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.1NG291400.1.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: 751aa    MW: 85186.8 Da    PI: 8.6495
Description C3H family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Pavir.1NG291400.1.pgenomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-CCCH22.91.5e-07226245625
                          -SGGGGTS--TTTTT-SS-S CS
              zf-CCCH   6 CrffartGtCkyGdrCkFaH 25 
                          C+f+++tG C++G rC++ H
  Pavir.1NG291400.1.p 226 CPFHLKTGACRFGVRCSRVH 245
                          ******************99 PP
2zf-CCCH23.11.3e-07355382126
                          --S---SGGGGTS..--TTTTT-SS-SS CS
              zf-CCCH   1 yktelCrffartG..tCkyGdrCkFaHg 26 
                          +k ++C  ++r+   tC++G  C+F+H+
  Pavir.1NG291400.1.p 355 WKAAICGEYMRSKykTCSHGVACNFIHC 382
                          7889***********************8 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PROSITE profilePS5010311.807220248IPR000571Zinc finger, CCCH-type
SMARTSM003562221247IPR000571Zinc finger, CCCH-type
PfamPF006421.9E-5225245IPR000571Zinc finger, CCCH-type
PRINTSPR018481.2E-37226245IPR009145U2 auxiliary factor small subunit
PRINTSPR018481.2E-37245265IPR009145U2 auxiliary factor small subunit
PROSITE profilePS501029.985252352IPR000504RNA recognition motif domain
Gene3DG3DSA:3.30.70.3303.9E-24252350IPR012677Nucleotide-binding alpha-beta plait domain
CDDcd125406.19E-50253350No hitNo description
SMARTSM003611.1E-5274348IPR003954RNA recognition motif domain, eukaryote
PRINTSPR018481.2E-37281296IPR009145U2 auxiliary factor small subunit
SuperFamilySSF549281.37E-15283351IPR012677Nucleotide-binding alpha-beta plait domain
PRINTSPR018481.2E-37309331IPR009145U2 auxiliary factor small subunit
PRINTSPR018481.2E-37336360IPR009145U2 auxiliary factor small subunit
PROSITE profilePS5010310.08354384IPR000571Zinc finger, CCCH-type
SMARTSM003560.072354383IPR000571Zinc finger, CCCH-type
PfamPF006423.0E-5355382IPR000571Zinc finger, CCCH-type
PRINTSPR018481.2E-37374386IPR009145U2 auxiliary factor small subunit
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0000398Biological ProcessmRNA splicing, via spliceosome
GO:0089701Cellular ComponentU2AF
GO:0000166Molecular Functionnucleotide binding
GO:0003723Molecular FunctionRNA binding
GO:0046872Molecular Functionmetal ion binding
Sequence ? help Back to Top
Protein Sequence    Length: 751 aa     Download sequence    Send to blast
MSASATAAGS EAAGPPEAAA AAGASRKEKR RERKKERRRR ARREAAARAR AADALAADPE  60
EERRLLEQEE AEAAAESERA RRAFEDAERR WLEAAAARAA EKAAAAAAAA EEARAAEAST  120
RQKSKDDHGN ESEEDGEWEY IEDGPAEIIW QGNEIIVKKK KVKVPKGGKE KPPIQEEDRP  180
TSNPLPPQSV AFAAQRTEPP MSAQEVLEKV AQETPNFGTE QDKAHCPFHL KTGACRFGVR  240
CSRVHFYPDK SSTLLMKNMY NGPGLALEQD EGLEFTDEEI EQSYEEFYED VHTEFLKFGE  300
LANFKVCRNG SFHLRGNVYV HYKSLDSALL SYSSMNGRYF AGKQITCEFV AVTRWKAAIC  360
GEYMRSKYKT CSHGVACNFI HCFRNPGGDY EWADWDNPPP RYWIRKMAAL FGPTADTMHD  420
KPSDTPAFER PQRSDRKRLK NSSDRYVSRR SLDEDVHPHS SRGYSRSSRS MNYEYSRHRR  480
GSSASDRHQG QDTVDTNGRQ FSITENESHP RKHKHEERRR SDHGDGGKYD DRIRSRKHRS  540
DRREPGSSDW PSDLTDTDVS KDPSGGKSSS RYDDHEKSRR KSSEDQSLEG RCTAHKSSGK  600
EHSSRRGSKH GTEDDYYDEK DGGRGKSRKH KDGNKYSDDR WVATYSDADS DVERYQRSSS  660
GGTKSGRKDD AHSDAEVRHQ RSSRRRKDDN RRRKTHSGNK QLSTTEEDTT DSDTRDLSSD  720
SWSCRSRSSE ENFSTLRSKR KRSQSKEKVE *
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4yh8_A2e-332173819167Splicing factor U2AF 23 kDa subunit
Search in ModeBase
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
12937RRERKKERR
23643RRRRARRE
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Pvr.171900.0root| stem
Cis-element ? help Back to Top
SourceLink
PlantRegMapPavir.1NG291400.1.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
GenBankJF6811440.0JF681144.1 Zea mays RGH3 splicing factor mRNA, complete cds.
GenBankJN7914190.0JN791419.1 Zea mays rough endosperm 3 alpha isoform (Rgh3) mRNA, complete cds, alternatively spliced.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_025808935.10.0zinc finger CCCH domain-containing protein 16
SwissprotQ6YVX90.0C3H16_ORYSJ; Zinc finger CCCH domain-containing protein 16
TrEMBLA0A2S3GPX50.0A0A2S3GPX5_9POAL; Uncharacterized protein
STRINGPavir.J30896.1.p0.0(Panicum virgatum)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MonocotsOGMP92961317
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT1G10320.11e-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]