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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgttgttgttgactttgtttatgctgtaatgtgggtaatggtctaatggctaatgatttttcatttaattttggtgtaacctggtaaatatgtttgcagaTTCCTTTGGCCCTAATTCGGGGAAGGGTTACCCATGTTGTGTGGCCTCCTCAAAGAATAGGAGCTGTCAAGAGTACTCCACCGCAACGATTATCTTCTTT

Basic information

species Glycine max
transcript GLYMA18G42910.1
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|207690690|gb|GD672468.1|GD672468
EST:     TGAAGGAGACAACACCGCTTCTAGCTTGGATTCAAATTCATTTGGACCAA                         TTCCTTTGGCCCTAATTCGGGGAAGGGTTACCC
genomic: TGAAGGAGACAACACCGCTTCTAGCTTGGATTCAAATTCATTTGGACCAGtaagttgcca ... tgtttgcagaTTCCTTTGGCCCTAATTCGGGGAAGGGTTACCC
EST: gi|192297913|gb|FG988369.1|FG988369
EST:     GAAGGAGACAACACCGCTTCTAGCTTGGATTCAAATTCATTTGGGACCAA                         TTCCTTTGGCCCTATTTCGGGGAAGGGTTACCCATGTTGTGTGGCCTCCT
genomic: GAAGGAGACAACACCGCTTCTAGCTTGGATTCAAATTCATTTGG-ACCAGtaagttgcca ... tgtttgcagaTTCCTTTGGCCCTAATTCGGGGAAGGGTTACCCATGTTGTGTGGCCTCCT
EST: gi|193660990|gb|FK603512.1|FK603512
EST:     ACAACACCGCTTCTAGCTTGGATTCAAATTCATTTGGACCAA                         TTCCTTTGGCCCTAATTCGGGGAAGGGGTTACCCATGTTGTGTGGCTTCCT
genomic: ACAACACCGCTTCTAGCTTGGATTCAAATTCATTTGGACCAGtaagttgcca ... tgtttgcagaTTCCTTTGGCCCTAATTCGGGGAA-GGGTTACCCATGTTGTGTGGCCTCCT
EST: gi|151410357|gb|EV280172.1|EV280172
EST:     TGAAGGAGACAACACCGCTTCTAGCTTGGATTCAAATTCATTTGGACCAA                         TTCCTTTGGCCCTAATTCGGGGAAGGGTTACCCATGTTGTGTGGCCTCCTC
genomic: TGAAGGAGACAACACCGCTTCTAGCTTGGATTCAAATTCATTTGGACCAGtaagttgcca ... tgtttgcagaTTCCTTTGGCCCTAATTCGGGGAAGGGTTACCCATGTTGTGTGGCCTCCTC
EST: gi|208208386|gb|GE004303.1|GE004303
EST:     AAGGAGACAACACCGCTTTCTTAGCTTGGATTCAAATTCATTTGGACCAA                         TTCCTTTGGCCCTAATTCGGGGAAGGGTTACCCATGTTGTGTGGCCTCCTC
genomic: AAGGAGACAACACCGC-TTC-TAGCTTGGATTCAAATTCATTTGGACCAGtaagttgcca ... tgtttgcagaTTCCTTTGGCCCTAATTCGGGGAAGGGTTACCCATGTTGTGTGGCCTCCTC
EST: gi|193719877|gb|FK650429.1|FK650429
EST:     TGAAGGAGACAACACCGCTTCTAGCTTGGATTCAAATTCATTTGGACCAA                         TTCCTTTGGCCCTAATTCGGGGGAAGGGTTACCCATGTTGTGTGGCCTCC
genomic: TGAAGGAGACAACACCGCTTCTAGCTTGGATTCAAATTCATTTGGACCAGtaagttgcca ... tgtttgcagaTTCCTTTGGCCCTAATTCGGGG-AAGGGTTACCCATGTTGTGTGGCCTCC
EST: gi|208040914|gb|GD843379.1|GD843379
EST:     TGAAGGAGACAACACCGCTTCTAGCTTGGATTCAAATTCATTTGGACCAA                         TTCCTTTGGCCCTAATTCGGGGAAGGGTTACCCATGTTGTGTGGCCTCCTC
genomic: TGAAGGAGACAACACCGCTTCTAGCTTGGATTCAAATTCATTTGGACCAGtaagttgcca ... tgtttgcagaTTCCTTTGGCCCTAATTCGGGGAAGGGTTACCCATGTTGTGTGGCCTCCTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atggctaatgatttttcatttaattttggtgtaacctggtaaatatgtttgcagaTTCCTTTGGCCCTAATTCGGGGAAGGGTTACCCATGTTGTGTGGCCTCCTCAAAGAATAGGAGCTGTCAAGAGTACTCCACCGCAACGATTATCTTCTTT
                            gtgtaac  putative branch site (score: 3)
     taatgatttttcattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgttgttgttgactttgtttatgctgtaatgtgggtaatggtctaatggctaatgatttttcatttaattttggtgtaacctggtaaatatgtttgcagaTTCCTTTGGCCCTAATTCGGGGAAGGGTTACCCATGTTGTGTGGCCTCCTCAAAGAATAGGAGCTGTCAAGAGTACTCCACCGCAACGATTATCTTCTTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - tgttgac
- - - - - - - - - - -tgctgta
- - - - - - - - - - - - - - -tgtgggt
- - - - - - - - - - - - - - - - - - - - - - - - gctaatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tttggtg