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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atattttcattttaaattttttaagaacacatgttagcatttttttataataaatatttatatttatatttatatttaatttgtaaatttgtaaatgtagTTTCCCAGAAGCAGCATTGGAGGCCGAATTGGGAGTGATCTTTCATTATCAGTGGCTGATCAACAACAGTGGCAAACCGGGCCTTCACGTTATTTAGCAA

Basic information

species Glycine max
transcript GLYMA05G18170.1
intron # 9
splice site 3'
intron type U2

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|193616512|gb|FK570216.1|FK570216
EST:     AGTCTCAAATGCTTCAAAATTTTGCGCACATTCACCCACCAAATTTTCAT                         TTTCCCAGAAGCAGCATTGGAG
genomic: AGTCTCAAATGCTTCAAAATTTTGCGCACATTCACCCACCAAATTTTCATgtgggtacct ... gtaaatgtagTTTCCCAGAAGCAGCATTGGAG
EST: gi|208163388|gb|GD959780.1|GD959780
EST:     TTCACCCACCAAATTTTCAT                         TTTCCCAGAAGCAGCATTGGAGGCCGAATTGGGAGTGATCTTTCATTATCA
genomic: TTCACCCACCAAATTTTCATgtgggtacct ... gtaaatgtagTTTCCCAGAAGCAGCATTGGAGGCCGAATTGGGAGTGATCTTTCATTATCA
EST: gi|193706774|gb|FK646337.1|FK646337
EST:     AGTCTCAAATGCTTCAAAATTTTGCGCACATTCACCCACCAAATTTTCATT                         TTTCCCAGAAGCAGCATTGGAGGCCGAATTGGGAGTGATCTTTCATTATC
genomic: AGTCTCAAATGCTTCAAAATTTTGCGCACATTCACCCACCAAATTTTCA-Tgtgggtacct ... gtaaatgtagTTTCCCAGAAGCAGCATTGGAGGCCGAATTGGGAGTGATCTTTCATTATC
EST: gi|208107377|gb|GD907964.1|GD907964
EST:     AGTCTCAAATGCTTCAAAATTTTGCGCACATTCACCCACCAAATTTTCAT                         TTTCCCAGAAGCAGCATTGGAGGCCGAATTGGGAGTGATCTTTCATTATCA
genomic: AGTCTCAAATGCTTCAAAATTTTGCGCACATTCACCCACCAAATTTTCATgtgggtacct ... gtaaatgtagTTTCCCAGAAGCAGCATTGGAGGCCGAATTGGGAGTGATCTTTCATTATCA
EST: gi|193685246|gb|FK626196.1|FK626196
EST:     AGTCTCAAATGCTTCAAAATTTTGCGCACATTCACCCACCAAATTTTCAT                         TTTCCCAGAAGCAGCATTGGAGGCCGAATTGGGAGTGATCTTTCATTATCA
genomic: AGTCTCAAATGCTTCAAAATTTTGCGCACATTCACCCACCAAATTTTCATgtgggtacct ... gtaaatgtagTTTCCCAGAAGCAGCATTGGAGGCCGAATTGGGAGTGATCTTTCATTATCA
EST: gi|207827545|gb|GD800754.1|GD800754
EST:     AGTCTCAAATGCTTCAAAATTTTGCGCACATTCACCCACCAAATTTTCAT                         TTTCCCAGAAGCAGCATTGGAGGCCGAATTGGGAGTGATCTTTCATTATCA
genomic: AGTCTCAAATGCTTCAAAATTTTGCGCACATTCACCCACCAAATTTTCATgtgggtacct ... gtaaatgtagTTTCCCAGAAGCAGCATTGGAGGCCGAATTGGGAGTGATCTTTCATTATCA
EST: gi|8402153|gb|BE057787.1|BE057787
EST:     GTCTCAAATGCTTCAAAATTTTGCGCACATTCACCCACCAAATTTTCAT                         TTTCCCAGAAGCAGCATTGGAGGCCGAATTGGGAGTGATCTTTCATTATCA
genomic: GTCTCAAATGCTTCAAAATTTTGCGCACATTCACCCACCAAATTTTCATgtgggtacct ... gtaaatgtagTTTCCCAGAAGCAGCATTGGAGGCCGAATTGGGAGTGATCTTTCATTATCA
EST: gi|207844380|gb|GD814425.1|GD814425
EST:     CGCACATTCACCCACCAAATTTTCAT                         TTTCCCAGAAGCAGCATTGGAGGCCGAATTGGGAGTGATCTTTCATTATCA
genomic: CGCACATTCACCCACCAAATTTTCATgtgggtacct ... gtaaatgtagTTTCCCAGAAGCAGCATTGGAGGCCGAATTGGGAGTGATCTTTCATTATCA
EST: gi|7283390|gb|AW595998.1|AW595998
EST:     AGTCTCAAATGCTTCAAAATTTTGCGCACATTCACCCACCAAATTTTCAT                         TTTCCCAGAAGCAGCATTGGAGGCCGAATTGGGAGTGATCTTTCATTATCA
genomic: AGTCTCAAATGCTTCAAAATTTTGCGCACATTCACCCACCAAATTTTCATgtgggtacct ... gtaaatgtagTTTCCCAGAAGCAGCATTGGAGGCCGAATTGGGAGTGATCTTTCATTATCA
EST: gi|208181585|gb|GD974166.1|GD974166
EST:     AGTCTCAAATGCTTCAAAATTTTGCGCACACTCACCCACCAAATTTTCAT                         TTTCCCAGAAGCAGCATTGGAGGCCGAATTGGGAGTGATCTTTCATTATCA
genomic: AGTCTCAAATGCTTCAAAATTTTGCGCACATTCACCCACCAAATTTTCATgtgggtacct ... gtaaatgtagTTTCCCAGAAGCAGCATTGGAGGCCGAATTGGGAGTGATCTTTCATTATCA
EST: gi|193435204|gb|FK399858.1|FK399858
EST:     AGTCTCAAATGCTTCAAAATTTTGCGCACATTCATCCACCAAATTTTCAT                         TTTCCCAGAAGCAGCATTGGAGGCCGAATTGGGAGTGATTCTTTCATT
genomic: AGTCTCAAATGCTTCAAAATTTTGCGCACATTCACCCACCAAATTTTCATgtgggtacct ... gtaaatgtagTTTCCCAGAAGCAGCATTGGAGGCCGAATTGGGAGTGAT-CTTTCATT
EST: gi|16280595|gb|BI944044.1|BI944044
EST:     AGTCTCAAATGCTTCAAAATTTTGCGCACATTCACCCACCAAATTTTCAT                         TTTCCCAGAAGCAGCATTGGAGGCCGAATTGGGAGTGATCTTTCATTATCN
genomic: AGTCTCAAATGCTTCAAAATTTTGCGCACATTCACCCACCAAATTTTCATgtgggtacct ... gtaaatgtagTTTCCCAGAAGCAGCATTGGAGGCCGAATTGGGAGTGATCTTTCATTATC-


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tataataaatatttatatttatatttatatttaatttgtaaatttgtaaatgtagTTTCCCAGAAGCAGCATTGGAGGCCGAATTGGGAGTGATCTTTCATTATCAGTGGCTGATCAACAACAGTGGCAAACCGGGCCTTCACGTTATTTAGCAA
                            atttaat  putative branch site (score: 4)
     taaatatttatattta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atattttcattttaaattttttaagaacacatgttagcatttttttataataaatatttatatttatatttatatttaatttgtaaatttgtaaatgtagTTTCCCAGAAGCAGCATTGGAGGCCGAATTGGGAGTGATCTTTCATTATCAGTGGCTGATCAACAACAGTGGCAAACCGGGCCTTCACGTTATTTAGCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - -aacacat