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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTCTGTATGACGCATTGATGAGGCAAGAAGAGCTGCTTGCTTACATTGACAGACAAGAAGAAGCCAAGTTGCGGGTAAgttggcaagtctatcttttgaataaagttaaaaccttgactcaatgtatcaaattttttatatttctgtttcctgtgttttaatcag

Basic information

species Glycine max
transcript GLYMA06G01260.1
intron # 13
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA06G01260.1 (Glycine max), 5'ss of exon 13
lower sequence: Vv03s0038g04470.t01 (Vitis vinifera), 5'ss of exon 14
GCTCTGTATGACGCATTGATGAGGCAAGAAGAGCTGCTTGCTTACATTGACAGACAAGAAGAAGCCAAGTTGCGGGTAAgttggcaagtctatctttt--gaataaagttaaaaccttgactcaatgtatcaaattttttatatttc--tgtttcctgtgttttaatcag-----
|| ||| |||| ||  |  ||||||| || ||  ||||||||||||| ||||| || |||||||| ||||| |||||||||||   ||| |  |   |  |  | || ||  ||   |  |       |  | | |  |  ||  ||  |||||  ||    |||    |     
GCCCTGCATGAAGCTCTATTGAGGCAGGAGGAATTGCTTGCTTACATAGACAGTCAGGAAGAAGCTAAGTTTCGGgtaagttgagtagttttacacataggggtgaacttctaattctttcagctctcaaaagactcctcctaggtcaatgttttgtgaagcttacattgcataa
















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|57575650|gb|CX548625.1|CX548625
EST:     AGAGCTGCTTGCTTACATTGACAGACAAGAAGAAGCCAAGTTGCGG--AA                         AAA--GAAGTTTTGCTGGTGAGATTCATTACTGGGAAAGAGATTGTGCAGA
genomic: AGAGCTGCTTGCTTACATTGACAGACAAGAAGAAGCCAAGTTGCGGGTAAgttggcaagt ... ttttaatcagAAAAAGAAGTTTTGCTGGTGAGATTCATTACTGGGAAAGAGATTGTGCAGA
EST: gi|254335758|gb|GR847286.1|GR847286
EST:     AGAGCTGCTTGCTTACATTGACAGACAAGAAGAAGCCAAGTTGCGG--AA                         AAA--GAAGTTTTGCTGGTGAGATTCATTACTGGGAAAGAGATTGTGCAGA
genomic: AGAGCTGCTTGCTTACATTGACAGACAAGAAGAAGCCAAGTTGCGGGTAAgttggcaagt ... ttttaatcagAAAAAGAAGTTTTGCTGGTGAGATTCATTACTGGGAAAGAGATTGTGCAGA
EST: gi|208209242|gb|GE005122.1|GE005122
EST:     AGAGCTGCTTGCTTACATTGACAGACAAGAAGAAGCCAAGTTGCGG--AA                         AAA--GAAGTTTTGCTGGTGAGATTCATTACTGGGAAAGAGATTGTGCAGA
genomic: AGAGCTGCTTGCTTACATTGACAGACAAGAAGAAGCCAAGTTGCGGGTAAgttggcaagt ... ttttaatcagAAAAAGAAGTTTTGCTGGTGAGATTCATTACTGGGAAAGAGATTGTGCAGA
EST: gi|254335757|gb|GR847285.1|GR847285
EST:     AGAGCTGCTTGCTTACATTGACAGACAAGAAGAAGCCAAGTTGCGG--AA                         AAA--GAAGTTTTGCTGGTGAGATTCATTACTGGGAAAGAGATTGTGCAGA
genomic: AGAGCTGCTTGCTTACATTGACAGACAAGAAGAAGCCAAGTTGCGGGTAAgttggcaagt ... ttttaatcagAAAAAGAAGTTTTGCTGGTGAGATTCATTACTGGGAAAGAGATTGTGCAGA
EST: gi|208130170|gb|GD926725.1|GD926725
EST:     AGAGCTGCTTGCTTACATTGACAGACAAGAAGAAGCCAAGTTGCGG--AA                         AAA--GAAGTTTTGCTGGTGAGATTCATTACTGGGAAAGAGATTGTGCAGA
genomic: AGAGCTGCTTGCTTACATTGACAGACAAGAAGAAGCCAAGTTGCGGGTAAgttggcaagt ... ttttaatcagAAAAAGAAGTTTTGCTGGTGAGATTCATTACTGGGAAAGAGATTGTGCAGA
EST: gi|209697051|gb|BW667041.1|BW667041
EST:     AGAGCTGCTTGCTTACATTGACAGACAAGAAGAAGCCAAGTTGCGG--AA                         AAA--GAAGTTTTGCTGGTGAGATTCATTACTGGGAAAGAGATTGTGCAGA
genomic: AGAGCTGCTTGCTTACATTGACAGACAAGAAGAAGCCAAGTTGCGGGTAAgttggcaagt ... ttttaatcagAAAAAGAAGTTTTGCTGGTGAGATTCATTACTGGGAAAGAGATTGTGCAGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCTCTGTATGACGCATTGATGAGGCAAGAAGAGCTGCTTGCTTACATTGACAGACAAGAAGAAGCCAAGTTGCGGGTAAgttggcaagtctatcttttgaataaagttaaaaccttgactcaatgtatcaaattttttatatttctgtttcctgtgttttaatcag

- - - - - - - - - - - - - -  AGAGCT
- - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC