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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aattctactctgattgttaatgatttatagttacatacttacatgtgatcttcattttcattatcttactggcattaccatatttgaatttcttaataagGATGAGTAAATACAATAAAGTGGAAATACTTGAGAAAGCTGAAAAGGATTTAGCAGCTGTGACAGATCAGTACATGTCACGACTAGTCAAAGAATTGCAG

Basic information

species Glycine max
transcript GLYMA11G01340.1
intron # 3
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|298165204|gb|HO011253.1|HO011253
EST:     AGTCGTGATGTAACAATGAATAGTAAGAAAGTCATATTTCAAGTGCACAG                         GATGAGTAAATACAATAAAGTGGAAATACTTGAGAAAGCTGAAAAGGATTT
genomic: AGTCGTGATGTAACAATGAATAGTAAGAAAGTCATATTTCAAGTGCACAGgttatctctt ... tcttaataagGATGAGTAAATACAATAAAGTGGAAATACTTGAGAAAGCTGAAAAGGATTT
EST: gi|17519493|gb|BM188535.1|BM188535
EST:     AGTCGTGATGTAACAATGAATAGTAAGAAAGTCATATTTCAAGTGCACAG                         GATGAGTAAATACAATAAAGTGGAAATACTTGAGAAAGCTGAAAAGGATTT
genomic: AGTCGTGATGTAACAATGAATAGTAAGAAAGTCATATTTCAAGTGCACAGgttatctctt ... tcttaataagGATGAGTAAATACAATAAAGTGGAAATACTTGAGAAAGCTGAAAAGGATTT
EST: gi|213593699|gb|DB971721.1|DB971721
EST:     AGTCGTGATGTAACAATGAATAGTAAGAAAGTCATATTTCAAGTGCACAG                         GATGAGTAAATACAATAAAGTGGAAATACTTGAGAAAGCTGAAAAGGATTT
genomic: AGTCGTGATGTAACAATGAATAGTAAGAAAGTCATATTTCAAGTGCACAGgttatctctt ... tcttaataagGATGAGTAAATACAATAAAGTGGAAATACTTGAGAAAGCTGAAAAGGATTT
EST: gi|192326479|gb|FK017256.1|FK017256
EST:     AGTCGTGATGTAACAATGAATAGTAAGAAAGTCATATTTCAAGTGCACAG                         GATGAGTAAATACAATAAAGTGGAAATACTTGAGAAAGCTGAAAAGGATTT
genomic: AGTCGTGATGTAACAATGAATAGTAAGAAAGTCATATTTCAAGTGCACAGgttatctctt ... tcttaataagGATGAGTAAATACAATAAAGTGGAAATACTTGAGAAAGCTGAAAAGGATTT
EST: gi|151394898|gb|EV264769.1|EV264769
EST:     AGTCGTGATGTAACAATGGATAGTAAGAAAGTCATATTTCAAGTGCACAG                         GATGAGTAAATACAATAAAGTGGAAATACTTGAGAAAGCTGAAAAGGATTT
genomic: AGTCGTGATGTAACAATGAATAGTAAGAAAGTCATATTTCAAGTGCACAGgttatctctt ... tcttaataagGATGAGTAAATACAATAAAGTGGAAATACTTGAGAAAGCTGAAAAGGATTT
EST: gi|298182210|gb|HO026385.1|HO026385
EST:     AGTCGTGATGTAACAATGAATAGTAAGAAAGTCATATTTCAAGTGCACAG                         GATGAGTAAATACAATAAAGTGGAAATACTTGAGAAAGCTGAAAAGGATTT
genomic: AGTCGTGATGTAACAATGAATAGTAAGAAAGTCATATTTCAAGTGCACAGgttatctctt ... tcttaataagGATGAGTAAATACAATAAAGTGGAAATACTTGAGAAAGCTGAAAAGGATTT
EST: gi|298174665|gb|HO014696.1|HO014696
EST:     AGTCGTGATGTAACAATGAATAGTAAGAAAGTCATATTTCAAGTGCACAG                         GATGAGTAAATACAATAAAGTGGAAATACTTGAGAAAGCTGAAAAGGATTT
genomic: AGTCGTGATGTAACAATGAATAGTAAGAAAGTCATATTTCAAGTGCACAGgttatctctt ... tcttaataagGATGAGTAAATACAATAAAGTGGAAATACTTGAGAAAGCTGAAAAGGATTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgatcttcattttcattatcttactggcattaccatatttgaatttcttaataagGATGAGTAAATACAATAAAGTGGAAATACTTGAGAAAGCTGAAAAGGATTTAGCAGCTGTGACAGATCAGTACATGTCACGACTAGTCAAAGAATTGCAG
                 atcttac  putative branch site (score: 3)
                                           tttctt  putative PPT
                                  atatttgaatttctta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aattctactctgattgttaatgatttatagttacatacttacatgtgatcttcattttcattatcttactggcattaccatatttgaatttcttaataagGATGAGTAAATACAATAAAGTGGAAATACTTGAGAAAGCTGAAAAGGATTTAGCAGCTGTGACAGATCAGTACATGTCACGACTAGTCAAAGAATTGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - -ctgattg
- - - - - - - - - - - - - - - -tacatac
- - - - - - - - - - - - - - - - - - - - acatgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cttactg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gcattac