PlantTFDB
Plant Transcription Factor Database
v4.0
Previous version: v1.0, v2.0, v3.0
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID AT1G03790.1
Common NameAtTZF4, F11M21.28, SOM, TZF4
Organism
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis
Family C3H
Protein Properties Length: 393aa    MW: 43614.5 Da    PI: 7.9029
Description C3H family protein
Gene Model
Gene Model ID Type Source Coding Sequence
AT1G03790.1genomeTAIRView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-CCCH33.66.5e-11125148326
                  S---SGGGGTS--TTTTT-SS-SS CS
      zf-CCCH   3 telCrffartGtCkyGdrCkFaHg 26 
                   e C+ f+r+G C++Gd C FaHg
  AT1G03790.1 125 GEVCPEFRRGGDCSRGDDCEFAHG 148
                  689********************9 PP

Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PROSITE profilePS5010313.535122150IPR000571Zinc finger, CCCH-type
SuperFamilySSF902293.79E-6122152IPR000571Zinc finger, CCCH-type
SMARTSM003568.4E-6122149IPR000571Zinc finger, CCCH-type
PfamPF006421.9E-8126148IPR000571Zinc finger, CCCH-type
Gene3DG3DSA:4.10.1000.102.1E-6126150IPR000571Zinc finger, CCCH-type
SMARTSM003562.5158181IPR000571Zinc finger, CCCH-type
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006355Biological Processregulation of transcription, DNA-templated
GO:0010187Biological Processnegative regulation of seed germination
GO:0005634Cellular Componentnucleus
GO:0003677Molecular FunctionDNA binding
GO:0003700Molecular Functiontranscription factor activity, sequence-specific DNA binding
GO:0005515Molecular Functionprotein binding
GO:0046872Molecular Functionmetal ion binding
Plant Ontology ? help Back to Top
PO Term PO Category PO Description
PO:0009001anatomyfruit
PO:0009010anatomyseed
PO:0009030anatomycarpel
PO:0007616developmental stageflowering stage
Sequence ? help Back to Top
Protein Sequence    Length: 393 aa     Download sequence    Send to blast
MDVVCTEHQM RKPTVEIPPR KLLLSSKSFP SDSSSPRSPR KHNWNKSNKI TSEHEEDNED  60
NNRENKEYCY DSDSDDPYAS DHFRMFEFKI RRCTRSRSHD WTDCPFAHPG EKARRRDPRR  120
FQYSGEVCPE FRRGGDCSRG DDCEFAHGVF ECWLHPIRYR TEACKDGKHC KRKVCFFAHS  180
PRQLRVLPPE NVSGVSASPS PAAKNPCCLF CSSSPTSTLL GNLSHLSRSP SLSPPMSPAN  240
KAAAFSRLRN RAASAVSAAA AAGSMNYKDV LSELVNSLDS MSLAEALQAS SSSPVTTPVS  300
AAAAAFASSC GLSNQRLHLQ QQQPSSPLQF ALSPSTPSYL TNSPQANFFS DDFTPRRRQM  360
NDFTAMTAVR ENTNIEDGSC GDPDLGWVND LLT
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
At.430100.0seed
Expression -- Microarray ? help Back to Top
Source ID E-value
Genevisible265084_at0.0
Expression AtlasAT1G03790-
AtGenExpressAT1G03790-
ATTED-IIAT1G03790-
Expression -- Description ? help Back to Top
Source Description
UniprotTISSUE SPECIFICITY: Specifically expressed in seeds. {ECO:0000269|PubMed:18487351}.
Functional Description ? help Back to Top
Source Description
TAIREncodes SOMNUS (SOM), a nucleus-localized CCCH-type zinc finger protein. SOM negatively regulates light-dependent seed germination downstream of PIL5 (AT2G20180).
UniProtProbable transcription repressor that functions as negative regulator of phytochrome-mediated promotion of seed germination. Inhibits seed germination by regulating the expression of gibberellic acid (GA) and abscisic acid (ABA) metabolic genes. Does not regulate the expression of the DELLA genes RGA and RGA1. Activated by PIL5, a phytochrome-interacting basic helix-loop-helix transcription factor. {ECO:0000269|PubMed:18487351}.
Function -- GeneRIF ? help Back to Top
  1. ABI3 and PIL5 collaboratively activate the expression of SOM mRNA by directly binding to and interacting with each other at the SOM promoter.
    [PMID: 21467583]
  2. AtTZF4, 5 and 6 affect seed germination by controlling genes critical for abscisic acid (ABA) and gibberellic acid (GA) response.
    [PMID: 23421766]
  3. ABI3, ABI5, and DELLAs mediate high-temperature signaling to activate the expression of SOM and other high-temperature-inducible genes, thereby inhibiting seed germination.
    [PMID: 24326588]
Cis-element ? help Back to Top
SourceLink
PlantRegMapAT1G03790.1
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Regulation -- ATRM (Manually Curated Upstream Regulators) ? help Back to Top
Source Upstream Regulator (A: Activate/R: Repress)
ATRM AT2G20180 (A), AT3G24650 (A)
Phenotype -- Mutation ? help Back to Top
Source ID
T-DNA ExpressAT1G03790
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAC0030270.0AC003027.1 Arabidopsis thaliana chromosome I BAC F21M11 genomic sequence, complete sequence.
GenBankCP0026840.0CP002684.1 Arabidopsis thaliana chromosome 1 sequence.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqNP_171875.10.0CCCH-type zinc finger protein SOMNUS
SwissprotQ9ZWA10.0C3H2_ARATH; Zinc finger CCCH domain-containing protein 2
TrEMBLD7KD800.0D7KD80_ARALL; Zinc finger (CCCH-type) family protein
STRINGAT1G03790.10.0(Arabidopsis thaliana)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM29872766
Representative plantOGRP11701644
Publications ? help Back to Top
  1. Riechmann JL, et al.
    Arabidopsis transcription factors: genome-wide comparative analysis among eukaryotes.
    Science, 2000. 290(5499): p. 2105-10
    [PMID:11118137]
  2. Seki M, et al.
    Functional annotation of a full-length Arabidopsis cDNA collection.
    Science, 2002. 296(5565): p. 141-5
    [PMID:11910074]
  3. Yamada K, et al.
    Empirical analysis of transcriptional activity in the Arabidopsis genome.
    Science, 2003. 302(5646): p. 842-6
    [PMID:14593172]
  4. Yazaki J, et al.
    Transcriptional profiling of genes responsive to abscisic acid and gibberellin in rice: phenotyping and comparative analysis between rice and Arabidopsis.
    Physiol. Genomics, 2004. 17(2): p. 87-100
    [PMID:14982972]
  5. Becerra C,Puigdomenech P,Vicient CM
    Computational and experimental analysis identifies Arabidopsis genes specifically expressed during early seed development.
    BMC Genomics, 2006. 7: p. 38
    [PMID:16504176]
  6. Wang D, et al.
    Genome-wide analysis of CCCH zinc finger family in Arabidopsis and rice.
    BMC Genomics, 2008. 9: p. 44
    [PMID:18221561]
  7. Kim DH, et al.
    SOMNUS, a CCCH-type zinc finger protein in Arabidopsis, negatively regulates light-dependent seed germination downstream of PIL5.
    Plant Cell, 2008. 20(5): p. 1260-77
    [PMID:18487351]
  8. Pomeranz M,Lin PC,Finer J,Jang JC
    AtTZF gene family localizes to cytoplasmic foci.
    Plant Signal Behav, 2010. 5(2): p. 190-2
    [PMID:20173417]
  9. Park J,Lee N,Kim W,Lim S,Choi G
    ABI3 and PIL5 collaboratively activate the expression of SOMNUS by directly binding to its promoter in imbibed Arabidopsis seeds.
    Plant Cell, 2011. 23(4): p. 1404-15
    [PMID:21467583]
  10. Cho JN, et al.
    Control of seed germination by light-induced histone arginine demethylation activity.
    Dev. Cell, 2012. 22(4): p. 736-48
    [PMID:22483719]
  11. Lee KP, et al.
    Spatially and genetically distinct control of seed germination by phytochromes A and B.
    Genes Dev., 2012. 26(17): p. 1984-96
    [PMID:22948663]
  12. Renault H, et al.
    γ-Aminobutyric acid transaminase deficiency impairs central carbon metabolism and leads to cell wall defects during salt stress in Arabidopsis roots.
    Plant Cell Environ., 2013. 36(5): p. 1009-18
    [PMID:23148892]
  13. Bogamuwa S,Jang JC
    The Arabidopsis tandem CCCH zinc finger proteins AtTZF4, 5 and 6 are involved in light-, abscisic acid- and gibberellic acid-mediated regulation of seed germination.
    Plant Cell Environ., 2013. 36(8): p. 1507-19
    [PMID:23421766]
  14. Lim S, et al.
    ABA-insensitive3, ABA-insensitive5, and DELLAs Interact to activate the expression of SOMNUS and other high-temperature-inducible genes in imbibed seeds in Arabidopsis.
    Plant Cell, 2013. 25(12): p. 4863-78
    [PMID:24326588]
  15. Jin J, et al.
    An Arabidopsis Transcriptional Regulatory Map Reveals Distinct Functional and Evolutionary Features of Novel Transcription Factors.
    Mol. Biol. Evol., 2015. 32(7): p. 1767-73
    [PMID:25750178]
  16. Bogamuwa S,Jang JC
    Plant Tandem CCCH Zinc Finger Proteins Interact with ABA, Drought, and Stress Response Regulators in Processing-Bodies and Stress Granules.
    PLoS ONE, 2016. 11(3): p. e0151574
    [PMID:26978070]