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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CACACTTCATTGAGCCCAGATGGGAAACTGGTTGTGATTGTTGGAGACAACCCAGAAGGGATACTAGTGGATTCTCAAACTGGAAAGgtggtgtactctgttgatttgtgttacaaattccataggtactgtttgcaggtaaattatgaataatttaaattttggttctttgtag

Basic information

species Glycine max
transcript GLYMA07G40060.1
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA07G40060.1 (Glycine max), 5'ss of exon 9
lower sequence: LOC_Os08g38880.6 (Oryza sativa), 5'ss of exon 7
CACACTTCATTGAGCCCAGATGGGAAACTGGTTGTGATTGTTGGAGACAACCCAGAAGGGATACTAGTGGATTCTCAAACTGGAAAGgtggtgtactctgttgatttgtgttacaaattccataggtactgtttgcaggt---aaattatgaataatttaaa--ttttggttctttgtag
||||| ||||||||||| ||||| ||||| ||||  |||||||| |||||||| |||||  |  |||| ||| || |  | ||||| ||   | |    |      |  |  |  || | |  |  |||||    ||  |   | |  | ||| |  | |    | || |||  | | ||
CACACATCATTGAGCCCGGATGGTAAACTTGTTGCTATTGTTGGGGACAACCCTGAAGGACTTATAGTCGATACTAATTCAGGAAAAgtaa-gcagaaagcaacgctcagcgattaacttc-caaatactgacctcacatttcagaaaaagaaaagctcatggctgtttgtttctcgcag

upper sequence: GLYMA07G40060.1 (Glycine max), 5'ss of exon 9
lower sequence: LOC_Os08g38880.3 (Oryza sativa), 5'ss of exon 7
CACACTTCATTGAGCCCAGATGGGAAACTGGTTGTGATTGTTGGAGACAACCCAGAAGGGATACTAGTGGATTCTCAAACTGGAAAGgtggtgtactctgttgatttgtgttacaaattccataggtactgtttgcaggt---aaattatgaataatt--taaattttggttctttgtag----
||||| ||||||||||| ||||| ||||| ||||  |||||||| |||||||| |||||  |  |||| ||| || |  | ||||| ||   | |    |      |  |  |  || | |  |  |||||    ||  |   | |  | ||| |  |  |   | || |||  | | ||    
CACACATCATTGAGCCCGGATGGTAAACTTGTTGCTATTGTTGGGGACAACCCTGAAGGACTTATAGTCGATACTAATTCAGGAAAAgtaa-gcagaaagcaacgctcagcgattaacttc-caaatactgacctcacatttcagaaaaagaaaagctcatggctgtttgtttctcgcagacag

upper sequence: GLYMA07G40060.1 (Glycine max), 5'ss of exon 9
lower sequence: Vv00s1206g00020.t01 (Vitis vinifera), 5'ss of exon 5
CACACTTCATTGAGCCCAGATGGGAAACTGGTTGTGATTGTTGGAGACAACCCAGAAGGGATACTAGTGGATTCTCAAACTGGAAAGgtggtgtactctgttgatttgtgttacaaattccataggtactgtttgcaggtaaattatgaataatttaaattttggttctttgtag
|| || || ||||| |||||||| || ||  |||| |||||||| ||||||||||| || ||||| ||||| ||||| |||||||||||    |  |   |    |     | |     |  ||||          ||  |   |   | | |||| || |||  |    |||||
CATACCTCTTTGAGTCCAGATGGTAAGCTTCTTGTCATTGTTGGTGACAACCCAGATGGAATACTGGTGGACTCTCAGACTGGAAAGgtacc-tgtttcctaacataaaacttct--cccagtagggggaaaaataagaaacggttccactcatttgaagttttttatcatgtag

