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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCTCAAAACAATTAGGCGAAGTAGAAGGATACTTTTCATTGGTTGTGGTACAAGTTATAATGCTGCTTTGGCAGCTAGACCCATATTGGAAGAACTTTCAggtcagtgctgtatcctgtatgacaaatcttttttaagtttggctgattaaaaagtatgcccattcttacaatgttttattttattttatacattattata

Basic information

species Glycine max
transcript GLYMA18G47860.1
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA18G47860.1 (Glycine max), 5'ss of exon 7
lower sequence: LOC_Os11g03900.1 (Oryza sativa), 5'ss of exon 6
CCTCAAAACAATTAGGCGAAGTAGAAGGATACTTTTCATTGGTTGTGGTACAAGTTATAATGCTGCTTTGGCAGCTAGACCCATATTGGAAGAACTTTCAggt----cagtgctgtatcctg------tatgacaaatcttttttaagtttggctgattaaaaagtatgcccattcttacaatgttttattttattttatacattattata---------------
 |||||||| |||||||| ||||||||| || |||||||||| |||||||||||||| |||||||| ||||| || |||||  |  |||| ||| |  | |||    ||      | |||||      ||||  | || ||||  | ||     | | | | || ||||      ||  |  | | ||     |  |  | |||  ||  |               
-CTCAAAACTATTAGGCGCAGTAGAAGGTTAGTTTTCATTGGCTGTGGTACAAGTTACAATGCTGCCTTGGCTGCAAGACCTTTTGTGGAGGAATTAACTGgtatgccaacttattgtcctgactccttatg-tagatattttagatgtcaacatcagtgacaa-tatgtattagctacctgtttcttgacccagatacttcatccttgcattatttggacaatag

upper sequence: GLYMA18G47860.1 (Glycine max), 5'ss of exon 7
lower sequence: LOC_Os12g03720.1 (Oryza sativa), 5'ss of exon 6
CCTCAAAACAATTAGGCGAAGTAGAAGGATACTTTTCATTGGTTGTGGTACAAGTTATAATGCTGCTTTGGCAGCTAGACCCATATTGGAAGAACTTTCAggt----cagtgctgtatcctg------tatg-acaaatctt---ttttaagtttggctg-attaaaaagta--tgcccattcttacaatgttttattttattttatacattattata-------
 |||||||| |||||||| ||||||||| || |||||||||| |||||||||||||| |||||||| ||||| || |||||  |  |||| ||| |  | |||    ||      | |||||      |||| | |||| ||   | | ||  |  |    | ||   | ||  | ||  ||  |  |      || ||  |  | | |||||||          
-CTCAAAACTATTAGGCGCAGTAGAAGGTTAGTTTTCATTGGCTGTGGTACAAGTTACAATGCTGCCTTGGCTGCAAGACCTTTTGTGGAGGAATTAACTGgtatgccaacttattgtcctgactccttatgtagaaattttagatgtcaacatcagtgacaatatgtattagctacctgtttcttgacccagatacttcttcct-tgcattatttggacaatag

upper sequence: GLYMA18G47860.1 (Glycine max), 5'ss of exon 7
lower sequence: GRMZM2G005849_T03 (Zea mays), 5'ss of exon 5
CCTCAAAACAATTAGGCGAAGTAGAAGGATACTTTTCATTGGTTGTGGTACAAGTTATAATGCTGCTTTGGCAGCTAGACCCATATTGGAAGAACTTTCAggtcagt--------------------gctgtatcctgtatgacaaatcttttttaagtttggctgattaaaaagtatgcccattcttacaatgtttta--ttttattttatacattattata------------
 ||||| |||||||||||  |||||||| |  | || ||||||||||| |||||||| |||||||| || || || |||||  |  ||||||||||  | ||| ||                     |||||||    |||  |||      |||    || |  ||  |  ||  |  ||     | |  ||  ||||  ||| |  ||   | ||  | ||            
-CTCAAGACAATTAGGCGCTGTAGAAGGGTGGTATTTATTGGTTGTGGAACAAGTTACAATGCTGCCTTAGCTGCAAGACCTTTTGTGGAAGAACTGACTGgtaagaccaatcaattaattactccagctgtattgcctataccaagaaaagtttggaatttgtcga--agcaatcagaccttagttaatgatcctttaggtttaacctttctccttgctttatttggatgacag

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|193597951|gb|FK550155.1|FK550155
EST:     CAAGTTATAATGCTGCTTTGGCAGCTAGACCCATCTTGGAAGAACTTTCT                         GGTGTTCCTGCTACTATGGAAATTGCTAGTGATCTATTGGATCGGGAGGGA
genomic: CAAGTTATAATGCTGCTTTGGCAGCTAGACCCATATTGGAAGAACTTTCAggtcagtgct ... cattattataGGTGTTCCTGTTACTATGGAAATTGCTAGTGATCTATTGGATCGAGAGGGA
EST: gi|6454585|gb|AW185268.1|AW185268
EST:     CAAGTTATAATGCTGCTTTGGCAGCTAGACCCATATTGGAAGAACTTTCA                         GGTGTTCCTGTTACTATGGAAATTGCTAGTGATCTATTGGATCGGGAGGGA
genomic: CAAGTTATAATGCTGCTTTGGCAGCTAGACCCATATTGGAAGAACTTTCAggtcagtgct ... cattattataGGTGTTCCTGTTACTATGGAAATTGCTAGTGATCTATTGGATCGAGAGGGA
EST: gi|151408304|gb|EV278112.1|EV278112
EST:     CAAGTTATAATGCTGCTTTGGCAGCTAGACCCATCTTGGAAGAACTTTCT                         GGTGTTCCTGTTACTATGGAAATTGCTAGTGATCTATTGGATCGGGAGGGA
genomic: CAAGTTATAATGCTGCTTTGGCAGCTAGACCCATATTGGAAGAACTTTCAggtcagtgct ... cattattataGGTGTTCCTGTTACTATGGAAATTGCTAGTGATCTATTGGATCGAGAGGGA
EST: gi|193602233|gb|FK559742.1|FK559742
EST:     CAAGTTATAATGCTGCTTTGGCAGCTAGACCCATCTTGGAAGAACTTTCT                         GGTGTTCCTGCTACTATGGAAATTGCTAGTGATCTATTGGATCGGGAGGGA
genomic: CAAGTTATAATGCTGCTTTGGCAGCTAGACCCATATTGGAAGAACTTTCAggtcagtgct ... cattattataGGTGTTCCTGTTACTATGGAAATTGCTAGTGATCTATTGGATCGAGAGGGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCTCAAAACAATTAGGCGAAGTAGAAGGATACTTTTCATTGGTTGTGGTACAAGTTATAATGCTGCTTTGGCAGCTAGACCCATATTGGAAGAACTTTCAggtcagtgctgtatcctgtatgacaaatcttttttaagtttggctgattaaaaagtatgcccattcttacaatgttttattttattttatacattattata

- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC