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 Sobic.004G259300.1.p
Common NameSb04g029760, SORBIDRAFT_04g029760
Organism
Sorghum bicolor
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; Liliopsida; Petrosaviidae; commelinids; Poales; Poaceae; PACMAD clade; Panicoideae; Andropogonodae; Andropogoneae; Sorghinae; Sorghum
Family C3H
Protein Properties Length: 366aa    MW: 40889.7 Da    PI: 7.2355
Description C3H family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Sobic.004G259300.1.pgenomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-CCCH17.38.6e-063450522
                          --SGGGGTS--TTTTT-S CS
               zf-CCCH  5 lCrffartGtCkyGdrCk 22
                           C f+++ G C++G+rC+
  Sobic.004G259300.1.p 34 VCTFYQK-GACSFGSRCR 50
                          5******.*********7 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PROSITE profilePS5010314.192128IPR000571Zinc finger, CCCH-type
SMARTSM003560.006227IPR000571Zinc finger, CCCH-type
SuperFamilySSF902291.22E-5426IPR000571Zinc finger, CCCH-type
PROSITE profilePS5010313.4132956IPR000571Zinc finger, CCCH-type
SMARTSM003560.00583155IPR000571Zinc finger, CCCH-type
PROSITE profilePS501038.502144171IPR000571Zinc finger, CCCH-type
SMARTSM003566.8146170IPR000571Zinc finger, CCCH-type
SuperFamilySSF578503.53E-14200277No hitNo description
Gene3DG3DSA:3.30.40.103.7E-10206272IPR013083Zinc finger, RING/FYVE/PHD-type
CDDcd001620.00187212272No hitNo description
PfamPF136394.1E-8212271IPR001841Zinc finger, RING-type
PROSITE profilePS5008912.297213271IPR001841Zinc finger, RING-type
SMARTSM001849.3E-7213270IPR001841Zinc finger, RING-type
PROSITE patternPS005180237246IPR017907Zinc finger, RING-type, conserved site
PROSITE profilePS5010314.314300329IPR000571Zinc finger, CCCH-type
SMARTSM003560.028300328IPR000571Zinc 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: 366 aa     Download sequence    Send to blast
MSRRVPCKFF LHGACFKGDY CEFSHDCNDQ PDNVCTFYQK GACSFGSRCR NEHVEAHRDC  60
PQPATTAARA SPNSSQLVAS SRDPRCSGCQ TDMCDQTQQI CKSTTTLSAH QPAWAVDYHD  120
NDTPDDTTSW PSYQAVQNQT SQHPAHLSNC SSAAVGTCPY GKDCSQMHGD LCAFCERQSL  180
NPNQPDERGV HVKLCKKNNR YLEAMRKSED IECGVCLDRV LSKPTAAERR FGLLSDCDHS  240
FCISCIRNWR STSPTSGMDV NSTLRACPIC RKLSYYVVPS ITWYSSKEEK QEIVEGYKAK  300
LRSIDCKHFD FGKGTCPFGS SCFYKHAYDD GRLEDALLNH HDAEDASAAI ARLMRLSYLL  360
TRVHV*
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Sbi.130710.0ovary| pollen
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
PlantRegMapSobic.004G259300.1.p
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankBT0545500.0BT054550.1 Zea mays full-length cDNA clone ZM_BFc0152O03 mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_002452642.10.0E3 ubiquitin-protein ligase makorin
SwissprotQ5ZA071e-161C3H41_ORYSJ; E3 ubiquitin-protein ligase makorin
TrEMBLC5XZU90.0C5XZU9_SORBI; Uncharacterized protein
STRINGSb04g029760.10.0(Sorghum bicolor)
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT3G08505.21e-126C3H 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. 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]
  3. 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]