21161161MEF2 CHIMERA
6byy_B3e-21161161MEF2 CHIMERA
6byy_C3e-21161161MEF2 CHIMERA
6byy_D3e-21161161MEF2 CHIMERA
6bz1_A3e-21161161MEF2 CHIMERA
6bz1_B3e-21161161MEF2 CHIMERA
6bz1_C3e-21161161MEF2 CHIMERA
6bz1_D3e-21161161MEF2 CHIMERA
Search in ModeBase
Functional Description ? help Back to Top
Source Description
UniProtMADS-box transcription factor that acts redundantly with J2 to control meristem maturation and inflorescence architecture. {ECO:0000269|PubMed:28528644}.
UniProtProbable transcription factor.
UniProtProbable transcription factor. May be involved in the control of flowering time. {ECO:0000269|PubMed:9339904, ECO:0000269|Ref.10}.
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAY9474649e-59AY947464.1 Prunus dulcis MADS-box transcription factor (MADS3) mRNA, complete cds.
GenBankEF4403529e-59EF440352.1 Prunus persica transcription factor MADS7 (MADS7) mRNA, complete cds.
GenBankJQ6867259e-59JQ686725.1 Prunus avium transcription factor MADS4 (MADS4) mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_009622386.17e-37PREDICTED: MADS-box protein CMB1-like
RefseqXP_022850778.11e-36MADS-box protein EJ2-like
SwissprotP0C5B01e-36MADS7_ORYSI; MADS-box transcription factor 7
SwissprotQ0J4661e-36MADS7_ORYSJ; MADS-box transcription factor 7
SwissprotQ7Y0401e-36EJ2_SOLLC; MADS-box protein EJ2
TrEMBLA0A2N9HF954e-36A0A2N9HF95_FAGSY; Uncharacterized protein
STRINGcassava4.1_033922m4e-37(Manihot esculenta)
STRINGLus100113498e-37(Linum usitatissimum)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM7828413
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT1G24260.31e-38MIKC_MADS family protein
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]
  2. Shitsukawa N, et al.
    Genetic and epigenetic alteration among three homoeologous genes of a class E MADS box gene in hexaploid wheat.
    Plant Cell, 2007. 19(6): p. 1723-37
    [PMID:17586655]
  3. Bai X,Wang Q,Chu C
    Excision of a selective marker in transgenic rice using a novel Cre/loxP system controlled by a floral specific promoter.
    Transgenic Res., 2008. 17(6): p. 1035-43
    [PMID:18437520]
  4. Qu L, et al.
    Expression pattern and functional analysis of a MADS-box gene M79 from rice.
    Sci. China, C, Life Sci., 2001. 44(2): p. 161-9
    [PMID:18726433]
  5. Cui R, et al.
    Functional conservation and diversification of class E floral homeotic genes in rice (Oryza sativa).
    Plant J., 2010. 61(5): p. 767-81
    [PMID:20003164]
  6. Li H, et al.
    The AGL6-like gene OsMADS6 regulates floral organ and meristem identities in rice.
    Cell Res., 2010. 20(3): p. 299-313
    [PMID:20038961]
  7. Seok HY, et al.
    Rice ternary MADS protein complexes containing class B MADS heterodimer.
    Biochem. Biophys. Res. Commun., 2010. 401(4): p. 598-604
    [PMID:20888318]
  8. Tang X, et al.
    Global gene profiling of laser-captured pollen mother cells indicates molecular pathways and gene subfamilies involved in rice meiosis.
    Plant Physiol., 2010. 154(4): p. 1855-70
    [PMID:20959420]
  9. Wang SS,Wang CS,Tseng TH,Hou YL,Chen KY
    High-resolution genetic mapping and candidate gene identification of the SLP1 locus that controls glume development in rice.
    Theor. Appl. Genet., 2011. 122(8): p. 1489-96
    [PMID:21327937]
  10. Li H, et al.
    Rice MADS6 interacts with the floral homeotic genes SUPERWOMAN1, MADS3, MADS58, MADS13, and DROOPING LEAF in specifying floral organ identities and meristem fate.
    Plant Cell, 2011. 23(7): p. 2536-52
    [PMID:21784949]
  11. Yoshida H
    Is the lodicule a petal: molecular evidence?
    Plant Sci., 2012. 184: p. 121-8
    [PMID:22284716]
  12. Tomato Genome Consortium
    The tomato genome sequence provides insights into fleshy fruit evolution.
    Nature, 2012. 485(7400): p. 635-41
    [PMID:22660326]
  13. Duan Y, et al.
    Characterization of Osmads6-5, a null allele, reveals that OsMADS6 is a critical regulator for early flower development in rice (Oryza sativa L.).
    Plant Mol. Biol., 2012. 80(4-5): p. 429-42
    [PMID:22933119]
  14. Wong CE,Singh MB,Bhalla PL
    Novel members of the AGAMOUS LIKE 6 subfamily of MIKCC-type MADS-box genes in soybean.
    BMC Plant Biol., 2013. 13: p. 105
    [PMID:23870482]
  15. Hu Z,Ding X,Hu S,Sun Y,Xia L
    Tissue-specifically regulated site-specific excision of selectable marker genes in bivalent insecticidal, genetically-modified rice.
    Biotechnol. Lett., 2013. 35(12): p. 2177-83
    [PMID:23974493]
  16. Bai X, et al.
    Regulatory role of FZP in the determination of panicle branching and spikelet formation in rice.
    Sci Rep, 2016. 6: p. 19022
    [PMID:26744119]
  17. Dreni L,Zhang D
    Flower development: the evolutionary history and functions of the AGL6 subfamily MADS-box genes.
    J. Exp. Bot., 2016. 67(6): p. 1625-38
    [PMID:26956504]
  18. Soyk S, et al.
    Bypassing Negative Epistasis on Yield in Tomato Imposed by a Domestication Gene.
    Cell, 2017. 169(6): p. 1142-1155.e12
    [PMID:28528644]