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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aacagacgaatacaacccgtttgttttttttccctcgtgttctaattactctgttccaccgtctaatgctaactggctctttctcttttctttatagcagATCAAAGTTTGATCTTCTGATTATCAACTTGCATGGTGGGAAATCCCTCTTCCTGGGAAGTGTGGCAATGATGTAATCAGAATATATACTTTTTATGCCA

Basic information

species Glycine max
transcript GLYMA06G19940.1
intron # 4
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|58018233|gb|CX704975.1|CX704975
EST:     TTCAAGGGAGATTTCAGGCTCTGCCAGATCAGAGCTAGCTTGAAAAGCAG                         ATCAAAGTTTGATCTTCTGATTATCAACTTGCATGGTGGGAAATCCCTCTT
genomic: TTCAAGGGAGATTTCAGGCTCTGCCAGATCAGAGCTAGCTTGAAAAGCAGgttcgctttc ... tttatagcagATCAAAGTTTGATCTTCTGATTATCAACTTGCATGGTGGGAAATCCCTCTT
EST: gi|192321764|gb|FK013184.1|FK013184
EST:     ATTTCAGGCTCTGCCAGATCAGAGCTAGCTTGAAAAGCAG                         ATCAAGGTTTGATCTTCTGATTATCAACTTGCATGGTGGGAAATCCCTCTT
genomic: ATTTCAGGCTCTGCCAGATCAGAGCTAGCTTGAAAAGCAGgttcgctttc ... tttatagcagATCAAAGTTTGATCTTCTGATTATCAACTTGCATGGTGGGAAATCCCTCTT
EST: gi|57576007|gb|CX548978.1|CX548978
EST:     TTCAAGGGAGATTTCAGGCTCTGCCAGATCAGAGCTAGCTTGAAAAGCAG                         ATCAAAGTTTGATCTTCTGATTATCAACTTGCATGGTGGGAAATCCCTCTT
genomic: TTCAAGGGAGATTTCAGGCTCTGCCAGATCAGAGCTAGCTTGAAAAGCAGgttcgctttc ... tttatagcagATCAAAGTTTGATCTTCTGATTATCAACTTGCATGGTGGGAAATCCCTCTT
EST: gi|58021370|gb|CX708111.1|CX708111
EST:     TTCAAGGGAGATTTCAGGCTCTGCCAGATCAGAGCTAGCTTGAAAAGCAG                         ATCAAAGTTTGATCTTCTGATTATCAACTTGCATGGTGGGAAATCCCTCTT
genomic: TTCAAGGGAGATTTCAGGCTCTGCCAGATCAGAGCTAGCTTGAAAAGCAGgttcgctttc ... tttatagcagATCAAAGTTTGATCTTCTGATTATCAACTTGCATGGTGGGAAATCCCTCTT
EST: gi|192328733|gb|FK022533.1|FK022533
EST:     TTCAAGGGAGATTTCAGGCTCTGCCAGATCAGAGCTAGCTTGAAAAGCAG                         ATCAAAGTTTGATCTTCTGATTATCAACTTGCATGGTGGGAAATCCCTCTT
genomic: TTCAAGGGAGATTTCAGGCTCTGCCAGATCAGAGCTAGCTTGAAAAGCAGgttcgctttc ... tttatagcagATCAAAGTTTGATCTTCTGATTATCAACTTGCATGGTGGGAAATCCCTCTT
EST: gi|209723134|gb|BW662510.1|BW662510
EST:     TTCAAGGGAGATTTCAGGCTCTGCCAGATCAGAGCTAGCTTGAAAAGCAGCAG                       
genomic: TTCAAGGGAGATTTCAGGCTCTGCCAGATCAGAGCTAGCTTG-AAA--AGCAGgttcgctttc ... tttatagc


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttactctgttccaccgtctaatgctaactggctctttctcttttctttatagcagATCAAAGTTTGATCTTCTGATTATCAACTTGCATGGTGGGAAATCCCTCTTCCTGGGAAGTGTGGCAATGATGTAATCAGAATATATACTTTTTATGCCA
                     tgctaac  putative branch site (score: 1)
                           ctggctctttctcttt  CT-rich tract
                                        ttttctttata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aacagacgaatacaacccgtttgttttttttccctcgtgttctaattactctgttccaccgtctaatgctaactggctctttctcttttctttatagcagATCAAAGTTTGATCTTCTGATTATCAACTTGCATGGTGGGAAATCCCTCTTCCTGGGAAGTGTGGCAATGATGTAATCAGAATATATACTTTTTATGCCA

- - - - - -acaaccc
- - - - - - - - - - - - - - -ttccctc
- - - - - - - - - - - - - - - - - - - - - - - - - - -ttccacc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctaatgc