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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagcatatattctatatcttctttcattggactatttattttggagtttaatttatgattgaacttcatgattttctacttagACTCTGGAAGAAGCAATTGCCTTGAACAATTCTGTACCTCAAGGATTAAGTAGTTCAATCTTTACCCAAAGACCTGGAACTATATTCAAGTGGATTGGGT

Basic information

species Glycine max
transcript GLYMA15G19670.3
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA15G19670.4 (Glycine max), 3'ss of exon 11
lower sequence: Vv11s0016g00900.t01 (Vitis vinifera), 3'ss of exon 11
-------gtagcatatatt-ctatatcttctttcattggactatttattttggagtttaa-tttatgattgaacttcatgattttctactt-----agACTCTGGAAGAAGCAATTGCCTTGAACAATTCTGTACCTCAAGGATTAAGTAGTTCAATCTTTACCCAAAGACCTGGAACTATATTCAAGTGGATTGGGT
       ||     || |  || |     || |   ||| |||||| | ||   | | ||  ||||  ||  |  |   ||   ||  |||     ||||| | ||||||||| |||   ||||||| |||||||| |||||||| |||||||||||||| || |  | ||||| |  ||| ||||| ||||||||  
gtagtctgttaatgatgtcactctcctccctcttggtggtctatttctcttcctgatcaaacttatcttttcatgtttggaaactcctctttgtgcagACTTTTGAAGAAGCAGTTGAAATGAACAACTCTGTACCACAAGGATTGAGTAGTTCAATCTTCACTCGCAAACCTGAAGTTATCTTCAAATGGATTGG--
















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|193511086|gb|FK468971.1|FK468971
EST:     TAGTTAAAGAAGAATTGTTTGGTCCAGTTCTGTATGTTATGAAATTTCAG                         ACTCTGGAAGAAGCAATTGCCTTGAAACAATTCTGTACCTCAAGGATTAAG
genomic: TAGTTAAAGAAGAATTGTTTGGTCCAGTTCTGTATGTTATGAAATTTCAGgtagcatata ... ttctacttagACTCTGGAAGAAGCAATTGCCTTGAA-CAATTCTGTACCTCAAGGATTAAG
EST: gi|20448705|gb|BQ252829.1|BQ252829
EST:     TAGTTAAAGAAGAATTGTTTGGTCCAGTTCTGTATGTTATGAAATTTCAG                         ACTCTGGAAGAAGCAATTGCCTTGAACAATTCTGTACCTCAAGGATTAAGT
genomic: TAGTTAAAGAAGAATTGTTTGGTCCAGTTCTGTATGTTATGAAATTTCAGgtagcatata ... ttctacttagACTCTGGAAGAAGCAATTGCCTTGAACAATTCTGTACCTCAAGGATTAAGT
EST: gi|193615341|gb|FK564765.1|FK564765
EST:     TAGTTAAAGAAGAATTGTTTGGTCCAGTTCTGTATGTTATGAAATTTCAG                         ACTCTGGAAGAAGCAATTGCCTTGAACAATTCTGTACCTCAAGGATTAAGT
genomic: TAGTTAAAGAAGAATTGTTTGGTCCAGTTCTGTATGTTATGAAATTTCAGgtagcatata ... ttctacttagACTCTGGAAGAAGCAATTGCCTTGAACAATTCTGTACCTCAAGGATTAAGT
EST: gi|193472436|gb|FK438643.1|FK438643
EST:     TAGTTAAAGAAGAATTGTTTGGTCCAGTTCTGTATGTTATGAAATTTCAG                         ACTCTGGAAGAAGCAATTGCCTTGAACAATTCTGTACCTCAAGGATTA
genomic: TAGTTAAAGAAGAATTGTTTGGTCCAGTTCTGTATGTTATGAAATTTCAGgtagcatata ... ttctacttagACTCTGGAAGAAGCAATTGCCTTGAACAATTCTGTACCTCAAGGATTA
EST: gi|192309267|gb|FG999144.1|FG999144
EST:     TAGTTAAAGAAGAATTGTTTGGTCCAGTTCTGTATGTTATGAAATTTCAG                         ACTCTGGAAGAAGCAATTGCCTTGAACAATTCTGTAC-TCAAGGAT-AAGT
genomic: TAGTTAAAGAAGAATTGTTTGGTCCAGTTCTGTATGTTATGAAATTTCAGgtagcatata ... ttctacttagACTCTGGAAGAAGCAATTGCCTTGAACAATTCTGTACCTCAAGGATTAAGT
EST: gi|208314647|gb|GE112191.1|GE112191
EST:     TAGTTAAAGAAGAATTGTTTGGTCCAGTTCTGTATGTTATGAAATTTCAG                         ACTCTGGAAGAAGCAATTGCCTTGGACAATTCTGTACCT
genomic: TAGTTAAAGAAGAATTGTTTGGTCCAGTTCTGTATGTTATGAAATTTCAGgtagcatata ... ttctacttagACTCTGGAAGAAGCAATTGCCTTGAACAATTCTGTACCT
EST: gi|15813675|gb|BI785950.1|BI785950
EST:     TAGTTAAAGAAGAATTGTTTGGTCCAGTTCTGTATGTTATGAAATTTCAG                         ACTCTGGAAGAAGCAATTGCCTTGAACAATTCTGTACCTCAAGGATTAAGT
genomic: TAGTTAAAGAAGAATTGTTTGGTCCAGTTCTGTATGTTATGAAATTTCAGgtagcatata ... ttctacttagACTCTGGAAGAAGCAATTGCCTTGAACAATTCTGTACCTCAAGGATTAAGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggactatttattttggagtttaatttatgattgaacttcatgattttctacttagACTCTGGAAGAAGCAATTGCCTTGAACAATTCTGTACCTCAAGGATTAAGTAGTTCAATCTTTACCCAAAGACCTGGAACTATATTCAAGTGGATTGGGT
                 gtttaat  putative branch site (score: 4)
                                           ttttctactt  putative PPT
     atttattttggagttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtagcatatattctatatcttctttcattggactatttattttggagtttaatttatgattgaacttcatgattttctacttagACTCTGGAAGAAGCAATTGCCTTGAACAATTCTGTACCTCAAGGATTAAGTAGTTCAATCTTTACCCAAAGACCTGGAACTATATTCAAGTGGATTGGGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA