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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttatatacttgagttaattggattcaacatacgaaatacttgattgtcttggtgcacgaatttgcttgattttttaagacacgatattttcgttttgcagAATGTGTATGATACACTTTTCTTCATTGTGGACCTGCACGCG

Basic information

species Glycine max
transcript GLYMA04G09130.1
intron # 3
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|23063730|gb|BU578612.1|BU578612
EST:     TTCACCTCGGAAACTATTTTGGCGCCATCAAGAATTGGGTTGCCCTTCAG                         AATGTGTATGATACACTTTTCTTCATTGTGGACCTGCACGCG
genomic: TTCACCTCGGAAACTATTTTGGCGCCATCAAGAATTGGGTTGCCCTTCAGgtttattatt ... cgttttgcagAATGTGTATGATACACTTTTCTTCATTGTGGACCTGCACGCG
EST: gi|6482637|gb|AW201882.1|AW201882
EST:     TTCACCTCGGAAACTATTTTGGCGCCATCAAGAATTGGGTTGCCCTTCAG                         AATGTGTATGATACACTTTTCTTCATTGTGGACCTGCACGCG
genomic: TTCACCTCGGAAACTATTTTGGCGCCATCAAGAATTGGGTTGCCCTTCAGgtttattatt ... cgttttgcagAATGTGTATGATACACTTTTCTTCATTGTGGACCTGCACGCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtcttggtgcacgaatttgcttgattttttaagacacgatattttcgttttgcagAATGTGTATGATACACTTTTCTTCATTGTGGACCTGCACGCG
                  gcttgat  putative branch site (score: 5)
                                         ttttcgtttt  putative PPT
                    ttgattttttaaga  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttatatacttgagttaattggattcaacatacgaaatacttgattgtcttggtgcacgaatttgcttgattttttaagacacgatattttcgttttgcagAATGTGTATGATACACTTTTCTTCATTGTGGACCTGCACGCG

- - - - - - - - - - - - - - - - gaaatac
- - - - - - - - - - - - - - - - - - - - - - tgtcttg
- - - - - - - - - - - - - - - - - - - - - - - - - - tgcacga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgcttga