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 Oropetium_20150105_11463A
Organism
Oropetium thomaeum
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; Liliopsida; Petrosaviidae; commelinids; Poales; Poaceae; PACMAD clade; Chloridoideae; Cynodonteae; Tripogoninae; Oropetium
Family C3H
Protein Properties Length: 761aa    MW: 87098.5 Da    PI: 8.3474
Description C3H family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Oropetium_20150105_11463AgenomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-CCCH22.52e-07238257625
                                -SGGGGTS--TTTTT-SS-S CS
                    zf-CCCH   6 CrffartGtCkyGdrCkFaH 25 
                                C+f+++tG C++G rC++ H
  Oropetium_20150105_11463A 238 CPFHLKTGACRFGVRCSRVH 257
                                ******************99 PP
2zf-CCCH24.16.2e-08367394126
                                --S---SGGGGTS..--TTTTT-SS-SS CS
                    zf-CCCH   1 yktelCrffartG..tCkyGdrCkFaHg 26 
                                +k ++C  ++r+   tC++G+ C+F+H+
  Oropetium_20150105_11463A 367 WKAAICGEYMRSRykTCSHGAACNFIHC 394
                                7889***********************8 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PROSITE profilePS512575117No hitNo description
PROSITE profilePS5010311.206232260IPR000571Zinc finger, CCCH-type
SMARTSM003562.6233259IPR000571Zinc finger, CCCH-type
PfamPF006422.6E-5238257IPR000571Zinc finger, CCCH-type
PRINTSPR018485.3E-36238257IPR009145U2 auxiliary factor small subunit
PRINTSPR018485.3E-36257277IPR009145U2 auxiliary factor small subunit
Gene3DG3DSA:3.30.70.3301.2E-24263362IPR012677Nucleotide-binding alpha-beta plait domain
PROSITE profilePS501029.098264364IPR000504RNA recognition motif domain
CDDcd125404.34E-49265362No hitNo description
SMARTSM003613.1E-4286360IPR003954RNA recognition motif domain, eukaryote
PRINTSPR018485.3E-36293308IPR009145U2 auxiliary factor small subunit
SuperFamilySSF549288.55E-16295362IPR012677Nucleotide-binding alpha-beta plait domain
PRINTSPR018485.3E-36321343IPR009145U2 auxiliary factor small subunit
PRINTSPR018485.3E-36348372IPR009145U2 auxiliary factor small subunit
PROSITE profilePS5010310.756366396IPR000571Zinc finger, CCCH-type
SMARTSM003560.03366395IPR000571Zinc finger, CCCH-type
PfamPF006421.6E-5367394IPR000571Zinc finger, CCCH-type
PRINTSPR018485.3E-36386398IPR009145U2 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: 761 aa     Download sequence    Send to blast
MTQARSLIHY GPSGTSCGHN ASERNSKEAS ALSPRPIPPF PVVFPRKERK KERRRRARRE  60
AAACARAAEA LAADPEEERR LLELEVAQAA EESERARQAF EDAERRWLQA AAARAAEKAA  120
AAEEAARAVE ASSQRKDVDG SNLEDDGDWE YVEDGPAEII WQGNEIIVKK KKVKVPKGVK  180
EKPEEERPTS NPLPPQSASL ASQRREPSLS AQEVLEKVAQ EIPNFGTEQA CTIDKAHCPF  240
HLKTGACRFG VRCSRVHFYP DKSCTLLMKH MYNGPGLALE QDEGLEFTDE EIEQSYEEFY  300
EDVHTEFLKF GELVNFKVCR NGSFHLRGNV YVHYKSLDSA LLAYNSMNGR YFAAKQISCE  360
FVALTKWKAA ICGEYMRSRY KTCSHGAACN FIHCFRNPGG DYEWADWDNP PPKYWIRKMT  420
ALFGLSADTK LSNIPDFEWS QGSERKRLKS SGDRYVLRRP KDEDGHKRHL SRDYSHSKEE  480
RGSHSMKNEQ GRHRRDPHAV DKHQNREIEG NTGRCSENGR ESHRHFLEER YGNDHSGGEK  540
GDGAKIRRKH LSDRQGSLEP RSSDWHSDYT DADLSKCSSG SRSTRRYDDH KRSRRQCSED  600
SNPEKQYSSM HRSREEHSTK RHSNHYTGDE YYDKKNDYYD EKNSGRGKSG KCRSHHNGSD  660
DRWVATNSDG DSDFGKYHRL SGKCSSRRKD DAHSDAEAQY QRSGMEAKDN KSRRKRHSEH  720
RQYSDTEEDT SYSDNTDSSS DAWSGRSRRS ENVSKHRARR *
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4yh8_A1e-302253939167Splicing factor U2AF 23 kDa subunit
Search in ModeBase
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
14553RKERKKERR
25259RRRRARRE
Cis-element ? help Back to Top
SourceLink
PlantRegMapOropetium_20150105_11463A
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.
GenBankJN7914170.0JN791417.1 Zea mays rough endosperm 3-umu1 alpha isoform (Rgh3) mRNA, Rgh3-umu1 allele, complete cds, alternatively spliced.
GenBankJN7914190.0JN791419.1 Zea mays rough endosperm 3 alpha isoform (Rgh3) mRNA, complete cds, alternatively spliced.
GenBankJN7914370.0JN791437.1 Zea mays rough endosperm 3 (Rgh3) mRNA, complete sequence; alternatively spliced.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_004952780.30.0LOW QUALITY PROTEIN: zinc finger CCCH domain-containing protein 16
SwissprotQ6YVX90.0C3H16_ORYSJ; Zinc finger CCCH domain-containing protein 16
TrEMBLA0A1D6HAP50.0A0A1D6HAP5_MAIZE; Rough endosperm3
STRINGTraes_5BL_938BFB459.20.0(Triticum aestivum)
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-139C3H 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]