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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGAAAATGCAAATGAAATCAAGGCCAAATTTATTGTGGAAGCAGCTAATCACCCAACTGACCCAGAAGCTGATGAGgttagtctgaattttctcttcctttcccttcttcaaacaagaaagaagaaatgcactattgttaactaccttcctaacttgcag

Basic information

species Glycine max
transcript GLYMA16G04560.2
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G04560.2 (Glycine max), 5'ss of exon 8
lower sequence: AT3G03910.1 (Arabidopsis thaliana), 5'ss of exon 7
GGAAAATGCAAATGAAATCAAGGCCAAATTTATTGTGGAAGCAGCTAATCACCCAACTGACCCAGAAGCTGATGAGgttagtctgaa---------ttttctcttcctttcccttcttcaaacaagaaag-aagaaatgcactattgttaactaccttcctaacttgcag
|||||||||||| ||||| || |||||||| ||  | ||||  ||||||||||||||||| || || ||||| ||||||| ||  ||         |||  | || || |  |||||||  | |     | || | |  | || |  | | ||  || |  |        
GGAAAATGCAAACGAAATAAAAGCCAAATTCATCATTGAAGGTGCTAATCACCCAACTGATCCTGAGGCTGACGAGgttattcgaaaatctgatactttgtttttgctctttcttcttctcaaactcgcgtaacagaaactctgtaat-atctgtctccgcag-------

upper sequence: GLYMA16G04560.2 (Glycine max), 5'ss of exon 8
lower sequence: Vv08s0007g07400.t01 (Vitis vinifera), 5'ss of exon 9
GGAAAATGCAAATGAAATCAAGGCCAAATTTATTGTGGAAGCAGCTAATCACCCAACTGACCCAGAAGCTGATGAGgttagtctgaattttctcttcctttcccttcttcaaacaagaaagaagaaatgcactattgttaactaccttcctaacttgcag
|||||||||||||||||| || |||||||||||| | |||||||| || || || || ||||| ||||| ||||||||||||   || |||    |   ||    |  | ||| || ||| || || |||| |    | ||||    |  |  |||||||
GGAAAATGCAAATGAAATTAAAGCCAAATTTATTATTGAAGCAGCCAACCATCCTACAGACCCTGAAGCAGATGAGgttagtgcaaactttgaaat---ttagagttctgaaaaaaaaaaaaaaaactgcaatgccat-aactgttgtattctcttgcag
















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|21994949|gb|BQ786477.1|BQ786477
EST:     AATTTATTGTGGAAGCAGCTAATCACCCAACTGACCCAGAAGCTGATGAG                         ATTTTGAAGAAGAAAGGGGTTGTGATCCTCCCAGACATATTTGCAAATTCA
genomic: AATTTATTGTGGAAGCAGCTAATCACCCAACTGACCCAGAAGCTGATGAGgttagtctga ... taacttgcagATTTTGAAGAAGAAAGGGGTTGTGATCCTCCCAGACATATTTGCAAATTCA
EST: gi|26058522|gb|CA801436.1|CA801436
EST:     AATTTATTGTGGAAGCAGCTAATCACCCAACTGACCCAGAAGCTGATGAG                         ATTTTGAAGAAGAAAGGGGTTGTGATCCTCCCAGACATATTTGCAAATTCA
genomic: AATTTATTGTGGAAGCAGCTAATCACCCAACTGACCCAGAAGCTGATGAGgttagtctga ... taacttgcagATTTTGAAGAAGAAAGGGGTTGTGATCCTCCCAGACATATTTGCAAATTCA
EST: gi|22541194|gb|BU091037.1|BU091037
EST:     AATTTATTGTGGAAGCAGCTAATCACCCAACTGACCCAGAAGCTGATGAG                         ATTTTGAAGAAGAAAGGGGTTGTGATCCTCCCAGACATATTTGCAAATTCA
genomic: AATTTATTGTGGAAGCAGCTAATCACCCAACTGACCCAGAAGCTGATGAGgttagtctga ... taacttgcagATTTTGAAGAAGAAAGGGGTTGTGATCCTCCCAGACATATTTGCAAATTCA
EST: gi|8404383|gb|BE060017.1|BE060017
EST:     AATTTATTGTGGAAGCAGCTAATCACCCAACTGACCCAGAAGCTGATGAG                         ATTTTGAAGAAGAAAGGGGTTGTGATCCTCCCAGACATATTTGCAAATTCA
genomic: AATTTATTGTGGAAGCAGCTAATCACCCAACTGACCCAGAAGCTGATGAGgttagtctga ... taacttgcagATTTTGAAGAAGAAAGGGGTTGTGATCCTCCCAGACATATTTGCAAATTCA
EST: gi|8403457|gb|BE059091.1|BE059091
EST:     AATTTATTGTGGAAGCAGCTAATCACCCAACTGACCCAGAAGCTGATGAG                         ATTTTGAAGAAGAAAGGGGTTGTGATCCTCCCAGACATATTTGCAAATTCA
genomic: AATTTATTGTGGAAGCAGCTAATCACCCAACTGACCCAGAAGCTGATGAGgttagtctga ... taacttgcagATTTTGAAGAAGAAAGGGGTTGTGATCCTCCCAGACATATTTGCAAATTCA
EST: gi|13252589|gb|BG363492.1|BG363492
EST:     CCAACTGACCCCGAAGCTGATGAG                         ATTTTGAAGAAGAAA-GGGTTGTGATCCTCCCAGACATATTTGCAAATTCA
genomic: CCAACTGACCCAGAAGCTGATGAGgttagtctga ... taacttgcagATTTTGAAGAAGAAAGGGGTTGTGATCCTCCCAGACATATTTGCAAATTCA
EST: gi|8827932|gb|BE211662.1|BE211662
EST:     AATTTATTGTGGAAGCAGCTAATCACCCAACTGACCCAGAAGCTGATGAG                         ATTTTGAAGAAGAAAGGGGTTGTGATCCTCCCAGACATATTTGCAAATTCA
genomic: AATTTATTGTGGAAGCAGCTAATCACCCAACTGACCCAGAAGCTGATGAGgttagtctga ... taacttgcagATTTTGAAGAAGAAAGGGGTTGTGATCCTCCCAGACATATTTGCAAATTCA
EST: gi|6200845|gb|AW152945.1|AW152945
EST:     TGACCCAGAAGCTGATGAG                         ATTTTGAAGAAGAAAGGGGTTGTGATCCTCCCAGACATATTTGCAAATTCA
genomic: TGACCCAGAAGCTGATGAGgttagtctga ... taacttgcagATTTTGAAGAAGAAAGGGGTTGTGATCCTCCCAGACATATTTGCAAATTCA
EST: gi|192308766|gb|FG999791.1|FG999791
EST:     AATTTATTGTGGAAGCAGCTAATCACCCAACTGACCCAGAAGCTGATGAG                         ATTTTGAAGAAGAAAGGGGTTGTGATCCTCCCAGACATATTTGCAAATTCA
genomic: AATTTATTGTGGAAGCAGCTAATCACCCAACTGACCCAGAAGCTGATGAGgttagtctga ... taacttgcagATTTTGAAGAAGAAAGGGGTTGTGATCCTCCCAGACATATTTGCAAATTCA
EST: gi|151413195|gb|EV283003.1|EV283003
EST:     AATTTATTGTGGAAGCAGCTAATCACCCAACTGACCCAGAAGCTGATGAG                         ATTTTGAAGAAGAAAGGGGTTGTGATCCTCCCAGACATATTTGCAAATTCA
genomic: AATTTATTGTGGAAGCAGCTAATCACCCAACTGACCCAGAAGCTGATGAGgttagtctga ... taacttgcagATTTTGAAGAAGAAAGGGGTTGTGATCCTCCCAGACATATTTGCAAATTCA
EST: gi|8402782|gb|BE058416.1|BE058416
EST:     AATTTATTGTGGAAGCAGCTAATCACCCAACTGACCCAGAAGCTGATGAG                         ATTTTGAAGAAGAAAGGGGTTGTGATCCTCCCAGACATATTTGCAAATTCA
genomic: AATTTATTGTGGAAGCAGCTAATCACCCAACTGACCCAGAAGCTGATGAGgttagtctga ... taacttgcagATTTTGAAGAAGAAAGGGGTTGTGATCCTCCCAGACATATTTGCAAATTCA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGAAAATGCAAATGAAATCAAGGCCAAATTTATTGTGGAAGCAGCTAATCACCCAACTGACCCAGAAGCTGATGAGgttagtctgaattttctcttcctttcccttcttcaaacaagaaagaagaaatgcactattgttaactaccttcctaacttgcag

- - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT