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 Solyc10g038000.1.1
Common NameLOC101259296
Organism
Solanum lycopersicum
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; asterids; lamiids; Solanales; Solanaceae; Solanoideae; Solaneae; Solanum; Lycopersicon
Family C3H
Protein Properties Length: 361aa    MW: 40524.7 Da    PI: 7.3694
Description C3H family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Solyc10g038000.1.1genomeITAGView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-CCCH18.53.7e-06426326
                        S---SGGGGTS--TTTTT-SS-SS CS
             zf-CCCH  3 telCrffartGtCkyGdrCkFaHg 26
                        ++lC+ffa  G C  Gd C F+H+
  Solyc10g038000.1.1  4 RVLCKFFAH-GACLKGDHCEFSHD 26
                        89***6666.*************5 PP
2zf-CCCH27.65e-093454526
                        --SGGGGTS--TTTTT-SS-SS CS
             zf-CCCH  5 lCrffartGtCkyGdrCkFaHg 26
                         C ++++ G C yG+rC++ H+
  Solyc10g038000.1.1 34 VCTYYQK-GACAYGSRCRYDHV 54
                        6******.*************7 PP
3zf-CCCH21.54.2e-07142164326
                         S---SGGGGTS--TTTTT-SS-SS CS
             zf-CCCH   3 telCrffartGtCkyGdrCkFaHg 26 
                         +++C  fa+ G C++G++C++ Hg
  Solyc10g038000.1.1 142 RSICA-FAAAGNCPRGEKCPRVHG 164
                         56788.*****************9 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PROSITE profilePS5010314.295128IPR000571Zinc finger, CCCH-type
SMARTSM003563.9E-6227IPR000571Zinc finger, CCCH-type
SuperFamilySSF902294.45E-7426IPR000571Zinc finger, CCCH-type
PfamPF156637.1E-8762No hitNo description
PROSITE profilePS5010314.5872956IPR000571Zinc finger, CCCH-type
SuperFamilySSF902293.4E-53153IPR000571Zinc finger, CCCH-type
SMARTSM003563.8E-43155IPR000571Zinc finger, CCCH-type
Gene3DG3DSA:4.10.1000.104.1E-43453IPR000571Zinc finger, CCCH-type
PROSITE profilePS5010312.746139166IPR000571Zinc finger, CCCH-type
SMARTSM003560.0092140165IPR000571Zinc finger, CCCH-type
PfamPF006421.6E-4142164IPR000571Zinc finger, CCCH-type
Gene3DG3DSA:3.30.40.102.9E-10201266IPR013083Zinc finger, RING/FYVE/PHD-type
SuperFamilySSF578501.33E-12202271No hitNo description
PfamPF136391.0E-7207265IPR001841Zinc finger, RING-type
CDDcd001620.00103207266No hitNo description
SMARTSM001847.7E-8208264IPR001841Zinc finger, RING-type
PROSITE profilePS5008912.519208265IPR001841Zinc finger, RING-type
PROSITE patternPS005180232241IPR017907Zinc finger, RING-type, conserved site
SMARTSM003560.22294322IPR000571Zinc finger, CCCH-type
PROSITE profilePS5010313.122294323IPR000571Zinc finger, CCCH-type
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0005515Molecular Functionprotein binding
GO:0008270Molecular Functionzinc ion binding
Sequence ? help Back to Top
Protein Sequence    Length: 361 aa     Download sequence    Send to blast
MSERVLCKFF AHGACLKGDH CEFSHDWNNP SNNVCTYYQK GACAYGSRCR YDHVKLSRSQ  60
PSAQSSAQPQ QCLLSSSTPI NVSPGMGAHN ADVLPGICTE YLASSRPYDA SSQSAWNQKS  120
ELQDALEIDD MIELNSDNPA DRSICAFAAA GNCPRGEKCP RVHGDLCPTC GKHCLHPFRP  180
EEREEHIKTC ENKQKHLDLL KRSQEIECSV CLERVLSKST AAERKFGILS ECDHPFCVSC  240
IRNWRGSSSS GMDVNSALRA CPICRKLSYF VIPSVIWYFT KEEKEEIVDN YKNKLRSIDC  300
KHFDFGNGTC PFGTSCFYKH QHRDGRVEEV VLRHLGSEDG STVIAKNIRL SDFLRNFEIR  360
*
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Les.167230.0fruit| leaf
Expression -- Description ? help Back to Top
Source Description
UniprotDEVELOPMENTAL STAGE: Expressed in dry seeds. Increased expression throughout imbibition and germination and when radicle and shoots are emerging. Up-regulated during cell differentiation. {ECO:0000269|PubMed:17870591}.
UniprotTISSUE SPECIFICITY: Expressed in primary roots and leaves. Detected in vascular bundle tissues. {ECO:0000269|PubMed:17870591}.
Functional Description ? help Back to Top
Source Description
UniProtE3 ubiquitin ligase catalyzing the covalent attachment of ubiquitin moieties onto substrate proteins. {ECO:0000250}.
Cis-element ? help Back to Top
SourceLink
PlantRegMapSolyc10g038000.1.1
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAC1717320.0Solanum lycopersicum chromosome 10 clone C10HBa0111D09, complete sequence
GenBankAC2402280.0Solanum lycopersicum strain Heinz 1706 chromosome 10 clone slm-141c17 map 10, complete sequence
GenBankAC2445790.0Solanum lycopersicum strain Heinz 1706 chromosome 10 clone hba-40g5 map 10, complete sequence
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqNP_001307876.10.0zinc finger transcription factor 57
RefseqXP_010327283.10.0zinc finger transcription factor 57 isoform X1
SwissprotE0X9N41e-164C3H69_ARATH; Putative RING-type E3 ubiquitin transferase C3H69
SwissprotQ5ZA071e-164C3H41_ORYSJ; E3 ubiquitin-protein ligase makorin
TrEMBLA0A0V0IGK50.0A0A0V0IGK5_SOLCH; Putative zinc finger CCCH domain-containing protein 69-like
STRINGSolyc10g038000.1.10.0(Solanum lycopersicum)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
AsteridsOGEA33862149
Representative plantOGRP40671523
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT3G08505.21e-149C3H 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. Wang Y,van der Hoeven RS,Nielsen R,Mueller LA,Tanksley SD
    Characteristics of the tomato nuclear genome as determined by sequencing undermethylated EcoRI digested fragments.
    Theor. Appl. Genet., 2005. 112(1): p. 72-84
    [PMID:16208505]
  3. Wang CT,Ho CH,Hseu MJ,Chen CM
    The subtelomeric region of the Arabidopsis thaliana chromosome IIIR contains potential genes and duplicated fragments from other chromosomes.
    Plant Mol. Biol., 2010. 74(1-2): p. 155-66
    [PMID:20652368]
  4. Sahi VP, et al.
    A molecular insight into Darwin's "plant brain hypothesis" through expression pattern study of the MKRN gene in plant embryo compared with mouse embryo.
    Plant Signal Behav, 2012. 7(3): p. 375-81
    [PMID:22499205]
  5. Wadekar HB,Sahi VP,Morita EH,Abe S
    MKRN expression pattern during embryonic and post-embryonic organogenesis in rice (Oryza sativa L. var. Nipponbare).
    Planta, 2013. 237(4): p. 1083-95
    [PMID:23262670]