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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtgttttgagttgagaaaaagagaagcgaagtttatttgttgttttggtactgattggtgttgaacgtggtgggtttttctttattttcttggtgggcagCTCTTTGATTTTTGAGTTAATAAAAAAAAAAAAATTAGGGTTTGATGGCTGACCAAGGATTGGAAGGGAGCCAGCCGGTGGATCTACAGAAGCATCCTTC

Basic information

species Glycine max
transcript GLYMA16G25450.1
intron # 1
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|163927309|gb|EH038590.1|EH038590
EST:     CCTCTGATTTAATTCATGCGCAGATCCAAACCCTAATCCCTCTCTCCGAG                         CTCTTTGATTTTTGAGTTAAT-NNNNNNNNNNNNTTAGGGTTTGATGGCTG
genomic: CCTCTGATTTAATTCATGCGCAGATCCAAACCCTAATCCATCTCTCCGAGgtctgatttc ... tggtgggcagCTCTTTGATTTTTGAGTTAATAAAAAAAAAAAAATTAGGGTTTGATGGCTG
EST: gi|120530268|gb|EH258402.1|EH258402
EST:     CCTCTGATTTAATTCATGCGCAGATCCAAACCCTAATCCATCTCTCCGAG                         CTCTTTGATTTTTGAGTTAATNNNNNNNNNNNNNTTAGGGTTTGATGGCTG
genomic: CCTCTGATTTAATTCATGCGCAGATCCAAACCCTAATCCATCTCTCCGAGgtctgatttc ... tggtgggcagCTCTTTGATTTTTGAGTTAATAAAAAAAAAAAAATTAGGGTTTGATGGCTG
EST: gi|13481866|gb|BG511209.1|BG511209
EST:     CCTCTGATTTAATTCATGCGCAGATCCAAACCCTAATCCATCTCTCCGAG                         CTCTTTGATTTTTGAGTTAA
genomic: CCTCTGATTTAATTCATGCGCAGATCCAAACCCTAATCCATCTCTCCGAGgtctgatttc ... tggtgggcagCTCTTTGATTTTTGAGTTAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggtactgattggtgttgaacgtggtgggtttttctttattttcttggtgggcagCTCTTTGATTTTTGAGTTAATAAAAAAAAAAAAATTAGGGTTTGATGGCTGACCAAGGATTGGAAGGGAGCCAGCCGGTGGATCTACAGAAGCATCCTTC
   tactgat  putative branch site (score: 2)
                             tttttctttattttct  putative PPT
                             tttttctttattttct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgttttgagttgagaaaaagagaagcgaagtttatttgttgttttggtactgattggtgttgaacgtggtgggtttttctttattttcttggtgggcagCTCTTTGATTTTTGAGTTAATAAAAAAAAAAAAATTAGGGTTTGATGGCTGACCAAGGATTGGAAGGGAGCCAGCCGGTGGATCTACAGAAGCATCCTTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
-tgttttg
- - - - - - -agaaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - ggtgttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tggtggg