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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ccttcttatgttctttgtatttgtcaaaatcttttcttatctattcatgtaatgctttatttgaatgaagcaacaaaatcataaatttaattttgagtagGTTAAAGCAATGGTGATCATAAATCCTGGAAACCCTACTGGTCAATGCCTTAGTGAAGCTAATCTAAGAGAGGTTTTGCAATTCTGTTATCAAGAAAATT

Basic information

species Glycine max
transcript GLYMA01G03260.3
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA01G03260.3 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os07g01760.1 (Oryza sativa), 3'ss of exon 5
ccttcttatgttctttgtatttgtcaaaatcttttcttatctattcatgtaatgctt----tatttgaatgaagcaacaaaatcataaatttaattttgagtagGTTAAAGCAATGGTGATCATAAATCCTGGAAACCCTACTGGTCAATGCCTTAGTGAAGCTAATCTAAGAGAGGTTTTGCAATTCTGTTATCAAGAAAATT
  |||||    | | | |  || ||||      |  ||   ||   |||||    ||    ||| || ||  |||    |  | ||    ||  | ||   ||||||  |||||||||||| || || || |||||||||||||| ||||||||||||||||  ||  |||  ||  || |  ||||||| |  || || || |
atttcttcccctttcttttattttcaatcatgctgtttgcataaaaatgtagcatttatactatctgtattcagctttgatgttat----tttttcttccatagGTTCGAGCAATGGTGATTATCAACCCAGGAAACCCTACTGGCCAATGCCTTAGTGAAGGAAACATAAAGGAACTTCTCAAATTCTGCTTCCATGAGAACT

upper sequence: GLYMA01G03260.3 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM5G840582_T01 (Zea mays), 3'ss of exon 6
ccttcttatgttctttgtatttgtcaaaatcttttcttatctattcatgta-atgc-tttatttgaatgaagcaacaaaatcataaatttaattttgagtagGTTAAAGCAATGGTGATCATAAATCCTGGAAACCCTACTGGTCAATGCCTTAGTGAAGCTAATCTAAGAGAGGTTTTGCAATTCTGTTATCAAGAAAATT
   || |     ||||||     |     ||   |  | |  || ||| |  |||| || |||    |      |      |         |   ||  ||||||  ||| | |||||| |||||||| ||||| || ||||| || |||||||||||||| ||| |||| ||  || ||| ||  || || || ||||| |
-tgtcgtgaacactttgtgac-atgggcttcaaataatgtacatacatatgtatgcattcattccgctctgatcatttcccccccttacctacgatgcttagGTTCGAGCGACGGTGATTATAAATCCAGGAAATCCCACTGGCCAGTGCCTTAGTGAAGCAAATATAAGGGAACTTGTGCGATATTGCTACCATGAAAACT
















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|19053398|gb|BM732065.1|BM732065
EST:     TTAATGAACTTCGTCAATCAGTTGAGCAGGCTCGCTTTAAAGGAATAACT                         GTTAAAGCAATGGTGATCATAAATCCTGGAAACCCTACTGGTCAATGCCTT
genomic: TTAATGAACTTCGTCAATCAGTTGAGCAGGCTCGCTTTAAAGGAATAACTgtatgtgttt ... ttttgagtagGTTAAAGCAATGGTGATCATAAATCCTGGAAACCCTACTGGTCAATGCCTT
EST: gi|120529201|gb|EH257335.1|EH257335
