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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acaaataattcttttaatgaattttatgctgcaagaaaacattggattatataaattttatattttatcacaaaagatctgtgcatcttgtcattttcagATTGTACAAGTTGATATACCTCAATCCTTGTTTGAGGAACAAGGAAGGCAGCTTTATGGAGCCAACCTATTAGAAATACAG

Basic information

species Glycine max
transcript GLYMA14G02220.2
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA14G02220.2 (Glycine max), 3'ss of exon 9
lower sequence: AT5G55220.1 (Arabidopsis thaliana), 3'ss of exon 9
acaaataattcttttaatgaattttatgctgcaagaaaacattggattatataaattttatattttatcacaaaagatctgtgcatcttgtcattttcagATTGTACAAGTTGATATACCTCAATCCTTGTTTGAGGAACAAGGAAGGCAGCTTTATGGAGCCAACCTATTAGAAATACAG
                       | ||  |  ||    | ||   ||| |  |   || | ||  |    ||||     | ||| |||| |  |||| |||| ||  |||| || || |||||||| || ||||||||||||||||| ||| |||||||||| |  ||  |||| || |||
----------------------gtcatcatctaattccatatatcatt-tgaagcattaacatcgttgatcaaacatcatttgcttctttt--tttttagATGGTTGAAGTAGAGATTCCTCAATCTTTATTTGAGGAACAAGGAAGACAGTTTTATGGAGCTAGGCTTCTAGAGATTCAG

upper sequence: GLYMA14G02220.2 (Glycine max), 3'ss of exon 9
lower sequence: Vv19s0090g01210.t01 (Vitis vinifera), 3'ss of exon 9
acaaataattcttttaatgaattttatgctgcaagaaaacattggattatataaattttatattttatcacaaaagatctgtgcatctt----gtcattttcagATTGTACAAGTTGATATACCTCAATCCTTGTTTGAGGAACAAGGAAGGCAGCTTTATGGAGCCAACCTATTAGAAATACAG
   || | || | |  ||||  |     |   |       ||   ||| | |     || ||  | ||||  |  | | | |   | ||    |||||||||||||  |  |||| ||||| ||||||||||||||||||||||| || |||||||| ||||||||| | || ||| | ||||||
tggaagatttatctggatgatatcctccccatatttgtgtataatattttct----cttttacatcatcatgatggttttttttttttttttggtcattttcagATGATTGAAGTAGATATTCCTCAATCCTTGTTTGAGGAACAGGGCAGGCAGCTCTATGGAGCCCAGCTTTTACAGATACAG
















