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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagaatagtttgttagtacttattgtatacagtctttttctctgaagtcatatcacgtttaacactgttcttgaaaataatagCATGCAAATGGAGAAAATGCATGGATTGGTATAGATGGAAATACTGGCAGTATCACTGACATGAAAGAGCGCAAG

Basic information

species Glycine max
transcript GLYMA09G28650.2
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G28650.2 (Glycine max), 3'ss of exon 12
lower sequence: Vv17s0000g08170.t01 (Vitis vinifera), 3'ss of exon 11
-----------gtaagaatagtttgttagtacttattgtatacagtctttt------tctctgaagtcatatcacgtttaacactgttcttgaaaataatagCATGCAAATGGAGAAAATGCATGGATTGGTATAGATGGAAATACTGGCAGTATCACTGACATGAAAGAGCGCAAG
            | || || |||| |  | |  |   | | | |    |||      |||||   |||   | | ||||   | |     |     |  |||||||||||||| |||||||| ||||| || |||||||||| ||||||    || ||||||||||| ||||| |||
tcgggcaattactcagcattgtttttctgcatcttcggaaaataaaaatttaacacatctcttttgtctcgt-atgtttcttattccatctttttctc-tagCATGCAAATGGTGAAAATGCCTGGATCGGAATAGATGGAAGTACTGGTGCAATTACTGACATGAAGGAGCGTAAG
















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|193575184|gb|FK530743.1|FK530743
EST:     AAAATTGTGGAGTAAATGTCATCCGGACTATGGCTGCTCTACAAGGAAAA                         CATGCAAATGGAGAAAATGCATGGATTGGTATAGATGGAAATACTGGCAGT
genomic: AAAATTGTGGAGTAAATGTCATCCGGACTATGACTGCTCTACAAGGAAAAgtaagaatag ... aaaataatagCATGCAAATGGAGAAAATGCATGGATTGGTATAGATGGAAATACTGGCAGT
EST: gi|192309233|gb|FG999124.1|FG999124
EST:     AAAATTGTGGAGTAAATGTCATCCGGACTATGACTGCTCTACAAGGAAAA                         CATGCAAATGGAGAAAATGCATGGATTGGTATAGATGGAAATACTGGCAGT
genomic: AAAATTGTGGAGTAAATGTCATCCGGACTATGACTGCTCTACAAGGAAAAgtaagaatag ... aaaataatagCATGCAAATGGAGAAAATGCATGGATTGGTATAGATGGAAATACTGGCAGT
EST: gi|58017480|gb|CX704222.1|CX704222
EST:     AAAATTGTGGAGTAAATGTCATCCGGACTATGACTGCTCTACAAGGAAAA                         CATGCAAATGGAGAAAATGCATGGATTGGTATAGATGGAAATACTGGCAGT
genomic: AAAATTGTGGAGTAAATGTCATCCGGACTATGACTGCTCTACAAGGAAAAgtaagaatag ... aaaataatagCATGCAAATGGAGAAAATGCATGGATTGGTATAGATGGAAATACTGGCAGT
EST: gi|209714673|gb|BW674236.1|BW674236
EST:     AAAATTGTGGAGTAAATGTCATCCGGACTATGACTGCTCTACAAGGAAAA                         CATGCAAATGGAGAAAATGCATGGATTGGTATAGATGGAAATACTGGCAGT
genomic: AAAATTGTGGAGTAAATGTCATCCGGACTATGACTGCTCTACAAGGAAAAgtaagaatag ... aaaataatagCATGCAAATGGAGAAAATGCATGGATTGGTATAGATGGAAATACTGGCAGT
EST: gi|193639863|gb|FK592320.1|FK592320
EST:     AAAATTGTGGAGTAAATGTCATCCGGACTATGACTGCTCTACAAGGAAAA                         CATGCAAATGGAGAAAATGCATGGATTGGTATAGATGGAAATACTGGCAGT
genomic: AAAATTGTGGAGTAAATGTCATCCGGACTATGACTGCTCTACAAGGAAAAgtaagaatag ... aaaataatagCATGCAAATGGAGAAAATGCATGGATTGGTATAGATGGAAATACTGGCAGT
EST: gi|22927071|gb|BU544210.1|BU544210
EST:     AAAATTGTGGAGTAAATGTCATCCGGACTATGACTGCTCTACAAGGAAAA                         CATGCAAATGGAGAAAATGCATGGATTGGTATAGATGGAAATACTGGCAGT
genomic: AAAATTGTGGAGTAAATGTCATCCGGACTATGACTGCTCTACAAGGAAAAgtaagaatag ... aaaataatagCATGCAAATGGAGAAAATGCATGGATTGGTATAGATGGAAATACTGGCAGT
EST: gi|192309232|gb|FG999123.1|FG999123
EST:     AAAATTGTGGAGTAAATGTCATCCGGACTATGACTGCTCTACAAGGAAAA                         CATGCAAATGGAGAAAATGCATGGATTGGTATAGATGGAAATACTGGCAGT
genomic: AAAATTGTGGAGTAAATGTCATCCGGACTATGACTGCTCTACAAGGAAAAgtaagaatag ... aaaataatagCATGCAAATGGAGAAAATGCATGGATTGGTATAGATGGAAATACTGGCAGT
EST: gi|26048688|gb|CA785141.1|CA785141
EST:     AAAATTGTGGAGTAAATGTCATCCGGACTATGACTGCTCTACAAGGAAAA                         CATGCAAATGGAGAAAATGCATGGATTGGTATAGATGGAAATACTGGCAGT
genomic: AAAATTGTGGAGTAAATGTCATCCGGACTATGACTGCTCTACAAGGAAAAgtaagaatag ... aaaataatagCATGCAAATGGAGAAAATGCATGGATTGGTATAGATGGAAATACTGGCAGT
EST: gi|193619682|gb|FK572642.1|FK572642
EST:     AAAATTGTGGAGTAAATGTCATCCGGACTATGACTGCTCTACAAGGAAAA                         CATGCAAATGGAGAAAATGCATGGATTGGTATAGATGGAAATACTGGCAGT
genomic: AAAATTGTGGAGTAAATGTCATCCGGACTATGACTGCTCTACAAGGAAAAgtaagaatag ... aaaataatagCATGCAAATGGAGAAAATGCATGGATTGGTATAGATGGAAATACTGGCAGT
EST: gi|193521393|gb|FK481638.1|FK481638
EST:     AAAATTGTGGAGTAAATGTCATCCGGACTATGACTGCTCTACAAGGAAAA                         CATGCAAATGGGGAAAATGCATGGATTGGTATAGATGGAAATACTGGCAG
genomic: AAAATTGTGGAGTAAATGTCATCCGGACTATGACTGCTCTACAAGGAAAAgtaagaatag ... aaaataatagCATGCAAATGGAGAAAATGCATGGATTGGTATAGATGGAAATACTGGCAG
EST: gi|193588325|gb|FK544060.1|FK544060
EST:     AAAATTGTGGAGTAAATGTCATCCGGACTATGACTGCTCTACAAGGAAAA                         CATGCAAATGGAGAAAATGCATGGATTGGTATAGATGGAAATACTGGCAGT
genomic: AAAATTGTGGAGTAAATGTCATCCGGACTATGACTGCTCTACAAGGAAAAgtaagaatag ... aaaataatagCATGCAAATGGAGAAAATGCATGGATTGGTATAGATGGAAATACTGGCAGT
EST: gi|209714674|gb|BW674237.1|BW674237
EST:     AAAATTGTGGAGTAAATGTCATCCGGACTATGACTGCTCTACAAGGAAAA                         CATGCAAATGGAGAAAATGCATGGATTGGTATAGATGGAAATACTGGCAGT
genomic: AAAATTGTGGAGTAAATGTCATCCGGACTATGACTGCTCTACAAGGAAAAgtaagaatag ... aaaataatagCATGCAAATGGAGAAAATGCATGGATTGGTATAGATGGAAATACTGGCAGT
