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 GRMZM5G849788_P01
Organism
Zea mays
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; Liliopsida; Petrosaviidae; commelinids; Poales; Poaceae; PACMAD clade; Panicoideae; Andropogonodae; Andropogoneae; Tripsacinae; Zea
Family C3H
Protein Properties Length: 272aa    MW: 30417.9 Da    PI: 5.16
Description C3H family protein
Gene Model
Gene Model ID Type Source Coding Sequence
GRMZM5G849788_P01genomeMaizeSequenceView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-CCCH23.78.4e-08181200625
                        -SGGGGTS--TTTTT-SS-S CS
            zf-CCCH   6 CrffartGtCkyGdrCkFaH 25 
                        C+f+++tG C++G rC++ H
  GRMZM5G849788_P01 181 CPFHLKTGACRFGLRCSRVH 200
                        ******************99 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PROSITE profilePS5010311.77175203IPR000571Zinc finger, CCCH-type
PRINTSPR018487.3E-18181200IPR009145U2 auxiliary factor small subunit
PfamPF006427.4E-6181200IPR000571Zinc finger, CCCH-type
PRINTSPR018487.3E-18200220IPR009145U2 auxiliary factor small subunit
Gene3DG3DSA:3.30.70.3305.4E-5208260IPR012677Nucleotide-binding alpha-beta plait domain
PRINTSPR018487.3E-18236251IPR009145U2 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: 272 aa     Download sequence    Send to blast
MSALAAGGGA AADGAPEATA APTRREKRRE RKKERRRRAR RQAAARARAA VEAEAPAVDP  60
EEERRLLEIQ EAEAAAESER ALRAFEDAER RWLEAAAARA AEKAAAAAAE EDARAAEASA  120
RNKPKDGQGN QSEEDSEWEY VEDGPAEIIW KGNEIIVKKK KVKVPKGSKE KLQIQEDKAH  180
CPFHLKTGAC RFGLRCSRVH FYPDKSITLL MKNMYNGPGL ALEQDEGLEF TDEEIEQSYE  240
EFYEDVHTEF LKFGELVNFK GRGCLSEREL EN
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4yh8_A2e-161752561290Splicing factor U2AF 23 kDa subunit
Search in ModeBase
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
12735RRERKKERR
22741RRERKKERRRRARRQ
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Zm.683150.0endosperm| glume| meristem| shoot
Expression -- Microarray ? help Back to Top
Source ID
Expression AtlasGRMZM5G849788
Cis-element ? help Back to Top
SourceLink
PlantRegMapGRMZM5G849788_P01
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.
GenBankJN7914200.0JN791420.1 Zea mays rough endosperm 3 beta isoform 1 (Rgh3) mRNA, complete cds, alternatively spliced.
GenBankJN7914210.0JN791421.1 Zea mays rough endosperm 3 beta isoform 2 (Rgh3) mRNA, complete cds, alternatively spliced.
GenBankJN7914220.0JN791422.1 Zea mays rough endosperm 3 beta isoform 3 (Rgh3) mRNA, complete cds, alternatively spliced.
GenBankJN7914230.0JN791423.1 Zea mays rough endosperm 3 beta isoform 4 (Rgh3) mRNA, complete cds, alternatively spliced.
GenBankJN7914240.0JN791424.1 Zea mays rough endosperm 3 gamma isoform 1 (Rgh3) mRNA, complete cds, alternatively spliced.
GenBankJN7914250.0JN791425.1 Zea mays rough endosperm 3 gamma isoform 2 (Rgh3) mRNA, complete cds, alternatively spliced.
GenBankJN7914260.0JN791426.1 Zea mays rough endosperm 3 gamma isoform 3 (Rgh3) mRNA, complete cds, alternatively spliced.
GenBankJN7914270.0JN791427.1 Zea mays rough endosperm 3 gamma isoform 4 (Rgh3) mRNA, complete cds, alternatively spliced.
GenBankJN7914280.0JN791428.1 Zea mays rough endosperm 3 gamma isoform 5 (Rgh3) mRNA, complete cds, alternatively spliced.
GenBankJN7914290.0JN791429.1 Zea mays rough endosperm 3 gamma isoform 6 (Rgh3) mRNA, complete cds, alternatively spliced.
GenBankJN7914300.0JN791430.1 Zea mays rough endosperm 3 gamma isoform 7 (Rgh3) mRNA, complete cds, alternatively spliced.
GenBankJN7914310.0JN791431.1 Zea mays rough endosperm 3 gamma isoform 8 (Rgh3) mRNA, complete cds, alternatively spliced.
GenBankJN7914320.0JN791432.1 Zea mays rough endosperm 3 gamma isoform 9 (Rgh3) mRNA, complete cds, alternatively spliced.
GenBankJN7914360.0JN791436.1 Zea mays rough endosperm 3 epsilon isoform (Rgh3) mRNA, complete cds, alternatively spliced.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqNP_001241852.13e-98uncharacterized protein LOC100857066
SwissprotQ6YVX91e-81C3H16_ORYSJ; Zinc finger CCCH domain-containing protein 16
TrEMBLA0A1D6HAP70.0A0A1D6HAP7_MAIZE; Rough endosperm3
STRINGGRMZM5G849788_P010.0(Zea mays)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MonocotsOGMP92961317
Representative plantOGRP592666
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT1G10320.16e-40C3H 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]