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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAGATTGGGCTTAGCCAAGTCTATTGGTGTTAGCAACTTCGGCATCAAAAAGCTAAGCCAGCTCCTGGAAAATGCAACCATCCCTCCTGCTGTCAATCAGgtatgaagttttagcaattgcatgcaggttgatatttacgcagcaatgaaacacttggcggtgttgattccttccattggttttag

Basic information

species Glycine max
transcript GLYMA16G34560.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G34560.1 (Glycine max), 5'ss of exon 2
lower sequence: Vv05s0077g02190.t01 (Vitis vinifera), 5'ss of exon 2
CAGATTGGGCTTAGCCAAGTCTATTGGTGTTAGCAACTTCGGCATCAAAAAGCTAAGCCAGCTCCTGGAAAATGCAACCATCCCTCCTGCTGTCAATCAGgtatgaagttttagcaattgcatg-caggttgatatttacgcagcaatgaaacactt---ggcggtgttgattccttccattggttttag
|||||||||| ||||||  ||||||||||| ||||||||| |   |||||||||   |||||| ||  || |||| ||||| ||||||||||| |||||||||   |      |   ||  ||| ||  |    |||  | |||   ||   |||||   |  |||| |||  |     ||  || | ||
CAGATTGGGCCTAGCCAGATCTATTGGTGTAAGCAACTTCAGTTCCAAAAAGCTCTCCCAGCTTCTCCAACATGCTACCATTCCTCCTGCTGTTAATCAGgtacacaaacagggatgttctatggcatatatgcattgccacagt--tgggtcacttacagttggtgatgaaactgaatatatgtctcag

upper sequence: GLYMA16G34560.1 (Glycine max), 5'ss of exon 2
lower sequence: Vv05s0077g02150.t01 (Vitis vinifera), 5'ss of exon 2
CAGATTGGGCTTAGCCAAGTCTATTGGTGTTAGCAACTTCGGCATCAAAAAGCTAAGCCAGCTCCTGGAAAATGCAACCATCCCTCCTGCTGTCAATCAGgtatgaagttttagcaattgcatgcaggttgatatttacgcagcaatgaaacacttggcggtgttgattccttccattggttttag
|||||||||||||||||| |||||||| || ||||||||| |   ||| |||||   |||||| ||  |  ||||  ||||||||||||| || |||||||||| ||     ||    ||     |||   ||| | | ||||   |    ||   |  | || |||       |    |||| ||
CAGATTGGGCTTAGCCAAATCTATTGGAGTCAGCAACTTCAGTTGCAAGAAGCTCTCCCAGCTTCTCCAGTATGCTGCCATCCCTCCTGCCGTTAATCAGgtattaaaac--agggggtgtgccgaggc--ataat-aggcagagctagttcatgagttgatgatgaaattgaacgcgtgtttcag

upper sequence: GLYMA16G34560.1 (Glycine max), 5'ss of exon 2
lower sequence: Vv05s0077g02180.t01 (Vitis vinifera), 5'ss of exon 3
CAGATTGGGCTTAGCCAAGTCTATTGGTGTTAGCAACTTCGGCATCAAAAAGCTAAGCCAGCTCCTGGAAAATGCAACCATCCCTCCTGCTGTCAATCAGgt-atgaagttttagcaattgcatgcaggttgatatttacgcagcaatgaaacacttggcggtgttgattccttccattggttttag
|||||||||| |||||||||||||||| || ||||||||| |   |||||||||    ||||| ||  || |||| || |||||||||||||| |||||||| | |||     ||  ||    || ||  | || |    |  | | |  |   ||||  | || |||         ||| ||| ||
CAGATTGGGCCTAGCCAAGTCTATTGGCGTAAGCAACTTCAGTTGCAAAAAGCTCTCTCAGCTTCTCCAATATGCTACTATCCCTCCTGCTGTTAATCAGgttacgaa----caggcatgttctgtagcataat-tgggagaggtagtccatggcttgatgatgatgaaattgaatgttg-tttcag

upper sequence: GLYMA16G34560.1 (Glycine max), 5'ss of exon 2
lower sequence: Vv18s0001g09570.t01 (Vitis vinifera), 5'ss of exon 4
CAGATTGGGCTTAGCCAAGTCTATTGGTGTTAGCAACTTCGGCATCAAAAAGCTAAGCCAGCTCCTGGAAAATGCAACCATCCCTCCTGCTGTCAATCAGgtatgaagttttagcaattgcatgcaggttgatatttacgcagcaatga-aacacttggcggtgttgattccttccattggttttag
|||||||||| |||||||||||||||| || ||||||||| | | |||||||||    ||||| ||  || |||| ||||||||||||||||| |||||||| |  |     ||   |    ||  |  | | || ||    |||  |  |   | ||||  || |||  |      ||| ||| ||
CAGATTGGGCCTAGCCAAGTCTATTGGCGTAAGCAACTTCAGTAGCAAAAAGCTCTCTCAGCTTCTCCAATATGCTACCATCCCTCCTGCTGTTAATCAGgtttacaaac--aggcgtgttctgtggcataa-atataattggcagaggtagttcatggct-tgatgaaactgaatgttg-tttcag

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|254346211|gb|GR859824.1|GR859824
EST:     AGCTAAGCCAGCTCCTGGAAAATGCAACCATCCCTCCTGCTGTCAATCAG                         -TGGAAATGAGCCCAGCATGGCAGCAGGGGAAACTCAAAGAATTCTGCAAG
genomic: AGCTAAGCCAGCTCCTGGAAAATGCAACCATCCCTCCTGCTGTCAATCAGgtatgaagtt ... ttggttttagGTGGAAATGAGCCCAGCATGGCAGCAGGGGAAACTCAAAGAATTCTGCAAG
EST: gi|254326727|gb|GR832879.1|GR832879
EST:     AGCTAAGCCAGCTCCTGGAAAATGCAACCATCCCTCCTGCTGTCAATCAT                         GTGGAAATGAGCCCAGCATGGCAGCAGGGGAAACTCAAAGAATTCTGCAAG
genomic: AGCTAAGCCAGCTCCTGGAAAATGCAACCATCCCTCCTGCTGTCAATCAGgtatgaagtt ... ttggttttagGTGGAAATGAGCCCAGCATGGCAGCAGGGGAAACTCAAAGAATTCTGCAAG
EST: gi|192318392|gb|FK006512.1|FK006512
EST:     AGCTAAGCCAGCTCCTGGAAAATGCAACCATCCCTCCTGCTGTCAATCAG                         GTGGAAATGAGCCCAGCATGGCAGCAGGGGAAACTCAAAGAATTCTGCAAG
genomic: AGCTAAGCCAGCTCCTGGAAAATGCAACCATCCCTCCTGCTGTCAATCAGgtatgaagtt ... ttggttttagGTGGAAATGAGCCCAGCATGGCAGCAGGGGAAACTCAAAGAATTCTGCAAG
EST: gi|23057505|gb|BU578179.1|BU578179
EST:     AGCTAAGCCAGCTCCTGGAAAATGCAACCATCCCTCCTGCTGTCAATCAG                         GTGGAAATGAGCCCAGCATGGCAGCAGGGGAAACTCAAAGAATTCTGCAAG
genomic: AGCTAAGCCAGCTCCTGGAAAATGCAACCATCCCTCCTGCTGTCAATCAGgtatgaagtt ... ttggttttagGTGGAAATGAGCCCAGCATGGCAGCAGGGGAAACTCAAAGAATTCTGCAAG
EST: gi|9203435|gb|BE329588.1|BE329588
EST:     AGCTAAGCCAGCTCCTGGAAAATGCAACCATCCCTCCTGCTGTCAATCAG                         GTGGAAATGAGCCCAGCATGGCAGCAGGGGAAACTCAAAGAATTCTGCGAG
genomic: AGCTAAGCCAGCTCCTGGAAAATGCAACCATCCCTCCTGCTGTCAATCAGgtatgaagtt ... ttggttttagGTGGAAATGAGCCCAGCATGGCAGCAGGGGAAACTCAAAGAATTCTGCAAG
EST: gi|6455653|gb|AW186336.1|AW186336
EST:     AGCTAAGCCAGCTCCTGGAAAATGCAACCATCCCTCCTGCTGTCAATCAG                         GTGGAAATGAGCCCAGCATGGCAGCAGGGGAAACTCANAGAATTCTGCAAG
genomic: AGCTAAGCCAGCTCCTGGAAAATGCAACCATCCCTCCTGCTGTCAATCAGgtatgaagtt ... ttggttttagGTGGAAATGAGCCCAGCATGGCAGCAGGGGAAACTCAAAGAATTCTGCAAG
EST: gi|31310975|gb|CD396178.1|CD396178
EST:     AGCTAAGCCAGCTCCTGGAAAATGCAACCATCCCTCCTGCTGTCAATCAG                         GTGGAAATGAGCCCAGCATGGCAGCAGGGGAAACTCAAAGAATTCTGCAAG
genomic: AGCTAAGCCAGCTCCTGGAAAATGCAACCATCCCTCCTGCTGTCAATCAGgtatgaagtt ... ttggttttagGTGGAAATGAGCCCAGCATGGCAGCAGGGGAAACTCAAAGAATTCTGCAAG
EST: gi|213598887|gb|DB964490.1|DB964490
EST:     AGCTAAGCCAGCTCCTGGAAAATGCAACCATCCCTCCTGCTGTCAATCAG                         GTGGAAATGAGCCCAGCA