EST: gi|193529449|gb|FK487832.1|FK487832
EST:     AAAATTGTGGAGTAAATGTCATCCGGACTATGGCTGCTCTACAAGGAAAA                         CATGCAAATGGAGAAAATGCATGGATTGGTATAGATGGAAATACTGGCAGT
genomic: AAAATTGTGGAGTAAATGTCATCCGGACTATGACTGCTCTACAAGGAAAAgtaagaatag ... aaaataatagCATGCAAATGGAGAAAATGCATGGATTGGTATAGATGGAAATACTGGCAGT
EST: gi|208325439|gb|GE124105.1|GE124105
EST:     AAAATTGTGGAGTAAATGTCATCCGGACTATGACTGCTCTACAAGGAAAA                         CATGCAAATGGAGAAAATGCATGGATTGGTATAGATGGAAAATAACTAGGA
genomic: AAAATTGTGGAGTAAATGTCATCCGGACTATGACTGCTCTACAAGGAAAAgtaagaatag ... aaaataatagCATGCAAATGGAGAAAATGCATGGATTGGTATAGATGGAAA-TA-CT-GG-
EST: gi|15199729|gb|BI423980.1|BI423980
EST:     AAAATTGTGGAGTAAATGTCATCCGGACTATGACTGCTCTACAAGGAAAA                         CATGCAAATGGAGAAAATGCATGGATTGGTATAGATGGAAATACTGGCAGT
genomic: AAAATTGTGGAGTAAATGTCATCCGGACTATGACTGCTCTACAAGGAAAAgtaagaatag ... aaaataatagCATGCAAATGGAGAAAATGCATGGATTGGTATAGATGGAAATACTGGCAGT
EST: gi|207786727|gb|GD757958.1|GD757958
EST:     AAAATTGTGGAGTAAATGTCATCCGGACTATGACTGCTCTACAAGGAAAA                         CATGCAAATGGAGAAAATGCATGGATTGGTATAGATGGAAATACTGGCAGT
genomic: AAAATTGTGGAGTAAATGTCATCCGGACTATGACTGCTCTACAAGGAAAAgtaagaatag ... aaaataatagCATGCAAATGGAGAAAATGCATGGATTGGTATAGATGGAAATACTGGCAGT
EST: gi|208095316|gb|GD892046.1|GD892046
EST:     TTGTGGAGTAAATGTTCTATTCCGGTACTATGACTGCTCTACAAGGAAAA                         CATGCAAATGGAGAAAATGCATGGATTGGTATAGATGGAAATACTGGCAGT
genomic: TTGTGGAGTAAATG-TC-A-TCCGG-ACTATGACTGCTCTACAAGGAAAAgtaagaatag ... aaaataatagCATGCAAATGGAGAAAATGCATGGATTGGTATAGATGGAAATACTGGCAGT
EST: gi|208209540|gb|GE001809.1|GE001809
EST:     AAATTGTGGAGTAAATGTCATCCGGACTATGACTGCTCTACAAGGAAAA                         CATGCAAATGGAGAAAATGCATGGATTGGTATAGATGGAAATACTGGCAGT
genomic: AAATTGTGGAGTAAATGTCATCCGGACTATGACTGCTCTACAAGGAAAAgtaagaatag ... aaaataatagCATGCAAATGGAGAAAATGCATGGATTGGTATAGATGGAAATACTGGCAGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acagtctttttctctgaagtcatatcacgtttaacactgttcttgaaaataatagCATGCAAATGGAGAAAATGCATGGATTGGTATAGATGGAAATACTGGCAGTATCACTGACATGAAAGAGCGCAAG
                            gtttaac  putative branch site (score: 3)
                                       ttcttgaaaataata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagaatagtttgttagtacttattgtatacagtctttttctctgaagtcatatcacgtttaacactgttcttgaaaataatagCATGCAAATGGAGAAAATGCATGGATTGGTATAGATGGAAATACTGGCAGTATCACTGACATGAAAGAGCGCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA