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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacataatttaatttaatgtcatatttgtatcgatttttatttattttacatagcctttgaaatttaagtgttaattactcactgaattgtatactttttttattcagCTTGCACAGTTGCAAGTGGAGCTTCAACGCATGAACGCTGAGAACAAGAAGCTGAAAGAGATGCTCAGCCATGTCACCGGTAACTACACCGCCTTGCAGA

Basic information

species Glycine max
transcript GLYMA09G00820.1
intron # 2
splice site 3'
intron type U2

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|21993769|gb|BQ785297.1|BQ785297
EST:     ATGACGGGCTTTCATCGGATGCAGAAGATAAGCGAGCCAAAACCACCGAG                         CTTGCACAGTTGCAAGTGGAGCTTCAACGCATGAACGCTGAGAACAAGAAG
genomic: ATGACGGGCTTTCATCGGATGCAGAAGATAAGCGAGCCAAAACCACCGAGgtacataatt ... ttttattcagCTTGCACAGTTGCAAGTGGAGCTTCAACGCATGAACGCTGAGAACAAGAAG
EST: gi|21995158|gb|BQ786686.1|BQ786686
EST:     ATGACGGGCTTTCATCGGATGCAGAAGATAAGCGAGCCAAAACCACCGAG                         CTTGCACAGTTGCAAGTGGAGCTTCAACGCATGAACGCTGAGAACAAGAAG
genomic: ATGACGGGCTTTCATCGGATGCAGAAGATAAGCGAGCCAAAACCACCGAGgtacataatt ... ttttattcagCTTGCACAGTTGCAAGTGGAGCTTCAACGCATGAACGCTGAGAACAAGAAG
EST: gi|209698051|gb|BW680372.1|BW680372
EST:     ATGACGGGCTTTCATCGGATGCAGAAGATAAGCGAGCCAAAACCACCGAG                         CTTGCACAGTTGCAAGTGGAGCTTCAACGCATGAACGCTGAGAACAAGAAG
genomic: ATGACGGGCTTTCATCGGATGCAGAAGATAAGCGAGCCAAAACCACCGAGgtacataatt ... ttttattcagCTTGCACAGTTGCAAGTGGAGCTTCAACGCATGAACGCTGAGAACAAGAAG
EST: gi|14990745|gb|BI316418.1|BI316418
EST:     ATGACGGGCTTTCATCGGATGCAGAAGATAAGCGAGCCAAAACCACCGAG                         CTTGCACAGTTGCAAGTGGAGCTTCAACGCATGAACGCTGAGAACAAGAAG
genomic: ATGACGGGCTTTCATCGGATGCAGAAGATAAGCGAGCCAAAACCACCGAGgtacataatt ... ttttattcagCTTGCACAGTTGCAAGTGGAGCTTCAACGCATGAACGCTGAGAACAAGAAG
EST: gi|213614601|gb|DB969531.1|DB969531
EST:     ATGACGGGCTTTCATCGGATGCAGAAGATAAGCGAGCCAAAACCACCGAG                         CTTGCACAGTTGCAAGTGGAGCTTCAACGCATGAACGCTGAGAACAAGAAG
genomic: ATGACGGGCTTTCATCGGATGCAGAAGATAAGCGAGCCAAAACCACCGAGgtacataatt ... ttttattcagCTTGCACAGTTGCAAGTGGAGCTTCAACGCATGAACGCTGAGAACAAGAAG
EST: gi|17964331|gb|BM271068.1|BM271068
EST:     GAGCTAAAACCACCGAG                         CTTGCACAGTTGCAAGTGGAGCTTCAACGCATGAACGCTGAGAACAAGAAG
genomic: GAGCCAAAACCACCGAGgtacataatt ... ttttattcagCTTGCACAGTTGCAAGTGGAGCTTCAACGCATGAACGCTGAGAACAAGAAG
EST: gi|14205880|gb|BG839558.1|BG839558
EST:     ATGACGGGCTTTCATCGGATGCAGAAGATAAGCGAGCCAAAACCACCGAG                         CTTGCACAGTTGCAAGTGGAGCTTCAACGCATGAACGCTGAGAACAAGAAG
genomic: ATGACGGGCTTTCATCGGATGCAGAAGATAAGCGAGCCAAAACCACCGAGgtacataatt ... ttttattcagCTTGCACAGTTGCAAGTGGAGCTTCAACGCATGAACGCTGAGAACAAGAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcctttgaaatttaagtgttaattactcactgaattgtatactttttttattcagCTTGCACAGTTGCAAGTGGAGCTTCAACGCATGAACGCTGAGAACAAGAAGCTGAAAGAGATGCTCAGCCATGTCACCGGTAACTACACCGCCTTGCAGA
                       tactcac  putative branch site (score: 1)
                                       tactttttttattc  putative PPT
                              tgaattgtatactttt  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacataatttaatttaatgtcatatttgtatcgatttttatttattttacatagcctttgaaatttaagtgttaattactcactgaattgtatactttttttattcagCTTGCACAGTTGCAAGTGGAGCTTCAACGCATGAACGCTGAGAACAAGAAGCTGAAAGAGATGCTCAGCCATGTCACCGGTAACTACACCGCCTTGCAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG