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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tctttggcctcacaacaacttgaaattcatgtagtttgagaaattcttaatggtttaacctcatggaagacgaaattaacttagcttttgttcatgacagTTTGCCCATATTTGGTATTGGTTCATCACTGAATAGATGGACGCATGAGATAGCCAGCATTGGCACTAATGCATTGTGTCGCCGGGCAAGACAGGAACAG

Basic information

species Glycine max
transcript GLYMA06G09560.1
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|13312771|gb|BG406422.1|BG406422
EST:     GTCATANCCTGTCAAGTAATCCTCCACCAATTTTATTGTGTGTGTGATAG                         TTTGCCCATATTTGGTATTGGTTCATCACTGAATAGATGGACGCATGAGAT
genomic: GTCATA-CCTGTCAAGTAATCCTCCACCAATTTTATTGTGTGTGTGATAGgtatgacctg ... ttcatgacagTTTGCCCATATTTGGTATTGGTTCATCACTGAATAGATGGACGCATGAGAT
EST: gi|298198820|gb|HO042183.1|HO042183
EST:     TGTCATACCTGTCAAGTAATCCTCCACCAATTTTATTGTGTGTGTGATAG                         TTTGCCCATATTTGGTATTGGTTCATCACTGAATAGATGGACGCATGAGAT
genomic: TGTCATACCTGTCAAGTAATCCTCCACCAATTTTATTGTGTGTGTGATAGgtatgacctg ... ttcatgacagTTTGCCCATATTTGGTATTGGTTCATCACTGAATAGATGGACGCATGAGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttaatggtttaacctcatggaagacgaaattaacttagcttttgttcatgacagTTTGCCCATATTTGGTATTGGTTCATCACTGAATAGATGGACGCATGAGATAGCCAGCATTGGCACTAATGCATTGTGTCGCCGGGCAAGACAGGAACAG
                            aattaac  putative branch site (score: 2)
                                       cttttgttc  putative PPT
                           aaattaactta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tctttggcctcacaacaacttgaaattcatgtagtttgagaaattcttaatggtttaacctcatggaagacgaaattaacttagcttttgttcatgacagTTTGCCCATATTTGGTATTGGTTCATCACTGAATAGATGGACGCATGAGATAGCCAGCATTGGCACTAATGCATTGTGTCGCCGGGCAAGACAGGAACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - -cctcaca
- - - - - - - - - - - - - tcatgta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -catggaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gaaattaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gcttttg