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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aactggcaaattacctttgttgggtcacgcttagcggtttgatgattgattaaaaatagttctttcatgcacataagtgaattgaattattatgcctcagGACCTAGAATTGGCACTGAGGGAATCAACAGCAAAATGGAAGATTGTTGTTGGTCATCATGCCATTAGAAGTGTTGGGCATCATGGTGATACTCAAGAAC

Basic information

species Glycine max
transcript GLYMA08G06090.1
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|6502194|gb|AW203567.1|AW203567
EST:     ATTGGCGGGGCATTGGCCCACAAAAACCTTATATTACTAACTTACTCAAG                         GACCTAGAATTGGCACTGAGGGAATCAACAGCAAAATGGAAGATTGTTGTT
genomic: ATTGGCGGGGCATTGGCCCACAAAAACCTTATATTACTAACTTACTCAAGgtatgcatag ... tatgcctcagGACCTAGAATTGGCACTGAGGGAATCAACAGCAAAATGGAAGATTGTTGTT
EST: gi|16343572|gb|BI969167.1|BI969167
EST:     TTGGCGGGGCATTGGCCCACAAANNNCCTTATATTACTAACTTACTCAAG                         GACCTAGAATTGGCACTGAGGGAATCAACAGCAAAATGGAAGATTGTTGTT
genomic: TTGGCGGGGCATTGGCCCACAAA-AACCTTATATTACTAACTTACTCAAGgtatgcatag ... tatgcctcagGACCTAGAATTGGCACTGAGGGAATCAACAGCAAAATGGAAGATTGTTGTT
EST: gi|254331979|gb|GR843722.1|GR843722
EST:     ATTGGCGGGGCATTGGCCCACAAAAACCTTATATTACTAACTTACTCAAG                         GACCTAGAATTGGCACTGAGGGAATCAACAGCAAAATGGAAGATTGTTGTT
genomic: ATTGGCGGGGCATTGGCCCACAAAAACCTTATATTACTAACTTACTCAAGgtatgcatag ... tatgcctcagGACCTAGAATTGGCACTGAGGGAATCAACAGCAAAATGGAAGATTGTTGTT
EST: gi|31460751|gb|CD402779.1|CD402779
EST:     ATTGGCGGGGCATTGGCCCACGAAAACCTTATATTACTAACTTACTCAAG                         GACCTAGAATTGGCACTGAGGGAATCAACAGCCAAATGGAAGATTGTTGTT
genomic: ATTGGCGGGGCATTGGCCCACAAAAACCTTATATTACTAACTTACTCAAGgtatgcatag ... tatgcctcagGACCTAGAATTGGCACTGAGGGAATCAACAGCAAAATGGAAGATTGTTGTT
EST: gi|192331088|gb|FK020308.1|FK020308
EST:     ATTGGCGGGGCATTGGCCCACAAAAACCTTATATTACTAACTTACTCAAG                         GACCTAGAATTGGCACTGAGGGAATCAACAGCAAAATGGAAGATTGTTGTT
genomic: ATTGGCGGGGCATTGGCCCACAAAAACCTTATATTACTAACTTACTCAAGgtatgcatag ... tatgcctcagGACCTAGAATTGGCACTGAGGGAATCAACAGCAAAATGGAAGATTGTTGTT
EST: gi|254331980|gb|GR843723.1|GR843723
EST:     TTGGCGGGGCATTGGCCCCACAAAAACCTTATATTACTAACTTACTCAAG                         GACCTAGAATTGGCACTGAGGGAATCAACAGCAAAATGGAAGATTGTTGTT
genomic: TTGGCGGGGCATTGG-CCCACAAAAACCTTATATTACTAACTTACTCAAGgtatgcatag ... tatgcctcagGACCTAGAATTGGCACTGAGGGAATCAACAGCAAAATGGAAGATTGTTGTT
EST: gi|9258428|gb|BE346575.1|BE346575
EST:     ATTGGCGGGGCATTGGCCCACAAAAACCTTATATTACTAACTTACTCAAG                         GACCTAGAATTGGCACTGAGGGAATCAACAGCAAAATGGAAGATTGTTGTT
genomic: ATTGGCGGGGCATTGGCCCACAAAAACCTTATATTACTAACTTACTCAAGgtatgcatag ... tatgcctcagGACCTAGAATTGGCACTGAGGGAATCAACAGCAAAATGGAAGATTGTTGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgattaaaaatagttctttcatgcacataagtgaattgaattattatgcctcagGACCTAGAATTGGCACTGAGGGAATCAACAGCAAAATGGAAGATTGTTGTTGGTCATCATGCCATTAGAAGTGTTGGGCATCATGGTGATACTCAAGAAC
 gattgat  putative branch site (score: 4)
                           ataagtgaattgaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aactggcaaattacctttgttgggtcacgcttagcggtttgatgattgattaaaaatagttctttcatgcacataagtgaattgaattattatgcctcagGACCTAGAATTGGCACTGAGGGAATCAACAGCAAAATGGAAGATTGTTGTTGGTCATCATGCCATTAGAAGTGTTGGGCATCATGGTGATACTCAAGAAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC