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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagccagcctcttactctaatcctttatcgttttgcattgcgattttcgtttttcctttttaagaaaacatcataatcgatttcaatcttctatttgaattattaattcgccttgttcttatgattatgatgtttgcttctgcggaaacagAAAGAGAGAGGTGAATCTGAAGGTGCTCAAGGTTCCGGAAATCGAACAGAAG

Basic information

species Glycine max
transcript GLYMA17G35000.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA17G35000.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os04g51120.3 (Oryza sativa), 3'ss of exon 1
gtgagccagcctcttactctaatcctttatcgttttgcattgcgattttcgtttttcctttttaagaaaacatcataatc-gatttcaatcttctatttgaattattaattcgccttgttcttatgattatgatgtttgcttctgcggaaacagAAAGAGAGAGGTGAATCTGAAGGTGCTCAAGGTTCCGGAAATCGAACAGAAG
       |   | |    | |  ||   |||        | || |||   |||     || |  || |     | |  || || ||  |||       |||  |  | || ||  ||     | ||  | ||    ||||||         ||||||||| ||||| ||| ||||||||||||||||||| ||  |||||||||||
-----gtaagttgtgggccgagcccgagatc--------tcgccattgctgttccgatttctcgaggatgtggcgtgttctgagttggatccg-----tgagatcctgatccgtttt----ctgtgtgtgtg----ttgcttt-------gcagAAAGAGGGAGGTCAATTTGAAGGTGCTCAAGGTTCCAGAGCTCGAACAGAAG

upper sequence: GLYMA17G35000.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os01g53670.2 (Oryza sativa), 3'ss of exon 1
gtgagccagcctcttactctaatcctttatcgttttgcattgcgattttcgtttttcctttttaagaaaacatcataatcgatttcaatcttctatttgaattattaattcgccttgttcttatgattatgatgtttgcttctgcggaaacagAAAGAGAGAGGTGAATCTGAAGGTGCTCAAGGTTCCGGAAATCGAACAGAAG
                                                          |    |  | ||  |     ||   |||      |  |||    |  |  |   |     |||| | |  || || |||  |  ||      ||||| ||| ||||| ||||| |||||||||||||| ||||||||||| ||||||
---------------------------------------------------------gtaagaatcagaatttttatttctccttctccgccccttttctcctcctggtgtactcctatcttgtaaagat-atttttcttcttgtactttcagAAGGAGGGAGGTAAATCTTAAGGTGCTCAAGGTGCCGGAAATCGAGCAGAAG

upper sequence: GLYMA17G35000.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G125728_T02 (Zea mays), 3'ss of exon 1
gtgagccagcctcttactctaatcctttatcgt-tttgcattgcgattttcgtttttcctttttaagaaaacatcataatcgatttcaatcttctatttgaattattaattcgccttgttcttatgattatgatgtttgcttctgcggaaacagAAAGAGAGAGGTGAATCTGAAGGTGCTCAAGGTTCCGGAAATCGAACAGAAG
                   |||    | | | | | |    |    ||  |||  ||   || | ||| |   | ||  | ||||  || ||||     | ||  || ||  || |  | |   ||       | || |            ||||||||| ||||| ||||||||||| |||||||| || || ||||| ||||||
------------------gtaagttctaaccctgtctatgatctcgttgccgtcgttagattctgagagatgtttat--tggattcgaaccttc-----ggatc-ttgatctgcgtgttgcgcgtg-------tattcgt----------gcagAAAGAGGGAGGTCAATCTGAAGGTACTCAAGGTCCCCGAGATCGAGCAGAAG

upper sequence: GLYMA17G35000.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv04s0008g00640.t01 (Vitis vinifera), 3'ss of exon 3
gtgagccagcctcttactctaatcctttatcgttttgcattgcgattttcgtttttcctttttaagaaaacatcataatcgatttcaatcttctatttgaattattaattcgccttgttcttatgattatgatgtttgcttctgcggaaacagAAAGAGAGAGGTGAATCTGAAGGTGCTCAAGGTTCCGGAAATCGAACAGAAG
                             |    |   | |||||||||| ||||      || || ||    |    |||| |  |   |   |||| ||||  | |||||  |   |    ||||| | || | |  ||||   |   ||||||||| |||||||||||||||||  | |||||||| || ||||| ||||||
----------------------------gtgagctccgaatgcgattttcattttcttagatttagcaatgtgctctttcgagtgaa---taagattttaatt--tgattcgattcaatt---tgatt-taatctcta-ttctcttggggcagAAAGAGGGAGGTGAATCTGAAGGTTTTGAAGGTTCCAGAGATCGAGCAGAAG

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|193689999|gb|FK627940.1|FK627940
EST:     CCCACCGCCATGGATTTCATGAAGGTCTTCGATCGAACCGTTCGAGAAAT                         AAAGAGAGAGGTGAATCTGAAGGTGCTCAAGGTTCCGGAAATCGAACAGAA
genomic: CCCACCGCCATGGATTTCATGAAGGTCTTCGATCAAACCGTTCGAGAAATgtgagccagc ... gcggaaacagAAAGAGAGAGGTGAATCTGAAGGTGCTCAAGGTTCCGGAAATCGAACAGAA
EST: gi|207736087|gb|GD711238.1|GD711238
EST:     CCCACCGCCATGGATTTCATGAAGGTCTTCGATCAAACCGTTCGAGAAAT                         AAAGAGAGAGGTGAATCTGAAGGTGCTCAAGGTTCCGGAAATCGAACAGAA
genomic: CCCACCGCCATGGATTTCATGAAGGTCTTCGATCAAACCGTTCGAGAAATgtgagccagc ... gcggaaacagAAAGAGAGAGGTGAATCTGAAGGTGCTCAAGGTTCCGGAAATCGAACAGAA
EST: gi|193345140|gb|FK309624.1|FK309624
EST:     CCCACCGCCATGGATTTCATGAAGGTCTTCGATCAAACCGTTCGAGAAAT                         AAAGAGAGAGGTGAATCTGAAGGTGCTCAAGGTTCCGGAAATCGAACAGAA
genomic: CCCACCGCCATGGATTTCATGAAGGTCTTCGATCAAACCGTTCGAGAAATgtgagccagc ... gcggaaacagAAAGAGAGAGGTGAATCTGAAGGTGCTCAAGGTTCCGGAAATCGAACAGAA
EST: gi|192323821|gb|FK015617.1|FK015617
EST:     CCCACCGCCATGGATTTCATGAAGGTCTTCGATCAAACCGTTCGAGAAAT                         AAAGAGAGAGGTGAATCTGAAGGTGCTCAAGGTTCCGGAAATCGAACAGAA
genomic: CCCACCGCCATGGATTTCATGAAGGTCTTCGATCAAACCGTTCGAGAAATgtgagccagc ... gcggaaacagAAAGAGAGAGGTGAATCTGAAGGTGCTCAAGGTTCCGGAAATCGAACAGAA
EST: gi|192323472|gb|FK019003.1|FK019003
EST:     CCCACCGCCATGGATTTCATGAAGGTCTTCGATCAAACCGTTCGAGAAAT                         AAAGAGAGAGGTGAATCTGAAGGTGCTCAAGGTTCCGGAAATCGAACAGAA
genomic: CCCACCGCCATGGATTTCATGAAGGTCTTCGATCAAACCGTTCGAGAAATgtgagccagc ... gcggaaacagAAAGAGAGAGGTGAATCTGAAGGTGCTCAAGGTTCCGGAAATCGAACAGAA
EST: gi|192330169|gb|FK020514.1|FK020514
EST:     CCCACCGCCATGGATTTCATGAAGGTCTTCGATCAAACCGTTCGAGAAAT                         AAAGAGAGAGGTGAATCTGAAGGTGCTCAAGGTTCCGGAAATCGAACAGAA
genomic: CCCACCGCCATGGATTTCATGAAGGTCTTCGATCAAACCGTTCGAGAAATgtgagccagc ... gcggaaacagAAAGAGAGAGGTGAATCTGAAGGTGCTCAAGGTTCCGGAAATCGAACAGAA
EST: gi|254331977|gb|GR843720.1|GR843720
EST:     CCCACCGCCATGGATTTCATGAAGGTCTTCGATCAAACCGTTCGAGAAAT                         AAAGAGAGAGGTGAATCTGAAGGTGCTCAAGGTTCCGGAAATCGAACAGAA
genomic: CCCACCGCCATGGATTTCATGAAGGTCTTCGATCAAACCGTTCGAGAAATgtgagccagc ... gcggaaacagAAAGAGAGAGGTGAATCTGAAGGTGCTCAAGGTTCCGGAAATCGAACAGAA
EST: gi|193409765|gb|FK375029.1|FK375029
EST:     CCCACCGCCATGGATTTCGTGAAGGTCTTCGATCAAACCGTTCGAGAAAT                         AAAGAGAGAGGTGAATCTGAAGGTGCTCAAGGTTCCGGAAATCGAACAGAA
genomic: CCCACCGCCATGGATTTCATGAAGGTCTTCGATCAAACCGTTCGAGAAATgtgagccagc ... gcggaaacagAAAGAGAGAGGTGAATCTGAAGGTGCTCAAGGTTCCGGAAATCGAACAGAA
EST: gi|208240582|gb|GE040112.1|GE040112
EST:     CCCACCGCCATGGATTTCATGAAGGTCTTCGATCAAACCGTTCGAGAAAT                         AAAGAGAGAGGTGAATCTGAAGGTGCTCAAGGTTCCGGAAATACGAACAGA
genomic: CCCACCGCCATGGATTTCATGAAGGTCTTCGATCAAACCGTTCGAGAAATgtgagccagc ... gcggaaacagAAAGAGAGAGGTGAATCTGAAGGTGCTCAAGGTTCCGGAAAT-CGAACAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaattattaattcgccttgttcttatgattatgatgtttgcttctgcggaaacagAAAGAGAGAGGTGAATCTGAAGGTGCTCAAGGTTCCGGAAATCGAACAGAAG
    tattaat  putative branch site (score: 2)
                                        cttctgc  putative PPT
                      ttatgattat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagccagcctcttactctaatcctttatcgttttgcattgcgattttcgtttttcctttttaagaaaacatcataatcgatttcaatcttctatttgaattattaattcgccttgttcttatgattatgatgtttgcttctgcggaaacagAAAGAGAGAGGTGAATCTGAAGGTGCTCAAGGTTCCGGAAATCGAACAGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG