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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtcatgttcaacctctgcattcactttaggcctgaagagcatatccaagattgacaaaactttgaaaattaattgttggctgaattgaactgttttgtgtagTGTCCTGTATGAAGTCTTCCCAATGTCATTCTTGATGGAACAGGCAGGAGGACAGTCTTTCACGGGCAAGGAACGG

Basic information

species Glycine max
transcript GLYMA16G28310.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G28310.1 (Glycine max), 3'ss of exon 11
lower sequence: LOC_Os01g64660.4 (Oryza sativa), 3'ss of exon 8
--gtatgtcatgttcaacctctgcat-tcactttaggcctgaagagcatatccaagattgacaaaactttgaaaattaattgttggctgaattgaactgttttgtgtagTGTCCTGTATGAAGTCTTCCCAATGTCATTCTTGATGGAACAGGCAGGAGGACAGTCTTTCACGGGCAAGGAACGG
    |  | | |   |  ||| |||| ||||||   || |  |  | |  |||||  |       |  |||| ||  |||| |    | |    | ||      |  ||||| ||||||||||| ||||| ||||||||| ||||||| ||||| ||||| ||||||||||| ||||| ||||||
gtacacattaagcctactctcggcatctcacttc--gctt--atggtacttccaatttc------atattgataaacaattctgaattcaccaaatcttggaattacagTGTTCTGTATGAAGTTTTCCCCATGTCATTCCTGATGGAGCAGGCTGGAGGCCAGTCTTTCACAGGCAAAGAACGG

upper sequence: GLYMA16G28310.1 (Glycine max), 3'ss of exon 11
lower sequence: LOC_Os05g36270.1 (Oryza sativa), 3'ss of exon 9
gtatgtcatgttcaacctctgcattcactttaggcctgaagagcatatccaagattgacaaaactttgaaaattaattgttggctgaattgaactgttttgtgtagTGTCCTGTATGAAGTCTTCCCAATGTCATTCTTGATGGAACAGGCAGGAGGACAGTCTTTCACGGGCAAGGAACGG
                   |    | | |  |   |||||  ||| |   |   | |   |||  | ||    | |  ||| |||  ||     ||   || | ||||| ||||| ||||| ||||||||||||||||||||||| || || ||||||||  ||||||| |||||  |||||
------------------gtatgctga-tgcaactctgaactgcaaaggtagagtagt--aaatgtagattgctgaa-gttcgctacatg----tggcatg-gcagTGTTCTGTACGAAGTGTTCCCAATGTCATTCTTGATGGAGCAAGCTGGAGGACAAGCTTTCACAGGCAAACAACGG

upper sequence: GLYMA16G28310.1 (Glycine max), 3'ss of exon 11
lower sequence: GRMZM2G322953_T03 (Zea mays), 3'ss of exon 8
gtatgtcatgttcaacctctgcattcactttaggcctgaagagcatatccaagattg--acaaaactttgaaaattaattgttggctgaattgaactgttttgtgtagTGTCCTGTATGAAGTCTTCCCAATGTCATTCTTGATGGAACAGGCAGGAGGACAGTCTTTCACGGGCAAGGAACGG
||||  ||    ||||       ||   ||||      |  |  |   ||  || ||      | |||       | |    ||| ||  |  |  ||   | || || || ||||||||||||||||| ||||||||| |||||||||| || ||||| ||| ||||||| |||||  |||||
gtataacaaagacaacaatc---ttttttttacttactattactactcccgggactgtagtttagcttcctgtcctcac-actggttggttctatgtggaat-tgcagCGTTCTGTATGAAGTCTTCCCGATGTCATTCCTGATGGAACAAGCTGGAGGCCAGGCTTTCACAGGCAAACAACGG

