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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atgaggcctttatttattgccgattgccactgaatactttatgtagacaattaagtaactggactcgatcatctagacctcatgctattattattttcagATACATTCAAGAAAACTATTCTAAAATTCGCAATGTGGAGCGTGAGCTTGCAAATCTTTCACTGGAGATGAAACTTACAGCTGGGCCAAAAAAAGCAG

Basic information

species Glycine max
transcript GLYMA20G29280.1
intron # 2
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|6455809|gb|AW186492.1|AW186492
EST:     ATCATCGAAGCAGAACAGCTTCAATTGCAGAA                         ATACATTCAAGAAAACTATTCTAAAATTCGCAATGTGGAGCGTGAGCTTGC
genomic: ATCATCGAAGCAGAACAGCTTCAATTGCAGAAgtaacttctt ... ttattttcagATACATTCAAGAAAACTATTCTAAAATTCGCAATGTGGAGCGTGAGCTTGC
EST: gi|6727086|gb|AW311440.1|AW311440
EST:     ATCATCGAAGCAGAACAGCTTCAATTGCAGAA                         ATACATTCAAGAAAACTATTCTAAAATTCGCAATGTGGAGCGTGAGCTTGC
genomic: ATCATCGAAGCAGAACAGCTTCAATTGCAGAAgtaacttctt ... ttattttcagATACATTCAAGAAAACTATTCTAAAATTCGCAATGTGGAGCGTGAGCTTGC
EST: gi|298198667|gb|HO042030.1|HO042030
EST:     ATCATCGAAGCAGAACAGCTTCAATTGCAGAA                         ATACATTCAAGAAAACTATTCTAAAATTCGCAATGTGGAGCGTGAGCTTGC
genomic: ATCATCGAAGCAGAACAGCTTCAATTGCAGAAgtaacttctt ... ttattttcagATACATTCAAGAAAACTATTCTAAAATTCGCAATGTGGAGCGTGAGCTTGC
EST: gi|213618278|gb|DB973048.1|DB973048
EST:     ATCATCGAAGCAGAACAGCTTCAATTGCAGAA                         ATACATTCAAGAAAACTATTCTAAAATTCGCAATGTGGAGCGTGAGCTTGC
genomic: ATCATCGAAGCAGAACAGCTTCAATTGCAGAAgtaacttctt ... ttattttcagATACATTCAAGAAAACTATTCTAAAATTCGCAATGTGGAGCGTGAGCTTGC
EST: gi|7589567|gb|AW705338.1|AW705338
EST:     ATCATCGAAGCAGAACAGCTTCAATTGCAGAA                         ATACATTCAAGAAAACTATTCTAAAATTCGCAATGTGGAGCGTGAGCT
genomic: ATCATCGAAGCAGAACAGCTTCAATTGCAGAAgtaacttctt ... ttattttcagATACATTCAAGAAAACTATTCTAAAATTCGCAATGTGGAGCGTGAGCT
EST: gi|213602217|gb|DB958477.1|DB958477
EST:     ATCATCGAAGCAGAACAGCTTCAATTGCAGAA                         ATACATTCAAGAAAACTATTCTAAAATTCGCAATGTGGAGCGTGAGCTTGC
genomic: ATCATCGAAGCAGAACAGCTTCAATTGCAGAAgtaacttctt ... ttattttcagATACATTCAAGAAAACTATTCTAAAATTCGCAATGTGGAGCGTGAGCTTGC
EST: gi|151398262|gb|EV268140.1|EV268140
EST:     ATCATCGAAGCAGAACAGCTTCAATTGCAGAA                         ATACATTCAAGAAAACTATTCTAAAATTCGCAATGTGGAGCGTGAGCTTGC
genomic: ATCATCGAAGCAGAACAGCTTCAATTGCAGAAgtaacttctt ... ttattttcagATACATTCAAGAAAACTATTCTAAAATTCGCAATGTGGAGCGTGAGCTTGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gacaattaagtaactggactcgatcatctagacctcatgctattattattttcagATACATTCAAGAAAACTATTCTAAAATTCGCAATGTGGAGCGTGAGCTTGCAAATCTTTCACTGGAGATGAAACTTACAGCTGGGCCAAAAAAAGCAG
       aagtaac  putative branch site (score: 2)
                                             ttattttc  putative PPT
                                    atgctattattatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atgaggcctttatttattgccgattgccactgaatactttatgtagacaattaagtaactggactcgatcatctagacctcatgctattattattttcagATACATTCAAGAAAACTATTCTAAAATTCGCAATGTGGAGCGTGAGCTTGCAAATCTTTCACTGGAGATGAAACTTACAGCTGGGCCAAAAAAAGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
atgaggc
- - - - - - - tattgcc
- - - - - - - - - - - - tgccact
- - - - - - - - - - - - - - - - - - - -tatgtag
- - - - - - - - - - - - - - - - - - - - - - - - - - - gtaactg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tcatgct