PlantTFDB
PlantRegMap/PlantTFDB v5.0
Plant Transcription Factor Database
Home  TFext  BLAST  Prediction  Download  Help  About  Links  PlantRegMap
(e.g., LFY)
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID Sobic.010G131900.1.p
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: 371aa    MW: 41692.1 Da    PI: 7.7808
Description C3H family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Sobic.010G131900.1.pgenomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-CCCH192.4e-06427226
                          -S---SGGGGTS--TTTTT-SS-SS CS
               zf-CCCH  2 ktelCrffartGtCkyGdrCkFaHg 26
                          k +lC+ff+  G C  G+ C F+H+
  Sobic.010G131900.1.p  4 KKVLCKFFMH-GACLKGEYCEFSHD 27
                          789***8888.*************5 PP
2zf-CCCH28.42.8e-093555526
                          --SGGGGTS--TTTTT-SS-SS CS
               zf-CCCH  5 lCrffartGtCkyGdrCkFaHg 26
                           C f+++ G C+yG+rC++ H+
  Sobic.010G131900.1.p 35 VCTFYQK-GACSYGSRCRYDHV 55
                          5******.*************7 PP
3zf-CCCH19.32e-06153174426
                           ---SGGGGTS--TTTTT-SS-SS CS
               zf-CCCH   4 elCrffartGtCkyGdrCkFaHg 26 
                           ++C+ fa+ G C+yG+ C+ +Hg
  Sobic.010G131900.1.p 153 PICS-FAAAGNCPYGEGCPQMHG 174
                           6788.*****************9 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SMARTSM003562.6E-5228IPR000571Zinc finger, CCCH-type
PROSITE profilePS5010314.023229IPR000571Zinc finger, CCCH-type
SuperFamilySSF902294.19E-7327IPR000571Zinc finger, CCCH-type
Gene3DG3DSA:4.10.1000.107.2E-4430IPR000571Zinc finger, CCCH-type
PROSITE profilePS5010314.2773057IPR000571Zinc finger, CCCH-type
SMARTSM003563.4E-43256IPR000571Zinc finger, CCCH-type
SuperFamilySSF902294.71E-53254IPR000571Zinc finger, CCCH-type
PfamPF006429.6E-73555IPR000571Zinc finger, CCCH-type
Gene3DG3DSA:4.10.1000.102.3E-43554IPR000571Zinc finger, CCCH-type
PROSITE profilePS5010312.343149176IPR000571Zinc finger, CCCH-type
SMARTSM003560.016150175IPR000571Zinc finger, CCCH-type
SuperFamilySSF578501.6E-11207282No hitNo description
Gene3DG3DSA:3.30.40.104.7E-10211277IPR013083Zinc finger, RING/FYVE/PHD-type
CDDcd001620.00104217277No hitNo description
SMARTSM001842.8E-7218275IPR001841Zinc finger, RING-type
PfamPF000972.4E-7218275IPR018957Zinc finger, C3HC4 RING-type
PROSITE profilePS5008912.224218276IPR001841Zinc finger, RING-type
PROSITE patternPS005180242251IPR017907Zinc finger, RING-type, conserved site
SMARTSM003560.011305333IPR000571Zinc finger, CCCH-type
PROSITE profilePS5010313.676305334IPR000571Zinc 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: 371 aa     Download sequence    Send to blast
MATKKVLCKF FMHGACLKGE YCEFSHDWSD QANNVCTFYQ KGACSYGSRC RYDHVKVSRN  60
PTVPPPPSTS SAARRVTSNS LQLLSYSHAP HTGHQTDSSN QRHQISVDVL AHSASKPAWR  120
NDFQHDIVSD DGIDWSSNRN LLNETSLKPA DLPICSFAAA GNCPYGEGCP QMHGDLCATC  180
GKMCLHPHRP DEREEHIKVC EKNHKRLEAL KRSQEIECSV CLDRVLSKPT AAERKFGLLS  240
ECDHPFCIAC IRNWRSNSPA SGMDVNSALR ACPICRKLSY YVIPSVLWYF SKEEKEEITE  300
SYKSKLKSID CKYFDFGTGS CPFGTSCFYR HAYRDGRLEE VVLRHLDADD GSTVIAKDIR  360
LSDFLGRMHL *
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Sbi.58553e-47callus| embryo| panicle| 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.010G131900.1.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
GenBankBT0656290.0BT065629.1 Zea mays full-length cDNA clone ZM_BFb0371O01 mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_021305364.10.0E3 ubiquitin-protein ligase makorin isoform X1
SwissprotQ5ZA070.0C3H41_ORYSJ; E3 ubiquitin-protein ligase makorin
TrEMBLA0A194YIW90.0A0A194YIW9_SORBI; Uncharacterized protein
STRINGSb10g012170.20.0(Sorghum bicolor)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MonocotsOGMP53263356
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. 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]