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 Solyc01g087030.2.1
Common NameLOC101268612
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: 40999.9 Da    PI: 8.4868
Description C3H family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Solyc01g087030.2.1genomeITAGView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-CCCH215.9e-073454526
                        --SGGGGTS--TTTTT-SS-SS CS
             zf-CCCH  5 lCrffartGtCkyGdrCkFaHg 26
                         C ++++ G C yG+rC++ H+
  Solyc01g087030.2.1 34 VCTYYQK-GLCAYGNRCRYRHV 54
                        5******.***********997 PP
2zf-CCCH17.66.9e-06141163326
                         S---SGGGGTS--TTTTT-SS-SS CS
             zf-CCCH   3 telCrffartGtCkyGdrCkFaHg 26 
                         +++C+  a+ G C++ ++C+++Hg
  Solyc01g087030.2.1 141 RSICS-LAAAGKCPREEQCPYIHG 163
                         56788.999**************9 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PROSITE profilePS5010312.634128IPR000571Zinc finger, CCCH-type
SMARTSM003561.0E-4227IPR000571Zinc finger, CCCH-type
SuperFamilySSF902291.13E-6426IPR000571Zinc finger, CCCH-type
PROSITE profilePS5010314.6712956IPR000571Zinc finger, CCCH-type
SMARTSM003560.00113055IPR000571Zinc finger, CCCH-type
SuperFamilySSF902291.16E-53253IPR000571Zinc finger, CCCH-type
Gene3DG3DSA:4.10.1000.102.4E-43453IPR000571Zinc finger, CCCH-type
PfamPF006422.2E-43454IPR000571Zinc finger, CCCH-type
PROSITE profilePS5010311.798138165IPR000571Zinc finger, CCCH-type
SMARTSM003560.64139164IPR000571Zinc finger, CCCH-type
SuperFamilySSF578501.83E-12198271No hitNo description
Gene3DG3DSA:3.30.40.102.1E-10200266IPR013083Zinc finger, RING/FYVE/PHD-type
CDDcd001623.49E-4206266No hitNo description
PfamPF000972.1E-7207264IPR018957Zinc finger, C3HC4 RING-type
SMARTSM001842.8E-7207264IPR001841Zinc finger, RING-type
PROSITE profilePS5008912.593207265IPR001841Zinc finger, RING-type
PROSITE patternPS005180231240IPR017907Zinc finger, RING-type, conserved site
PROSITE profilePS5010313.441294323IPR000571Zinc finger, CCCH-type
SMARTSM003560.18294322IPR000571Zinc 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
MSRRVLCKFF VNGACLKGEY CEFSHHWKDP PNNVCTYYQK GLCAYGNRCR YRHVKVSEQH  60
SLPSSSAPAQ HLFSASPPTT LSPGMLADGT GILSGISSEY LASGRPFYPP NQPVWSENSE  120
HHDAAVIDNI VELKRMNPAD RSICSLAAAG KCPREEQCPY IHGDLCPICA KNCLHPFRPQ  180
EREEHIRICE KRQKRLELLK HSQEIECSVC LERVLSKTTA AERKFGILFE CDHPFCISCI  240
RNWRSGTPSS GVDINSTFRT CPICRKLSYF VIPSVTWFST KEEKQIILDS YKAKLRSIDC  300
KHYDFGNGTC PFGNSCFYKH QYRDGHLEEV VPRHLGHENG RTLIAKNIRL SDLLGNLRRR  360
*
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Les.125210.0callus| flower| fruit| leaf| root| seed| stem
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
PlantRegMapSolyc01g087030.2.1
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqNP_001334310.10.0CCCH zinc finger familyprotein
SwissprotQ5ZA071e-154C3H41_ORYSJ; E3 ubiquitin-protein ligase makorin
TrEMBLA0A3Q7EIT00.0A0A3Q7EIT0_SOLLC; Uncharacterized protein
STRINGSolyc01g087030.2.10.0(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-147C3H 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. 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]
  4. 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]