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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...catccagtttcatatattaatatttctggataatctgagtacctattttctaaacagttggagttatttgtaactgtagttttccttttctgttgtacagTCCTGCTTGCAAATGAGGAGCGTTTGCAGATGTGTTGAAGAACCAGCTCCTAGGGTCACGTCAAAGATTCTGTATTTAGTTGTTGAGTGATTGAGTTCAA

Basic information

species Glycine max
transcript GLYMA17G06020.1
intron # 8
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|13479651|gb|BG508994.1|BG508994
EST:     TGCAGGATCTCCTCTTGCAACCTTATAAAAATTT                         TCCTGCTTGCAAATGAGGAGCGTTTGCAGATGTGTTGAAGAACCAGCTCCT
genomic: TGCAGGATCTCCTCTTGCAACCTTATAAAAATTTgtacgtttca ... tgttgtacagTCCTGCTTGCAAATGAGGAGCGTTTGCAGATGTGTTGAAGAACCAGCTCCT
EST: gi|192334428|gb|FK024443.1|FK024443
EST:     CAGCTTACTTCTCGAATGCAGGATCTCCTCTTGCAACCTTATAAAAATTT                         TCCTGCTTGCAAATGAGGAGCGTTTGCAGATGTGTTGAAGAACCAGCTCCT
genomic: CAGCTTACTTCTCGAATGCAGGATCTCCTCTTGCAACCTTATAAAAATTTgtacgtttca ... tgttgtacagTCCTGCTTGCAAATGAGGAGCGTTTGCAGATGTGTTGAAGAACCAGCTCCT
EST: gi|58024620|gb|CX711361.1|CX711361
EST:     CAGCTTACTTCTCGAATGCAGGATCTCCTCTTGCAACCTTATAAAAATTT                         TCCTGCTTGCAAATGAGGAGCGTTTGCAGATGTGTTGAAGAACCAGCTCCT
genomic: CAGCTTACTTCTCGAATGCAGGATCTCCTCTTGCAACCTTATAAAAATTTgtacgtttca ... tgttgtacagTCCTGCTTGCAAATGAGGAGCGTTTGCAGATGTGTTGAAGAACCAGCTCCT
EST: gi|23052983|gb|BU577474.1|BU577474
EST:     CAGCTTACTTCTCGAATGCAGGATCTCCTCTTGCAACCTTATAAAAATTT                         TCCTGCTTGCAAATGAGGAGCGTTTGCAGATGTGTTGAAG
genomic: CAGCTTACTTCTCGAATGCAGGATCTCCTCTTGCAACCTTATAAAAATTTgtacgtttca ... tgttgtacagTCCTGCTTGCAAATGAGGAGCGTTTGCAGATGTGTTGAAG
EST: gi|58017683|gb|CX704425.1|CX704425
EST:     CAGCTTACTTCTCGAATGCAGGATCTCCTCTTGCAACCTTATAAAAATTT                         TCCTGCTTGCAAATGAGGAGCGTTTGCAGATGTGTTGAAGAACCAGCTCCT
genomic: CAGCTTACTTCTCGAATGCAGGATCTCCTCTTGCAACCTTATAAAAATTTgtacgtttca ... tgttgtacagTCCTGCTTGCAAATGAGGAGCGTTTGCAGATGTGTTGAAGAACCAGCTCCT
EST: gi|58023602|gb|CX710343.1|CX710343
EST:     CAGCTTACTTCTCGAATGCAGGATCTCCTCTTGCAACCTTATAAAAATTT                         TCCTGCTTGCAAATGAGGAGCGTTTGCAGATGTGTTGAAGAACCAGCTCCT
genomic: CAGCTTACTTCTCGAATGCAGGATCTCCTCTTGCAACCTTATAAAAATTTgtacgtttca ... tgttgtacagTCCTGCTTGCAAATGAGGAGCGTTTGCAGATGTGTTGAAGAACCAGCTCCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttctaaacagttggagttatttgtaactgtagttttccttttctgttgtacagTCCTGCTTGCAAATGAGGAGCGTTTGCAGATGTGTTGAAGAACCAGCTCCTAGGGTCACGTCAAAGATTCTGTATTTAGTTGTTGAGTGATTGAGTTCAA
                      ttgtaac  putative branch site (score: 2)
                                  ttttccttttctgttg  putative PPT
                  ttatttgtaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
catccagtttcatatattaatatttctggataatctgagtacctattttctaaacagttggagttatttgtaactgtagttttccttttctgttgtacagTCCTGCTTGCAAATGAGGAGCGTTTGCAGATGTGTTGAAGAACCAGCTCCTAGGGTCACGTCAAAGATTCTGTATTTAGTTGTTGAGTGATTGAGTTCAA

catccag
- - - - - - - - - - - tttctgg
- - - - - - - - - - - - - - - - - - - - - - - - -ctaaaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - gttggag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gtaactg