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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgaggagatttttgtctattggaatataacattgacacaattttatatcttaattcatagttatttacctgtcatttctcatttatcattccttttgcattcaatacttgattttggaaaattcccatagGTATGAAGGGCCACGCACTGCTGATTCACTTGCTGAGTTTGTAAATACGGAAGGAG

Basic information

species Glycine max
transcript GLYMA06G24520.1
intron # 4
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|193731335|gb|FK664867.1|FK664867
EST:     GGGTACCCAACAATTCAGTGGTTTCCAAAAGGATCTCTTGAACCCAAAAA                         GTATGAAGGGCCACGTCACTGCTGATTCACTTGCTGAGTTTGTAAATACGG
genomic: GGGTACCCAACAATTCAGTGGTTTCCAAAAGGATCTCTTGAACCCAAAAAgtgaggagat ... attcccatagGTATGAAGGGCCACG-CACTGCTGATTCACTTGCTGAGTTTGTAAATACGG
EST: gi|208316849|gb|GE115855.1|GE115855
EST:     GGTTTACCAAAAGGATCTCTTGAACCCAAAAA                         GTATGAAGGGCCACGCACTGCTGATTCACTTGCTGAGTTTGTAAATACGGA
genomic: GGTTT-CCAAAAGGATCTCTTGAACCCAAAAAgtgaggagat ... attcccatagGTATGAAGGGCCACGCACTGCTGATTCACTTGCTGAGTTTGTAAATACGGA
EST: gi|208270669|gb|GE066919.1|GE066919
EST:     TGGTTTACCAAAAGGATCTCTTGAACCCAAAAA                         GTATGAAGGGCCACGCACTGCTGATTCACTTGCTGAGTTTGTAAATACGGA
genomic: TGGTTT-CCAAAAGGATCTCTTGAACCCAAAAAgtgaggagat ... attcccatagGTATGAAGGGCCACGCACTGCTGATTCACTTGCTGAGTTTGTAAATACGGA
EST: gi|193515760|gb|FK474330.1|FK474330
EST:     GGGTACCCAACAATTCAGTGGTTTCCAAAAGGATCTCTTGAACCCAAAAA                         GTATGAAGGGCCACGCACTGCTGATTCACTTGCTGAGTTTGTAAATACGGA
genomic: GGGTACCCAACAATTCAGTGGTTTCCAAAAGGATCTCTTGAACCCAAAAAgtgaggagat ... attcccatagGTATGAAGGGCCACGCACTGCTGATTCACTTGCTGAGTTTGTAAATACGGA
EST: gi|193585305|gb|FK540790.1|FK540790
EST:     GGGTACCCAACAATTCAGTGGTTTCCAAAAGGATCTCTTGAACCCAAAA-                         GTATGAAGGGCCACG
genomic: GGGTACCCAACAATTCAGTGGTTTCCAAAAGGATCTCTTGAACCCAAAAAgtgaggagat ... attcccatagGTATGAAGGGCCACG
EST: gi|193447299|gb|FK414558.1|FK414558
EST:     GGGTACCCAACAATTCAGTGGTTTCCAAAAGGATCTCTTGAACCCAAAAA                         GTATGAAGGGCCACG
genomic: GGGTACCCAACAATTCAGTGGTTTCCAAAAGGATCTCTTGAACCCAAAAAgtgaggagat ... attcccatagGTATGAAGGGCCACG
EST: gi|193488849|gb|FK453214.1|FK453214
EST:     GGGTACCCAACAATTCAGTGGTTTCCAAAAGGATCTCTTGAACCCAAAAA                         GTATGAAGGGCCACGCACTGCTGATTCACTTGCTGAGTTTGTAAATACGGA
genomic: GGGTACCCAACAATTCAGTGGTTTCCAAAAGGATCTCTTGAACCCAAAAAgtgaggagat ... attcccatagGTATGAAGGGCCACGCACTGCTGATTCACTTGCTGAGTTTGTAAATACGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttctcatttatcattccttttgcattcaatacttgattttggaaaattcccatagGTATGAAGGGCCACGCACTGCTGATTCACTTGCTGAGTTTGTAAATACGGAAGGAG
                              acttgat  putative branch site (score: 5)
                                              ttcccat  putative PPT
     atttatcatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgaggagatttttgtctattggaatataacattgacacaattttatatcttaattcatagttatttacctgtcatttctcatttatcattccttttgcattcaatacttgattttggaaaattcccatagGTATGAAGGGCCACGCACTGCTGATTCACTTGCTGAGTTTGTAAATACGGAAGGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG