PlantTFDB
PlantRegMap/PlantTFDB v5.0
Plant Transcription Factor Database
Home  TFext  BLAST  Prediction  Download  Help  About  Links  PlantRegMap
(e.g., LFY)
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID Vradi10g13530.1
Organism
Vigna radiata
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; fabids; Fabales; Fabaceae; Papilionoideae; Phaseoleae; Vigna
Family C3H
Protein Properties Length: 664aa    MW: 78208.6 Da    PI: 7.3484
Description C3H family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Vradi10g13530.1genomeSNUView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-CCCH18.43.7e-06189208625
                      -SGGGGTS--TTTTT-SS-S CS
          zf-CCCH   6 CrffartGtCkyGdrCkFaH 25 
                      C+f+++tG C++G rC++ H
  Vradi10g13530.1 189 CPFHLKTGACRFGRRCSRVH 208
                      ******************99 PP
2zf-CCCH29.89.9e-10369396126
                      --S---SGGGGTS..--TTTTT-SS-SS CS
          zf-CCCH   1 yktelCrffartG..tCkyGdrCkFaHg 26 
                      +k ++C  ++++G  tC++G  C+F+H+
  Vradi10g13530.1 369 WKVAICGEYMKSGfkTCSRGTACNFIHC 396
                      899************************8 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PROSITE profilePS5010311.92183211IPR000571Zinc finger, CCCH-type
SMARTSM003563.6184210IPR000571Zinc finger, CCCH-type
PRINTSPR018481.4E-28189208IPR009145U2 auxiliary factor small subunit
PRINTSPR018481.4E-28208228IPR009145U2 auxiliary factor small subunit
SuperFamilySSF549284.88E-8212281IPR012677Nucleotide-binding alpha-beta plait domain
Gene3DG3DSA:3.30.70.3301.7E-19215268IPR012677Nucleotide-binding alpha-beta plait domain
Gene3DG3DSA:3.30.70.3301.7E-19318364IPR012677Nucleotide-binding alpha-beta plait domain
PRINTSPR018481.4E-28323345IPR009145U2 auxiliary factor small subunit
SuperFamilySSF549284.88E-8328370IPR012677Nucleotide-binding alpha-beta plait domain
PRINTSPR018481.4E-28350374IPR009145U2 auxiliary factor small subunit
PROSITE profilePS5010310.878368398IPR000571Zinc finger, CCCH-type
SMARTSM003568.5E-5368397IPR000571Zinc finger, CCCH-type
PfamPF006424.2E-7369396IPR000571Zinc finger, CCCH-type
PRINTSPR018481.4E-28388400IPR009145U2 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: 664 aa     Download sequence    Send to blast
MEDGKSMGRK EKRKAMKKMK RKQTRKEAAE RERREEEDRL NDPEEQRRMQ LLEQEEAERM  60
QRDTILFQER EKAFMDMIIT RQRRQQQQER EQEQSIDHDH EFEYVVQEEG PPEIIWQGNE  120
IIFNKKQVRV RVQDTDTDTH NNHAQQNDDI RPTSNPLPPE SGLESRTQNL QDIAEQIPNF  180
GTEQDKAHCP FHLKTGACRF GRRCSRVHFI PDKSSTLLME NMYNGPGLAC DRDQDEGLEY  240
TDEEIDRCFE EFYEDVHTEF LKFGEIVNFK EPLELECLPK QRPNSSVPEP ISTPCTFCLL  300
LLAVKGHGKW TTEYAVREKV CKNGSFHLRG NVYVQYKALD SALHAANLMN HHDFAGKRVT  360
CQFVNLTRWK VAICGEYMKS GFKTCSRGTA CNFIHCFRNP GGDYEWADSD KPPPKFWVEK  420
MIALFGYSDD YETSREQGNF SLSKTDSDRY HCRRSRSREM DQISCGYSGR RKHEDERKQR  480
TPYEDRNASL KNTRKRKSRG RTPDTDSDRE WLEKEEIRER RHEYTRNGSF NKSRDENSRS  540
HEEDSDVDCD TRDNEKQHGR NPRKCDKDIR VWINEAAGLD GDRDVRKHRI RESSGHQSGD  600
ASESNKDLFG RVEMETLHDH SRKTYSHRRS GVQVSVKGRD QNDKVDRDGS RKDSYKRDHH  660
KRK*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4yh8_A8e-231804239182Splicing factor U2AF 23 kDa subunit
Search in ModeBase
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
1492497TRKRKS
Cis-element ? help Back to Top
SourceLink
PlantRegMapVradi10g13530.1
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAP0150380.0AP015038.1 Vigna angularis var. angularis DNA, chromosome 5, almost complete sequence, cultivar: Shumari.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_014518349.10.0zinc finger CCCH domain-containing protein 5 isoform X2
SwissprotQ9SY741e-153C3H5_ARATH; Zinc finger CCCH domain-containing protein 5
TrEMBLA0A1S3VJT60.0A0A1S3VJT6_VIGRR; zinc finger CCCH domain-containing protein 5 isoform X2
STRINGXP_007148590.10.0(Phaseolus vulgaris)
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-133C3H 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]