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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcttcctttatacatattcttttccgttggctttattgtgcatggatgttttgtagattgactcaatacgctaaagcacacaattattcctttccatgcagGAAAAGTCTTTACTCAGAGTAAAGAGAATAATGAAAGTCAAAGTAGAGAGCAAAGAGATGAGAAATCACCGGTGAAACTGGATGACAGTTTACAGAAAAG

Basic information

species Glycine max
transcript GLYMA20G27030.1
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|17963691|gb|BM270437.1|BM270437
EST:     GGGTAGTACTGGGCAGGTTGGTCGAAGCAATGGTCAAAGGGAAGCTGGTG                         GAAAAGTCTTTACTCAGAGTAAAGAGAATAATGAAAGTCAAAGTAGAGAGC
genomic: GGGTAGTACTGGGCAGGTTGGTCGAAGCAATGGTCAAAGGGAAGCTGGTGgtaagcttcc ... ttccatgcagGAAAAGTCTTTACTCAGAGTAAAGAGAATAATGAAAGTCAAAGTAGAGAGC
EST: gi|18734241|gb|BM528070.1|BM528070
EST:     GGGTAGTACTGGGCAGGTTGGTCGAAGCAATGGTCAAAGGGAAGCTGGTG                         GAAAAGTCTTTACTCAGAGTAAAGAGAATAATGAAAGTCAAAGTAGAGAGC
genomic: GGGTAGTACTGGGCAGGTTGGTCGAAGCAATGGTCAAAGGGAAGCTGGTGgtaagcttcc ... ttccatgcagGAAAAGTCTTTACTCAGAGTAAAGAGAATAATGAAAGTCAAAGTAGAGAGC
EST: gi|192299355|gb|FG990751.1|FG990751
EST:     GGGTAGTACTGGGCAGGTTGGTCGAAGCAATGGTCAAAGGGAAGCTGGTG                         GAAAAGTCTTTACTCAGAGTAAGGAGAATAATGAAAGTCAAAGTAGAGAGC
genomic: GGGTAGTACTGGGCAGGTTGGTCGAAGCAATGGTCAAAGGGAAGCTGGTGgtaagcttcc ... ttccatgcagGAAAAGTCTTTACTCAGAGTAAAGAGAATAATGAAAGTCAAAGTAGAGAGC
EST: gi|4291324|gb|AI441745.1|AI441745
EST:     GGGTAGTACTGGGCAGGTTGGTCGAAGCAATGGTCAAAGGGAAGCTGGTG                         GAAAAGTCTTTACTCAGAGTAAAGAGAATAATGAAAGTCA
genomic: GGGTAGTACTGGGCAGGTTGGTCGAAGCAATGGTCAAAGGGAAGCTGGTGgtaagcttcc ... ttccatgcagGAAAAGTCTTTACTCAGAGTAAAGAGAATAATGAAAGTCA
EST: gi|298197509|gb|HO044988.1|HO044988
EST:     GGGTAGTACTGGGCAGGTTGGTCGAAGCAATGGTCAAAGGGAAGCTGGTG                         GAAAAGTCTTTACTCAGAGTAAAGAGAATAATGAAAGTCAAAGTAGAGAGC
genomic: GGGTAGTACTGGGCAGGTTGGTCGAAGCAATGGTCAAAGGGAAGCTGGTGgtaagcttcc ... ttccatgcagGAAAAGTCTTTACTCAGAGTAAAGAGAATAATGAAAGTCAAAGTAGAGAGC
EST: gi|298189778|gb|HO038181.1|HO038181
EST:     GGGTAGTACTGGGCAGGTTGGTCGAAGCAATGGTCAAAGGGAAGCTGGTG                         GAAAAGTCTTTACTCAGAGTAAAGAGAATAATGAAAGTCAAAGTAGAGAGC
genomic: GGGTAGTACTGGGCAGGTTGGTCGAAGCAATGGTCAAAGGGAAGCTGGTGgtaagcttcc ... ttccatgcagGAAAAGTCTTTACTCAGAGTAAAGAGAATAATGAAAGTCAAAGTAGAGAGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgttttgtagattgactcaatacgctaaagcacacaattattcctttccatgcagGAAAAGTCTTTACTCAGAGTAAAGAGAATAATGAAAGTCAAAGTAGAGAGCAAAGAGATGAGAAATCACCGGTGAAACTGGATGACAGTTTACAGAAAAG
                      cgctaaa  putative branch site (score: 3)
                                     ttattcctttccat  putative PPT
                                 acaattatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagcttcctttatacatattcttttccgttggctttattgtgcatggatgttttgtagattgactcaatacgctaaagcacacaattattcctttccatgcagGAAAAGTCTTTACTCAGAGTAAAGAGAATAATGAAAGTCAAAGTAGAGAGCAAAGAGATGAGAAATCACCGGTGAAACTGGATGACAGTTTACAGAAAAG

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