Displaying DV492067 on SAM Chip 1.0 (GPL2557): SAM vs Whole Seedling

Accession 1: DV492067 (GenBank)  Gene: 0
Accession 2:   Library Index: IUG35_RS-L-5
Gene Names:
  • retrotransposon Xilon1 LTR
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 0.00082273 228.013
Medium 2.34e-06 50.2665
High 1.32e-05 41.5773
BLAST results for DV492067   
BLASTN E-value: 0.0 Longest MEC sequence 
BLASTX E-value: None    
MAGI blast Fresh results
Show/Hide Reading Frames/PsortPrediction
Researcher: Julia Struble; Steve Olree (BB, djb checked)   Last Updated: 2007-05-14
Notes:

Replaces accession AI855009

This hits with the LTR of Xilon (BB)

 

Matches xilon1 retrotransposon region inside
>gi|18092333|gb|AF448416.1| Zea mays B73 chromosome 9S bz genomic region
Length=106186

Identified a loinger sequence on MAGI and ran it through interproscan and repeatmasker, then performed blastn of repeat sequences at MAGI database:

Repeat masker results Repeats

>MEC_29766_p95-May05 P95clusters.fas 1264 bp (1233 bp masked -- 97.55% masked)
tNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNgnnnnaanacnnnnnnnnnnaaaaaaaccc

MAGI repeat database blastn results:

                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

ZRSiTERTOOT0311 xilon_af448416-1 xilon1 af448416 bases 999. .127...  1003   0.0  
ZRSiTERTOOT0308 xilon_138B04-1part xilon_138B04-1 Z138B04 bases ...   977   0.0  
ZRSiTERTOOT0312 xilon_af448416-2hdnm xilon_af448416-2hdnm af4484...   456   e-128
ZRSiTERTOOT0149 diguus_123C01-1 diguus_123C01-1 merge bases 2074...   194   1e-49
ZRSiTERTOOT0306 tekay_af448416-1 tekay_af448416-1 af448416 bases...   84   3e-16
ZRSiTERTOOT0294 prem1_276N13-4 prem1_276N13-4 276N13 bases 39168...   70   4e-12
ZRSiTERTOOT0290 prem1_195D10-1 prem1_Z195D10-1 prem1ji_Z195D10-1...   70   4e-12
ZRSiTERT0020050 gi|3420038|gb|AF050455.1|AF050455 Zea mays gypsy...   68   2e-11
ZRSiTERTOOT0087 gi|433042|gb|U03683.1|ZMU03683 Zea mays W-22 clo...   66   6e-11
ZRSiTERTOOT0300 prem1_af090447-2hdnm prem1_af090447-2hdnm af0904...   64   2e-10
ZRSiTERTOOT0298 prem1_573F08-1 prem1_Z573F08-1 Z573F08 bases 127...   64   2e-10

TOP HIT FROM REPEAT DATABASE: 

>ZRSiTERTOOT0311 xilon_af448416-1 xilon1 af448416 bases 999. .12701
||retrotransposon
Length = 11703

Score = 1850 bits (933), Expect = 0.0
Identities = 1164/1235 (94%), Gaps = 11/1235 (0%)
Strand = Plus / Plus