Displaying DV621178 on SAM Chip 1.0 (GPL2557): SAM vs Whole Seedling

Accession 1: DV621178 (GenBank)  Gene: 0
Accession 2:   Library Index: UGIV_1091T4_RS-D-16
Gene Names:
  • Zea mays retrotransposon Opie-2 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 0.000749349 201.277
Medium 0.000196884 33.0402
High 5.35e-05 22.4126
BLAST results for DV621178   
BLASTN E-value: 0.0 Longest MEC sequence 
BLASTX E-value: None    
MAGI blast Fresh results
Show/Hide Reading Frames/PsortPrediction
Researcher: Clint Pogue   Last Updated: 2009-02-02
Notes:

BLASTn top hits from the original sequence are as follows:

 

Sequences producing significant alignments:(Click headers to sort columns)

Accession Description Max score Total score Query coverage E value Max ident Links
BT018479.1
Zea mays clone EL01N0424B06.d mRNA sequence
 915 915 74% 0.0 97%  
AY371488.1
Zea mays clone BAC 276N12-123C01, partial sequence
 867 5402 98% 0.0 100%  
AF546188.1
Contiguous genomic DNA sequence comprising the 19-kDa-zein gene family from Zea mays, complete sequence
 776 2263 98% 0.0 97%  
AY664414.1
Zea mays cultivar B73 locus 9008, complete sequence
 713 7297 98% 0.0 100%  
DQ493646.1
Zea mays cultivar CML258 bz locus region
 697 2041 98% 0.0 94%  
DQ493649.1
Zea mays cultivar Coroico bz locus region
 691 3965 98% 0.0 94%  
AC165174.2
Zea mays clone ZMMBBb-127F19, complete sequence
 686 3192 98% 0.0 97%  
AC152494.1
Zea mays BAC clone Z418K17, complete sequence
 682 4472 98% 0.0 97%  
AY078063.2
Zea mays B transcriptional activator (b1) gene, b1-B' allele, exons 1 through 3 and partial cds
 676 3119 94% 0.0 96%  
AY664419.1
Zea mays cultivar Mo17 locus 9009, complete sequence
 673 8490 98% 0.0 100%  
AY664415.1
Zea mays cultivar B73 locus 9009, complete sequence
 673 8202 98% 0.0 100%  
AF466932.1
Zea mays clone BAC 206C17, complete sequence
 669 6107 98% 0.0 94%  
U68408.1
Zea mays retrotransposon Opie-2 5' LTR, primer binding site, gag gene, pol gene, complete cds, polypurine tract and 3' LTR
 667 2015 94% 0.0 94%  
AF123535.1
Zea mays alcohol dehydrogenase 1 (adh1) gene, adh1-F allele, complete cds
 667 3111 94% 0.0 94%  
AY691949.1
Zea mays alcohol dehydrogenase 1 (adh1A) gene, complete cds; Fourf copia_LTR and Huck gypsy_LTR retrotransposons, complete sequence; Opie2 copia_LTR retrotransposon Zeon gypsy_LTR and Opie1 copia_LTR retrotransposons, complete sequence; Ji copia_LTR retrotransposon, complete sequence; and unknown protein (adh1B), cyclin H-1 (adh1C), unknown protein (adh1D), hypothetical protein (adh1E), and unknown protein (adh1F) genes, complete cds
 662 2125 94% 0.0 94%  
DQ417752.1
Zea mays B73 pathogenesis-related protein 2 and GASA-like protein genes, complete cds
 660 2596 98% 0.0 97%  
AC152495.1
Zea mays BAC clone Z486N13, complete sequence
 656 6042 98% 0.0 95%  
AF466931.1
Zea mays clone BAC 163K15, complete sequence
 656 4174 98% 0.0 95% 
BLASTx top hits from the original sequence:














                                                                   Score     E
Sequences producing significant alignments:                       (Bits)  Value

gb|ACG32268.1|  hypothetical protein [Zea mays]                    41.6    0.060







BLASTn at the MAGI database produced these top hits:


                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

ZRSiTERTOOT0264  opie_276N13-4part opie_276N13-4part 276N13 ...   864   0.0   
ZRSiTERTOOT0286  opie_af546188-1 opie_af546188-1 af546188 ba...   729   0.0   
ZRSiTERTOOT0083  gi|1657766|gb|U68408.1|ZMU68408 Zea mays re...   559   e-159 
ZRSiTERTOOT0259  opie_238E11-3 ||retrotransposon                  539   e-153 
ZRSiTERTOOT0274  opie_5BL-1solo opie_5BL-1solo 5BL.fasta.scr...   537   e-153 
ZRSiTERTOOT0272  opie_573F08-2hdnm opie_573F08-2hdnm 573F08 ...   496   e-140 
ZRSiTERTOOT0257  opie_238E11-1 ||retrotransposon                  476   e-134 
ZRSiTERT0010029  gi|4185305|gb|AF090446.1|AF090446|20714-296...   440   e-124 
ZRSiTERTOOT0261  opie_276N13-1 opie_276N13-1 276N13.fasta.sc...   387   e-107 
ZRSiTERTOOT0271  opie_573F08-1 opie_573F08-1 ZM573F08.fasta....   379   e-105 
ZRSiTERTOOT0268  opie_334B07-3 1-1260 5'LTR; 7702-8960 3'LTR...   359   3e-99 
ZRSiTERTOOT0265  opie_333J11-1 opie_Z333J11-1 Z333J11final b...   339   2e-93 
ZRSiTERTOOT0254  opie_138B04-1 GAP of: 138B04_contig13.seq c...   327   9e-90 
ZRSiTERTOOT0266  opie_333J11-2 opie_Z333J11-2 Z333J11final b...   325   4e-89 
ZRSiTERTOOT0267  opie_334B07-1 ||retrotransposon                  311   6e-85 
ZRSiTERTOOT0282  opie_af391808-2 opie_af391808-2 af391808 ba...   283   1e-76 
ZRSiTERTOOT0260  opie_238E11-4 ||retrotransposon                  283   1e-76 
ZRSiTERTOOT0277  opie_af090447-1 opie_af090447-1 af090447 ba...   258   7e-69 
ZRSiTERTOOT0262  opie_276N13-2 opie_276N13-2 276N13.fasta.sc...   250   2e-66 
ZRSiTERTOOT0275  opie_9C20-1 GAP of: 9C20.fasta.screen.Conti...   240   2e-63 
ZRSiTERTOOT0279  opie_af090447-3 opie_af090447-3 af090447 ba...   238   7e-63 
ZRSiTERTOOT0285  opie_af448416-1part opie_af448416-1part af4...   230   2e-60


Most likely a retrotransposon, which can be found in many differing genes in a single organism.






 



NSF Logo

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

Truman State University | Math & CS Department | Biology Department