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_009144452.1
Organism
Brassica rapa
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: 747aa    MW: 87741.2 Da    PI: 8.0361
Description C3H family protein
Gene Model
Gene Model ID Type Source Coding Sequence
XP_009144452.1genomeNCBIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-CCCH23.21.2e-07226245625
                     -SGGGGTS--TTTTT-SS-S CS
         zf-CCCH   6 CrffartGtCkyGdrCkFaH 25 
                     C+f+++tG C++G+rC++ H
  XP_009144452.1 226 CPFHLKTGACRFGPRCSRVH 245
                     ******************99 PP
2zf-CCCH29.51.3e-09355382126
                     --S---SGGGGTS..--TTTTT-SS-SS CS
         zf-CCCH   1 yktelCrffartG..tCkyGdrCkFaHg 26 
                     +k ++C  ++++   tC++G++C+F+H+
  XP_009144452.1 355 WKVAICGEYMKSRlkTCSRGSSCNFIHC 382
                     899************************8 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PROSITE profilePS5010312.681220248IPR000571Zinc finger, CCCH-type
SMARTSM003561.1221247IPR000571Zinc finger, CCCH-type
PfamPF006421.5E-5225245IPR000571Zinc finger, CCCH-type
PRINTSPR018483.2E-37226245IPR009145U2 auxiliary factor small subunit
PRINTSPR018483.2E-37245265IPR009145U2 auxiliary factor small subunit
Gene3DG3DSA:3.30.70.3302.6E-26251350IPR012677Nucleotide-binding alpha-beta plait domain
CDDcd125406.11E-50253351No hitNo description
SMARTSM003611.6E-4274348IPR003954RNA recognition motif domain, eukaryote
PRINTSPR018483.2E-37281296IPR009145U2 auxiliary factor small subunit
SuperFamilySSF549281.33E-16284352IPR012677Nucleotide-binding alpha-beta plait domain
PROSITE profilePS501029.49289352IPR000504RNA recognition motif domain
PRINTSPR018483.2E-37309331IPR009145U2 auxiliary factor small subunit
PRINTSPR018483.2E-37336360IPR009145U2 auxiliary factor small subunit
PROSITE profilePS5010311.62354384IPR000571Zinc finger, CCCH-type
SMARTSM003560.013354383IPR000571Zinc finger, CCCH-type
PfamPF006422.6E-7355382IPR000571Zinc finger, CCCH-type
PRINTSPR018483.2E-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: 747 aa     Download sequence    Send to blast
MEPQNEKPEE GGRLEEAMGG LEESKDKSAE MSRKEKRKAM KKLKRKQVRK EIASKEREDA  60
EAKLNDPAEQ EKLKAIEEEE ARKREKELRE FEESERAWRE AMEIKRKKEE EEERRWKEIE  120
ELRKLEASRD GECGEDGEYE YIEEGPPEII FKGNEIILRK NKVRVPKKSV PQVEGNEIAD  180
RPTSNPLPPG TEALSKYHNV SSAQQILDSV AQEVPNFGTE QDKAHCPFHL KTGACRFGPR  240
CSRVHFYPDK SCTILMKNMY NGPGIAWEQD EGLEYTDEEA EHCYEEFYED VHTEFLKYGE  300
LINFKVCRNG SFHLKGNVYV HYRSLESAML AYQSINGRYF AGKQVNCEFV NISRWKVAIC  360
GEYMKSRLKT CSRGSSCNFI HCFRNPGGDY EWADYDKPPP RFWIRKMTSL FGYSDEYLKH  420
MEREYSGSLS EFRSDQPTDL QRQPSRRSRS RDHDHVNVGS KPSYRSRTRD SSRGHKHSRH  480
EENCHGGDES PSSTRDGSVE RETYKEPRYA KETSRHESKW SEHSPRHRVM RKRIYEKYSD  540
DDSGVEDGRG ETSHKRKSSR RYGKRGSDSE VQEGLDDEEN TRTHWSSSDR RSRKEDDREG  600
SSADHKEKSH GHDRVHEVGE KSRRERSSSR YSHEGDSSES KHRPHKGSGE NERKRSVETS  660
PRDKDRDKSK ERHRYNKTGD PDSDRSRKGK QGRESQEVKR NASGSSSDEE REERRKERSH  720
SSHRKRRRSD EQTRKEPEEE IERWRPM
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4yh8_A3e-312173819167Splicing factor U2AF 23 kDa subunit
Search in ModeBase
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
1660665PRDKDR
2713727RRKERSHSSHRKRRR
3723727RKRRR
4723728RKRRRS
Cis-element ? help Back to Top
SourceLink
PlantRegMapXP_009144452.1
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAK2266840.0AK226684.1 Arabidopsis thaliana mRNA for hypothetical protein, complete cds, clone: RAFL07-54-F13.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_009144452.10.0PREDICTED: zinc finger CCCH domain-containing protein 5-like
SwissprotQ9SY740.0C3H5_ARATH; Zinc finger CCCH domain-containing protein 5
TrEMBLM4DPK50.0M4DPK5_BRARP; Uncharacterized protein
STRINGBra018446.1-P0.0(Brassica rapa)
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]