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 Rsa1.0_03642.1_g00002.1
Organism
Raphanus sativus
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Brassiceae; Raphanus
Family B3
Protein Properties Length: 309aa    MW: 34451.4 Da    PI: 10.695
Description B3 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Rsa1.0_03642.1_g00002.1genomeRGDView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B3361.2e-115732798
                             ---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE-SS.SEE..EEEEE- CS
                       B3 27 ggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfvvFkldgr.sefelvvkvfr 98
                             g++  +  ++tl  e+ r+W+ +l    ++g++ l+ GW eF+ ang+  g++++++++++ +++++v+++++
  Rsa1.0_03642.1_g00002.1  5 GIN--RLGKITLLGENKREWSAYL--LTRDGTVALGIGWDEFCVANGVSLGESFTLEFSKErNKTTPVLQFCS 73
                             444..2338***************..99999****************************888******99997 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PROSITE profilePS5086310.969174IPR003340B3 DNA binding domain
CDDcd100171.04E-7164No hitNo description
SMARTSM010191.7E-5175IPR003340B3 DNA binding domain
Gene3DG3DSA:2.40.330.101.1E-10272IPR015300DNA-binding pseudobarrel domain
SuperFamilySSF1019361.96E-11272IPR015300DNA-binding pseudobarrel domain
PfamPF023625.2E-10473IPR003340B3 DNA binding domain
Gene3DG3DSA:3.30.70.3301.7E-2175156IPR012677Nucleotide-binding alpha-beta plait domain
SuperFamilySSF549283.76E-2179169IPR012677Nucleotide-binding alpha-beta plait domain
PROSITE profilePS5010215.44381150IPR000504RNA recognition motif domain
SMARTSM003601.3E-1682146IPR000504RNA recognition motif domain
CDDcd123731.89E-3582150No hitNo description
PfamPF000762.6E-1683140IPR000504RNA recognition motif domain
SuperFamilySSF577561.83E-8159197IPR001878Zinc finger, CCHC-type
Gene3DG3DSA:4.10.60.102.1E-6173196IPR001878Zinc finger, CCHC-type
PROSITE profilePS5015810.889176192IPR001878Zinc finger, CCHC-type
SMARTSM003438.3E-5176192IPR001878Zinc finger, CCHC-type
PfamPF000986.5E-7176191IPR001878Zinc finger, CCHC-type
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0005730Cellular Componentnucleolus
GO:0005829Cellular Componentcytosol
GO:0000166Molecular Functionnucleotide binding
GO:0003677Molecular FunctionDNA binding
GO:0008270Molecular Functionzinc ion binding
Sequence ? help Back to Top
Protein Sequence    Length: 309 aa     Download sequence    Send to blast
MKANGINRLG KITLLGENKR EWSAYLLTRD GTVALGIGWD EFCVANGVSL GESFTLEFSK  60
ERNKTTPVLQ FCSLETNKKM SRVYVGNLDP RVTERELEDE FRVYGVIKSV WVARRPPGYA  120
FLDFEDSRDA RDAIRDLDGK NGWRVEQSHN RGGGGGGRGG GGGRDGGRGR GGSDLKCYEC  180
GESGHFAREC RSRGGGGSRR GRSPSPRGRS RSRSPPRYRK SPTYGGRRSY SPRARSPPPR  240
RRSPSPRGRN FSRSPPPYRA RDEKWSERCA QKPQLSGEGS GEQLFSCGRQ DDSLREISIC  300
ESLAKRDMF
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
2i38_A4e-168214075133Fusion protein consists of immunoglobulin G-Binding Protein G and Splicing factor, arginine/serine-rich 3
Search in ModeBase
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
1150163RGGGGGGRGGGGGR
2155162GGRGGGGG
Functional Description ? help Back to Top
Source Description
UniProtProbably involved in intron recognition and spliceosome assembly.
Cis-element ? help Back to Top
SourceLink
PlantRegMapRsa1.0_03642.1_g00002.1
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankDQ2460101e-173DQ246010.1 Zea mays clone 94573 mRNA sequence.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_018433814.14e-65PREDICTED: serine/arginine-rich splicing factor RSZ22A
RefseqXP_018433815.14e-65PREDICTED: serine/arginine-rich splicing factor RSZ22A
SwissprotQ9SJA62e-61RZ22A_ARATH; Serine/arginine-rich splicing factor RSZ22A
TrEMBLA0A3P5YPX31e-89A0A3P5YPX3_BRACM; Uncharacterized protein
STRINGBra007840.1-P3e-83(Brassica rapa)
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT2G24650.11e-25DNA binding;DNA binding;sequence-specific DNA binding transcription factors
Publications ? help Back to Top
  1. Kalyna M,Barta A
    A plethora of plant serine/arginine-rich proteins: redundancy or evolution of novel gene functions?
    Biochem. Soc. Trans., 2004. 32(Pt 4): p. 561-4
    [PMID:15270675]
  2. Iida K, et al.
    Genome-wide analysis of alternative pre-mRNA splicing in Arabidopsis thaliana based on full-length cDNA sequences.
    Nucleic Acids Res., 2004. 32(17): p. 5096-103
    [PMID:15452276]
  3. Iida K,Go M
    Survey of conserved alternative splicing events of mRNAs encoding SR proteins in land plants.
    Mol. Biol. Evol., 2006. 23(5): p. 1085-94
    [PMID:16520337]
  4. de la Fuente van Bentem S, et al.
    Phosphoproteomics reveals extensive in vivo phosphorylation of Arabidopsis proteins involved in RNA metabolism.
    Nucleic Acids Res., 2006. 34(11): p. 3267-78
    [PMID:16807317]
  5. Tillemans V,Leponce I,Rausin G,Dispa L,Motte P
    Insights into nuclear organization in plants as revealed by the dynamic distribution of Arabidopsis SR splicing factors.
    Plant Cell, 2006. 18(11): p. 3218-34
    [PMID:17114353]
  6. Tanabe N,Yoshimura K,Kimura A,Yabuta Y,Shigeoka S
    Differential expression of alternatively spliced mRNAs of Arabidopsis SR protein homologs, atSR30 and atSR45a, in response to environmental stress.
    Plant Cell Physiol., 2007. 48(7): p. 1036-49
    [PMID:17556373]
  7. Schindler S, et al.
    Alternative splicing at NAGNAG acceptors in Arabidopsis thaliana SR and SR-related protein-coding genes.
    BMC Genomics, 2008. 9: p. 159
    [PMID:18402682]
  8. Barta A,Kalyna M,Reddy AS
    Implementing a rational and consistent nomenclature for serine/arginine-rich protein splicing factors (SR proteins) in plants.
    Plant Cell, 2010. 22(9): p. 2926-9
    [PMID:20884799]
  9. Richardson DN, et al.
    Comparative analysis of serine/arginine-rich proteins across 27 eukaryotes: insights into sub-family classification and extent of alternative splicing.
    PLoS ONE, 2011. 6(9): p. e24542
    [PMID:21935421]