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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttcttggttatatgagtattttaaatttgttttgagtggattgttctctaaagtctctactgcatcattcatttgattcacttttaacataaatatctagCTTGGTCATGATGCTTATGTAAACCAACAAAGCACTGGTTTTGGAGGCGAGGGTGGCTTCAATCCTTTTGAGCAGATATTCCGTGATCAT

Basic information

species Glycine max
transcript GLYMA09G00580.1
intron # 6
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|208111987|gb|GD911077.1|GD911077
EST:     GTTTTGAAGGATGAGGAAAGGCGTCAACAGTATGATCAG                         CTTGGTCATGATGCTTATGTAAACCAACAAAGCACTGGTTTTGGAGGCGAG
genomic: GTTTTGAAGGATGAGGAAAGGCGTCAACAGTATGATCAGgtttagcact ... aaatatctagCTTGGTCATGATGCTTATGTAAACCAACAAAGCACTGGTTTTGGAGGCGAG
EST: gi|192326652|gb|FK017309.1|FK017309
EST:     GTTTTGAAGGATGAGGAAAGGCGTCAACAGTATGATCAG                         CTTGGTCATGATGCTTATGTAAACCAACAAAGCACTGGTTTTGGAGGCGAG
genomic: GTTTTGAAGGATGAGGAAAGGCGTCAACAGTATGATCAGgtttagcact ... aaatatctagCTTGGTCATGATGCTTATGTAAACCAACAAAGCACTGGTTTTGGAGGCGAG
EST: gi|7924054|gb|AW830062.1|AW830062
EST:     GTTTTGAAGGATGAGGAAAGGCGTCAACAGTATGATCAG                         CTTGGTCATGATGCTTATGTAAACCAACAAAGCACTGGTTTTGGAGGCGAG
genomic: GTTTTGAAGGATGAGGAAAGGCGTCAACAGTATGATCAGgtttagcact ... aaatatctagCTTGGTCATGATGCTTATGTAAACCAACAAAGCACTGGTTTTGGAGGCGAG
EST: gi|193368168|gb|FK329984.1|FK329984
EST:     GTTTTTGAAGGATGAGGAAAGGCGTCAACAGTATGATCAG                         CTTGGTCATGATGCTTATGTAAACCAACAAAGCACTGGTTTTGGAGGCGAG
genomic: G-TTTTGAAGGATGAGGAAAGGCGTCAACAGTATGATCAGgtttagcact ... aaatatctagCTTGGTCATGATGCTTATGTAAACCAACAAAGCACTGGTTTTGGAGGCGAG
EST: gi|151401621|gb|EV271434.1|EV271434
EST:     GTTTTGAAG-ATGAGGAAAGGCGTCAACAGTATGATCAG                         CTTGGTCATGATGCTTATGTAA-CCA-CAA-GCACTGGTTT
genomic: GTTTTGAAGGATGAGGAAAGGCGTCAACAGTATGATCAGgtttagcact ... aaatatctagCTTGGTCATGATGCTTATGTAAACCAACAAAGCACTGGTTT
EST: gi|193702972|gb|FK639236.1|FK639236
EST:     GTTTTGAAGGATGAGGAAAGGCGTCAACAGTATGATCAG                         CTTGGTCATGATGCTTATGTAAACCAACAAAGCACTGGTTTTGGAGGCGAG
genomic: GTTTTGAAGGATGAGGAAAGGCGTCAACAGTATGATCAGgtttagcact ... aaatatctagCTTGGTCATGATGCTTATGTAAACCAACAAAGCACTGGTTTTGGAGGCGAG
EST: gi|7284029|gb|AW596629.1|AW596629
EST:     GTTNTGAAGGATGAGGAAAGGCGTCAACAGTATGATCAG                         CTTGGTCATGATGCTTATGTAAACCAACAAAGCACTGGTTTTGGAGGCGAG
genomic: GTTTTGAAGGATGAGGAAAGGCGTCAACAGTATGATCAGgtttagcact ... aaatatctagCTTGGTCATGATGCTTATGTAAACCAACAAAGCACTGGTTTTGGAGGCGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctctaaagtctctactgcatcattcatttgattcacttttaacataaatatctagCTTGGTCATGATGCTTATGTAAACCAACAAAGCACTGGTTTTGGAGGCGAGGGTGGCTTCAATCCTTTTGAGCAGATATTCCGTGATCAT
                                    ttttaac  putative branch site (score: 2)
                              attcacttttaacata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttcttggttatatgagtattttaaatttgttttgagtggattgttctctaaagtctctactgcatcattcatttgattcacttttaacataaatatctagCTTGGTCATGATGCTTATGTAAACCAACAAAGCACTGGTTTTGGAGGCGAGGGTGGCTTCAATCCTTTTGAGCAGATATTCCGTGATCAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT
- - - - - - - - - - - - - -tgttttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - ctactgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cattcat