EST:     TTAATGAACTTCGTCAATCAGTTGAGCAGGCTCGCTTTAAAGGAATAACT                         GTTAAAGCAATGGTGATCATAAATCCTGGAAACCCTACTGGTCAATGC-TT
genomic: TTAATGAACTTCGTCAATCAGTTGAGCAGGCTCGCTTTAAAGGAATAACTgtatgtgttt ... ttttgagtagGTTAAAGCAATGGTGATCATAAATCCTGGAAACCCTACTGGTCAATGCCTT
EST: gi|15815783|gb|BI788058.1|BI788058
EST:     CAGGCTCGCTTTAAAGGAATAACT                         GTTAAAGCAATGGTGATCATAAATCCTGGAAACCCTACTGGTCAATGCCTT
genomic: CAGGCTCGCTTTAAAGGAATAACTgtatgtgttt ... ttttgagtagGTTAAAGCAATGGTGATCATAAATCCTGGAAACCCTACTGGTCAATGCCTT
EST: gi|15285990|gb|BI469890.1|BI469890
EST:     TAATGAACTTCGTCCATCAGTTGAGCAGGCTCGCTTTAAAAGGAA-AACT                         GGTAAAGCAATGGGGATCATAAAT
genomic: TAATGAACTTCGTCAATCAGTTGAGCAGGCTCGCTTTAAA-GGAATAACTgtatgtgttt ... ttttgagtagGTTAAAGCAATGGTGATCATAAAT
EST: gi|20498717|gb|BQ273647.1|BQ273647
EST:     TTAATGAACTTCGTCAATCAGTTGAGCAGGCTCGCTTTAAAGGAATAACT                         GTTAAAGCAATGGTGATCATAAATCCTGGAAACCCTACTGGTCAATGCCTT
genomic: TTAATGAACTTCGTCAATCAGTTGAGCAGGCTCGCTTTAAAGGAATAACTgtatgtgttt ... ttttgagtagGTTAAAGCAATGGTGATCATAAATCCTGGAAACCCTACTGGTCAATGCCTT
EST: gi|9902378|gb|BE611346.1|BE611346
EST:     TTAATGAACTTCGTCAATCAGTTGAGCAGGCTCGCTTTAAAGGAATAACT                         GTTAAAGCAATGGTGATCATAAATCCTGGAAACCCTACTGGTCAATGCCTT
genomic: TTAATGAACTTCGTCAATCAGTTGAGCAGGCTCGCTTTAAAGGAATAACTgtatgtgttt ... ttttgagtagGTTAAAGCAATGGTGATCATAAATCCTGGAAACCCTACTGGTCAATGCCTT
EST: gi|20814673|gb|BQ299151.1|BQ299151
EST:     TTAATGAACTTCGTCAATCAGTTGAGCAGGCTCGCTTTAAAGGAATAACT                         GTTAAAGCAATGGTGATCATAAATCCTGGAAACCCTACTGGTCAATGCCTT
genomic: TTAATGAACTTCGTCAATCAGTTGAGCAGGCTCGCTTTAAAGGAATAACTgtatgtgttt ... ttttgagtagGTTAAAGCAATGGTGATCATAAATCCTGGAAACCCTACTGGTCAATGCCTT
EST: gi|21887563|gb|BQ740776.1|BQ740776
EST:     TTAATGAACTTCGTCAATCAGTTGAGCAGGCTCGCTTTAAAGGAATAACT                         GTTAAAGCAATGGTGATCATAAATCCTGGGAACCCTACTGGTCAATGCCTT
genomic: TTAATGAACTTCGTCAATCAGTTGAGCAGGCTCGCTTTAAAGGAATAACTgtatgtgttt ... ttttgagtagGTTAAAGCAATGGTGATCATAAATCCTGGAAACCCTACTGGTCAATGCCTT
EST: gi|31561480|gb|CD487318.1|CD487318
EST:     TTAATGAACTTCGTCAATCAGTTGAGCAGGCTCGCTTTAAAGGAATAACT                         GTTAAAGCAATGGTGATCATAAATCCTGGAAACCCTACTGGTCAATGCCTT
genomic: TTAATGAACTTCGTCAATCAGTTGAGCAGGCTCGCTTTAAAGGAATAACTgtatgtgttt ... ttttgagtagGTTAAAGCAATGGTGATCATAAATCCTGGAAACCCTACTGGTCAATGCCTT
EST: gi|23064381|gb|BU579154.1|BU579154
EST:     TTAATGAACTTCGTCAATCAGTTGAGCAGGCTCGCTTTAAAGGAATAACT                         GTTAAAGCAATGGTGATCATAAATCCTGGAAACCCTACTGGTCAATGCCTT
genomic: TTAATGAACTTCGTCAATCAGTTGAGCAGGCTCGCTTTAAAGGAATAACTgtatgtgttt ... ttttgagtagGTTAAAGCAATGGTGATCATAAATCCTGGAAACCCTACTGGTCAATGCCTT
EST: gi|13480374|gb|BG509717.1|BG509717
EST:     TTAATGAACTTCGTCAATCAGTTGAGCAGGCTCGCTTTAAAGGAATAACT                         GTTAAAGCAATGGTGATCATAAATCCTGGAAACCCTACTGGTCAATGCCTT
genomic: TTAATGAACTTCGTCAATCAGTTGAGCAGGCTCGCTTTAAAGGAATAACTgtatgtgttt ... ttttgagtagGTTAAAGCAATGGTGATCATAAATCCTGGAAACCCTACTGGTCAATGCCTT
EST: gi|20498442|gb|BQ273372.1|BQ273372
EST:     TTAATGAACTTCGTCAATCAGTTGAGCAGGCTCGCTTTAAAGGAATAACT                         GTTAAAGCAATGGTGATCATAAATCCTGGAAACCCTACTGGTCAATGCCTT
genomic: TTAATGAACTTCGTCAATCAGTTGAGCAGGCTCGCTTTAAAGGAATAACTgtatgtgttt ... ttttgagtagGTTAAAGCAATGGTGATCATAAATCCTGGAAACCCTACTGGTCAATGCCTT
EST: gi|15285988|gb|BI469879.1|BI469879
EST:     TTAATGAACTTCGTCAATCAGTTGAGCAGGCTCGCTTTAAAGGAATAACT                         GTTAAAGCAATGGTGATCATAAATCCTGGAAACCCTACT
genomic: TTAATGAACTTCGTCAATCAGTTGAGCAGGCTCGCTTTAAAGGAATAACTgtatgtgttt ... ttttgagtagGTTAAAGCAATGGTGATCATAAATCCTGGAAACCCTACT
EST: gi|193366000|gb|FK329021.1|FK329021
EST:     TAATGAACTTCGTCAATCAGTTGAGCAGGTCTCGCTTTAAAGGAATAACT                         GTTAAAGCAATGGTGATCATAAATCCTGGAAACCCTACTGGTCAATGCCTT
genomic: TAATGAACTTCGTCAATCAGTTGAGCAGG-CTCGCTTTAAAGGAATAACTgtatgtgttt ... ttttgagtagGTTAAAGCAATGGTGATCATAAATCCTGGAAACCCTACTGGTCAATGCCTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catgtaatgctttatttgaatgaagcaacaaaatcataaatttaattttgagtagGTTAAAGCAATGGTGATCATAAATCCTGGAAACCCTACTGGTCAATGCCTTAGTGAAGCTAATCTAAGAGAGGTTTTGCAATTCTGTTATCAAGAAAATT
                                       atttaat  putative branch site (score: 4)
                          aacaaaatcataaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ccttcttatgttctttgtatttgtcaaaatcttttcttatctattcatgtaatgctttatttgaatgaagcaacaaaatcataaatttaattttgagtagGTTAAAGCAATGGTGATCATAAATCCTGGAAACCCTACTGGTCAATGCCTTAGTGAAGCTAATCTAAGAGAGGTTTTGCAATTCTGTTATCAAGAAAATT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
ccttctt
- - - - - - - - - - - - caaaatc
- - - - - - - - - - - - - - - - - - - - - - -catgtaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aatgaag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aacaaaa