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_180_f_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 B3
Protein Properties Length: 905aa    MW: 99513 Da    PI: 6.696
Description B3 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Neem_180_f_1genomeNGDView Nucleic Acid
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B354.81.7e-17314413299
                   EEE-..-HHHHTT-EE--HHH.HTT..---..--SEEEEEETTS-EEEEEE....EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE-SSSEE..EE CS
            B3   2 fkvltpsdvlksgrlvlpkkfaeeh..ggkkeesktltledesgrsWevkliy..rkksgryvltkGWkeFvkangLkegDfvvFkldgrsefelvv 94 
                   f+vl+ sd+++ grlvlpk +ae++   ++++e+  l+++d +g++W +++++  +++s++yvl+ G     ++ +L++gD+v+F++++  e++lv+
  Neem_180_f_1 314 FTVLSASDAGRIGRLVLPKACAEAYfpPISQPEGLPLRIQDVKGKEWVFQFRFwpNNNSRMYVLE-GVTPCIQSMQLQAGDTVTFSRMD-PEGKLVM 408
                   57899**********************555567778***************9989999999***9.********************876.7777888 PP

                   EEE-S CS
            B3  95 kvfrk 99 
                   +++++
  Neem_180_f_1 409 GFRKA 413
                   77765 PP

Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SMARTSM010191.7E-18313414IPR003340B3 DNA binding domain
PROSITE profilePS5086310.447313414IPR003340B3 DNA binding domain
CDDcd100172.62E-20314412No hitNo description
PfamPF023623.9E-15314413IPR003340B3 DNA binding domain
SuperFamilySSF1019367.59E-18314413IPR015300DNA-binding pseudobarrel domain
Gene3DG3DSA:2.40.330.106.7E-27315417IPR015300DNA-binding pseudobarrel domain
PROSITE profilePS5105013.718579629IPR011124Zinc finger, CW-type
PfamPF074964.1E-11584626IPR011124Zinc finger, CW-type
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0010030Biological Processpositive regulation of seed germination
GO:2000034Biological Processregulation of seed maturation
GO:0003677Molecular FunctionDNA binding
GO:0008270Molecular Functionzinc ion binding
Sequence ? help Back to Top
Protein Sequence    Length: 905 aa     Download sequence    Send to blast
MAREYDRGIE YGGCSELSLE QMESRTCMNE ACRASTSIEW RKGWALRSGD FAVLCDKCGS  60
VFEQLIFCDE FHSKDSGWRE CTSCGKRLHC GCIASRALIE LLDSGGVSCI NCAKKSELDL  120
VAGNEKPNGF GTLKADNASD LQSTSVDNQL GGSIKLVQLG NSSEGAGLRH LLQFRNDDPD  180
GSFGKTKLEE AAKPDVSKAD IGAKGIYESL AHTNLSITLG SPGVNSNSFP SAVVDEKEHS  240
KTSPFIQQGN RSRHLLPKPP KLALATGSEA NAAMSQVRVA RPPAEGRGRN QLLPRYWPRI  300
TDQELQQISG EYPFTVLSAS DAGRIGRLVL PKACAEAYFP PISQPEGLPL RIQDVKGKEW  360
VFQFRFWPNN NSRMYVLEGV TPCIQSMQLQ AGDTVTFSRM DPEGKLVMGF RKASSSAALQ  420
DAQPSAIPNG AHSSESFFSG VFENLSIISG YSGVLQSLKG STDPHLNALS KHLNATSGDI  480
SWVKSEKHED KPRDSLLLPS MLAPERKRSR NIGSKSKRLL IDRLDALELK LTWEEAQDML  540
RPPPTVMPSI VTIEDHAFEE YEGSGWINSS NLELLSLIFR GQEQWAQCDG CSKWRRLPID  600
VLLPPKWTCM DNAWDHSRSS CSTPDELTPR ELENLLRLHK DFKKRRIATS HRPSQEHEPS  660
GLDALSNAAI LGENMGEPGT ASVATTTKHP RHRPGCSCIV CIQPPSGKGK HKPTCTCNVC  720
MTVKRRFKTL MMRKKKRQSE REAEVAQRNQ PTWGSKEEAE VESSSKHISS HLDPSENEAR  780
SGNELESKIQ SNNMSSKLPE AGKSEIDLNC QPERDDMQAG LNRVSMMKLL QVASLPLETY  840
LKQNGLTSLM SEQQQASSAS HAPPAQATGE SDGRLNEFAS ATQDRESGGE ENCEAVSDKI  900
PDDPQ
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
6j9a_A6e-612984202131B3 domain-containing transcription repressor VAL1
Search in ModeBase
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
1723734KRRFKTLMMRKK
2723736KRRFKTLMMRKKKR
Functional Description ? help Back to Top
Source Description
UniProtTranscriptional repressor of gene expression involved in embryonic pathways, such as LEC1, ABI3, and FUS3. Repressor of the sugar-inducible genes involved in the seed maturation program in seedlings. Plays an essential role in regulating the transition from seed maturation to seedling growth. Functionally redundant with VAL1/HSI2. {ECO:0000269|PubMed:17158584, ECO:0000269|PubMed:17267611}.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_006429577.10.0B3 domain-containing transcription repressor VAL2 isoform X1
RefseqXP_006481190.10.0B3 domain-containing transcription repressor VAL2 isoform X1
RefseqXP_006481191.10.0B3 domain-containing transcription repressor VAL2 isoform X1
RefseqXP_024037446.10.0B3 domain-containing transcription repressor VAL2 isoform X1
RefseqXP_024037447.10.0B3 domain-containing transcription repressor VAL2 isoform X1
RefseqXP_024955576.10.0B3 domain-containing transcription repressor VAL2 isoform X1
SwissprotQ5CCK40.0VAL2_ARATH; B3 domain-containing transcription repressor VAL2
TrEMBLA0A067FKW80.0A0A067FKW8_CITSI; Uncharacterized protein
STRINGXP_006481189.10.0(Citrus sinensis)
STRINGXP_006429577.10.0(Citrus clementina)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM72032639
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT4G32010.10.0HSI2-like 1
Publications ? help Back to Top
  1. Jia H,McCarty DR,Suzuki M
    Distinct roles of LAFL network genes in promoting the embryonic seedling fate in the absence of VAL repression.
    Plant Physiol., 2013. 163(3): p. 1293-305
    [PMID:24043445]
  2. Chhun T, et al.
    HSI2 Repressor Recruits MED13 and HDA6 to Down-Regulate Seed Maturation Gene Expression Directly During Arabidopsis Early Seedling Growth.
    Plant Cell Physiol., 2016. 57(8): p. 1689-706
    [PMID:27335347]
  3. Yuan W, et al.
    A cis cold memory element and a trans epigenome reader mediate Polycomb silencing of FLC by vernalization in Arabidopsis.
    Nat. Genet., 2016. 48(12): p. 1527-1534
    [PMID:27819666]
  4. Li C,Cui Y
    A DNA element that remembers winter.
    Nat. Genet., 2016. 48(12): p. 1451-1452
    [PMID:27898079]