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 RrC20665_p1
Organism
Raphanus raphanistrum
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 NAC
Protein Properties Length: 450aa    MW: 49923.6 Da    PI: 9.1605
Description NAC family protein
Gene Model
Gene Model ID Type Source Coding Sequence
RrC20665_p1genomeMSUView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1NAM84.71.8e-262874101127
          NAM   1 lppGfrFhPtdeelvveyLkkkvegkkleleevikevdiykvePwdLp.kkvkaeekewyfFskrdkkyatgkrknratksgyWkatgkdkevlskkg 97 
                  lp Gf F+Ptde+l+++yL++k+++k+ +   +i+e++iy+++P++Lp  ++ ++++ w+fF++r  k        r t sg+W + g  k++++k++
  RrC20665_p1 287 LPTGFLFRPTDEDLLDYYLRRKLANKTYPN--AISELGIYDHDPSELPsLSILKSTEVWFFFARRILKD---GLVIRETPSGVWLSDGDVKHIKDKSD 379
                  699************************887..8***************656667788999999998876...4789999******************* PP

          NAM  98 elvglkktLvfy.kgrapkgektdWvmheyr 127
                  + +g+k+++ f  k ++   e+t+W+m+ey+
  RrC20665_p1 380 RFIGTKQSFKFClKPNNTPLEETNWMMEEYQ 410
                  ***********9444666668*********7 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF549281.03E-13149IPR012677Nucleotide-binding alpha-beta plait domain
PROSITE profilePS5010210.974147IPR000504RNA recognition motif domain
Gene3DG3DSA:3.30.70.3301.8E-14147IPR012677Nucleotide-binding alpha-beta plait domain
PfamPF000765.4E-8241IPR000504RNA recognition motif domain
Gene3DG3DSA:3.30.70.3303.2E-1775167IPR012677Nucleotide-binding alpha-beta plait domain
SuperFamilySSF549283.8E-1981180IPR012677Nucleotide-binding alpha-beta plait domain
PROSITE profilePS5010214.11290165IPR000504RNA recognition motif domain
CDDcd123541.34E-3290165No hitNo description
SMARTSM003605.0E-1591161IPR000504RNA recognition motif domain
PfamPF000762.5E-1092158IPR000504RNA recognition motif domain
SuperFamilySSF1019411.57E-31282428IPR003441NAC domain
PROSITE profilePS5100532.776287428IPR003441NAC domain
PfamPF023658.5E-18288410IPR003441NAC domain
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006355Biological Processregulation of transcription, DNA-templated
GO:0000166Molecular Functionnucleotide binding
GO:0003677Molecular FunctionDNA binding
Sequence ? help Back to Top
Protein Sequence    Length: 450 aa     Download sequence    Send to blast
MWDQKTGRSR GFGFVSFRNQ QDAQTAIDEA GGKWLGTRQI RCNWATKGAT SGEDKMSSDS  60
KSVVELTSGV SEDGKDTSNG DAPENNAQYT TVYVGNLGPE VSQVDLHRHF YSLGAGVIEE  120
VRVQRDKGFG FVRYSTHVEA ALAIQLGNTH SYLGGRQMKC SWGSKPTPPG TASNPVPPPG  180
PAPIPGFSAS DLLAYERQLA MSNMTGMSPM MHHPQGQHAL MQAAMGTTGS NQAIYDGGFQ  240
NAKQLMYNVL PRTKNWFLGL KGRALERGRE SLPLSSAPTP SPMAIDLPTG FLFRPTDEDL  300
LDYYLRRKLA NKTYPNAISE LGIYDHDPSE LPSLSILKST EVWFFFARRI LKDGLVIRET  360
PSGVWLSDGD VKHIKDKSDR FIGTKQSFKF CLKPNNTPLE ETNWMMEEYQ RHLQVDNHGF  420
VLCKIFLKKP PVKRTPVKRT PPATVTDTVM
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
2mjn_A3e-23316341185Nucleolysin TIA-1 isoform p40
Search in ModeBase
Functional Description ? help Back to Top
Source Description
UniProtHeterogeneous nuclear ribonucleoprotein (hnRNP)-like protein that acts as a component of the pre-mRNA processing machinery. Functions to facilitate the nuclear maturation of plant pre-mRNAs (By similarity). {ECO:0000250}.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAY0857050.0AY085705.1 Arabidopsis thaliana clone 17210 mRNA, complete sequence.
GenBankBT0264770.0BT026477.1 Arabidopsis thaliana At1g17370 mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_013599485.11e-164PREDICTED: oligouridylate-binding protein 1B
RefseqXP_013733234.11e-164oligouridylate-binding protein 1B
RefseqXP_022563785.11e-164oligouridylate-binding protein 1B-like
SwissprotQ9LQI91e-156UBP1B_ARATH; Oligouridylate-binding protein 1B
TrEMBLA0A3N6QP961e-164A0A3N6QP96_BRACR; Uncharacterized protein (Fragment)
STRINGBo8g104900.11e-163(Brassica oleracea)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM2388444
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT5G04410.11e-18NAC domain containing protein 2
Publications ? help Back to Top
  1. Lambermon MH, et al.
    UBP1, a novel hnRNP-like protein that functions at multiple steps of higher plant nuclear pre-mRNA maturation.
    EMBO J., 2000. 19(7): p. 1638-49
    [PMID:10747031]
  2. Lambermon MH, et al.
    UBA1 and UBA2, two proteins that interact with UBP1, a multifunctional effector of pre-mRNA maturation in plants.
    Mol. Cell. Biol., 2002. 22(12): p. 4346-57
    [PMID:12024044]
  3. Arteaga-Vázquez M,Caballero-Pérez J,Vielle-Calzada JP
    A family of microRNAs present in plants and animals.
    Plant Cell, 2006. 18(12): p. 3355-69
    [PMID:17189346]
  4. Peal L,Jambunathan N,Mahalingam R
    Phylogenetic and expression analysis of RNA-binding proteins with triple RNA recognition motifs in plants.
    Mol. Cells, 2011. 31(1): p. 55-64
    [PMID:21120628]
  5. McCue AD,Nuthikattu S,Reeder SH,Slotkin RK
    Gene expression and stress response mediated by the epigenetic regulation of a transposable element small RNA.
    PLoS Genet., 2012. 8(2): p. e1002474
    [PMID:22346759]
  6. McCue AD,Slotkin RK
    Transposable element small RNAs as regulators of gene expression.
    Trends Genet., 2012. 28(12): p. 616-23
    [PMID:23040327]
  7. Nguyen CC, et al.
    Oligouridylate Binding Protein 1b Plays an Integral Role in Plant Heat Stress Tolerance.
    Front Plant Sci, 2016. 7: p. 853
    [PMID:27379136]
  8. Nguyen CC, et al.
    Overexpression of oligouridylate binding protein 1b results in ABA hypersensitivity.
    Plant Signal Behav, 2017. 12(2): p. e1282591
    [PMID:28112571]