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|208308345|gb|GE102871.1|GE102871
EST:     TTGTTGGAGACAACCCAGAAGGGATACTAGTGGATTCTCAAACTGGAAAG                         ACTGTCAAGCCTTTATGTGGACACTTGGATTACTCATTTGCATCTGCGTGG
genomic: TTGTTGGAGACAACCCAGAAGGGATACTAGTGGATTCTCAAACTGGAAAGgtggtgtact ... ttctttgtagACTGTCAAGCCTTTATGTGGACACTTGGATTACTCATTTGCATCTGCGTGG
EST: gi|254336522|gb|GR842701.1|GR842701
EST:     AGAAGGGATACTAGTGGATTCTCAAACTGGAAAG                         ACTGTCAAGCCTTTATGTGGACACTTGGATTACTCATTTGCATCTGCGTGG
genomic: AGAAGGGATACTAGTGGATTCTCAAACTGGAAAGgtggtgtact ... ttctttgtagACTGTCAAGCCTTTATGTGGACACTTGGATTACTCATTTGCATCTGCGTGG
EST: gi|58022343|gb|CX709084.1|CX709084
EST:     TTGTTGGAGACAACCCAGAAGGGATACTAGTGGATTCTCAAACTGGAAAG                         ACTGTCAAGCCTTTATGTGGACACTTGGATTACTCATTTGCATCTGCGTGG
genomic: TTGTTGGAGACAACCCAGAAGGGATACTAGTGGATTCTCAAACTGGAAAGgtggtgtact ... ttctttgtagACTGTCAAGCCTTTATGTGGACACTTGGATTACTCATTTGCATCTGCGTGG
EST: gi|58024987|gb|CX711728.1|CX711728
EST:     TTGTTGGAGACAACCCAGAAGGGATACTAGTGGATTCTCAAACTGGAAAG                         ACTGTCAAGCCTTTATGTGGACACTTGGATTACTCATTTGCATCTGCGTGG
genomic: TTGTTGGAGACAACCCAGAAGGGATACTAGTGGATTCTCAAACTGGAAAGgtggtgtact ... ttctttgtagACTGTCAAGCCTTTATGTGGACACTTGGATTACTCATTTGCATCTGCGTGG
EST: gi|254327492|gb|GR837047.1|GR837047
EST:     TTGTTGGAGACAACCCAGAAGGGATACTAGTGGATTCTCAAACTGGAAAG                         ACTGTCAAGCCTTTATGTGGACACTTGGATTACTCATTTGCATCTGCGTGG
genomic: TTGTTGGAGACAACCCAGAAGGGATACTAGTGGATTCTCAAACTGGAAAGgtggtgtact ... ttctttgtagACTGTCAAGCCTTTATGTGGACACTTGGATTACTCATTTGCATCTGCGTGG
EST: gi|193584456|gb|FK543278.1|FK543278
EST:     TTGTTGGAGACAACCCAGAAGGGATACTAGTGGATTCTCAAACTGGAAAG                         ACTGTCAAGCCTTTATGTGGACACTTGGATTACTCATTTGCATCTGCGTGG
genomic: TTGTTGGAGACAACCCAGAAGGGATACTAGTGGATTCTCAAACTGGAAAGgtggtgtact ... ttctttgtagACTGTCAAGCCTTTATGTGGACACTTGGATTACTCATTTGCATCTGCGTGG
EST: gi|254327491|gb|GR837046.1|GR837046
EST:     TTGTTGGAGACAACCCAGAAGGGATACTAGTGGATTCTCAAACTGGAAAG                         ACTGTCAAGCCTTTATGTGGACACTTGGATTACTCATTTGCATCTGCGTGG
genomic: TTGTTGGAGACAACCCAGAAGGGATACTAGTGGATTCTCAAACTGGAAAGgtggtgtact ... ttctttgtagACTGTCAAGCCTTTATGTGGACACTTGGATTACTCATTTGCATCTGCGTGG
EST: gi|193689306|gb|FK632665.1|FK632665
EST:     TTGTTGGAGACAACCCAGAAGGGATACTAGTGGATTCTCAAACTGGAAAG                         ACTGTCAAGCCTTTATGTGGACACTTGGATTACTCATTTGCATCTGCGTGG
genomic: TTGTTGGAGACAACCCAGAAGGGATACTAGTGGATTCTCAAACTGGAAAGgtggtgtact ... ttctttgtagACTGTCAAGCCTTTATGTGGACACTTGGATTACTCATTTGCATCTGCGTGG
EST: gi|193490569|gb|FK456394.1|FK456394
EST:     TTGTTGGAGACAACCCAGAAGGGATACTAGTGGATTCTCAAACTGGAAAG                         ACTGTCAAGCCTTTATGTGGACACTTGGATTACTCATTTGCATCTGC
genomic: TTGTTGGAGACAACCCAGAAGGGATACTAGTGGATTCTCAAACTGGAAAGgtggtgtact ... ttctttgtagACTGTCAAGCCTTTATGTGGACACTTGGATTACTCATTTGCATCTGC
EST: gi|57575319|gb|CX548294.1|CX548294
EST:     TTGTTGGAGACAACCCAGAAGGGATACTAGTGGATTCTCAAACTGGAAAG                         ACTGTCAAGCCTTTATGTGGACACTTGGATTACTCATTTGCATCTGCGTGG
genomic: TTGTTGGAGACAACCCAGAAGGGATACTAGTGGATTCTCAAACTGGAAAGgtggtgtact ... ttctttgtagACTGTCAAGCCTTTATGTGGACACTTGGATTACTCATTTGCATCTGCGTGG
