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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGGGCAATGTTAGTATGGAGGAAAAGCAAATCTTCCAAAATGTTCAACTGAGTGTTAACTTCCTTGTCTCTTTGTTGAAAAAGAACTGGCAAAATGTGAgtagtagtccacactcaatatttcttaaactcattgcctctggtgccttcttttttattgtgcttttcttgaaattatatgttcttgttgctgttttatg...

Basic information

species Glycine max
transcript GLYMA11G35450.2
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G35450.2 (Glycine max), 5'ss of exon 5
lower sequence: AT5G22440.1 (Arabidopsis thaliana), 5'ss of exon 5
----GTGGGCAATGTTAGTATGGAGGAAAAGCAAATCTTCCAAAATGTTCAACTGAGTGTTAACTTCCTTGTCTCTTTGTTGAAAAAGAACTGGCAAAATGTGAgtagtagtccacactcaatatttcttaaactcattgcctctggtgccttctttttta---ttgtgcttttcttgaaattatatgttcttgttgctgttttatg
    || || ||| ||   |||||||| ||||| ||||| |||||||||||  |||||||||||||||| || ||| | ||||| || |||||||||||||| ||||  |   | | ||  | | ||||  | ||   | | |    |      | | | |    || | | ||| |   | |  |                     
TGCTGTCGGTAATCTTTCCATGGAGGAGAAGCAGATCTTTCAAAATGTTCAGATGAGTGTTAACTTCCTCGTTTCTCTCTTGAAGAAAAACTGGCAAAATgttagtaacaacaccctcttga-acttctcgatctttctccatacatttatcagtatctaaaacctgagttgttcctttgactgcag--------------------

upper sequence: GLYMA11G35450.2 (Glycine max), 5'ss of exon 5
lower sequence: Vv06s0080g00400.t01 (Vitis vinifera), 5'ss of exon 8
----GTGGGCAATGTTAGTATGGAGGAAAAGCAAATCTTCCAAAATGTTCAACTGAGTGTTAACTTCCTTGTCTCTTTGTTGAAAAAGAACTGGCAAAATGTGAgtagtagtccacactcaatatttcttaaactcattgcctctggtgccttcttttttattgtgcttttcttgaaattatatgttcttgtt--gctgttttatg
    ||||| ||    ||||||||||| ||||| ||||| |||||||| |||||||| ||||| ||||||||||| |||||||| |||||||||||||||||||||  |  | |||  | |    |  |  |  | || |           |   || | ||   | || | || |   | |   |   | ||  | |   | |  
TGCTGTGGGTAACTGCAGTATGGAGGAGAAGCAGATCTTTCAAAATGTGCAACTGAGCGTTAATTTCCTTGTCTCCTTGTTGAAGAAGAACTGGCAAAATgtgagt--tgattcac--ttagctctgtt--agtttatggaactaaaccaataggttatgataaagtttatattaaggctctcaatcagtctttaggtacctcact

upper sequence: GLYMA11G35450.2 (Glycine max), 5'ss of exon 5
lower sequence: PP1S40_297V6.1 (Physcomitrella patens), 5'ss of exon 3
----GTGGGCAATGTTAGTATGGAGGAAAAGCAAATCTTCCAAAATGTTCAACTGAGTGTTAACTTCCTTGTCTCTTTGTTGAAAAAGAACTGGCAAAATGTGAgtag---tagtccacact---------caatatttcttaaactcattgcctctggtgccttcttttttattgtgcttttcttgaaattatatgttcttgtt-gctgttttatg-----------------------
     | || ||   |  |||||||||||||||||||||||| ||    ||| || ||||||||||||| || ||  ||||||| ||||||||||| ||||| ||||    |  |||   ||         || ||| ||| ||  |  |  | | || ||| |   |||| ||| |    |  | |  ||   ||||    |||   | ||||||                        
CGCCATCGGTAACTGTGATATGGAGGAAAAGCAAATCTTCCAGAACACACAAATGGGTGTTAACTTCCTCGTGTCCCTGTTGAAGAAGAACTGGCAGAATgtaagtacatttgttcctttctatttgaatgcagtatatctgaaggtgtt--cttgtgatgcttgtattttcattattaagtgatggtcatacaatgtctaagttcagtattttatctaacgtttgaatttttgtaacag

upper sequence: GLYMA11G35450.2 (Glycine max), 5'ss of exon 5
lower sequence: EFJ34353 (Selaginella moellendorffii), 5'ss of exon 3
----GTGGGCAATGTTAGTATGGAGGAAAAGCAAATCTTCCAAAATGTTCAACTGAGTGTTAACTTCCTTGTCTCTTTGTTGAAAAAGAACTGGCAAAATGTGAgtagtagtccacactcaatatttcttaaactcattgcctctggtgccttcttttttattgtgcttttcttgaaattatatgttcttgttgctgttttatg
    ||||||||  |    |||||||| |||||  ||||||| || ||||| || || ||||||||||| |||||  || | || |||||||||||||| || |||||||||      ||  | |||  |     | |  | ||   ||  | |                                                  
AGCGGTGGGCAACATCGAGATGGAGGAGAAGCAGGTCTTCCAGAACGTTCAGCTCAGCGTTAACTTCCTCGTCTCGCTGCTCAAGAAGAACTGGCAAAACgtaagtagtagtagcgcttctctcttttctcgtggcttaacttcgattgattccag------------------------------------------------

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|151400505|gb|EV270319.1|EV270319
EST:     GAGTGTTAACTTCCTTGTCTCTTTGTTGAAAA-GAACTGGCAAAATGTTA                         GTGCTTGTATCTGAAGAGTACAATGGGGAAATGTTACCGTGTCTTTTGAGG
genomic: GAGTGTTAACTTCCTTGTCTCTTTGTTGAAAAAGAACTGGCAAAATGTGAgtagtagtcc ... ttcaggttagGTGCTTGTATCTGAAGAGTACAATGGGGAAATGTTACCGTGTCTTTTGAGG
EST: gi|24136835|gb|BU927345.1|BU927345
EST:     GAGTGTTAACTTCCTTGTCTCTTTGTTGAAAAAGAACTGGCAAAATGTTA                         GGTGCTTGTATCTGA
genomic: GAGTGTTAACTTCCTTGTCTCTTTGTTGAAAAAGAACTGGCAAAATGTGAgtagtagtcc ... ttcaggttagG-TGCTTGTATCTGA
EST: gi|308099186|gb|HO761027.1|HO761027
EST:     GAGTGCTAACTTCCTTGTCTCTTTGTTGAAAAAGAACTGGCAAAATGTTA                         GGTGCTTGTATCTGAAGAGT
genomic: GAGTGTTAACTTCCTTGTCTCTTTGTTGAAAAAGAACTGGCAAAATGTGAgtagtagtcc ... ttcaggttagG-TGCTTGTATCTGAAGAGT
EST: gi|151393924|gb|EV263795.1|EV263795
EST:     GAGTGTTAACTTCCTTGTCTCTTTGTTGAAAAAGAACTGGCAAAATGTTA                         GGTGCTTGTATCTGAAGAGTACAATGGGGAAATGTTACCGTGTCTTTTGAG
genomic: GAGTGTTAACTTCCTTGTCTCTTTGTTGAAAAAGAACTGGCAAAATGTGAgtagtagtcc ... ttcaggttagG-TGCTTGTATCTGAAGAGTACAATGGGGAAATGTTACCGTGTCTTTTGAG
EST: gi|18848831|gb|BM567943.1|BM567943
EST:     GAGTGTTAACTTCCTTGTCTCTTTGTTGAAAAAGAACTGGCAAAATGTTA                         GGTGCTTGTATCTGAAGAG
genomic: GAGTGTTAACTTCCTTGTCTCTTTGTTGAAAAAGAACTGGCAAAATGTGAgtagtagtcc ... ttcaggttagG-TGCTTGTATCTGAAGAG
EST: gi|214004726|gb|DB985379.1|DB985379
EST:     GAGTGTTAACTTCCTTGTCTCTTTGTTGAAAAAGAACTGGCAAAATGTTA                         GGTGCTTGTATCTGAAGAGTACAATGGGGAAATGTTACCGTGTCTTTTGAG
genomic: GAGTGTTAACTTCCTTGTCTCTTTGTTGAAAAAGAACTGGCAAAATGTGAgtagtagtcc ... ttcaggttagG-TGCTTGTATCTGAAGAGTACAATGGGGAAATGTTACCGTGTCTTTTGAG
EST: gi|192305924|gb|FG995796.1|FG995796
EST:     GAGTGTTAACTTCCTTGTCTCTTTGTTGAAAAAGAACTGGCAAAATGTTA                         GGTGCTTGTATCTGAAGAGTACAATGGGGAAATGTTACCGTGTCTTTTGAG
genomic: GAGTGTTAACTTCCTTGTCTCTTTGTTGAAAAAGAACTGGCAAAATGTGAgtagtagtcc ... ttcaggttagG-TGCTTGTATCTGAAGAGTACAATGGGGAAATGTTACCGTGTCTTTTGAG
EST: gi|151400830|gb|EV270644.1|EV270644
EST:     GAGTGTTAACTTCCTTGTCTCTTTGTTGAAAAAGAACTGGCAAAATGTTA                         GGTGCTTGTATCTGAAGAGTACAATGGGGGAAATGTTACCGTGTCTTTTGA
genomic: GAGTGTTAACTTCCTTGTCTCTTTGTTGAAAAAGAACTGGCAAAATGTGAgtagtagtcc ... ttcaggttagG-TGCTTGTATCTGAAGAGTACAATGGGG-AAATGTTACCGTGTCTTTTGA
EST: gi|58014260|gb|CX701002.1|CX701002
EST:     GAGTGTTAACTTCCTTGTCTCTTTGTTGAAAAAGAACTGGCAAAATGTTA                         GGTGCTTGTATCTGAAGAGTACAATGGGGAAATGTTACCGTGTCTTTTGAG
genomic: GAGTGTTAACTTCCTTGTCTCTTTGTTGAAAAAGAACTGGCAAAATGTGAgtagtagtcc ... ttcaggttagG-TGCTTGTATCTGAAGAGTACAATGGGGAAATGTTACCGTGTCTTTTGAG
EST: gi|254316554|gb|GR828091.1|GR828091
EST:     GAGTGTTAACTTCCTTGTCTCTTTGTTGAAAAAGAACTGGCAAAATGTTA                         GGTGCTTGTATCTGAAGAGTACAATGGGGAAATGTTACCGTGTCTTTTGAG
genomic: GAGTGTTAACTTCCTTGTCTCTTTGTTGAAAAAGAACTGGCAAAATGTGAgtagtagtcc ... ttcaggttagG-TGCTTGTATCTGAAGAGTACAATGGGGAAATGTTACCGTGTCTTTTGAG
EST: gi|209701463|gb|BW667324.1|BW667324
EST:     GAGTGTTAACTTCCTTGTCTCTTTGTTGAAAAAGAACTGGCAAAATGTTA                         GGTGCTTGTATCTGAAGAGTACAATGGGGAAATGTTACCGTGTCTTTTGAG
genomic: GAGTGTTAACTTCCTTGTCTCTTTGTTGAAAAAGAACTGGCAAAATGTGAgtagtagtcc ... ttcaggttagG-TGCTTGTATCTGAAGAGTACAATGGGGAAATGTTACCGTGTCTTTTGAG
EST: gi|58017635|gb|CX704377.1|CX704377
EST:     GAGTGTTAACTTCCTTGTCTCTTTGTTGAAAAAGAACTGGCAAAATGTTA                         GGTGCTTGTATCTGAAGAGTACAATGGGGAAATGTTACCGTGTCTTTTGAG
genomic: GAGTGTTAACTTCCTTGTCTCTTTGTTGAAAAAGAACTGGCAAAATGTGAgtagtagtcc ... ttcaggttagG-TGCTTGTATCTGAAGAGTACAATGGGGAAATGTTACCGTGTCTTTTGAG
EST: gi|254316553|gb|GR828090.1|GR828090
EST:     GAGTGTTAACTTCCTTGTCTCTTTGTTGAAAAAGAACTGGCAAAATGTTA                         GGTGCTTGTATCTGAAGAGTACAATGGGGAAATGTTACCGTGTCTTTTGAG
genomic: GAGTGTTAACTTCCTTGTCTCTTTGTTGAAAAAGAACTGGCAAAATGTGAgtagtagtcc ... ttcaggttagG-TGCTTGTATCTGAAGAGTACAATGGGGAAATGTTACCGTGTCTTTTGAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGGGCAATGTTAGTATGGAGGAAAAGCAAATCTTCCAAAATGTTCAACTGAGTGTTAACTTCCTTGTCTCTTTGTTGAAAAAGAACTGGCAAAATGTGAgtagtagtccacactcaatatttcttaaactcattgcctctggtgccttcttttttattgtgcttttcttgaaattatatgttcttgttgctgttttatg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC