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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTTCTTTATGCGTGAAACGTCTTGTGTACACAAATGAAAACGGAGAACTTGTCAAAGGAGTTTGCTCAAATTTCTTGTgtaaggatcaatgattttagtttttatatgatatttatgaaatagtaataaatatgatatcatgttataaaaagaattcattcaatatgttaaaataaat...

Basic information

species Glycine max
transcript GLYMA11G08230.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G08230.1 (Glycine max), 5'ss of exon 4
lower sequence: Vv04s0023g03510.t01 (Vitis vinifera), 5'ss of exon 4
GTTTCTTTATGCGTGAAACGTCTTGTGTACACAAATGAAAACGGAGAACTTGTCAAAGGAGTTTGCTCAAATTTCTTGTgtaag---gatcaatgattttagtttttatatgatatttatgaaatagtaataaatatgatatcatgttataaaaag--aat---tcattcaatatgttaaaataaat------------------------------------------------
|||||| | || |||||||| ||||| ||||| ||||| || || ||||| || || ||||| |||||||||||||||||||||   | ||||  |||||  |  ||  ||   | |        |       || | | |   |  |||   ||   |||   ||  | || |  |||   |||                                                  
GTTTCTCTTTGTGTGAAACGGCTTGTCTACACCAATGAGAATGGGGAACTAGTTAAGGGAGTCTGCTCAAATTTCTTGTgtaagtctgctcaa-aattttcttaattgcataggaatc-cagcccaccttctgatttcaaacagttgtatgggaaatcaatctctcggtgaagacattagtctaagagatgcttctgttaatgtacttttgagctctaaatctcttccatttcag

upper sequence: GLYMA11G08230.1 (Glycine max), 5'ss of exon 4
lower sequence: Vv18s0001g14450.t01 (Vitis vinifera), 5'ss of exon 4
GTTTCTTTATGCGTGAAACGTCTTGTGTACACAAATGAAAACGGAGAACTTGTCAAAGGAGTTTGCTCAAATTTCTTGTgtaaggatcaatgatt--ttagtttttatatgatatttatgaaatagtaataaatatgatatcatgttataaaaagaattcattcaatatgttaaaataaat-
||||| || || || ||| | ||||| ||||| |||||  | |||||  | || ||||||||||||||||||||||||||||||  ||   ||    ||  || ||  |   || || |    ||  |||  || ||||||  || |||      |   ||  |   |   |     |  | 
GTTTCATTGTGTGTAAAAAGGCTTGTCTACACCAATGACCAAGGAGAGATAGTTAAAGGAGTTTGCTCAAATTTCTTGTgtaagtctctgagaacacttgattctttcagtttagtttttc--taacaatgcatttgatattttggtattttcttagcccacccc-cactctcccccatctc
















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|120534406|gb|EH262539.1|EH262539
EST:     CACAAATGAAAACGGAGAACTTGTCAAAGGAGTTTGCTCAAATTTCTTGT                         GCGACTTGAAGCCAGGAGCCGAAGTAAAGATTACTGGACCTGTTGGTAAAG
genomic: CACAAATGAAAACGGAGAACTTGTCAAAGGAGTTTGCTCAAATTTCTTGTgtaaggatca ... gtttattcagGCGACTTGAAGCCAGGAGCCGAAGTAAAGATTACTGGACCTGTTGGTAAAG
EST: gi|192306166|gb|FG995030.1|FG995030
EST:     CACAAATGAAAACGGAGAACTTGTCAAAGGAGTTTGCTCAAATTTCTTGT                         GCGACTTGAAGCCAGGAGCCGAAGTAAAGATTACTGGACCTGTTGGTAAAG
genomic: CACAAATGAAAACGGAGAACTTGTCAAAGGAGTTTGCTCAAATTTCTTGTgtaaggatca ... gtttattcagGCGACTTGAAGCCAGGAGCCGAAGTAAAGATTACTGGACCTGTTGGTAAAG
EST: gi|12773001|gb|BG237928.1|BG237928
EST:     CACAAATGAAAACGGAGAACTTGTCAAAGGAGTTTGCTCAAATTTCTTGT                         GCGACTTGAAGCCATGAGCCGAAGTAAAGATTACTGGACCTGTTGG
genomic: CACAAATGAAAACGGAGAACTTGTCAAAGGAGTTTGCTCAAATTTCTTGTgtaaggatca ... gtttattcagGCGACTTGAAGCCAGGAGCCGAAGTAAAGATTACTGGACCTGTTGG
EST: gi|16105591|gb|BI893331.1|BI893331
EST:     CACAAATGAAAACGGAGAACTTGTCAAAGGAGTTTGCTCAAATTTCTTGT                         GCGACTTGAAGCCAGGAGCC
genomic: CACAAATGAAAACGGAGAACTTGTCAAAGGAGTTTGCTCAAATTTCTTGTgtaaggatca ... gtttattcagGCGACTTGAAGCCAGGAGCC
EST: gi|120531421|gb|EH259554.1|EH259554
EST:     CACAAATGAAAACGGAGAACTTGTCAAAGGAGTTTGCTCAAATTTCTTGT                         GCGACTTGAAGCCAGGAGCCGAAGTAAAGATTACTGGACCTGTTGGTAAAG
genomic: CACAAATGAAAACGGAGAACTTGTCAAAGGAGTTTGCTCAAATTTCTTGTgtaaggatca ... gtttattcagGCGACTTGAAGCCAGGAGCCGAAGTAAAGATTACTGGACCTGTTGGTAAAG
EST: gi|120534689|gb|EH262822.1|EH262822
EST:     CACAAATGAAAACGGAGAACTTGTCAAAGGAGTTTGCTCAAATTTCTTGT                         GCGACTTGAAGCCAGGAGCCGAAGTAAAGATTACTGGACCTGTTGGTAAAG
genomic: CACAAATGAAAACGGAGAACTTGTCAAAGGAGTTTGCTCAAATTTCTTGTgtaaggatca ... gtttattcagGCGACTTGAAGCCAGGAGCCGAAGTAAAGATTACTGGACCTGTTGGTAAAG
EST: gi|16342619|gb|BI968214.1|BI968214
EST:     CACAAATGNNNNNNGAGAACTTGTCAAAGGAGTTTGCTCAAATTTCTTGT                         GCGACTTGAAGCCAGGAGCCGAAGTAAAGATTACTGGACCTGTTGGTAAAG
genomic: CACAAATGAAAACGGAGAACTTGTCAAAGGAGTTTGCTCAAATTTCTTGTgtaaggatca ... gtttattcagGCGACTTGAAGCCAGGAGCCGAAGTAAAGATTACTGGACCTGTTGGTAAAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTTCTTTATGCGTGAAACGTCTTGTGTACACAAATGAAAACGGAGAACTTGTCAAAGGAGTTTGCTCAAATTTCTTGTgtaaggatcaatgattttagtttttatatgatatttatgaaatagtaataaatatgatatcatgttataaaaagaattcattcaatatgttaaaataaat

- - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaaagaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaataaa