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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttggtggttcatgtccacaataatttttctttactatgtctcagatgcccattctttgattaaaaaatatttttttaaactatcattttttgttctgaagGGTTTTGCTAGCGGAAGTCTAGATGCAGATGCCCAGCCTGTTCGTTTGTTTGTTGCTGATGGGGGTGAATTGCTGGTGGCACAAAGCTATGCAAAGAATC

Basic information

species Glycine max
transcript GLYMA04G08560.1
intron # 7
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|192306581|gb|FG996243.1|FG996243
EST:     TGCTAATAAGATCAAAAGCTTTGTTACCTTTCTTTGACAGTGCTTATCAG                         GGTTTTGCTAGCGGAAGTCTAGATGCAGATGCCCAGCCTGTTCGTTTGTTT
genomic: TGCTAATAAGATCAAAAGCTTTGTTACCTTTCTTTGACAGTGCTTATCAGgtaagctctc ... tgttctgaagGGTTTTGCTAGCGGAAGTCTAGATGCAGATGCCCAGCCTGTTCGTTTGTTT
EST: gi|14009070|gb|BG725683.1|BG725683
EST:     CTTTCTTTGACAGTGCTTATCAG                         GGTTTTGCTAGCGGAAGTCTANATGCAGATGCCCAGCCTGTTCGTTTGTTT
genomic: CTTTCTTTGACAGTGCTTATCAGgtaagctctc ... tgttctgaagGGTTTTGCTAGCGGAAGTCTAGATGCAGATGCCCAGCCTGTTCGTTTGTTT
EST: gi|254321007|gb|GR827456.1|GR827456
EST:     TGCTAATAAGATCAAAAGCTTTGTTACCTTTCTTTGACAGTGCTTATCAG                         GGTTTTGCTAGCGGAAGTCTAGATGCAGATGCCCAGCCTGTTCGTTTGTTT
genomic: TGCTAATAAGATCAAAAGCTTTGTTACCTTTCTTTGACAGTGCTTATCAGgtaagctctc ... tgttctgaagGGTTTTGCTAGCGGAAGTCTAGATGCAGATGCCCAGCCTGTTCGTTTGTTT
EST: gi|17022645|gb|BM093679.1|BM093679
EST:     TGCTAATAAGATCAAAAGCTTTGTTACCTTTCTTTGACAGTGCTTATCAG                         GGTTTTGCTAGCGGAAGTCTAGATGCAGATGCCCAGCCTGTTCGTTTGTTT
genomic: TGCTAATAAGATCAAAAGCTTTGTTACCTTTCTTTGACAGTGCTTATCAGgtaagctctc ... tgttctgaagGGTTTTGCTAGCGGAAGTCTAGATGCAGATGCCCAGCCTGTTCGTTTGTTT
EST: gi|192334120|gb|FK026277.1|FK026277
EST:     TAATAAGATCAAAAGCTTTGTTACCTTTCTTTGACAGTGCTTATCAG                         GGTTTTGCTAGCGGAAGTCTAGATGCAGATGCCCAGCCTGTTCGTTTGTTT
genomic: TAATAAGATCAAAAGCTTTGTTACCTTTCTTTGACAGTGCTTATCAGgtaagctctc ... tgttctgaagGGTTTTGCTAGCGGAAGTCTAGATGCAGATGCCCAGCCTGTTCGTTTGTTT
EST: gi|17153142|gb|BM143075.1|BM143075
EST:     TGCTAATAAGATCAAAAGCTTTGTTACCTTTCTTTGACAGTGCTTATCAG                         GGTTTTGCTAGCGGAAGTCTAGATGCAGATGCCCAGCCTGTTCGTTTGTTT
genomic: TGCTAATAAGATCAAAAGCTTTGTTACCTTTCTTTGACAGTGCTTATCAGgtaagctctc ... tgttctgaagGGTTTTGCTAGCGGAAGTCTAGATGCAGATGCCCAGCCTGTTCGTTTGTTT
EST: gi|17153235|gb|BM143168.1|BM143168
EST:     TGCTAATAAGATCAAAAGCTTTGTTACCTTTCTTTGACAGTGCTTATCAG                         GGTTTTGCTAGCGGAAGTCTAGATGCAGATGCCCAGCCTGTTCGTTTGTTT
genomic: TGCTAATAAGATCAAAAGCTTTGTTACCTTTCTTTGACAGTGCTTATCAGgtaagctctc ... tgttctgaagGGTTTTGCTAGCGGAAGTCTAGATGCAGATGCCCAGCCTGTTCGTTTGTTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcccattctttgattaaaaaatatttttttaaactatcattttttgttctgaagGGTTTTGCTAGCGGAAGTCTAGATGCAGATGCCCAGCCTGTTCGTTTGTTTGTTGCTGATGGGGGTGAATTGCTGGTGGCACAAAGCTATGCAAAGAATC
        ctttgat  putative branch site (score: 5)
                                     tcattttttgttct  putative PPT
     attctttgattaaaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttggtggttcatgtccacaataatttttctttactatgtctcagatgcccattctttgattaaaaaatatttttttaaactatcattttttgttctgaagGGTTTTGCTAGCGGAAGTCTAGATGCAGATGCCCAGCCTGTTCGTTTGTTTGTTGCTGATGGGGGTGAATTGCTGGTGGCACAAAGCTATGCAAAGAATC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
-tggtggt
- - - - -catgtcc
- - - - - - - - - - - - - - - - -ctatgtc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaaaat