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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttgatttgtttaccatgcatactttctttactgggagagaacatgggaacaagtttcttatgctaactttatgatttcttctcccccccctcccagCTGTATGGTGTGGAGCCAGCTGAAAGTCCAGTTTTGAATGGAGGACAGCCAG

Basic information

species Glycine max
transcript GLYMA20G37280.2
intron # 6
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|151409405|gb|EV279213.1|EV279213
EST:     CAATAGCAGGAGCTGGAAGATTCCTCAGGGAGAAAAACCCGGATATTAAG                         CTGTATGGTGTGGAGCCAGCTGAAAGTCCAGTTTTGAATGGAGGACAGCCA
genomic: CAATAGCAGGAGCTGGAAGATTCCTCAGGGAGAAAAACCCGGATATTAAGgttgatttgt ... cccctcccagCTGTATGGTGTGGAGCCAGCTGAAAGTCCAGTTTTGAATGGAGGACAGCCA
EST: gi|192297614|gb|FG989562.1|FG989562
EST:     CAATAGCAG-AGCTGGAAGATTCCTCAGG-AGAAAA-CCCGGATATTAAG                         CTGTATGGTGTGGAGCCAGCTGAAAGTCCAGTTTTGAATGGAGGA
genomic: CAATAGCAGGAGCTGGAAGATTCCTCAGGGAGAAAAACCCGGATATTAAGgttgatttgt ... cccctcccagCTGTATGGTGTGGAGCCAGCTGAAAGTCCAGTTTTGAATGGAGGA
EST: gi|254338389|gb|GR845639.1|GR845639
EST:     CAATAGCAGGAGCTGGAAGATTCCTCAGGGAGAAAAACCCGGATATTAAG                         CTGTATGGTGTGGAGCCAGCTGAAAGTCCAGTTTTGAATGGAGGACAGCCA
genomic: CAATAGCAGGAGCTGGAAGATTCCTCAGGGAGAAAAACCCGGATATTAAGgttgatttgt ... cccctcccagCTGTATGGTGTGGAGCCAGCTGAAAGTCCAGTTTTGAATGGAGGACAGCCA
EST: gi|254340199|gb|GR858324.1|GR858324
EST:     CAATAGCAGGAGCTGGAAGATTCCTCAGGGAGAAAAACCCGGATATTAAG                         CTGTATGGTGTGGAGCCAGCTGAAAGTCCAGTTTTGAATGGAGGACAGCCA
genomic: CAATAGCAGGAGCTGGAAGATTCCTCAGGGAGAAAAACCCGGATATTAAGgttgatttgt ... cccctcccagCTGTATGGTGTGGAGCCAGCTGAAAGTCCAGTTTTGAATGGAGGACAGCCA
EST: gi|254348058|gb|GR854307.1|GR854307
EST:     CAATAGCAGGAGCTGGAAGATTCCTCAGGGAGAAAAACCCGGATATTAAG                         CTGTATGGTGTGGAGCCAGCTGAAAGTCCAGTTTTGAATGGAGGACAGCCA
genomic: CAATAGCAGGAGCTGGAAGATTCCTCAGGGAGAAAAACCCGGATATTAAGgttgatttgt ... cccctcccagCTGTATGGTGTGGAGCCAGCTGAAAGTCCAGTTTTGAATGGAGGACAGCCA
EST: gi|254340198|gb|GR858323.1|GR858323
EST:     CAATAGCAGGAGCTGGAAGATTCCTCAGGGAGAAAAACCCGGATATTAAG                         CTGTATGGTGTGGAGCCAGCTGAAAGTCCAGTTTTGAATGGAGGACAGCCA
genomic: CAATAGCAGGAGCTGGAAGATTCCTCAGGGAGAAAAACCCGGATATTAAGgttgatttgt ... cccctcccagCTGTATGGTGTGGAGCCAGCTGAAAGTCCAGTTTTGAATGGAGGACAGCCA
EST: gi|308098448|gb|HO760189.1|HO760189
EST:     CAATAGCAGGAGCTGGAAGATTCCTCAGGGAGAAAAACCCGGATATTAAG                         CTGTATGGTGTGGAGCCAGCTGAAAGTCCAGTTTTGAATGGAGGACAGCCA
genomic: CAATAGCAGGAGCTGGAAGATTCCTCAGGGAGAAAAACCCGGATATTAAGgttgatttgt ... cccctcccagCTGTATGGTGTGGAGCCAGCTGAAAGTCCAGTTTTGAATGGAGGACAGCCA
EST: gi|254338246|gb|GR849771.1|GR849771
EST:     CAATAGCAGGAGCTGGAAGATTCCTCAGGGAGAAAAACCCGGATATTAAG                         CTGTATGGTGTGGAGCCAGCTGAAAGTCCAGTTTTGAATGGAGGACAGCCA
genomic: CAATAGCAGGAGCTGGAAGATTCCTCAGGGAGAAAAACCCGGATATTAAGgttgatttgt ... cccctcccagCTGTATGGTGTGGAGCCAGCTGAAAGTCCAGTTTTGAATGGAGGACAGCCA
EST: gi|208279577|gb|GE074134.1|GE074134
EST:     AGATTCCTCAGGGAGAAAAACCCGGATATTAAG                         CTGTATGGTGTGGAGCCAGCTGAAAGTCCAGTTTTGAATGGAGGACAGCCA
genomic: AGATTCCTCAGGGAGAAAAACCCGGATATTAAGgttgatttgt ... cccctcccagCTGTATGGTGTGGAGCCAGCTGAAAGTCCAGTTTTGAATGGAGGACAGCCA
EST: gi|5820065|gb|AI988271.1|AI988271
EST:     CTCAGGGAGAAAAACCCGGATATTAAG                         CTGTATGGTGTGGAGCCAGCTGAAAGTCCAGTTTTGAATGGAGGACAGCCA
genomic: CTCAGGGAGAAAAACCCGGATATTAAGgttgatttgt ... cccctcccagCTGTATGGTGTGGAGCCAGCTGAAAGTCCAGTTTTGAATGGAGGACAGCCA
EST: gi|58019268|gb|CX706010.1|CX706010
EST:     CAATAGCAGGAGCTGGAAGATTCCTCAGGGAGAAAAACCCGGATATTAAG                         CTGTATGGTGTGGAGCCAGCTGAAAGTCCAGTTTTGAATGGAGGACAGCCA
genomic: CAATAGCAGGAGCTGGAAGATTCCTCAGGGAGAAAAACCCGGATATTAAGgttgatttgt ... cccctcccagCTGTATGGTGTGGAGCCAGCTGAAAGTCCAGTTTTGAATGGAGGACAGCCA
EST: gi|58024841|gb|CX711582.1|CX711582
EST:     CAATAGCAGGAGCTGGAAGATTCCTCAGGGAGAAAAACCCGGATATTAAG                         CTGTATGGTGTGGAGCCAGCTGAAAGTCCAGTTTTGAATGGAGGACAGCCA
genomic: CAATAGCAGGAGCTGGAAGATTCCTCAGGGAGAAAAACCCGGATATTAAGgttgatttgt ... cccctcccagCTGTATGGTGTGGAGCCAGCTGAAAGTCCAGTTTTGAATGGAGGACAGCCA
EST: gi|58019608|gb|CX706350.1|CX706350
EST:     CAATAGCAGGAGCTGGAAGATTCCTCAGGGAGAAAAACCCGGATATTAAG                         CTGTATGGTGTGGAGCCAGCTGAAAGTCCAGTTTTGAATGGAGGACAGCCA
genomic: CAATAGCAGGAGCTGGAAGATTCCTCAGGGAGAAAAACCCGGATATTAAGgttgatttgt ... cccctcccagCTGTATGGTGTGGAGCCAGCTGAAAGTCCAGTTTTGAATGGAGGACAGCCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catgggaacaagtttcttatgctaactttatgatttcttctcccccccctcccagCTGTATGGTGTGGAGCCAGCTGAAAGTCCAGTTTTGAATGGAGGACAGCCAG
                   tgctaac  putative branch site (score: 1)
                         ctttatgatttcttct  CT-rich tract
                      taactttatgattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttgatttgtttaccatgcatactttctttactgggagagaacatgggaacaagtttcttatgctaactttatgatttcttctcccccccctcccagCTGTATGGTGTGGAGCCAGCTGAAAGTCCAGTTTTGAATGGAGGACAGCCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA