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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgtattgcaacataatttctcatggcattttggttttagtaactgattaagtttgatgatgggttctgtttggcagATTCGTCCTGGCACCCAACCTGGTCAGAAGGTGGTTCTGAAAAAGAAAG

Basic information

species Glycine max
transcript GLYMA15G42640.1
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA15G42640.1 (Glycine max), 3'ss of exon 15
lower sequence: Vv13s0064g01360.t01 (Vitis vinifera), 3'ss of exon 15
------------gtttgtattgcaacataatttctcatgg-----cattttggttttagt--aactgattaagtttgatga--tgggttctgtttggcagATTCGTCCTGGCACCCAACCTGGTCAGAAGGTGGTTCTGAAAAAGAAAG
             ||  ||||   |  |  |||||  | |     | || | ||| | ||  ||   | || |  || | |  ||  |||   || |||| | ||||||||||| ||||||||||||||||| ||| |||| |  ||||
ctcggttgtcaaattattattattattttgtttcttgttgatgtaccttcttgttattgttcaatcaagtaggagtgttaaattgatttccaatttgcagGTCCGTCCTGGCACTCAACCTGGTCAGAAGGTAGTTTTGAAGAGAAAAG
















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|17518777|gb|BM187819.1|BM187819
EST:     TGGGTGGAACCATTCAGGTCCCAACTCTTACTGGAGATGTTGTTCTAAAG                         ATTCGTCCTGGCACCCAACCTGGTCAGAAGGTGGTTCTGAAAAAGAAAGGG
genomic: TGGGTGGAACCATTCAGGTCCCAACTCTTACTGGAGATGTTGTTCTAAAGgtttgtattg ... tgtttggcagATTCGTCCTGGCACCCAACCTGGTCAGAAGGTGGTTCTGAAAAAGAAAGGG
EST: gi|58018599|gb|CX705341.1|CX705341
EST:     TGGGTGGAACCATTCAGGTCCCAACTCTTACTGGAGATGTTGTTCTAAAG                         ATTCGTCCTGGCACCCAACCTGGTCAGAAGGTGGTTCTGAAAAAGAAAG
genomic: TGGGTGGAACCATTCAGGTCCCAACTCTTACTGGAGATGTTGTTCTAAAGgtttgtattg ... tgtttggcagATTCGTCCTGGCACCCAACCTGGTCAGAAGGTGGTTCTGAAAAAGAAAG
EST: gi|18040165|gb|BM308459.1|BM308459
EST:     TGGGTGGAACCATTCAGGTCCCAACTCTTACTGGAGATGTTGTTCTAAAG                         ATTCGTCCTGGCACCCAACCTGGTCAGAAGGTGGTTCTGAAAAAGAAAG
genomic: TGGGTGGAACCATTCAGGTCCCAACTCTTACTGGAGATGTTGTTCTAAAGgtttgtattg ... tgtttggcagATTCGTCCTGGCACCCAACCTGGTCAGAAGGTGGTTCTGAAAAAGAAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atggcattttggttttagtaactgattaagtttgatgatgggttctgtttggcagATTCGTCCTGGCACCCAACCTGGTCAGAAGGTGGTTCTGAAAAAGAAAG
                                          ttctgttt  CT-rich tract
            ttttagtaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgtattgcaacataatttctcatggcattttggttttagtaactgattaagtttgatgatgggttctgtttggcagATTCGTCCTGGCACCCAACCTGGTCAGAAGGTGGTTCTGAAAAAGAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA