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.1KG481300.1.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: 366aa    MW: 40911.8 Da    PI: 7.1957
Description C3H family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Pavir.1KG481300.1.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+
  Pavir.1KG481300.1.p 34 VCTFYQK-GACSFGSRCR 50
                         5******.*********7 PP
2zf-CCCH18.24.5e-061541691126
                          GTS--TTTTT-SS-SS CS
              zf-CCCH  11 rtGtCkyGdrCkFaHg 26 
                          + GtC+yG  C+ +Hg
  Pavir.1KG481300.1.p 154 AAGTCPYGKDCSQMHG 169
                          57*************9 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PROSITE profilePS5010314.023128IPR000571Zinc finger, CCCH-type
SMARTSM003560.083127IPR000571Zinc finger, CCCH-type
SuperFamilySSF902291.19E-5426IPR000571Zinc finger, CCCH-type
PROSITE profilePS5010313.312956IPR000571Zinc finger, CCCH-type
SMARTSM003560.0033055IPR000571Zinc finger, CCCH-type
PROSITE profilePS5010311.066144171IPR000571Zinc finger, CCCH-type
SMARTSM003560.68144170IPR000571Zinc finger, CCCH-type
SuperFamilySSF578502.72E-13198277No hitNo description
Gene3DG3DSA:3.30.40.103.5E-10207272IPR013083Zinc finger, RING/FYVE/PHD-type
CDDcd001620.00136212272No hitNo description
PfamPF136395.5E-8212271IPR001841Zinc finger, RING-type
PROSITE profilePS5008912.297213271IPR001841Zinc finger, RING-type
SMARTSM001841.2E-6213270IPR001841Zinc finger, RING-type
PROSITE patternPS005180237246IPR017907Zinc finger, RING-type, conserved site
PROSITE profilePS5010313.516300329IPR000571Zinc finger, CCCH-type
SMARTSM003560.067300328IPR000571Zinc 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
MSKRVPCKFF LHGACYKGDY CEFSHDCNDR PDNVCTFYQK GACSFGSRCR NEHVEIHWNR  60
PQPATTAAHV SSNSSQLVAS SGGPHCSECQ TDQCDQTQQI CKSTTTHSAQ QPAWADDYHE  120
HDTPGDANSW PSDQAVENQT SQHPAHMPLC SSAAAGTCPY GKDCSQMHGD LCTFCEKQCL  180
HPHRPDESGL HVELCKKNNR LLEALRKSED IECGVCLDRV LSKPMAAERR FGLLSDCDHS  240
FCISCIRNWR STSPTSGMDV NSTLRACPIC RKLSYYVVPS TTWYSSKEEK QEIIEGYKAK  300
LRSIDCKHFD FGKGTCPFGG SCFYKHAYRD GRLEEALLNH NDADGARATI ARLMRLSYLL  360
TRLHV*
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.1KG481300.1.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_025798940.10.0E3 ubiquitin-protein ligase makorin-like isoform X1
SwissprotQ5ZA071e-166C3H41_ORYSJ; E3 ubiquitin-protein ligase makorin
TrEMBLA0A2T7FBC20.0A0A2T7FBC2_9POAL; Uncharacterized protein
STRINGPavir.Ab03056.1.p0.0(Panicum virgatum)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MonocotsOGMP53263356
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT3G08505.21e-128C3H 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]