EST: gi|193308655|gb|FK277030.1|FK277030
EST:     TGGATTCTCAAACTGGAAAG                         ACTGTCAAGCCTTTATGTGGACACTTGGATTACTCATTTGCATCTGCGTGG
genomic: TGGATTCTCAAACTGGAAAGgtggtgtact ... ttctttgtagACTGTCAAGCCTTTATGTGGACACTTGGATTACTCATTTGCATCTGCGTGG
EST: gi|58022583|gb|CX709324.1|CX709324
EST:     TTGTTGGAGACAACCCAGAAGGGATACTAGTGGATTCTCAAACTGGAAAG                         ACTGTCAAGCCTTTATGTGGACACTTGGATTACTCATTTGCATCTGCGTGG
genomic: TTGTTGGAGACAACCCAGAAGGGATACTAGTGGATTCTCAAACTGGAAAGgtggtgtact ... ttctttgtagACTGTCAAGCCTTTATGTGGACACTTGGATTACTCATTTGCATCTGCGTGG
EST: gi|254341974|gb|GR853111.1|GR853111
EST:     GGATACTAGTGGATTCTCAAACTGGAAAG                         ACTGTCAAGCCTTTATGTGGACACTTGGATTACTCATTTGCATCTGCGTGG
genomic: GGATACTAGTGGATTCTCAAACTGGAAAGgtggtgtact ... ttctttgtagACTGTCAAGCCTTTATGTGGACACTTGGATTACTCATTTGCATCTGCGTGG
EST: gi|193348336|gb|FK309544.1|FK309544
EST:     TTGTTGGAGACAACCCAGAAGGGATACTAGTGGATTCTCAAACTGGAAAG                         ACTGTCAAGCCTTTATGTGGACACTTGGATTACTCATTTGCATCTGCGTGG
genomic: TTGTTGGAGACAACCCAGAAGGGATACTAGTGGATTCTCAAACTGGAAAGgtggtgtact ... ttctttgtagACTGTCAAGCCTTTATGTGGACACTTGGATTACTCATTTGCATCTGCGTGG
EST: gi|193645157|gb|FK592967.1|FK592967
EST:     TTGTTGGAGACAACCCAGAAGGGATACTAGTGGATTCTCAAACTGGAAAG                         ACTGTCAAGCCTTTATGTGGACACTTGGATTACTCATTTGCATCTGCGTGG
genomic: TTGTTGGAGACAACCCAGAAGGGATACTAGTGGATTCTCAAACTGGAAAGgtggtgtact ... ttctttgtagACTGTCAAGCCTTTATGTGGACACTTGGATTACTCATTTGCATCTGCGTGG
EST: gi|57575083|gb|CX548058.1|CX548058
EST:     TTGTTGGAGACAACCCAGAAGGGATACTAGTGGATTCTCAAACTGGAAAG                         ACTGTCAAGCCTTTATGTGGACACTTGGATTACTCATTTGCATCTGCGTGG
genomic: TTGTTGGAGACAACCCAGAAGGGATACTAGTGGATTCTCAAACTGGAAAGgtggtgtact ... ttctttgtagACTGTCAAGCCTTTATGTGGACACTTGGATTACTCATTTGCATCTGCGTGG
EST: gi|209725666|gb|BW663155.1|BW663155
EST:     CAAACTGGAAAG                         ACTGTCAAGCCTTTATGTGGACACTTGGATTACTCATTTGCATCTGCGTGG
genomic: CAAACTGGAAAGgtggtgtact ... ttctttgtagACTGTCAAGCCTTTATGTGGACACTTGGATTACTCATTTGCATCTGCGTGG
EST: gi|192332288|gb|FK023937.1|FK023937
EST:     TTGTTGGAGACAACCCAGAAGGGATACTAGTGGATTCTCAAACTGGAAAG                         ACTGTCAAGCCTTTATGTGGACACTTGGATTACTCATTTGCATCTGCGTGG
genomic: TTGTTGGAGACAACCCAGAAGGGATACTAGTGGATTCTCAAACTGGAAAGgtggtgtact ... ttctttgtagACTGTCAAGCCTTTATGTGGACACTTGGATTACTCATTTGCATCTGCGTGG
EST: gi|207732145|gb|GD706680.1|GD706680
EST:     TTGTTGGAGACAACC-AGAAGGGATACTAGTGGATTCTCAAACTGGAAAG                         ACTGTCAAGCCTTTATGTGGACACTTGGAATTACTCATTTG
genomic: TTGTTGGAGACAACCCAGAAGGGATACTAGTGGATTCTCAAACTGGAAAGgtggtgtact ... ttctttgtagACTGTCAAGCCTTTATGTGGACACTTGGA-TTACTCATTTG
EST: gi|193325781|gb|FK290220.1|FK290220
EST:     TGGATTCTCAAACNGGAAAG                         ACTGTCAAGCCTTTATGTGGACACTTGGATTAACTCATTTGCATCTGCGTG
genomic: TGGATTCTCAAACTGGAAAGgtggtgtact ... ttctttgtagACTGTCAAGCCTTTATGTGGACACTTGGATT-ACTCATTTGCATCTGCGTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CACACTTCATTGAGCCCAGATGGGAAACTGGTTGTGATTGTTGGAGACAACCCAGAAGGGATACTAGTGGATTCTCAAACTGGAAAGgtggtgtactctgttgatttgtgttacaaattccataggtactgtttgcaggtaaattatgaataatttaaattttggttctttgtag

- - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA