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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cattgtgatgaagattatgctgtttaaagggtagttatctttcgatttatttttgtatgtaatgtaatgtgatgtgtgactagagctagttttgatgcagCTGATAGTTCAAAGAAGGCTGATCCAAAGGCACAGGCCTTGAAAACTGCCAAGGCAGTTAAGTCCGGTGCTAACTTTAAGAAGAAGACCAAGAAGATCCG

Basic information

species Glycine max
transcript GLYMA13G40780.2
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G40780.2 (Glycine max), 3'ss of exon 1
lower sequence: Vv06s0004g04090.t01 (Vitis vinifera), 3'ss of exon 2
----cattgtgatgaagattatgctgtttaaagggtagttatctttcgatttatttttgtatgtaatgtaatgtgatgtgtgactagagctagttttgatgcagCTGATAGTTCAAAGAAGGCTGATCCAAAGGCACAGGCCTTGAAAACTGCCAAGGCAGTTAAGTCCGGTGC--TAACTTT-AAGAAGAAGACCAAGAAGATCCG
    |     | |    |  ||       ||| |  ||| |   |   ||||  | || | | |    |  |    | | | | | ||  |   | | ||| ||||||||||||||| |||||||| ||||||||||| |||   ||  |||| || ||||| || |  |||||   |||||| ||||||||  | ||||||||   
attaccccacgctaggaaacatagaaaagaaatgaaagtaacagt---attttatgttctctctttcttccttctctatctaaat-gatatgtctctcatgtagCTGATAGTTCAAAAAAGGCTGACCCAAAGGCACAAGCCGCAAAGGCTGCTAAAGCAGTCAAATTGGGTGCATCAACTTTCAAGAAGAAAGCGAAGAAGAT---
















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|298179404|gb|HO027875.1|HO027875
EST:     AATTTAACAATTAGGGTTGCTTCTCCTTTGTCGACCCATGGCTCCCAAAG                         CTGATAGTTCAAAGAAGGCTGATCCAAAGGCACAGGCCTTGAAAACTGCCA
genomic: AATTTAACAATTAGGGTTGCTTCTCCTTTGCCGACCCATGGCTCCCAAAGgtattattct ... tttgatgcagCTGATAGTTCAAAGAAGGCTGATCCAAAGGCACAGGCCTTGAAAACTGCCA
EST: gi|192333698|gb|FK025463.1|FK025463
EST:     AATTTAACAATTAGGGTTGCTTCTCCTTTGCCGACCCATGGCTCCCAAAG                         CTGATAGTTCAAAGAAGGCTGATCCAAAGGCACAGGCCTTGAAAACTGCCA
genomic: AATTTAACAATTAGGGTTGCTTCTCCTTTGCCGACCCATGGCTCCCAAAGgtattattct ... tttgatgcagCTGATAGTTCAAAGAAGGCTGATCCAAAGGCACAGGCCTTGAAAACTGCCA
EST: gi|38193232|gb|CF922438.1|CF922438
EST:     AATTTAACAATTAGGGTTGCTTCTCCTTTGCCGACCCATGGCTCCCAAAG                         CTGATAGTTCAAAGAAGGCTGATCCAAAGGCACAGGCCTTGAAAACTGCCA
genomic: AATTTAACAATTAGGGTTGCTTCTCCTTTGCCGACCCATGGCTCCCAAAGgtattattct ... tttgatgcagCTGATAGTTCAAAGAAGGCTGATCCAAAGGCACAGGCCTTGAAAACTGCCA
EST: gi|213611065|gb|DB970992.1|DB970992
EST:     AATTTAACAATTAGGGTTGCTTCTCCTTTGTCGACCCATGGCTCCCAAAG                         CTGATAGTTCAAAGAAGGCTGATCCAAAGGCACAGGCCTTGAAAACTGCCA
genomic: AATTTAACAATTAGGGTTGCTTCTCCTTTGCCGACCCATGGCTCCCAAAGgtattattct ... tttgatgcagCTGATAGTTCAAAGAAGGCTGATCCAAAGGCACAGGCCTTGAAAACTGCCA
EST: gi|8402069|gb|BE057703.1|BE057703
EST:     AATTTAACAATTAGGGTTGCTTCTCCTTTGCCGACCCATGGCTCCCAAAG                         CTGATAGTTCAAAGAAGGCTGATCCAAAGGCACAGGCCTTGAAAACTGCCA
genomic: AATTTAACAATTAGGGTTGCTTCTCCTTTGCCGACCCATGGCTCCCAAAGgtattattct ... tttgatgcagCTGATAGTTCAAAGAAGGCTGATCCAAAGGCACAGGCCTTGAAAACTGCCA
EST: gi|6951766|gb|AW423834.1|AW423834
EST:     AATTTAACAATTAGGGTTGCTTCTCCTTTGCCGACCCATGGCTCCCAAAG                         CTGATAGTTCAAAGAAGGCTGATCCAAAGGCACAGGCCTTGAAAACTGCCA
genomic: AATTTAACAATTAGGGTTGCTTCTCCTTTGCCGACCCATGGCTCCCAAAGgtattattct ... tttgatgcagCTGATAGTTCAAAGAAGGCTGATCCAAAGGCACAGGCCTTGAAAACTGCCA
EST: gi|151394626|gb|EV264497.1|EV264497
EST:     AATTTAACAATTAGGGTTGCTTCTCCTTTGCCGACCCATGGCTCCCAAAG                         CTGATAGTTCAAAGAAGGCTGATCCAAAGGCACAGGCCTTGAAAACTGCCA
genomic: AATTTAACAATTAGGGTTGCTTCTCCTTTGCCGACCCATGGCTCCCAAAGgtattattct ... tttgatgcagCTGATAGTTCAAAGAAGGCTGATCCAAAGGCACAGGCCTTGAAAACTGCCA
EST: gi|6666174|gb|AW277633.1|AW277633
EST:     AATTTAACAATTAGGGTTGCTTCTCCTTTGCCGACCCATGGCTCCCAAAG                         CTGATAGTTCAAAGAAGGCTGATCCAAAGGCACAGGCCTTGAAAACTGCCA
genomic: AATTTAACAATTAGGGTTGCTTCTCCTTTGCCGACCCATGGCTCCCAAAGgtattattct ... tttgatgcagCTGATAGTTCAAAGAAGGCTGATCCAAAGGCACAGGCCTTGAAAACTGCCA
EST: gi|6913503|gb|AW395033.1|AW395033
EST:     AATTTAACAATTAGGGTTGCTTCTCCTTTGCCGACCCATGGCTCCCAAAG                         CTGATAGTTCAAAGAAGGCTGATCCAAAGGCACAGGCCTTGAAAACTGCCA
genomic: AATTTAACAATTAGGGTTGCTTCTCCTTTGCCGACCCATGGCTCCCAAAGgtattattct ... tttgatgcagCTGATAGTTCAAAGAAGGCTGATCCAAAGGCACAGGCCTTGAAAACTGCCA
EST: gi|51337227|gb|CO981093.1|CO981093
EST:     AATTTAACAATTAGGGTTGCTTCTCCTTTGCCGACCCATGGCTCCCAAAG                         CTGATAGTTCAAAGAAGGCTGATCCAAAGGCACAGGCCTTGAAAACTGCCA
genomic: AATTTAACAATTAGGGTTGCTTCTCCTTTGCCGACCCATGGCTCCCAAAGgtattattct ... tttgatgcagCTGATAGTTCAAAGAAGGCTGATCCAAAGGCACAGGCCTTGAAAACTGCCA
EST: gi|8285163|gb|BE022722.1|BE022722
EST:     AATTTAACAATTAGGGTTGCTTCTCCTTTGCCGACCCATGGCTCCCAAAG                         CTGATAGTTCAAAGAAGGCTGATCCAAAGGCACAGGCCTTGAAAACTGCCA
genomic: AATTTAACAATTAGGGTTGCTTCTCCTTTGCCGACCCATGGCTCCCAAAGgtattattct ... tttgatgcagCTGATAGTTCAAAGAAGGCTGATCCAAAGGCACAGGCCTTGAAAACTGCCA
EST: gi|8286339|gb|BE023898.1|BE023898
EST:     AATTTAACAATTAGGGTTGCTTCTCCTTTGCCGACCCATGGCTCCCAAAG                         CTGATAGTTCAAAGAAGGCTGATCCAAAGGCACAGGCCTTGAAAACTGCCA
genomic: AATTTAACAATTAGGGTTGCTTCTCCTTTGCCGACCCATGGCTCCCAAAGgtattattct ... tttgatgcagCTGATAGTTCAAAGAAGGCTGATCCAAAGGCACAGGCCTTGAAAACTGCCA
EST: gi|192315065|gb|FK010435.1|FK010435
EST:     AATTTAACAATTAGGGTTGCTTCTCCTTTGCCGACCCATGGCTCCCAAAG                         CTGATAGTTCAAAGAAGGCTGATCCAAAGGCACAGGCCTTGAAAACTGCCA
genomic: AATTTAACAATTAGGGTTGCTTCTCCTTTGCCGACCCATGGCTCCCAAAGgtattattct ... tttgatgcagCTGATAGTTCAAAGAAGGCTGATCCAAAGGCACAGGCCTTGAAAACTGCCA
EST: gi|31561020|gb|CD486858.1|CD486858
EST:     AATTTAACAATTAGGGTTGCTTCTCCTTTGTCGACCCATGGCTCCCAAAG                         CTGATGAGTTCAAAGAAGGCTGATCCAAAGGCACAGGCCTTGAAAACTGCC
genomic: AATTTAACAATTAGGGTTGCTTCTCCTTTGCCGACCCATGGCTCCCAAAGgtattattct ... tttgatgcagCTGAT-AGTTCAAAGAAGGCTGATCCAAAGGCACAGGCCTTGAAAACTGCC
EST: gi|13181470|gb|BG352810.1|BG352810
EST:     AATTTAACAATTAGGGTTGCTTCTCCTTTGCCGACCCATGGCTCCCAAAG                         CTGATAGTTCAAAGAAGGCTGATCCAAAGGCACAGGCCTTGAAAACTGCCA
genomic: AATTTAACAATTAGGGTTGCTTCTCCTTTGCCGACCCATGGCTCCCAAAGgtattattct ... tttgatgcagCTGATAGTTCAAAGAAGGCTGATCCAAAGGCACAGGCCTTGAAAACTGCCA
EST: gi|192333713|gb|FK025464.1|FK025464
EST:     AATTTAACAATTAGGGTTGCTTCTCCTTTGCCGACCCATGGCTCCCAAAG                         CTGATAGTTCAAAGAAGGCTGATCCAAAGGCACAGGCCTTGAAAACTGCCA
genomic: AATTTAACAATTAGGGTTGCTTCTCCTTTGCCGACCCATGGCTCCCAAAGgtattattct ... tttgatgcagCTGATAGTTCAAAGAAGGCTGATCCAAAGGCACAGGCCTTGAAAACTGCCA
EST: gi|10254581|gb|BE822347.1|BE822347
EST:     TTTGCCGACCCATGGCTCCCAAAG                         CTGATAGTTCAAAGAAGGCTGATCCAAAGGCACAGGCCTTGAAAACTGCCA
genomic: TTTGCCGACCCATGGCTCCCAAAGgtattattct ... tttgatgcagCTGATAGTTCAAAGAAGGCTGATCCAAAGGCACAGGCCTTGAAAACTGCCA
EST: gi|38193398|gb|CF922604.1|CF922604
EST:     AATTTAACAATTAGGGTTGCTTCTCCTTTGCCGACCCATGGCTCCCAAAG                         CTGATAGTTCAAAGAAGGCTGATCCAAAGGCACAGGCCTTGAAAACTGCCA
genomic: AATTTAACAATTAGGGTTGCTTCTCCTTTGCCGACCCATGGCTCCCAAAGgtattattct ... tttgatgcagCTGATAGTTCAAAGAAGGCTGATCCAAAGGCACAGGCCTTGAAAACTGCCA
EST: gi|22525561|gb|BU084372.1|BU084372
EST:     AATTTAACAATTAGGGTTGCTTCTCCTTTGCCGACCCATGGCTCCCAAAG                         CTGATAGTTCAAAGAAGGCTGATCCAAAGGCACAGGCCTTGAAAACTGCCA
genomic: AATTTAACAATTAGGGTTGCTTCTCCTTTGCCGACCCATGGCTCCCAAAGgtattattct ... tttgatgcagCTGATAGTTCAAAGAAGGCTGATCCAAAGGCACAGGCCTTGAAAACTGCCA
EST: gi|192311405|gb|FK003498.1|FK003498
EST:     AATTTAACAATTAGGGTTGCTTCTCCTTTGCCGACCCATGGCTCCCAAAG                         CTGATAGTTCAAAGAAGGCTGATCCAAAGGCACAGGCCTTGAAAACTGCCA
genomic: AATTTAACAATTAGGGTTGCTTCTCCTTTGCCGACCCATGGCTCCCAAAGgtattattct ... tttgatgcagCTGATAGTTCAAAGAAGGCTGATCCAAAGGCACAGGCCTTGAAAACTGCCA
EST: gi|15814025|gb|BI786300.1|BI786300
EST:     AATTTAACAATTAGGGTTGCTTCTCCTTTGCCGACCCATGGCTCCCAAAG                         CTGATAGTTCAAAGAAGGCTGATCCAAAGGCACAGGCCTTGAAAACTGCCA
genomic: AATTTAACAATTAGGGTTGCTTCTCCTTTGCCGACCCATGGCTCCCAAAGgtattattct ... tttgatgcagCTGATAGTTCAAAGAAGGCTGATCCAAAGGCACAGGCCTTGAAAACTGCCA
EST: gi|192316257|gb|FK011644.1|FK011644
EST:     AATTTAACAATTAGGGTTGCTTCTCCTTTGCCGACCCATGGCTCCCAAAG                         CTGATAGTTCAAAGAAGGCTGATCCAAAGGCACAGGCCTTGAAAACTGCCA
genomic: AATTTAACAATTAGGGTTGCTTCTCCTTTGCCGACCCATGGCTCCCAAAGgtattattct ... tttgatgcagCTGATAGTTCAAAGAAGGCTGATCCAAAGGCACAGGCCTTGAAAACTGCCA
EST: gi|38192506|gb|CF921712.1|CF921712
EST:     AATTTAACAATTAGGGTTGCTTCTCCTTTGCCGACCCATGGCTCCCAAAG                         CTGATAGTTCAAAGAAGGCTGATCCAAAGGCACAGGCCTTGAAAACTGCCA
genomic: AATTTAACAATTAGGGTTGCTTCTCCTTTGCCGACCCATGGCTCCCAAAGgtattattct ... tttgatgcagCTGATAGTTCAAAGAAGGCTGATCCAAAGGCACAGGCCTTGAAAACTGCCA
EST: gi|192317447|gb|FK011265.1|FK011265
EST:     AATTTAACAATTAGGGTTGCTTCTCCTTTGCCGACCCATGGCTCCCAAAG                         CTGATAGTTCAAAGAAGGCTGATCCAAAGGCACAGGCCTTGAAAACTGCCA
genomic: AATTTAACAATTAGGGTTGCTTCTCCTTTGCCGACCCATGGCTCCCAAAGgtattattct ... tttgatgcagCTGATAGTTCAAAGAAGGCTGATCCAAAGGCACAGGCCTTGAAAACTGCCA
EST: gi|192301545|gb|FG994113.1|FG994113
EST:     AATTTAACAATTAGGGTTGCTTCTCCTTTGCCGACCCATGGCTCCCAAAG                         CTGATAGTTCAAAGAAGGCTGATCCAAAGGCACAGGCCTTGAAAACTGCCA
genomic: AATTTAACAATTAGGGTTGCTTCTCCTTTGCCGACCCATGGCTCCCAAAGgtattattct ... tttgatgcagCTGATAGTTCAAAGAAGGCTGATCCAAAGGCACAGGCCTTGAAAACTGCCA
EST: gi|213620120|gb|DB965412.1|DB965412
EST:     AATTTAACAATTAGGGTTGCTTCTCCTTTGTCGACCCATGGCTCCCAAAG                         CTGATAGTTCAAAGAAGGCTGATCCAAAGGCACAGGCCTTGAAAACTGCCA
genomic: AATTTAACAATTAGGGTTGCTTCTCCTTTGCCGACCCATGGCTCCCAAAGgtattattct ... tttgatgcagCTGATAGTTCAAAGAAGGCTGATCCAAAGGCACAGGCCTTGAAAACTGCCA
EST: gi|192300561|gb|FG991513.1|FG991513
EST:     AATTTAACAATTAGGGTTGCTTCTCCTTTGCCGACCCATGGCTCCCAAAG                         CTGATAGTTCAAAGAAGGCTGATCCAAAGGCACAGGCCTTGAAAACTGCCA
genomic: AATTTAACAATTAGGGTTGCTTCTCCTTTGCCGACCCATGGCTCCCAAAGgtattattct ... tttgatgcagCTGATAGTTCAAAGAAGGCTGATCCAAAGGCACAGGCCTTGAAAACTGCCA
EST: gi|192315066|gb|FK010436.1|FK010436
EST:     AATTTAACAATTAGGGTTGCTTCTCCTTTGCCGACCCATGGCTCCCAAAG                         CTGATAGTTCAAAGAAGGCTGATCCAAAGGCACAGGCCTTGAAAACTGCCA
genomic: AATTTAACAATTAGGGTTGCTTCTCCTTTGCCGACCCATGGCTCCCAAAGgtattattct ... tttgatgcagCTGATAGTTCAAAGAAGGCTGATCCAAAGGCACAGGCCTTGAAAACTGCCA
EST: gi|20812652|gb|BQ297130.1|BQ297130
EST:     AATTTAACAATTAGGGTTGCTTCTCCTTTGTCGACCCATGGCTCCCAAAG                         CTGATAGTTCAAAGAAGGCTGATCCAAAGGCACAGGCCTTGAAAACTGCCA
genomic: AATTTAACAATTAGGGTTGCTTCTCCTTTGCCGACCCATGGCTCCCAAAGgtattattct ... tttgatgcagCTGATAGTTCAAAGAAGGCTGATCCAAAGGCACAGGCCTTGAAAACTGCCA
EST: gi|192316256|gb|FK011643.1|FK011643
EST:     AATTTAACAATTAGGGTTGCTTCTCCTTTGCCGACCCATGGCTCCCAAAG                         CTGATAGTTCAAAGAAGGCTGATCCAAAGGCACAGGCCTTGAAAACTGCCA
genomic: AATTTAACAATTAGGGTTGCTTCTCCTTTGCCGACCCATGGCTCCCAAAGgtattattct ... tttgatgcagCTGATAGTTCAAAGAAGGCTGATCCAAAGGCACAGGCCTTGAAAACTGCCA
EST: gi|192311404|gb|FK003497.1|FK003497
EST:     AATTTAACAATTAGGGTTGCTTCTCCTTTGCCGACCCATGGCTCCCAAAG                         CTGATAGTTCAAAGAAGGCTGATCCAAAGGCACAGGCCTTGAAAACTGCCA
genomic: AATTTAACAATTAGGGTTGCTTCTCCTTTGCCGACCCATGGCTCCCAAAGgtattattct ... tttgatgcagCTGATAGTTCAAAGAAGGCTGATCCAAAGGCACAGGCCTTGAAAACTGCCA
EST: gi|57575683|gb|CX548658.1|CX548658
EST:     AATTTAACAATTAGGGTTGCTTCTCCTTTGCCGACCCATGGCTCCCAAAG                         CTGATAGTTCAAAGAAGGCTGATCCAAAGGCACAGGCCTTGAAAACTGCCA
genomic: AATTTAACAATTAGGGTTGCTTCTCCTTTGCCGACCCATGGCTCCCAAAGgtattattct ... tttgatgcagCTGATAGTTCAAAGAAGGCTGATCCAAAGGCACAGGCCTTGAAAACTGCCA
EST: gi|192301643|gb|FG997599.1|FG997599
EST:     AATTTAACAATTAGGGTTGCTTCTCCTTTGTCGACCCATGGCTCCCAAAG                         CTGATAGTTCAAAGAAGGCTGATCCAAAGGCACAGGCCTTGAAAACTGCCA
genomic: AATTTAACAATTAGGGTTGCTTCTCCTTTGCCGACCCATGGCTCCCAAAGgtattattct ... tttgatgcagCTGATAGTTCAAAGAAGGCTGATCCAAAGGCACAGGCCTTGAAAACTGCCA
EST: gi|8826760|gb|BE210490.1|BE210490
EST:     CTTCTCCTTTGCCGACCCATGGCTCCCAAAG                         CTGATAGTTCAAAGAAGGCTGATCCAAAGGCACAGGCCTTGAAAACTGCCA
genomic: CTTCTCCTTTGCCGACCCATGGCTCCCAAAGgtattattct ... tttgatgcagCTGATAGTTCAAAGAAGGCTGATCCAAAGGCACAGGCCTTGAAAACTGCCA
EST: gi|151398829|gb|EV268700.1|EV268700
EST:     TCCTTTGCCGACCCATGGCTCCCAAAG                         CTGATAGTTCAAAGAAGGCTGATCCAAAGGCACAGGCCTTGAAAACTGCCA
genomic: TCCTTTGCCGACCCATGGCTCCCAAAGgtattattct ... tttgatgcagCTGATAGTTCAAAGAAGGCTGATCCAAAGGCACAGGCCTTGAAAACTGCCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttatttttgtatgtaatgtaatgtgatgtgtgactagagctagttttgatgcagCTGATAGTTCAAAGAAGGCTGATCCAAAGGCACAGGCCTTGAAAACTGCCAAGGCAGTTAAGTCCGGTGCTAACTTTAAGAAGAAGACCAAGAAGATCCG
                                            ttttgat  putative branch site (score: 4)
              taatgtaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cattgtgatgaagattatgctgtttaaagggtagttatctttcgatttatttttgtatgtaatgtaatgtgatgtgtgactagagctagttttgatgcagCTGATAGTTCAAAGAAGGCTGATCCAAAGGCACAGGCCTTGAAAACTGCCAAGGCAGTTAAGTCCGGTGCTAACTTTAAGAAGAAGACCAAGAAGATCCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG