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.4NG219700.5.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: 358aa    MW: 40219.4 Da    PI: 7.764
Description C3H family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Pavir.4NG219700.5.pgenomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-CCCH28.13.4e-092444526
                         --SGGGGTS--TTTTT-SS-SS CS
              zf-CCCH  5 lCrffartGtCkyGdrCkFaHg 26
                          C f+++ G C+yG+rC++ H+
  Pavir.4NG219700.5.p 24 VCTFYQK-GACSYGSRCRYDHV 44
                         5******.*************7 PP
2zf-CCCH19.41.9e-06140161426
                          ---SGGGGTS--TTTTT-SS-SS CS
              zf-CCCH   4 elCrffartGtCkyGdrCkFaHg 26 
                          ++C+ fa+ G C+yG+ C+ +Hg
  Pavir.4NG219700.5.p 140 PICS-FAAAGNCPYGEGCPQMHG 161
                          6788.*****************9 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PROSITE profilePS501038.681118IPR000571Zinc finger, CCCH-type
PROSITE profilePS5010313.9391946IPR000571Zinc finger, CCCH-type
SMARTSM003560.00112045IPR000571Zinc finger, CCCH-type
SuperFamilySSF902295.1E-52143IPR000571Zinc finger, CCCH-type
PfamPF006429.2E-72444IPR000571Zinc finger, CCCH-type
Gene3DG3DSA:4.10.1000.102.6E-42443IPR000571Zinc finger, CCCH-type
PROSITE profilePS5010312.343136163IPR000571Zinc finger, CCCH-type
SMARTSM003560.016137162IPR000571Zinc finger, CCCH-type
SuperFamilySSF578504.62E-12193269No hitNo description
Gene3DG3DSA:3.30.40.106.4E-9198264IPR013083Zinc finger, RING/FYVE/PHD-type
CDDcd001620.00168204264No hitNo description
PROSITE profilePS5008911.929205263IPR001841Zinc finger, RING-type
PfamPF000973.6E-6205262IPR018957Zinc finger, C3HC4 RING-type
SMARTSM001843.2E-6205262IPR001841Zinc finger, RING-type
PROSITE patternPS005180229238IPR017907Zinc finger, RING-type, conserved site
PROSITE profilePS5010313.676292321IPR000571Zinc finger, CCCH-type
SMARTSM003560.011292320IPR000571Zinc 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: 358 aa     Download sequence    Send to blast
MHGACLKGEY CEFSHDWKDQ VNNVCTFYQK GACSYGSRCR YDHVKVSRNP TVPLPSPSSS  60
TARPSSTYLQ LSSSGHPPRT GHQTDSKNQR NQISVDVPAH SASKPAWRND FQHVVSEDGI  120
DWSSNQTLQN QTSLKPADLP ICSFAAAGNC PYGEGCPQMH GDLCSTCGKM CLHPYRPDER  180
EEHIKLCEKN HKRLESLKRS QEIECSVCLD CVLSKPTAAE RKFGLLSECD HPFCIACIRN  240
WRSNSPASGM DVNSALRACP ICRKLSYYVI PSVLWYFSKE EKEEIIESYK SKLKSIDCKY  300
FDFGTGSCPF GTSCFYRHAY RDGRLEEVVL RHLDADDGST VIAKNIRLSD FLSRMHL*
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
1194199ESLKRS
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.4NG219700.5.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-131C3H 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]