upper sequence: GLYMA16G28310.1 (Glycine max), 3'ss of exon 11
lower sequence: GRMZM5G836250_T03 (Zea mays), 3'ss of exon 9
----gtatg-tcatgttcaacctctgcattcactttaggcctgaagagcatatccaagattgacaaaactttgaaaattaattgttggctgaattgaactgttttgtgtagTGTCCTGTATGAAGTCTTCCCAATGTCATTCTTGATGGAACAGGCAGGAGGACAGTCTTTCACGGGCAAGGAACGG
     || | |   |||   ||||   | || || |  | || |   ||   |   | |    |    |  ||||  |    | | || ||  |||   || ||| |||||| ||||||| ||||| ||||| ||||| ||| | ||||| ||||||||||| ||||| ||||| ||||| ||||||
gtaattaagcttccgttacccctccagactcgctctcagtctcagctgctcgtaacacaccaccccggccctgaacctg---tctcggttggtttgctttggttt-tgtagTATCCTGTACGAAGTTTTCCCCATGTCGTTCCTAATGGAGCAGGCAGGAGGCCAGTCCTTCACAGGCAAAGAACGG

upper sequence: GLYMA16G28310.1 (Glycine max), 3'ss of exon 11
lower sequence: GRMZM5G836250_T02 (Zea mays), 3'ss of exon 9
----gtatg-tcatgttcaacctctgcattcactttaggcctgaagagcatatccaagattgacaaaactttgaaaattaattgttggctgaattgaactgttttgtgtagTGTCCTGTATGAAGTCTTCCCAATGTCATTCTTGATGGAACAGGCAGGAGGACAGTCTTTCACGGGCAAGGAACGG------------------------
     || | |   |||   ||||   | || || |  | || |   ||   |   | |    |    |  ||||  |    | | || ||  |||   || ||| |||||| ||||||| ||||| ||||| ||||| ||| | ||||| ||||||||||| ||||| ||||| ||||| ||||||                        
gtaattaagcttccgttacccctccagactcgctctcagtctcagctgctcgtaacacaccaccccggccctgaacctg---tctcggttggtttgctttggttt-tgtagTATCCTGTACGAAGTTTTCCCCATGTCGTTCCTAATGGAGCAGGCAGGAGGCCAGTCCTTCACAGGCAAAGAACGGGTAGGGTTTACGCCTCTCCATTTC

upper sequence: GLYMA16G28310.1 (Glycine max), 3'ss of exon 11
lower sequence: Vv18s0072g00770.t01 (Vitis vinifera), 3'ss of exon 10
----------gtatgtcatgttcaac-ctctgcattcacttt--aggcctgaagagcatatccaagattgacaaaactttgaaaattaattgttgg--ctgaattgaactgttttgtgtagTGTCCTGTATGAAGTCTTCCCAATGTCATTCTTGATGGAACAGGCAGGAGGACAGTCTTTCACGGGCAAGGAACGG
           | | |||  |||  | |||| | |  ||||   |   |  |   ||| || ||   ||   | |||  | ||  ||  |   ||    ||  || |  ||| | |   ||||| || ||||||||||| ||||||||||||||||||||||| |||||||| ||  |||| || || ||| |||||
gtaagtactgatgtttcaccttcctctctctccctcaacttctcaaaacaaatttgcaaatgcagatttacaacaacaattaatttttgtgactgaatttggtttaacttgtatggaacagTGTTCTCTATGAAGTCTTTCCAATGTCATTCTTGATGGAACAAGCAGGAGGTCAAGCTTTTACTGGAAAGCAACGG

