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.4NG219700.3.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: 369aa    MW: 41547 Da    PI: 7.9435
Description C3H family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Pavir.4NG219700.3.pgenomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-CCCH18.24.5e-06527326
                         S---SGGGGTS--TTTTT-SS-SS CS
              zf-CCCH  3 telCrffartGtCkyGdrCkFaHg 26
                         ++lC+ff+  G C  G+ C F+H+
  Pavir.4NG219700.3.p  5 RVLCKFFMH-GACLKGEYCEFSHD 27
                         78***8888.*************5 PP
2zf-CCCH28.13.6e-093555526
                         --SGGGGTS--TTTTT-SS-SS CS
              zf-CCCH  5 lCrffartGtCkyGdrCkFaHg 26
                          C f+++ G C+yG+rC++ H+
  Pavir.4NG219700.3.p 35 VCTFYQK-GACSYGSRCRYDHV 55
                         5******.*************7 PP
3zf-CCCH19.32e-06151172426
                          ---SGGGGTS--TTTTT-SS-SS CS
              zf-CCCH   4 elCrffartGtCkyGdrCkFaHg 26 
                          ++C+ fa+ G C+yG+ C+ +Hg
  Pavir.4NG219700.3.p 151 PICS-FAAAGNCPYGEGCPQMHG 172
                          6788.*****************9 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PROSITE profilePS5010313.77229IPR000571Zinc finger, CCCH-type
SuperFamilySSF902294.97E-7327IPR000571Zinc finger, CCCH-type
SMARTSM003564.9E-5328IPR000571Zinc finger, CCCH-type
PROSITE profilePS5010313.9393057IPR000571Zinc finger, CCCH-type
SMARTSM003560.00113156IPR000571Zinc finger, CCCH-type
SuperFamilySSF902295.23E-53254IPR000571Zinc finger, CCCH-type
Gene3DG3DSA:4.10.1000.102.7E-43554IPR000571Zinc finger, CCCH-type
PfamPF006429.5E-73555IPR000571Zinc finger, CCCH-type
PROSITE profilePS5010312.343147174IPR000571Zinc finger, CCCH-type
SMARTSM003560.016148173IPR000571Zinc finger, CCCH-type
SuperFamilySSF578501.21E-11204280No hitNo description
Gene3DG3DSA:3.30.40.106.7E-9209275IPR013083Zinc finger, RING/FYVE/PHD-type
CDDcd001620.00218215275No hitNo description
PfamPF000973.7E-6216273IPR018957Zinc finger, C3HC4 RING-type
SMARTSM001843.2E-6216273IPR001841Zinc finger, RING-type
PROSITE profilePS5008911.929216274IPR001841Zinc finger, RING-type
PROSITE patternPS005180240249IPR017907Zinc finger, RING-type, conserved site
SMARTSM003560.011303331IPR000571Zinc finger, CCCH-type
PROSITE profilePS5010313.676303332IPR000571Zinc 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: 369 aa     Download sequence    Send to blast
MSTNRVLCKF FMHGACLKGE YCEFSHDWKD QVNNVCTFYQ KGACSYGSRC RYDHVKVSRN  60
PTVPLPSPSS STARPSSTYL QLSSSGHPPR TGHQTDSKNQ RNQISVDVPA HSASKPAWRN  120
DFQHVVSEDG IDWSSNQTLQ NQTSLKPADL PICSFAAAGN CPYGEGCPQM HGDLCSTCGK  180
MCLHPYRPDE REEHIKLCEK NHKRLESLKR SQEIECSVCL DCVLSKPTAA ERKFGLLSEC  240
DHPFCIACIR NWRSNSPASG MDVNSALRAC PICRKLSYYV IPSVLWYFSK EEKEEIIESY  300
KSKLKSIDCK YFDFGTGSCP FGTSCFYRHA YRDGRLEEVV LRHLDADDGS TVIAKNIRLS  360
DFLSRMHL*
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
1205210ESLKRS
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Pvr.10940.0callus| leaf| root
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.4NG219700.3.p
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_004965338.10.0E3 ubiquitin-protein ligase makorin
SwissprotQ5ZA070.0C3H41_ORYSJ; E3 ubiquitin-protein ligase makorin
TrEMBLK3XXQ20.0K3XXQ2_SETIT; Uncharacterized protein
STRINGPavir.J40916.1.p0.0(Panicum virgatum)
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT3G08505.21e-137C3H 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]