Displaying DV491914 on SAM Chip 1.0 (GPL2557): SAM vs Whole Seedling

Accession 1: DV491914 (GenBank)  Gene: 0
Accession 2:   Library Index: IUG33_RS-K-15
Gene Names:
  • statistically defined repeat
Categories:   
 ATPase
 Cell Division
 Cell Cycle
 DNA Replication
 Chromatin
 Chromatin Remodeling
 Chromatin Structure
 Cytoskeletal
 DNA Repair
 Defense
 Development
 Extracellular Matrix/Cell Wall
 Gene Silencing
  Metabolism
 Lipid
 Nucleotide
 Amino Acid
 Sugar
 Energy
 MySEG
 No hits
 Other
 Photosynthesis-related
 Protein Fate
 Proteolysis
 Chaperone
 RNA Binding Protein
 RNA Processing
 Respiration
  Signal Transduction
 Phosphatase
 G-proteins and Associated Proteins
 Signal Molecules
 Kinases
 Receptors
 Stress-related
 Transcription
 Transcription-Associated Proteins
 Transcription Factors
 Translation
 Ribosome
 Translation-Associated Proteins
 Transport
 Transposable Elements
 DNA Transposons
 Retrotransposon
 Unknown
 Vesicle Trafficking
GO Categories:
Molecular Function
molecular_function unknown
signal transducer activity
transporter activity
antioxidant activity
catalytic activity
triplet codon-amino acid adaptor activity
enzyme regulator activity
transcription regulator activity
binding
motor activity
structural molecule activity
nutrient reservoir activity
chaperone regulator activity
 Biological Process
behavior
physiological process
cellular process
biological_process unknown
regulation of biological process
development
viral life cycle
 Cell Component
cellular_component unknown
extracellular region
virion
cell
organelle
extracellular matrix
protein complex
Light Intensity Reads P-Value Fold Change
Low 8.41e-06 816.409
Medium 0.003562939 62.953
High 1.64e-05 30.6207
BLAST results for DV491914   
BLASTN E-value: 5e-69 Longest MEC sequence 
BLASTX E-value: None    
MAGI blast Fresh results
Show/Hide Reading Frames/PsortPrediction
Researcher: Lisa Grantham (djb and BB checked)   Last Updated: 2006-07-19
Notes:

Replaces accession AI666171

558 bps
no significant blastX hits
BlastN: unconclusive
UniGene: E. coli - B Chain B, Lactose Operon Repressor Bound To 21-Base Pair Symmetric Operator Dna, Alpha Carbons Only 96.67 % / 30 aa
InterPro (nucleotide sequence entered): signal peptide

Sequence was run through repeatmasker at MAGI database and got the following results:

Repeats

>AI666171 606005G10.x1 606 - Ear tissue cDNA library from Schmidt lab Zea mays cDNA, mRNA sequence. (520 bp masked -- 93.19% masked)
TNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTCACACACTAANNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTACTTTGGGGAGAGAGG
TAGGAGGTAGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN

tBlastx of sesquence at MAGI's repeat database produced lots of hits with retrotransposons.

Repeats blast showed best hits with:

zm_SDRv3.1_12481                                                      170   1e-42 
zm_SDRv3.1_12077                                                      155   8e-38 
zm_SDRv3.1_12702                                                      151   1e-36 
zm_SDRv3.1_11340                                                      125   7e-29

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Partial support for this work is provided by the National Science Foundation.

Truman State University | Math & CS Department | Biology Department