genomic: AGCTAAGCCAGCTCCTGGAAAATGCAACCATCCCTCCTGCTGTCAATCAGgtatgaagtt ... ttggttttagGTGGAAATGAGCCCAGCA
EST: gi|7686056|gb|AW756704.1|AW756704
EST:     GCTAAGCCCA-CTCCTGAAAAATGCAACCATCCCTGCTGCTGTCAATCAA                         GTGGAAATGATCCCATCATGG
genomic: GCTAAGCC-AGCTCCTGGAAAATGCAACCATCCCTCCTGCTGTCAATCAGgtatgaagtt ... ttggttttagGTGGAAATGAGCCCAGCATGG
EST: gi|213603474|gb|DB966625.1|DB966625
EST:     AGCTAAGCCAGCTCCTGGAAAATGCAACCATCCCTCCTGCTGTCAATCAG                         GTGGAAATGAGCCCAGCATGGCAG
genomic: AGCTAAGCCAGCTCCTGGAAAATGCAACCATCCCTCCTGCTGTCAATCAGgtatgaagtt ... ttggttttagGTGGAAATGAGCCCAGCATGGCAG
EST: gi|254346212|gb|GR859825.1|GR859825
EST:     GAAAATGCAACCATCCCT-CTGCTGTCAATCAG                         GTGGAAATGAGCCCAGCATGGCAGCAGGGGAAACTCAAAGAATTCTGCAAG
genomic: GAAAATGCAACCATCCCTCCTGCTGTCAATCAGgtatgaagtt ... ttggttttagGTGGAAATGAGCCCAGCATGGCAGCAGGGGAAACTCAAAGAATTCTGCAAG
EST: gi|254317844|gb|GR826828.1|GR826828
EST:     AGCTAAGCCAGCT-CTGGAAAATGCAACCATCCCTCCTGCTGTCAATCAG                         GTGGAAATGAGCCCAGCATGGCAGCAGGGGAAACTCAAAGAATTCTGCAAG
genomic: AGCTAAGCCAGCTCCTGGAAAATGCAACCATCCCTCCTGCTGTCAATCAGgtatgaagtt ... ttggttttagGTGGAAATGAGCCCAGCATGGCAGCAGGGGAAACTCAAAGAATTCTGCAAG
EST: gi|192318391|gb|FK006511.1|FK006511
EST:     AGCTAAGCCAGCTCCTGGAAAATGCAACCATCCCTCCTGCTGTCAATCAG                         GTGGAAATGAGCCCAGCATGGCAGCAGGGGAAACTCAAAGAATTCTGCAAG
genomic: AGCTAAGCCAGCTCCTGGAAAATGCAACCATCCCTCCTGCTGTCAATCAGgtatgaagtt ... ttggttttagGTGGAAATGAGCCCAGCATGGCAGCAGGGGAAACTCAAAGAATTCTGCAAG
EST: gi|9985768|gb|BE659876.1|BE659876
EST:     AGCTAAGCCAGCTCCTGGAAAATGCAACCATCCCTCCTGCTGTCAATCAG                         GTGGAAATGAGCCCAGCATGGCAGCAGGGGAAACTCAAAGAATTCTGCAAG
genomic: AGCTAAGCCAGCTCCTGGAAAATGCAACCATCCCTCCTGCTGTCAATCAGgtatgaagtt ... ttggttttagGTGGAAATGAGCCCAGCATGGCAGCAGGGGAAACTCAAAGAATTCTGCAAG
EST: gi|254317843|gb|GR826827.1|GR826827
EST:     AGCTAAGCCAGCTCCTGGAAAATGCAACCATCCCTCCTGCTGTCAATCAT                         GTGGAAATGAGCCCAGCATGGCAGCAGGGGAAACTCAA
genomic: AGCTAAGCCAGCTCCTGGAAAATGCAACCATCCCTCCTGCTGTCAATCAGgtatgaagtt ... ttggttttagGTGGAAATGAGCCCAGCATGGCAGCAGGGGAAACTCAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAGATTGGGCTTAGCCAAGTCTATTGGTGTTAGCAACTTCGGCATCAAAAAGCTAAGCCAGCTCCTGGAAAATGCAACCATCCCTCCTGCTGTCAATCAGgtatgaagttttagcaattgcatgcaggttgatatttacgcagcaatgaaacacttggcggtgttgattccttccattggttttag

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