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 Pavir.1NG461800.2.p
Organism
Panicum virgatum
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; Liliopsida; Petrosaviidae; commelinids; Poales; Poaceae; PACMAD clade; Panicoideae; Panicodae; Paniceae; Panicinae; Panicum
Family C3H
Protein Properties Length: 360aa    MW: 40215.1 Da    PI: 7.2606
Description C3H family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Pavir.1NG461800.2.pgenomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-CCCH18.24.4e-061481631126
                          GTS--TTTTT-SS-SS CS
              zf-CCCH  11 rtGtCkyGdrCkFaHg 26 
                          + GtC+yG  C+ +Hg
  Pavir.1NG461800.2.p 148 AAGTCPYGKDCSQMHG 163
                          57*************9 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SMARTSM003560.67127IPR000571Zinc finger, CCCH-type
PROSITE profilePS5010313.479128IPR000571Zinc finger, CCCH-type
SuperFamilySSF902292.88E-5426IPR000571Zinc finger, CCCH-type
SMARTSM00356162849IPR000571Zinc finger, CCCH-type
PROSITE profilePS501037.4133350IPR000571Zinc finger, CCCH-type
PROSITE profilePS5010311.066138165IPR000571Zinc finger, CCCH-type
SMARTSM003560.68138164IPR000571Zinc finger, CCCH-type
SuperFamilySSF578502.44E-14193271No hitNo description
Gene3DG3DSA:3.30.40.105.0E-10201266IPR013083Zinc finger, RING/FYVE/PHD-type
CDDcd001620.00161206266No hitNo description
PfamPF136394.0E-8206265IPR001841Zinc finger, RING-type
SMARTSM001849.3E-7207264IPR001841Zinc finger, RING-type
PROSITE profilePS5008912.297207265IPR001841Zinc finger, RING-type
PROSITE patternPS005180231240IPR017907Zinc finger, RING-type, conserved site
SMARTSM003560.028294322IPR000571Zinc finger, CCCH-type
PROSITE profilePS5010314.202294323IPR000571Zinc 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: 360 aa     Download sequence    Send to blast
MSKRVPCKFF LHGGCYKGDY CDFSHDCNDR PDNKGACSFG SRCRNEHVEV HRNRLQPETT  60
AALISSNSSQ LVNSSGGPHC SECQKDQCDQ TQQICKSTTA LSAQQPAWAD DYHQHDAPED  120
ANSWPSYQTV ENQTSQHPAH MPLCSSAAAG TCPYGKDCSQ MHGDLCTFCE KQCLHPHRPD  180
ESGLHVELCK KNNRLLEALR KGEDIECGVC LDRVLSKPTA AERRFGLLSD CDHSFCISCI  240
RNWRSTSPTS GMDVNSTLRA CPICRKLSYY VVPSTTWYSS KEEKQEIIEG YKAKLRSIDC  300
KHFDFGKGTC PFGSSCFYKH AYRDGRLEEA LLNHNDADGA RAAIARLMRL SYLLTRLDV*
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Pvr.186430.0callus| leaf| 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
PlantRegMapPavir.1NG461800.2.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_025798941.10.0E3 ubiquitin-protein ligase makorin-like isoform X2
SwissprotQ5ZA071e-158C3H41_ORYSJ; E3 ubiquitin-protein ligase makorin
TrEMBLA0A2T7FBC60.0A0A2T7FBC6_9POAL; Uncharacterized protein
STRINGPavir.Aa00659.1.p0.0(Panicum virgatum)
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT3G08505.21e-118C3H 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]