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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctttacgcttttggaagacctagttctttgcctggtttcttgatttgaattatttgatgtaattttctccaggattgttaagttgaaattttcattacagGAAAACCTCCCCTCCCTGACACTCCTAACCCCCCTGAAGGGATTCGAGCTCGGATTGTGGTAGCTCTAACTGTCTTCTTTATGACGCTGTTTACTCTCTT

Basic information

species Glycine max
transcript GLYMA12G04460.1
intron # 11
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|193627598|gb|FK575288.1|FK575288
EST:     TGCTGCCTGGAAGAACCAAGCATCACTCCAGAGGTCTCAAACTTCAAAAG                         GAAAACCTCCCCTCCCTGACACTCCTAACCCCC-TGAAGGGATTCGAGCTC
genomic: TGCTGCCTGGAAGAACCAAGCATCACTCCAGAGGTCTCAAACTTCAAAAGgttaacaact ... ttcattacagGAAAACCTCCCCTCCCTGACACTCCTAACCCCCCTGAAGGGATTCGAGCTC
EST: gi|208161112|gb|GD961718.1|GD961718
EST:     TGCTGCCTGGAAGAACCAAGCATCACTCCAGAGGTCTCAAACTTCAAAAG                         GAAA-CCTCCCCTCCCTGACACTCC
genomic: TGCTGCCTGGAAGAACCAAGCATCACTCCAGAGGTCTCAAACTTCAAAAGgttaacaact ... ttcattacagGAAAACCTCCCCTCCCTGACACTCC
EST: gi|57575734|gb|CX548709.1|CX548709
EST:     TGCTGCCTGGAAGAACCAAGCATCACTCCAGAGGTCTCAAACTTCAAAAG                         GAAAACCTCCCCCTNCCTGACACTCCTAACCCCCCTGAAGGGATTCGAGCT
genomic: TGCTGCCTGGAAGAACCAAGCATCACTCCAGAGGTCTCAAACTTCAAAAGgttaacaact ... ttcattacagGAAAACCT-CCCCTCCCTGACACTCCTAACCCCCCTGAAGGGATTCGAGCT
EST: gi|193342761|gb|FK309037.1|FK309037
EST:     CTGCCTGGAAGAACCAAGCATCACTCCAGAGGTCTCAAACTTCAAAAG                         GAAAACCTCCCCTCCCTGACACTCCTAACCTCCCTGAAGGGATTCGAGCTC
genomic: CTGCCTGGAAGAACCAAGCATCACTCCAGAGGTCTCAAACTTCAAAAGgttaacaact ... ttcattacagGAAAACCTCCCCTCCCTGACACTCCTAACCCCCCTGAAGGGATTCGAGCTC
EST: gi|19053078|gb|BM731745.1|BM731745
EST:     TGCTGCCTGGAAGAACCAAGCATCACTCCAGAGGTCTCAAACTTCAAAAG                         GAAAACCTCCCCTCCCTGACACTCCTAACCCCCCTGAAGGGATTCGAGCTC
genomic: TGCTGCCTGGAAGAACCAAGCATCACTCCAGAGGTCTCAAACTTCAAAAGgttaacaact ... ttcattacagGAAAACCTCCCCTCCCTGACACTCCTAACCCCCCTGAAGGGATTCGAGCTC
EST: gi|193453091|gb|FK419007.1|FK419007
EST:     TGCTGCCTGGAAGAACCAAGCATCACTCCAGAGGTCTCAAACTTCAAAAG                         GAAAACCTCCCCTCCCTGACACTCCTAACCCCCCTGAAGGGATTCGAGCTC
genomic: TGCTGCCTGGAAGAACCAAGCATCACTCCAGAGGTCTCAAACTTCAAAAGgttaacaact ... ttcattacagGAAAACCTCCCCTCCCTGACACTCCTAACCCCCCTGAAGGGATTCGAGCTC
EST: gi|193419035|gb|FK382265.1|FK382265
EST:     TGCTGCCTGGAAGAACCAAGCATCACTCCAGAGGTCTCAAACTTCAAAAG                         GAAAACCTCCCCTCCCTGACACTCCTAACCCCCCTGAAGGGATTCGAGCT
genomic: TGCTGCCTGGAAGAACCAAGCATCACTCCAGAGGTCTCAAACTTCAAAAGgttaacaact ... ttcattacagGAAAACCTCCCCTCCCTGACACTCCTAACCCCCCTGAAGGGATTCGAGCT
EST: gi|57575553|gb|CX548528.1|CX548528
EST:     TGCTGCCTGGAAGAACCAAGCATCACTCCAGAGGTCTCAAACTTCAAAAG                         GAAAACCTCCCCTTCCTGACACTCCTAACCCCCCTGAAGGGATTCGAGCTC
genomic: TGCTGCCTGGAAGAACCAAGCATCACTCCAGAGGTCTCAAACTTCAAAAGgttaacaact ... ttcattacagGAAAACCTCCCCTCCCTGACACTCCTAACCCCCCTGAAGGGATTCGAGCTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgaattatttgatgtaattttctccaggattgttaagttgaaattttcattacagGAAAACCTCCCCTCCCTGACACTCCTAACCCCCCTGAAGGGATTCGAGCTCGGATTGTGGTAGCTCTAACTGTCTTCTTTATGACGCTGTTTACTCTCTT
      atttgat  putative branch site (score: 5)
 ttttcatt  putative PPT
 tatttgatgtaatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctttacgcttttggaagacctagttctttgcctggtttcttgatttgaattatttgatgtaattttctccaggattgttaagttgaaattttcattacagGAAAACCTCCCCTCCCTGACACTCCTAACCCCCCTGAAGGGATTCGAGCTCGGATTGTGGTAGCTCTAACTGTCTTCTTTATGACGCTGTTTACTCTCTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - gcttttg
- - - - - - - - - - - - -ctttgcc
- - - - - - - - - - - - - - - - - - - - tgatttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - tgatgta