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.4KG115700.2.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: 372aa    MW: 41743.2 Da    PI: 8.0514
Description C3H family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Pavir.4KG115700.2.pgenomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-CCCH18.82.9e-06628326
                         S---SGGGGTS--TTTTT-SS-SS CS
              zf-CCCH  3 telCrffartGtCkyGdrCkFaHg 26
                         ++lC+ff+  G C  G+ C F+H+
  Pavir.4KG115700.2.p  6 RVLCKFFMH-GACLKGEYCEFSHD 28
                         79***8888.*************5 PP
2zf-CCCH28.42.8e-093656526
                         --SGGGGTS--TTTTT-SS-SS CS
              zf-CCCH  5 lCrffartGtCkyGdrCkFaHg 26
                          C f+++ G C+yG+rC++ H+
  Pavir.4KG115700.2.p 36 VCTFYQK-GACSYGSRCRYDHV 56
                         5******.*************7 PP
3zf-CCCH19.32e-06154175426
                          ---SGGGGTS--TTTTT-SS-SS CS
              zf-CCCH   4 elCrffartGtCkyGdrCkFaHg 26 
                          ++C+ fa+ G C+yG+ C+ +Hg
  Pavir.4KG115700.2.p 154 PICS-FAAAGNCPYGEGCPQMHG 175
                          6788.*****************9 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PROSITE profilePS5010313.526330IPR000571Zinc finger, CCCH-type
SMARTSM003562.7E-5429IPR000571Zinc finger, CCCH-type
SuperFamilySSF902296.41E-7628IPR000571Zinc finger, CCCH-type
PROSITE profilePS5010314.2773158IPR000571Zinc finger, CCCH-type
SuperFamilySSF902295.36E-53355IPR000571Zinc finger, CCCH-type
SMARTSM003563.4E-43357IPR000571Zinc finger, CCCH-type
Gene3DG3DSA:4.10.1000.102.4E-43655IPR000571Zinc finger, CCCH-type
PfamPF006429.6E-73656IPR000571Zinc finger, CCCH-type
PROSITE profilePS5010312.343150177IPR000571Zinc finger, CCCH-type
SMARTSM003560.016151176IPR000571Zinc finger, CCCH-type
SuperFamilySSF578507.83E-12208283No hitNo description
Gene3DG3DSA:3.30.40.104.7E-10212278IPR013083Zinc finger, RING/FYVE/PHD-type
CDDcd001620.00132218278No hitNo description
PROSITE profilePS5008912.224219277IPR001841Zinc finger, RING-type
SMARTSM001842.8E-7219276IPR001841Zinc finger, RING-type
PfamPF000972.4E-7219276IPR018957Zinc finger, C3HC4 RING-type
PROSITE patternPS005180243252IPR017907Zinc finger, RING-type, conserved site
PROSITE profilePS5010313.676306335IPR000571Zinc finger, CCCH-type
SMARTSM003560.011306334IPR000571Zinc 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: 372 aa     Download sequence    Send to blast
MSASSRVLCK FFMHGACLKG EYCEFSHDWK DQANNVCTFY QKGACSYGSR CRYDHVKVSR  60
NPTVPLPSPS PSSSTARLAS TSRQLSSFGH PPRTGHQTDS STQRNQISVD VPAHSASKPA  120
WRNDFQHVVS EDGIDWSSNQ TLQNQTSLKP ADLPICSFAA AGNCPYGEGC PQMHGDLCST  180
CGKMCLHPYR PDEREEHIKL CEKNHKRLEA LKRSQEIECS VCLDRVLSKP TAAERKFGLL  240
SECDHPFCIA CIRNWRSNSP ASGMDVNSAL RACPICRKLS YYVIPSVLWY FSKEEKEEII  300
ESYKSKLKSI DCKYFDFGTG SCPFGTSCFY RHAYRDGRLE EVVLRHLDAD DGSTVIAKNI  360
RLSDFLSRMH L*
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.4KG115700.2.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
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
STRINGSi006712m0.0(Setaria italica)
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT3G08505.21e-138C3H 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]