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|192301996|gb|FG995166.1|FG995166
EST:     TGGAGCAAACAGCTAGAGAACAAGCCACTGATAATGCTATCTTAGATCAGGTTTCTAAG                 
genomic: TGGAGCAAACAGCTAGAGAACAAGCCACTGATAATGCTATCTTAG---A----TC--AGgtttctaagg ... tc
EST: gi|31457278|gb|CD399306.1|CD399306
EST:     ACAGCTAGAGAACAAGCCACTGATAATGCTATCTTAGATCAG                         ATTGTACAAGTTGATATACCTCAATCCTTGTTTGAGGAACAAGGAAGGCAG
genomic: ACAGCTAGAGAACAAGCCACTGATAATGCTATCTTAGATCAGgtttctaagg ... tcattttcagATTGTACAAGTTGATATACCTCAATCCTTGTTTGAGGAACAAGGAAGGCAG
EST: gi|31466922|gb|CD408950.1|CD408950
EST:     TGGAGCAAACAGCTAGAGAACAAGCCACTGATAATGCTATCTTAGATCAGGTTTCTAAG                 
genomic: TGGAGCAAACAGCTAGAGAACAAGCCACTGATAATGCTATCTTAG---A----TC--AGgtttctaagg ... tc
EST: gi|9898860|gb|BE607828.1|BE607828
EST:     TGGAGCAAACAGCTAGAGAACAAGCCACTGATAATGCTATCTTAGATCAG                         G
genomic: TGGAGCAAACAGCTAGAGAACAAGCCACTGATAATGCTATCTTAGATCAGgtttctaagg ... tcattttcag-
EST: gi|9898860|gb|BE607828.1|BE607828
EST:     TGGAGCAAACAGCTAGAGAACAAGCCACTGATAATGCTATCTTAGATCAG                         G
genomic: TGGAGCAAACAGCTAGAGAACAAGCCACTGATAATGCTATCTTAGATCAGgtttctaagg ... tcattttcag-
EST: gi|9898860|gb|BE607828.1|BE607828
EST:     TGGAGCAAACAGCTAGAGAACAAGCCACTGATAATGCTATCTTAGATCAG                         G
genomic: TGGAGCAAACAGCTAGAGAACAAGCCACTGATAATGCTATCTTAGATCAGgtttctaagg ... tcattttcag-
EST: gi|9898860|gb|BE607828.1|BE607828
EST:     TGGAGCAAACAGCTAGAGAACAAGCCACTGATAATGCTATCTTAGATCAG                         G
genomic: TGGAGCAAACAGCTAGAGAACAAGCCACTGATAATGCTATCTTAGATCAGgtttctaagg ... tcattttcag-
EST: gi|9898860|gb|BE607828.1|BE607828
EST:     TGGAGCAAACAGCTAGAGAACAAGCCACTGATAATGCTATCTTAGATCAG                         G
genomic: TGGAGCAAACAGCTAGAGAACAAGCCACTGATAATGCTATCTTAGATCAGgtttctaagg ... tcattttcag-
EST: gi|9898860|gb|BE607828.1|BE607828
EST:     TGGAGCAAACAGCTAGAGAACAAGCCACTGATAATGCTATCTTAGATCAG                         G
genomic: TGGAGCAAACAGCTAGAGAACAAGCCACTGATAATGCTATCTTAGATCAGgtttctaagg ... tcattttcag-
EST: gi|9898860|gb|BE607828.1|BE607828
EST:     TGGAGCAAACAGCTAGAGAACAAGCCACTGATAATGCTATCTTAGATCAG                         G
genomic: TGGAGCAAACAGCTAGAGAACAAGCCACTGATAATGCTATCTTAGATCAGgtttctaagg ... tcattttcag-
EST: gi|151410964|gb|EV280779.1|EV280779
EST:     TGGAGCAAACAGCTAGAGAACAAGCCACTGATAATGCTATCTTAGATCAG                         G
genomic: TGGAGCAAACAGCTAGAGAACAAGCCACTGATAATGCTATCTTAGATCAGgtttctaagg ... tcattttcag-
EST: gi|151410964|gb|EV280779.1|EV280779
EST:     TGGAGCAAACAGCTAGAGAACAAGCCACTGATAATGCTATCTTAGATCAG                         G
genomic: TGGAGCAAACAGCTAGAGAACAAGCCACTGATAATGCTATCTTAGATCAGgtttctaagg ... tcattttcag-
EST: gi|151410964|gb|EV280779.1|EV280779
EST:     TGGAGCAAACAGCTAGAGAACAAGCCACTGATAATGCTATCTTAGATCAG                         G
genomic: TGGAGCAAACAGCTAGAGAACAAGCCACTGATAATGCTATCTTAGATCAGgtttctaagg ... tcattttcag-
EST: gi|151410964|gb|EV280779.1|EV280779
EST:     TGGAGCAAACAGCTAGAGAACAAGCCACTGATAATGCTATCTTAGATCAG                         G
genomic: TGGAGCAAACAGCTAGAGAACAAGCCACTGATAATGCTATCTTAGATCAGgtttctaagg ... tcattttcag-
EST: gi|151410964|gb|EV280779.1|EV280779
EST:     TGGAGCAAACAGCTAGAGAACAAGCCACTGATAATGCTATCTTAGATCAG                         G
genomic: TGGAGCAAACAGCTAGAGAACAAGCCACTGATAATGCTATCTTAGATCAGgtttctaagg ... tcattttcag-
EST: gi|151410964|gb|EV280779.1|EV280779
EST:     TGGAGCAAACAGCTAGAGAACAAGCCACTGATAATGCTATCTTAGATCAG                         G
genomic: TGGAGCAAACAGCTAGAGAACAAGCCACTGATAATGCTATCTTAGATCAGgtttctaagg ... tcattttcag-
EST: gi|151410964|gb|EV280779.1|EV280779
EST:     TGGAGCAAACAGCTAGAGAACAAGCCACTGATAATGCTATCTTAGATCAG                         G
genomic: TGGAGCAAACAGCTAGAGAACAAGCCACTGATAATGCTATCTTAGATCAGgtttctaagg ... tcattttcag-
EST: gi|12773062|gb|BG237989.1|BG237989
EST:     TGGAGCAAACAGCTAGAGAACAAGCCACTGATAATGCTATCTTAGATCAGGTTTCTAAG                 
genomic: TGGAGCAAACAGCTAGAGAACAAGCCACTGATAATGCTATCTTAG---A----TC--AGgtttctaagg ... tc


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attatataaattttatattttatcacaaaagatctgtgcatcttgtcattttcagATTGTACAAGTTGATATACCTCAATCCTTGTTTGAGGAACAAGGAAGGCAGCTTTATGGAGCCAACCTATTAGAAATACAG
                                             tcattttc  CT-rich tract
     ataaattttatatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acaaataattcttttaatgaattttatgctgcaagaaaacattggattatataaattttatattttatcacaaaagatctgtgcatcttgtcattttcagATTGTACAAGTTGATATACCTCAATCCTTGTTTGAGGAACAAGGAAGGCAGCTTTATGGAGCCAACCTATTAGAAATACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - tttatgc
- - - - - - - - - - - - - - -tgcaaga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tctgtgc