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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttttggaagagatataactataaatatataacttcaatttcaatcttttatgcggaaattaaggttgtcgtgttttgcgtgagcttcaattaaattgattgacttggttcatttcatttgttattttgcagGAAGTGGAAGGAAATTGTGGATGAGTGGGTGAAGTTGAATCCACGGGGAGGAAGCAACACTCTGATGG

Basic information

species Glycine max
transcript GLYMA04G39470.2
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|20449163|gb|BQ253287.1|BQ253287
EST:     CGGAAGCATCCTTCAAACGACCTTCGGCGATTGGTGAAGTTGCTTGTCAG                         GAAGTGGAAGGAAATTGTGGATGAGTGGGTGAAGTTGAATCCACGGGGAGG
genomic: CGGAAGCATCCTTCAAACGACCTTCGGCGATTGGTGAAGTTGCTTGTCAGgttttggaag ... tattttgcagGAAGTGGAAGGAAATTGTGGATGAGTGGGTGAAGTTGAATCCACGGGGAGG
EST: gi|20812089|gb|BQ296567.1|BQ296567
EST:     CGGAAGCATCCTTCAAACGACCTTCGGCGATTGGTGAAGTTGCTTGTCAG                         GAAGTGGAAGGAAATTGTGGATGAGTGGGTGAAGTTGAATCCACGGGGAGG
genomic: CGGAAGCATCCTTCAAACGACCTTCGGCGATTGGTGAAGTTGCTTGTCAGgttttggaag ... tattttgcagGAAGTGGAAGGAAATTGTGGATGAGTGGGTGAAGTTGAATCCACGGGGAGG
EST: gi|6070892|gb|AW100279.1|AW100279
EST:     CGGAAGCATCCTTCAAACGACCTTCGGCGATTGGTGAAGTTGCTTGTCAG                         GAAGTGGAAGGAAATTGTGGATGAGTGGGTGAA
genomic: CGGAAGCATCCTTCAAACGACCTTCGGCGATTGGTGAAGTTGCTTGTCAGgttttggaag ... tattttgcagGAAGTGGAAGGAAATTGTGGATGAGTGGGTGAA
EST: gi|10844098|gb|BF067435.1|BF067435
EST:     CGGAAGCATCCTTCAAACGACCTTCGGCGATTGGTGAAGTTGCTTGTCAG                         GAAGTGGAAGGAAATTGTGGATGAGTGGGTGAAGTTGAATCCACGGNGAGG
genomic: CGGAAGCATCCTTCAAACGACCTTCGGCGATTGGTGAAGTTGCTTGTCAGgttttggaag ... tattttgcagGAAGTGGAAGGAAATTGTGGATGAGTGGGTGAAGTTGAATCCACGGGGAGG
EST: gi|8286013|gb|BE023501.1|BE023501
EST:     CGGAAGCATCCTTCAAACGACCTTCGGCGATTGGTGAAGTTGCTTGTCAG                         GAAGTGGAAGGAAATTGTGGATGAGTGGGTG-AGTTGAATCCACGGGGAGG
genomic: CGGAAGCATCCTTCAAACGACCTTCGGCGATTGGTGAAGTTGCTTGTCAGgttttggaag ... tattttgcagGAAGTGGAAGGAAATTGTGGATGAGTGGGTGAAGTTGAATCCACGGGGAGG
EST: gi|10847263|gb|BF069975.1|BF069975
EST:     CGGAAGCATCCTTCAAACGACCTTCGGCGATTGGTGAAGTTGCTTGTCAG                         GAAGTGGAAGGAAATTGTGGATGAGTGGGTGAAGTTGAATCCACGGGGAGG
genomic: CGGAAGCATCCTTCAAACGACCTTCGGCGATTGGTGAAGTTGCTTGTCAGgttttggaag ... tattttgcagGAAGTGGAAGGAAATTGTGGATGAGTGGGTGAAGTTGAATCCACGGGGAGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcgtgagcttcaattaaattgattgacttggttcatttcatttgttattttgcagGAAGTGGAAGGAAATTGTGGATGAGTGGGTGAAGTTGAATCCACGGGGAGGAAGCAACACTCTGATGG
                    gattgac  putative branch site (score: 3)
                                            ttatttt  putative PPT
                                  atttcatttgttattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttttggaagagatataactataaatatataacttcaatttcaatcttttatgcggaaattaaggttgtcgtgttttgcgtgagcttcaattaaattgattgacttggttcatttcatttgttattttgcagGAAGTGGAAGGAAATTGTGGATGAGTGGGTGAAGTTGAATCCACGGGGAGGAAGCAACACTCTGATGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA