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 GSBRNA2T00012823001
Common NameGSBRNA2T00012823001
Organism
Brassica napus
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: 1428aa    MW: 161015 Da    PI: 7.7657
Description C3H family protein
Gene Model
Gene Model ID Type Source Coding Sequence
GSBRNA2T00012823001genomeGenoscopeView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-CCCH22.22.5e-07680699625
                          -SGGGGTS--TTTTT-SS-S CS
              zf-CCCH   6 CrffartGtCkyGdrCkFaH 25 
                          C+f+++tG C++G+rC++ H
  GSBRNA2T00012823001 680 CPFHLKTGACRFGPRCSRVH 699
                          ******************99 PP
2zf-CCCH283.7e-09809836126
                          --S---SGGGGTS..--TTTTT-SS-SS CS
              zf-CCCH   1 yktelCrffartG..tCkyGdrCkFaHg 26 
                          +k ++C  f+++   tC++G+ C+F+H+
  GSBRNA2T00012823001 809 WKVAICGEFMKSRlkTCSRGSACNFIHC 836
                          899************************8 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PROSITE profilePS5029716.6867215IPR020683Ankyrin repeat-containing domain
SMARTSM00248236796IPR002110Ankyrin repeat
SuperFamilySSF484033.94E-1569215IPR020683Ankyrin repeat-containing domain
Gene3DG3DSA:1.25.40.201.8E-1770216IPR020683Ankyrin repeat-containing domain
CDDcd002044.41E-1370182No hitNo description
PfamPF127961.4E-672156IPR020683Ankyrin repeat-containing domain
SMARTSM002480.62101131IPR002110Ankyrin repeat
SMARTSM00248440135166IPR002110Ankyrin repeat
SMARTSM00248460173204IPR002110Ankyrin repeat
PfamPF139623.7E-29280389IPR026961PGG domain
PROSITE profilePS5010312.681674702IPR000571Zinc finger, CCCH-type
SMARTSM003561.1675701IPR000571Zinc finger, CCCH-type
PfamPF006423.1E-5679699IPR000571Zinc finger, CCCH-type
PRINTSPR018485.7E-36680699IPR009145U2 auxiliary factor small subunit
PRINTSPR018485.7E-36699719IPR009145U2 auxiliary factor small subunit
Gene3DG3DSA:3.30.70.3302.5E-26705804IPR012677Nucleotide-binding alpha-beta plait domain
PROSITE profilePS501029.661706806IPR000504RNA recognition motif domain
CDDcd125401.02E-51707805No hitNo description
SMARTSM003614.4E-5728802IPR003954RNA recognition motif domain, eukaryote
PRINTSPR018485.7E-36735750IPR009145U2 auxiliary factor small subunit
SuperFamilySSF549283.36E-16738806IPR012677Nucleotide-binding alpha-beta plait domain
PRINTSPR018485.7E-36763785IPR009145U2 auxiliary factor small subunit
PRINTSPR018485.7E-36790814IPR009145U2 auxiliary factor small subunit
PROSITE profilePS5010311.413808838IPR000571Zinc finger, CCCH-type
SMARTSM003560.015808837IPR000571Zinc finger, CCCH-type
PfamPF006426.3E-7809836IPR000571Zinc finger, CCCH-type
PRINTSPR018485.7E-36828840IPR009145U2 auxiliary factor small subunit
SuperFamilySSF517354.11E-5412021397IPR016040NAD(P)-binding domain
Gene3DG3DSA:3.40.50.7201.4E-5712021394IPR016040NAD(P)-binding domain
PfamPF001062.3E-4712031390IPR002347Short-chain dehydrogenase/reductase SDR
CDDcd052337.37E-5612051390No hitNo description
PROSITE patternPS00061013381366IPR020904Short-chain dehydrogenase/reductase, conserved site
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0000398Biological ProcessmRNA splicing, via spliceosome
GO:0055114Biological Processoxidation-reduction process
GO:0016021Cellular Componentintegral component of membrane
GO:0089701Cellular ComponentU2AF
GO:0000166Molecular Functionnucleotide binding
GO:0003723Molecular FunctionRNA binding
GO:0005515Molecular Functionprotein binding
GO:0016491Molecular Functionoxidoreductase activity
GO:0046872Molecular Functionmetal ion binding
Sequence ? help Back to Top
Protein Sequence    Length: 1428 aa     Download sequence    Send to blast
MELRIKALNV ESNSKNLIAS ITNNSSVPEL YGIVADILSI SYFFYYIILE RFPDLAREEA  60
WPVQGGSLSS LLHHACDRGD LELTRILLGL DQRLEEALNT NGLSPLHLAV LRGSVVILEE  120
FINKAPLSFL SHTPSKETVF HLAARNKNMD AFVFMAERLG SNSQFLLQKT DENGNTVLHT  180
AASVACGAPL IRYIIAMKIV DISNKNKMGF AAYHLLPHDA QDFELLSSWL RFDTETSDEL  240
DSDLLNLIGL NTSEMVERKT RKAHGVKKGS ENLEYDMYIE ALQNARNTIT IVAVLIASVA  300
YAGGINPPGG VYQDGPWRGK SIVGKTTAFK VFAICNNIAL FTSLAIVILL VSIIPYKRKP  360
LKKLLVATHR MMWVSIGFMA TAYVAASWVT IPHYHGTRWL FPAIVAVAGG ALAVLFSYLG  420
VEAIGHWFKK KARVGSVPSS SSTSEREVNA IGIMEPRNEK EEGERLEEAM GGFEESKEKS  480
AEMSRKEKRK AMKKMKRKQV RKEIASKERE EAEAKLNDPA EQEKLKAIEE EEERKREKEL  540
REFEDSERAW REAMEIQRKK EEVEEKRWKE LEELRKLEAS GDDECGEDDD GEYEYIEEGP  600
PEIIFQGNEI ILRKNKVKVP KRSVAQVEGN EIADRPTSNP LPPGTEAFPK NHNVSSAQQI  660
LDSVAQEVPN FGTEQDKAHC PFHLKTGACR FGPRCSRVHF YPDKSCTILM KNMYNGPGIA  720
WEQDEGLEYT DEEAEQCYEE FYEDVHTEFL KYGELINFKV CRNGSFHLKG NVYVHYRSLE  780
SAMLAYQSIN GRYFAGKQVN CEFVNISRWK VAICGEFMKS RLKTCSRGSA CNFIHCFRNP  840
GGDYEWADFD KPPPRFWIRK MAALFGYSDE DLKHMEREYS GSLSEFRSDQ PSDSQRQASR  900
RSRSRDHDHV NVGSKPSYRS RKNHGDTRDS SRGHKLSRHE ENCHGSPSSN RDGSLEREIY  960
KEPRHAKETS RHESKWSEHS PTHRGMRKRI HERYSDDDSG DDDGRGETDH KRKSSRRYGR  1020
RGSNSEVQER LDDEEDTRCH WSSSDRRSRK EDHREGSLGD QEESHAVGEK SKRERSSSRH  1080
SHEGDSSGSR HRRHKRSDLR DKDGNERKRS VETSPRDKDR DKSKQRRRYK TGDPDYDRSR  1140
NGKRENVSGS SSDEKREERH KEGSGSSHRK RRRSSHEQTP KEPEEIIEPT PFSGAANSVT  1200
SAKTVLITGV SKGLGRALSL EMAKRGHTVI GCARTQEKFT ALQSELSSPE NHLLLTADVK  1260
SDSSVKEMAH TIMEKKGVPD IIVNNAGTIN KNSKIWEVSA EDFDSVMDTN VKGVVNVLRH  1320
FIPLMLPRKQ GIIVNMSSGW GRSGAALVAP YCASKWAIEG LSRSVAKEVA EGMAVVALNP  1380
GVINTEMLTS CFGNTASLYQ APDAWAVKAA TMILNLTAGD NGGSLTV*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4yh8_A1e-326718359167Splicing factor U2AF 23 kDa subunit
Search in ModeBase
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
111141119PRDKDR
211681172RKRRR
311681173RKRRRS
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Bna.73940.0flower| seed
Cis-element ? help Back to Top
SourceLink
PlantRegMapGSBRNA2T00012823001
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAK1766700.0AK176670.1 Arabidopsis thaliana mRNA, complete cds, clone: RAFL25-20-N20.
GenBankAY0879730.0AY087973.1 Arabidopsis thaliana clone 40058 mRNA, complete sequence.
GenBankBT0257890.0BT025789.1 Arabidopsis thaliana At1g10310 mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_013604855.10.0PREDICTED: zinc finger CCCH domain-containing protein 5
TrEMBLA0A078G6P90.0A0A078G6P9_BRANA; BnaC08g14160D 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. Chalhoub B, et al.
    Plant genetics. Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome.
    Science, 2014. 345(6199): p. 950-3
    [PMID:25146293]