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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATTCTGCTCGATTATGGTGGTTTCAAGTTTGCACTGAAGTTGCATACTTTCAGGTGGCTCCCTCAAATGACAGTATTCGCTCCTCAAAAGTGGACATAAAgcaagttcctcatccttgtcattcactttacatgctcctctattgacaggattctatcactattacaccattctttgttcttgactttttttctttataatgttgttaatttgtacaaagtggggtctcatacattgcag

Basic information

species Glycine max
transcript GLYMA16G24290.1
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G24290.1 (Glycine max), 5'ss of exon 8
lower sequence: LOC_Os10g36760.1 (Oryza sativa), 5'ss of exon 9
ATTCTGCTCGATTATGGTGGTTTCAAGTTTGCACTGAAGTTGCATACTTTCAGGTGGCTCCCTCAAATGACAGTATTCGCTCCTCAAAAGTGGACATAAAgcaagttcctcatccttgtcattcactttacatgctcctctattgacaggattctatcactattacaccattctttgttcttgactttttttctttataatgttgtta-atttgtacaaagtggggtctcatacattgcag------------
   |   | | ||||||||||  |||||||||| |||||||||||| || || ||||||||   |||||| ||| | || ||  ||||  | |||| || |  |   |   |||    |   |||  | | ||  ||| ||     |    ||   | |    |  |    |  |   | |   ||| | || || |  ||||   ||   || || | | ||   |   |||  || |              
---CATATAGGTTATGGTGGTACCAAGTTTGCAGTGAAGTTGCATATTTCCAAGTGGCTCCAAAAAATGATAGTGTCCGTTCTGCAAAGATTGACACAAGgtta---ctagatctactttcctcaaataa-atattccactggaagctatcttaccttatcgatttagatctgctatctataatcttctctttttcaagatgtgactatgcttctagatattgtatttatataagttcctcttttctttctag

upper sequence: GLYMA16G24290.1 (Glycine max), 5'ss of exon 8
lower sequence: Vv04s0023g03020.t01 (Vitis vinifera), 5'ss of exon 8
ATTCTGCTCGATTATGGTGGTTTCAAGTTTGCACTGAAGTTGCATACTTTCAGGTGGCTCCCTCAAATGACAGTATTCGCTCCTCAAAAGTGGACATAAAgcaagt-tcctcatcctt----gtcattcac----tttacatgctc----ctctattgacaggattctatcactattacaccattctttgt------------tcttgactttttttctttataatgttgttaat------ttgtacaaagtggggtctcatacattgcag
  |||| ||| || |||||||| |||||||||||||||||||||| ||| |||||||| |||||| |||| || || ||||| ||| |  |  | | ||||   || | | || |  |    ||  |||||    | ||| | | |       | || | |  |||  |   ||||  ||  ||| |||||            | | |  ||  || |||||   | ||||  ||      || |||||| |||   ||||||  | ||||
CATCTGATCGGTTGTGGTGGTTCCAAGTTTGCACTGAAGTTGCATTCTTCCAGGTGGCACCCTCAGATGATAGCATGCGCTCTTCAGAGATTAATACAAAgtgcgtcttcgcacctctttacgtgtttcacagtttctacttacccaacttcttttttatattattaaaatgctatggcatgattatttgtgagttataagtatttggttttgcttactttactcttttgtacatgtatgattatacaaattggttgctcatatgtggcag
















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|254323221|gb|GR840026.1|GR840026
EST:     CAGGTGGCTCCCTCAAATGACAGTATTCGCTCCTCAAAAGTGGACATAAA                         ATACCATTTGGACCTTTGCAAAAATGTCTTTGGAGAGGGCATCTTTCCTGA
genomic: CAGGTGGCTCCCTCAAATGACAGTATTCGCTCCTCAAAAGTGGACATAAAgcaagttcct ... tacattgcagATACCATTTGGACCTTTGCAAAAATGTCTTTGGAGAGGGCATCTTTCCTGA
EST: gi|193547219|gb|FK499588.1|FK499588
EST:     CAGGTGGCTCCCTCAAATGACAGTATTCGCTCCTCAAAAGTGGACATAAA                         ATACCATTTGGACCTTTGCAAAAATGTCTTTGGAGAGGGCATCTTTCCTGA
genomic: CAGGTGGCTCCCTCAAATGACAGTATTCGCTCCTCAAAAGTGGACATAAAgcaagttcct ... tacattgcagATACCATTTGGACCTTTGCAAAAATGTCTTTGGAGAGGGCATCTTTCCTGA
EST: gi|7283896|gb|AW596498.1|AW596498
EST:     CAGGTGGCTCCCTCAAATGACAGTATTCGCTCCTCAAAAGTGGACATAAA                         ATACCATTTGGACCTTTGCAAAAATGTCTTTGGAGAAGGCATCTTTCCTGA
genomic: CAGGTGGCTCCCTCAAATGACAGTATTCGCTCCTCAAAAGTGGACATAAAgcaagttcct ... tacattgcagATACCATTTGGACCTTTGCAAAAATGTCTTTGGAGAGGGCATCTTTCCTGA
EST: gi|193731955|gb|FK664073.1|FK664073
EST:     CAGGTGGCTCCCTCAAATGACAGTATTCGCTCCTCAAAAGTGGACATAAA                         ATACCATTTGGACCTTTGCAAAAATGTCTTTGGAGAGGGCATCTTTCCTGA
genomic: CAGGTGGCTCCCTCAAATGACAGTATTCGCTCCTCAAAAGTGGACATAAAgcaagttcct ... tacattgcagATACCATTTGGACCTTTGCAAAAATGTCTTTGGAGAGGGCATCTTTCCTGA
EST: gi|193469219|gb|FK435467.1|FK435467
EST:     CAGGTGGCTCCCTCAAATGACAGTATTCGCTCCTCAAAAGTGGACATAAA                         ATACCATTTGGACCTTTGCAAAAAATGTCTTTGGAGAGGGCATCTTTCCTG
genomic: CAGGTGGCTCCCTCAAATGACAGTATTCGCTCCTCAAAAGTGGACATAAAgcaagttcct ... tacattgcagATACCATTTGGACCTTTGCAAAAA-TGTCTTTGGAGAGGGCATCTTTCCTG
EST: gi|193547333|gb|FK499646.1|FK499646
EST:     CAGGTGGCTCCCTCAAATGACAGTATTCGCTCCTCAAAAGTGGACATAAA                         ATACCATTTGGACCTTTGCAAAAATGTCTTTGGAGAGGGCATCTTTCCTGA
genomic: CAGGTGGCTCCCTCAAATGACAGTATTCGCTCCTCAAAAGTGGACATAAAgcaagttcct ... tacattgcagATACCATTTGGACCTTTGCAAAAATGTCTTTGGAGAGGGCATCTTTCCTGA
EST: gi|163918185|gb|EH039901.1|EH039901
EST:     CAGGTGGCTCCCTCAAATGACAGTATTCGCTCCTCAAAAGTGGACATAAA                         ATACCATTTGGACCTTTGCAAAAATGTCTTTGGAGAGGGCATCTTTCCTGA
genomic: CAGGTGGCTCCCTCAAATGACAGTATTCGCTCCTCAAAAGTGGACATAAAgcaagttcct ... tacattgcagATACCATTTGGACCTTTGCAAAAATGTCTTTGGAGAGGGCATCTTTCCTGA
EST: gi|193657700|gb|FK606347.1|FK606347
EST:     CAGGTGGCTCCCTCAAATGACAGTATTCGCTCCTCAAAAGTGGACATAAA                         ATACCATTTGGACCTTTGCAAAAATGTCTTTGGAGAGGGCATCTTTCCTGA
genomic: CAGGTGGCTCCCTCAAATGACAGTATTCGCTCCTCAAAAGTGGACATAAAgcaagttcct ... tacattgcagATACCATTTGGACCTTTGCAAAAATGTCTTTGGAGAGGGCATCTTTCCTGA
EST: gi|208098374|gb|GD894767.1|GD894767
EST:     CCTCAAAAGTGGACATAAA                         ATACCATTTGGACCTTTGCAAAAATGTCTTTGGAGAGGGCATCTTTCCTGA
genomic: CCTCAAAAGTGGACATAAAgcaagttcct ... tacattgcagATACCATTTGGACCTTTGCAAAAATGTCTTTGGAGAGGGCATCTTTCCTGA
EST: gi|254333270|gb|GR850520.1|GR850520
EST:     CAGGTGGCTCCCTCAAATGACAGTATTCGCTCCTCAAAAGTGGACATAAA                         ATACCATTTGGACCTTTGCAAAAATGTCTTTGGAGAGGGCATCTTTCCTGA
genomic: CAGGTGGCTCCCTCAAATGACAGTATTCGCTCCTCAAAAGTGGACATAAAgcaagttcct ... tacattgcagATACCATTTGGACCTTTGCAAAAATGTCTTTGGAGAGGGCATCTTTCCTGA
EST: gi|192325369|gb|FK018355.1|FK018355
EST:     CAGGTGGCTCCCTCAAATGACAGTATTCGCTCCTCAAAAGTGGACATAAA                         ATACCATTTGGACCTTTGCAAAAATGTCTTTGGAGAGGGCATCTTTCCTGA
genomic: CAGGTGGCTCCCTCAAATGACAGTATTCGCTCCTCAAAAGTGGACATAAAgcaagttcct ... tacattgcagATACCATTTGGACCTTTGCAAAAATGTCTTTGGAGAGGGCATCTTTCCTGA
EST: gi|193704130|gb|FK647450.1|FK647450
EST:     CAGGTGGCTCCCTCAAATGACAGTATTCGCTCCTCAAAAGTGGACATAAA                         ATACCATTTGGACCTTTGCAAAAATGTCTTTGGAGAGGGCATCTTTCCTGA
genomic: CAGGTGGCTCCCTCAAATGACAGTATTCGCTCCTCAAAAGTGGACATAAAgcaagttcct ... tacattgcagATACCATTTGGACCTTTGCAAAAATGTCTTTGGAGAGGGCATCTTTCCTGA
EST: gi|254333269|gb|GR850519.1|GR850519
EST:     CAGGTGGCTCCCTCAAATGACAGTATTCGCTCCTCAAAAGTGGACATAAA                         ATACCATTTGGACCTTTGCAAAAATGTCTTTGGAGAGGGCATCTTTCCTGA
genomic: CAGGTGGCTCCCTCAAATGACAGTATTCGCTCCTCAAAAGTGGACATAAAgcaagttcct ... tacattgcagATACCATTTGGACCTTTGCAAAAATGTCTTTGGAGAGGGCATCTTTCCTGA
EST: gi|192318972|gb|FK010592.1|FK010592
EST:     CAGGTGGCTCCCTCAAATGACAGTATTCGCTCCTCAAAAGTGGACATAAA                         ATACCATTTGGACCTTTGCAAAAATGTCTTTGGAGAGGGCATCTTTCCTGA
genomic: CAGGTGGCTCCCTCAAATGACAGTATTCGCTCCTCAAAAGTGGACATAAAgcaagttcct ... tacattgcagATACCATTTGGACCTTTGCAAAAATGTCTTTGGAGAGGGCATCTTTCCTGA
EST: gi|192318971|gb|FK010591.1|FK010591
EST:     CAGGTGGCTCCCTCAAATGACAGTATTCGCTCCTCAAAAGTGGACATAAA                         ATACCATTTGGACCTTTGCAAAAATGTCTTTGGAGAGGGCATCTTTCCTGA
genomic: CAGGTGGCTCCCTCAAATGACAGTATTCGCTCCTCAAAAGTGGACATAAAgcaagttcct ... tacattgcagATACCATTTGGACCTTTGCAAAAATGTCTTTGGAGAGGGCATCTTTCCTGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATTCTGCTCGATTATGGTGGTTTCAAGTTTGCACTGAAGTTGCATACTTTCAGGTGGCTCCCTCAAATGACAGTATTCGCTCCTCAAAAGTGGACATAAAgcaagttcctcatccttgtcattcactttacatgctcctctattgacaggattctatcactattacaccattctttgttcttgactttttttctttataatgttgttaatttgtacaaagtggggtctcatacattgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA