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 XP_013604855.1
Organism
Brassica oleracea
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Brassiceae; Brassica
Family C3H
Protein Properties Length: 739aa    MW: 86756 Da    PI: 7.2447
Description C3H family protein
Gene Model
Gene Model ID Type Source Coding Sequence
XP_013604855.1genomeNCBIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-CCCH23.21.2e-07227246625
                     -SGGGGTS--TTTTT-SS-S CS
         zf-CCCH   6 CrffartGtCkyGdrCkFaH 25 
                     C+f+++tG C++G+rC++ H
  XP_013604855.1 227 CPFHLKTGACRFGPRCSRVH 246
                     ******************99 PP
2zf-CCCH29.11.7e-09356383126
                     --S---SGGGGTS..--TTTTT-SS-SS CS
         zf-CCCH   1 yktelCrffartG..tCkyGdrCkFaHg 26 
                     +k ++C  f+++   tC++G+ C+F+H+
  XP_013604855.1 356 WKVAICGEFMKSRlkTCSRGSACNFIHC 383
                     899************************8 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PROSITE profilePS5010312.681221249IPR000571Zinc finger, CCCH-type
SMARTSM003561.1222248IPR000571Zinc finger, CCCH-type
PfamPF006421.5E-5226246IPR000571Zinc finger, CCCH-type
PRINTSPR018481.4E-37227246IPR009145U2 auxiliary factor small subunit
PRINTSPR018481.4E-37246266IPR009145U2 auxiliary factor small subunit
Gene3DG3DSA:3.30.70.3301.0E-26252351IPR012677Nucleotide-binding alpha-beta plait domain
PROSITE profilePS501029.661253353IPR000504RNA recognition motif domain
CDDcd125401.03E-49254352No hitNo description
SMARTSM003614.4E-5275349IPR003954RNA recognition motif domain, eukaryote
PRINTSPR018481.4E-37282297IPR009145U2 auxiliary factor small subunit
SuperFamilySSF549281.34E-16285353IPR012677Nucleotide-binding alpha-beta plait domain
PRINTSPR018481.4E-37310332IPR009145U2 auxiliary factor small subunit
PRINTSPR018481.4E-37337361IPR009145U2 auxiliary factor small subunit
SMARTSM003560.015355384IPR000571Zinc finger, CCCH-type
PROSITE profilePS5010311.413355385IPR000571Zinc finger, CCCH-type
PfamPF006423.0E-7356383IPR000571Zinc finger, CCCH-type
PRINTSPR018481.4E-37375387IPR009145U2 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: 739 aa     Download sequence    Send to blast
MEPRNEKEEG ERLEEAMGGF EESKEKSAEM SRKEKRKAMK KMKRKQVRKE IASKEREEAE  60
AKLNDPAEQE KLKAIEEEEE RKREKELREF EESERAWREA MEIKRKKEEE EERRWKELEE  120
LRKLEASGDD ECGEDDDGEY EYIEEGPPEI IFQGNEIILR KNKVKVPKRS VAQVEGNEIA  180
DRPTSNPLPP GTEAFPKNHN VSSAQQILDS VAQEVPNFGT EQDKAHCPFH LKTGACRFGP  240
RCSRVHFYPD KSCTILMKNM YNGPGIAWEQ DEGLEYTDEE AEQCYEEFYE DVHTEFLKYG  300
ELINFKVCRN GSFHLKGNVY VHYRSLESAM LAYQSINGRY FAGKQVNCEF VNISRWKVAI  360
CGEFMKSRLK TCSRGSACNF IHCFRNPGGD YEWADFDKPP PRFWIRKMAA LFGYSDEDLK  420
HMEREYSGSL SEFRSDQPSD SQRQASRRSR SRDHDHVNVG SKPSYRSRKN HGDTRDSSRG  480
HKLSRHEENC HGSPSSTRDG SLEREIYKEQ RHAKETSRHE SKWSEHSPTH RGMRKRIHES  540
YSDDDSGDDD GKGETDHKRK SSRRYGRRES NSEVQERLDD EEDTRCHWSS SDRRSRKEDH  600
REGSLGDQEE SHAVGEKSQR ERSSSRHSHE GDSSGSRHRP HKRSDLRDKD GNERKRSVET  660
SPRDKDRDKS KQRRRYKTGD PDYDRSRNGK RENVSGSSSD EKREERHKER SGSSHRKRRR  720
SSHEQTPKEP EEIERWRPI
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4yh8_A3e-312183829167Splicing factor U2AF 23 kDa subunit
Search in ModeBase
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
1661666PRDKDR
2715719RKRRR
3715720RKRRRS
Cis-element ? help Back to Top
SourceLink
PlantRegMapXP_013604855.1
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_013604855.10.0PREDICTED: zinc finger CCCH domain-containing protein 5
SwissprotQ9SY740.0C3H5_ARATH; Zinc finger CCCH domain-containing protein 5
TrEMBLA0A0D3DNW40.0A0A0D3DNW4_BRAOL; Uncharacterized protein
STRINGBo8g059320.10.0(Brassica oleracea)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM59752025
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT1G10320.10.0C3H 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]