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 maker-scaffold02226-augustus-gene-0.29-mRNA-1
Organism
Castanea mollissima
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; fabids; Fagales; Fagaceae; Castanea
Family C3H
Protein Properties Length: 880aa    MW: 104210 Da    PI: 6.4999
Description C3H family protein
Gene Model
Gene Model ID Type Source Coding Sequence
maker-scaffold02226-augustus-gene-0.29-mRNA-1genomeTHGPView Nucleic Acid
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-CCCH19.22.2e-06244263625
                                                    -SGGGGTS--TTTTT-SS-S CS
                                        zf-CCCH   6 CrffartGtCkyGdrCkFaH 25 
                                                    C+f+++tG C++G rC++ H
  maker-scaffold02226-augustus-gene-0.29-mRNA-1 244 CPFHLKTGACRFGQRCSRVH 263
                                                    ******************99 PP
2zf-CCCH24.54.5e-08398425126
                                                    --S---SGGGGTS..--TTTTT-SS-SS CS
                                        zf-CCCH   1 yktelCrffartG..tCkyGdrCkFaHg 26 
                                                    +k ++C  ++++   tC++G  C+F+H+
  maker-scaffold02226-augustus-gene-0.29-mRNA-1 398 WKVAICGEYMKSRfkTCSHGTACNFIHC 425
                                                    899************************8 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PROSITE profilePS5010312.23238266IPR000571Zinc finger, CCCH-type
SMARTSM003563.4239265IPR000571Zinc finger, CCCH-type
PfamPF006422.3E-4243263IPR000571Zinc finger, CCCH-type
PRINTSPR018485.1E-33244263IPR009145U2 auxiliary factor small subunit
PRINTSPR018485.1E-33263283IPR009145U2 auxiliary factor small subunit
Gene3DG3DSA:3.30.70.3304.0E-24269393IPR012677Nucleotide-binding alpha-beta plait domain
PROSITE profilePS501029.695299395IPR000504RNA recognition motif domain
SMARTSM003611.1E-4320391IPR003954RNA recognition motif domain, eukaryote
SuperFamilySSF549285.96E-16327396IPR012677Nucleotide-binding alpha-beta plait domain
PRINTSPR018485.1E-33352374IPR009145U2 auxiliary factor small subunit
PRINTSPR018485.1E-33379403IPR009145U2 auxiliary factor small subunit
PROSITE profilePS5010310.465397427IPR000571Zinc finger, CCCH-type
SMARTSM003560.016397426IPR000571Zinc finger, CCCH-type
PfamPF006422.2E-5398425IPR000571Zinc finger, CCCH-type
PRINTSPR018485.1E-33417429IPR009145U2 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: 880 aa     Download sequence    Send to blast
MAEPIAGKED EDEEEEKEEE REMMEEVEEE SVRKETEGMA ERMRRKEKRK AKKKMKRKQV  60
RKEMAEKERE EEEARLNDPE EQRKLRMMEE EEKERMERDR KEFEEREKAW IEAMEMKKKK  120
EEEEEEEEER RKKALEEDSR RQQQAENENE LNEDDDWEYV EGPAEIIWKG NEIIVKKKRV  180
KVPKKDANQQ RIDNADRPTS NPLPPQSEAF ADYKNAPKLS AEQIIENVTQ QVPNFGTEQD  240
KAHCPFHLKT GACRFGQRCS RVHFYPDKSC TLLIRNMYNG PGLAWEQDEG LELLLLLNHD  300
VTVSSMQNYM LLPILSYHTD EEVEGCFEEF YEDVHTEFLK FGEIVNFKVC KNGAFHLRGN  360
VYVQYKSLDS AVLVYNSING RYFAGKQISC EFVNVTRWKV AICGEYMKSR FKTCSHGTAC  420
NFIHCFRNPG GDYEWADFDK PPPRYWVRKM ASLFGYSDEV GYQKEVEQEN LGQLRHSRKR  480
LTDVDRYYSR SKSKEIDYLN GGGSSRRNDN KNDIQKSTQR RGRTSNDRKQ MEVLDKDMRG  540
ENMNFKGSYY RKSRSHDTDS DGEWSDRYKD RYYGSARKSS GHQNRDVNHR THEIESEGGY  600
SDRSEDRETH DGHARKSSRH SRNAKFVDDC EGQEKFGGNW SDRDGDQETH DAYMTKSSRH  660
RRKVGHPDDH MDSKNRTHDT DGEWSDGERD RDRHHRKRSE SSRHLRKVGH SDDHKDSKNR  720
SHDPEGEWSD RDTNRDRHHH KKRKSSRRDH DRGGSKNRAD DTNLSSDWLD SDGEKHKSQT  780
RKHTRHRNEV SDYSDHEGEP AKKLKDKYYS RESSIEKSGL ERGSMHSHSR WDSINENLES  840
DGSHESNSSD QYVQRHKSHD LESSYNSDKY IDKQDRWEPD
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4yh8_A8e-262354249167Splicing factor U2AF 23 kDa subunit
Search in ModeBase
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
14349RRKEKRK
24357RRKEKRKAKKKMKRK
34856RKAKKKMKR
45158KKKMKRKQ
5117132KKKEEEEEEEEERRKK
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAM4760953e-48AM476095.1 Vitis vinifera, whole genome shotgun sequence, contig VV78X038396.7, clone ENTAV 115.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_023904779.10.0zinc finger CCCH domain-containing protein 5 isoform X2
SwissprotQ9SY740.0C3H5_ARATH; Zinc finger CCCH domain-containing protein 5
TrEMBLA0A2N9HQF20.0A0A2N9HQF2_FAGSY; Uncharacterized protein
STRINGEMJ278120.0(Prunus persica)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
FabidsOGEF47132433
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT1G10320.11e-141C3H family protein
Publications ? help Back to Top
  1. Lorković ZJ,Wieczorek Kirk DA,Lambermon MH,Filipowicz W
    Pre-mRNA splicing in higher plants.
    Trends Plant Sci., 2000. 5(4): p. 160-7
    [PMID:10740297]
  2. Domon C,Lorković ZJ,Valcárcel J,Filipowicz W
    Multiple forms of the U2 small nuclear ribonucleoprotein auxiliary factor U2AF subunits expressed in higher plants.
    J. Biol. Chem., 1998. 273(51): p. 34603-10
    [PMID:9852132]