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|31474714|gb|CD416742.1|CD416742
EST:     GGCATCTTTTTGTACCCTGCTGACNNNNNNNGTCCAAATGGAAAACTTCG                         TGTCCTGTATGAAGTCTTCCCAATGTCATTCTTGATGGAACAGGCAGGAGG
genomic: GGCATCTTTTTGTACCCTGCTGACAAAAAAAGTCCAAATGGAAAACTTCGgtatgtcatg ... ttttgtgtagTGTCCTGTATGAAGTCTTCCCAATGTCATTCTTGATGGAACAGGCAGGAGG
EST: gi|26269057|gb|CA820120.1|CA820120
EST:     GGCATCTTTTTGTACCCTGCTGACNNNNNNNGTCCAAATGGAAAACTTCG                         TGTCCTGTATGAAGTCTTCCCAATGTCATTCTTGATGGAACAGGCAGGAGG
genomic: GGCATCTTTTTGTACCCTGCTGACAAAAAAAGTCCAAATGGAAAACTTCGgtatgtcatg ... ttttgtgtagTGTCCTGTATGAAGTCTTCCCAATGTCATTCTTGATGGAACAGGCAGGAGG
EST: gi|15204366|gb|BI427134.1|BI427134
EST:     GGCATCTTTTTGTACCCTGCTGACNNNNNNNGTCCAAATGGAAAACTTCG                         TGTCCTGTATGAAGTCTTCCCAATGTCATTCTTGATGGAACAGGCAGGAGG
genomic: GGCATCTTTTTGTACCCTGCTGACAAAAAAAGTCCAAATGGAAAACTTCGgtatgtcatg ... ttttgtgtagTGTCCTGTATGAAGTCTTCCCAATGTCATTCTTGATGGAACAGGCAGGAGG
EST: gi|31457542|gb|CD399570.1|CD399570
EST:     GGCATCTTTTTGTACCCTGCTGACNNNNNNNGTCCAAATGGAAAACTTCG                         TGTCCTGTATGAAGTCTTCCCAATGTCATTCTTGATGGAACAGGCAGGAGG
genomic: GGCATCTTTTTGTACCCTGCTGACAAAAAAAGTCCAAATGGAAAACTTCGgtatgtcatg ... ttttgtgtagTGTCCTGTATGAAGTCTTCCCAATGTCATTCTTGATGGAACAGGCAGGAGG
EST: gi|31473114|gb|CD415142.1|CD415142
EST:     GGCATCTTTTTGTACCCTGCTGACCAAAAAAGTCCAAATGGAAAACTTCG                         TGTCCTGTATGAAGTCTTCCCAATGTCATTCTTGATGGAACAGGCAGGAGG
genomic: GGCATCTTTTTGTACCCTGCTGACAAAAAAAGTCCAAATGGAAAACTTCGgtatgtcatg ... ttttgtgtagTGTCCTGTATGAAGTCTTCCCAATGTCATTCTTGATGGAACAGGCAGGAGG
EST: gi|22928833|gb|BU545972.1|BU545972
EST:     GGCATCTTTTTGTACCCTGCTGACNNNNNNNGTCCAAATGGAAAACTTCG                         TGTCCTGTATGAAGTCTTCCCAATGTCATTCTTGATGGAACAGGCAGGAGG
genomic: GGCATCTTTTTGTACCCTGCTGACAAAAAAAGTCCAAATGGAAAACTTCGgtatgtcatg ... ttttgtgtagTGTCCTGTATGAAGTCTTCCCAATGTCATTCTTGATGGAACAGGCAGGAGG
EST: gi|31469604|gb|CD411632.1|CD411632
EST:     GGCATCTTTTTGTACCCTGCTGACNNNNNNNGTCCAAATGGAAAACTTCG                         TGTCCTGTATGAAGTCTTCCCAATGTCATTCTTGATGGAACAGGCAGGAGG
genomic: GGCATCTTTTTGTACCCTGCTGACAAAAAAAGTCCAAATGGAAAACTTCGgtatgtcatg ... ttttgtgtagTGTCCTGTATGAAGTCTTCCCAATGTCATTCTTGATGGAACAGGCAGGAGG
EST: gi|192304055|gb|FG993885.1|FG993885
EST:     TTTTTGTACCCTGCTGAC-AAAAAAGTCCAAATGGAAAACTTCG                         TGTCCTGTATGAAGTCTTCCCAATGTCATTCTTGATGGAACAGGCAGGAGG
genomic: TTTTTGTACCCTGCTGACAAAAAAAGTCCAAATGGAAAACTTCGgtatgtcatg ... ttttgtgtagTGTCCTGTATGAAGTCTTCCCAATGTCATTCTTGATGGAACAGGCAGGAGG
EST: gi|151398810|gb|EV268681.1|EV268681
EST:     GGCATCTTTTTGTACCCTGCTGACNNNNNNNGTCCAAATGGAAAACTTCG                         TGTCCTGTATGAAGTCTTCCCAATGTCATTCTTGATGGAACAGGCAGGAGG
genomic: GGCATCTTTTTGTACCCTGCTGACAAAAAAAGTCCAAATGGAAAACTTCGgtatgtcatg ... ttttgtgtagTGTCCTGTATGAAGTCTTCCCAATGTCATTCTTGATGGAACAGGCAGGAGG
EST: gi|31456318|gb|CD398346.1|CD398346
EST:     GGCATCTTTTTGTACCCTGCTGACCAAAAAAGTCCAAATGGAAAACTTCG                         TGTCCTGTATGAAGTCTTCCCAATGTCATTCTTGATGGAACAGGCAGGAGG
genomic: GGCATCTTTTTGTACCCTGCTGACAAAAAAAGTCCAAATGGAAAACTTCGgtatgtcatg ... ttttgtgtagTGTCCTGTATGAAGTCTTCCCAATGTCATTCTTGATGGAACAGGCAGGAGG
EST: gi|7692550|gb|AW760653.1|AW760653
EST:     GGCATCTTTTTGTACCCTGCTGACNNNNNNNGTCCAAATGGAAAACTTCG                         TGTCCTGTATGAAGTCTTCCCAATGTCATTCTTGATGGAACAGGCAGGAGG
genomic: GGCATCTTTTTGTACCCTGCTGACAAAAAAAGTCCAAATGGAAAACTTCGgtatgtcatg ... ttttgtgtagTGTCCTGTATGAAGTCTTCCCAATGTCATTCTTGATGGAACAGGCAGGAGG
EST: gi|192304054|gb|FG993884.1|FG993884
EST:     GGCATCTTTTTGTACCCTGCTGACAAAAAA-GTCCAAATGGAAAACTTCG                         TGTCCTGTATGAAGTCTTCCCAATGTCATTCTTGATGGA
genomic: GGCATCTTTTTGTACCCTGCTGACAAAAAAAGTCCAAATGGAAAACTTCGgtatgtcatg ... ttttgtgtagTGTCCTGTATGAAGTCTTCCCAATGTCATTCTTGATGGA
EST: gi|21675556|gb|BQ627907.1|BQ627907
EST:     GGCATCTTTTTGTACCCTGCTGACNNNNNNNGTCCAAATGGAAAACTTCG                         TGTCCTGTATGAAGTCTTCCCAATGTCATTCTTGATGGAACAGGCAGGAGG
genomic: GGCATCTTTTTGTACCCTGCTGACAAAAAAAGTCCAAATGGAAAACTTCGgtatgtcatg ... ttttgtgtagTGTCCTGTATGAAGTCTTCCCAATGTCATTCTTGATGGAACAGGCAGGAGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agattgacaaaactttgaaaattaattgttggctgaattgaactgttttgtgtagTGTCCTGTATGAAGTCTTCCCAATGTCATTCTTGATGGAACAGGCAGGAGGACAGTCTTTCACGGGCAAGGAACGG
                   aattaat  putative branch site (score: 3)
                                          ctgtttt  putative PPT
        aaaactttgaaaatta  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtcatgttcaacctctgcattcactttaggcctgaagagcatatccaagattgacaaaactttgaaaattaattgttggctgaattgaactgttttgtgtagTGTCCTGTATGAAGTCTTCCCAATGTCATTCTTGATGGAACAGGCAGGAGGACAGTCTTTCACGGGCAAGGAACGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA