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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattttgcttcttactttttacatctcttcatctcctcagttaattatatgaatggcttctgctagctgtttggcaaaaataagcttatattataggattgataggaaacctcttgctgtacgcatcattaaacctctgaggatgtttaagttttgatctagtttggctccttccttctcagGGTTGTTATGTCTGCATCATTATAGGTTATTGTGAGGGAGGAGATAT

Basic information

species Glycine max
transcript GLYMA20G36690.1
intron # 4
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|14990832|gb|BI316505.1|BI316505
EST:     AATTAAGAAACCCATTCATTGGGGAGTACAAAGATTCATGGGTAGAAAAG                         GGTTGNTATGTCTGCATCATTATAGGTTATTGGGAAGGAGGAGATCT
genomic: AATTAAGAAACCCATTCATTGTGGAGTACAAAGATTCATGGGTAGAAAAGgtattttgct ... tccttctcagGGTTGTTATGTCTGCATCATTATAGGTTATTGTGAGGGAGGAGATAT
EST: gi|209702825|gb|BW660690.1|BW660690
EST:     AATTAAGAAACCCATTCATTGTGGAGTACAAAGATTCATGGGTAGAAAAG                         GGTTGTTATGTCTGCATCATTATAGGTTATTGTGAGGGAGGAGATAT
genomic: AATTAAGAAACCCATTCATTGTGGAGTACAAAGATTCATGGGTAGAAAAGgtattttgct ... tccttctcagGGTTGTTATGTCTGCATCATTATAGGTTATTGTGAGGGAGGAGATAT
EST: gi|193548153|gb|FK504810.1|FK504810
EST:     AATTAAGAAACCCATTCATTGTGGAGTACAAAGATTCATGGGTAGAAAAG                         GGTTGTTATGTCTGCATCATTATAGGTTATTGTGAGGGAGGAGATAT
genomic: AATTAAGAAACCCATTCATTGTGGAGTACAAAGATTCATGGGTAGAAAAGgtattttgct ... tccttctcagGGTTGTTATGTCTGCATCATTATAGGTTATTGTGAGGGAGGAGATAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attaaacctctgaggatgtttaagttttgatctagtttggctccttccttctcagGGTTGTTATGTCTGCATCATTATAGGTTATTGTGAGGGAGGAGATAT
                        ttttgat  putative branch site (score: 4)
                                   tttggctccttccttc  putative PPT
                  tttaagtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtattttgcttcttactttttacatctcttcatctcctcagttaattatatgaatggcttctgctagctgtttggcaaaaataagcttatattataggattgataggaaacctcttgctgtacgcatcattaaacctctgaggatgtttaagttttgatctagtttggctccttccttctcagGGTTGTTATGTCTGCATCATTATAGGTTATTGTGAGGGAGGAGATAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT