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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATGTTCCTTTAAGTGCTAGAAACATTTTGGAGGATCCTGAACTGAAAAATGCTGTAAAAGCTTTCAGgtatgttcatttttactggttttattactcttgcttcataagagagtactctatttctcttacagtgagcacaatttttcaaaattcacatttgtggtgg...

Basic information

species Glycine max
transcript GLYMA13G44000.2
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G44000.2 (Glycine max), 5'ss of exon 3
lower sequence: Vv09s0002g06040.t01 (Vitis vinifera), 5'ss of exon 5
ATGTTCCTTTAAGTGCTAGAAACATTTTGGAGGATCCTGAACTGAAAAATGCTGTAAAAGCTTTCAGgtatgttcattttt-------actggttttattactcttgcttcataag--agagtactctatttctcttacagtgagcacaatttttcaaaattcacatttgtggtgg
|||||||||| ||||||||||| |||||||| || ||||| ||||| | ||||||||||   |||||||| ||||  | |        | ||  |||||| ||  |   | |  ||  | || |||  |   | ||     |  | |    || |   |  ||| | |        
ATGTTCCTTTGAGTGCTAGAAATATTTTGGAAGACCCTGAGCTGAAGATTGCTGTAAAAAAATTCAGgtaagttctctctacacccgaagtgcgtttattgcttattgataaccagctaaagaactacaagaccct---gtttggaatggcttcttggaggtcaaaatct------
















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|17154054|gb|BM143987.1|BM143987
EST:     AGAAACATTTTGGAGGATCCTGAACTGAAAAATGCTGTAAAAGCTTTCAG                         TAACTGGCCAACATTTCCACAAGTTTTCATTAAGGGAGAGTTTATCGGTGG
genomic: AGAAACATTTTGGAGGATCCTGAACTGAAAAATGCTGTAAAAGCTTTCAGgtatgttcat ... ttctctgcagTAACTGGCCAACATTTCCACAAGTTTTCATTAAGGGAGAGTTTATCGGTGG
EST: gi|151403951|gb|EV273761.1|EV273761
EST:     AGAAACATTTTGGAGGATCCTGAACTGAAAAATGCTGTAAAAGCTTTCAG                         TAACTGGCCAACATTTCCACAAGTTTTCATTAAGGGAGAGTTTATCGGTGG
genomic: AGAAACATTTTGGAGGATCCTGAACTGAAAAATGCTGTAAAAGCTTTCAGgtatgttcat ... ttctctgcagTAACTGGCCAACATTTCCACAAGTTTTCATTAAGGGAGAGTTTATCGGTGG
EST: gi|208136320|gb|GD933246.1|GD933246
EST:     AAAGCTTTCAG                         TAACTTGGCCAACATTTCCACAAGTTTTCATTAAGGGAGAGTTTATCGGTG
genomic: AAAGCTTTCAGgtatgttcat ... ttctctgcagTAAC-TGGCCAACATTTCCACAAGTTTTCATTAAGGGAGAGTTTATCGGTG
EST: gi|58019023|gb|CX705765.1|CX705765
EST:     AGAAACA-TTTGGAAGATCCTGAACTGAAAAATGCTGTAAAAGCTTTCAG                         TAACTGGCCAACATTTCCACAAGTTTTCATTAAGGGAGAGTTTATCGGTGG
genomic: AGAAACATTTTGGAGGATCCTGAACTGAAAAATGCTGTAAAAGCTTTCAGgtatgttcat ... ttctctgcagTAACTGGCCAACATTTCCACAAGTTTTCATTAAGGGAGAGTTTATCGGTGG
EST: gi|58018776|gb|CX705518.1|CX705518
EST:     AGAAACATTTTGGAGGATCCTGAACTGAAAAATGCTGTAAAAGCTTTCAG                         TAACTGGCCAACATTTCCACAAGTTTTCATTAAGGGAGAGTTTATCGGTGG
genomic: AGAAACATTTTGGAGGATCCTGAACTGAAAAATGCTGTAAAAGCTTTCAGgtatgttcat ... ttctctgcagTAACTGGCCAACATTTCCACAAGTTTTCATTAAGGGAGAGTTTATCGGTGG
EST: gi|193689192|gb|FK631403.1|FK631403
EST:     AGAAACATTTTGGAGGATCCTGAACTGAAAAATGCTGTAAAAGCTTTCAG                         TAACTGGCCAACATTTCCACAAGTTTTCATTAAGGGAGAGTTTATCGGTGG
genomic: AGAAACATTTTGGAGGATCCTGAACTGAAAAATGCTGTAAAAGCTTTCAGgtatgttcat ... ttctctgcagTAACTGGCCAACATTTCCACAAGTTTTCATTAAGGGAGAGTTTATCGGTGG
EST: gi|31462442|gb|CD404470.1|CD404470
EST:     AGAAACATTTTGGAGGATCCTGAACTGAAAAATGCTGTAAAAGCTTTCAG                         TAACTGGCCAACATTTCCACAAGTTTTCATTAAGGGAGAGTTTATCGGTGG
genomic: AGAAACATTTTGGAGGATCCTGAACTGAAAAATGCTGTAAAAGCTTTCAGgtatgttcat ... ttctctgcagTAACTGGCCAACATTTCCACAAGTTTTCATTAAGGGAGAGTTTATCGGTGG
EST: gi|208240966|gb|GE037780.1|GE037780
EST:     GGATCCTGAACTGAAAAATGCTGTAAAAGCTCTCAG                         TAACTGGCCAACATTTCCACAAGTTTTCATTAAGGGAGAGTTTATCGGTGG
genomic: GGATCCTGAACTGAAAAATGCTGTAAAAGCTTTCAGgtatgttcat ... ttctctgcagTAACTGGCCAACATTTCCACAAGTTTTCATTAAGGGAGAGTTTATCGGTGG
EST: gi|22541152|gb|BU090995.1|BU090995
EST:     AAACATTTTGGAGGATCCTGAACTGAATAATGCTGTAAAAGCTTTCAG                         TAACTGGCCAACATTTCCACAAGTTTTCATTAAGGGAGAGTTTATCGGTGG
genomic: AAACATTTTGGAGGATCCTGAACTGAAAAATGCTGTAAAAGCTTTCAGgtatgttcat ... ttctctgcagTAACTGGCCAACATTTCCACAAGTTTTCATTAAGGGAGAGTTTATCGGTGG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATGTTCCTTTAAGTGCTAGAAACATTTTGGAGGATCCTGAACTGAAAAATGCTGTAAAAGCTTTCAGgtatgttcatttttactggttttattactcttgcttcataagagagtactctatttctcttacagtgagcacaatttttcaaaattcacatttgtggtgg

- - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - -  GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - ATGCTG