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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgagtcatggcgacgtcgtttacgaccctgtgaatttcagattgtacttaacgtgtttgtaatttgatcgcagGCGAAAGAGATCAGAAGACTCGCGGATAATATGGTGCAGCTTGGAAAGGAG

Basic information

species Glycine max
transcript GLYMA04G39250.1
intron # 2
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|26268298|gb|CA819361.1|CA819361
EST:     TGGTCTCGCAGTTGGTGAAGCACGAGCGCATCGAAACTACTGTCGCCAAG                         GCGAAAGAGATCAGAAGACTCGCGGATAATATGGTGCAGCTTGGAAAGGAG
genomic: TGGTCTCGCAGTTGGTGAAGCACGAGCGCATCGAAACTACTGTCGCCAAGgtacgagtca ... ttgatcgcagGCGAAAGAGATCAGAAGACTCGCGGATAATATGGTGCAGCTTGGAAAGGAG
EST: gi|298187006|gb|HO034155.1|HO034155
EST:     TGGTCTCGCAGTTGGTGAAGCACGAGCGCATCGAAACTACTGTCGCCAAG                         GCGAAAGAGATCAGAAGACTCGCGGATAATATGGTGCAGCTTGGAAAGGAG
genomic: TGGTCTCGCAGTTGGTGAAGCACGAGCGCATCGAAACTACTGTCGCCAAGgtacgagtca ... ttgatcgcagGCGAAAGAGATCAGAAGACTCGCGGATAATATGGTGCAGCTTGGAAAGGAG
EST: gi|192311623|gb|FK003106.1|FK003106
EST:     TGGTCTCGCAGTTGGTGAAGCACGAGCGCATCGAAACTACTGTCGCCAAG                         GCGAAAGAGATCAGAAGACTCGCGGATAATATGGTGCAGCTTGGAAAGGAG
genomic: TGGTCTCGCAGTTGGTGAAGCACGAGCGCATCGAAACTACTGTCGCCAAGgtacgagtca ... ttgatcgcagGCGAAAGAGATCAGAAGACTCGCGGATAATATGGTGCAGCTTGGAAAGGAG
EST: gi|192310244|gb|FK002600.1|FK002600
EST:     TGGTCTCGTAGTTGGTGAAGCACGAGCGCATCGAAACTACTGTCGCCAAG                         GCGAAAGAGATCAGAAGACTCGCGGATAATATGGTGCAGCTTGGAAAGGAG
genomic: TGGTCTCGCAGTTGGTGAAGCACGAGCGCATCGAAACTACTGTCGCCAAGgtacgagtca ... ttgatcgcagGCGAAAGAGATCAGAAGACTCGCGGATAATATGGTGCAGCTTGGAAAGGAG
EST: gi|192310245|gb|FK002601.1|FK002601
EST:     TGGTCTCGTAGTTGGTGAAGCACGAGCGCATCGAAACTACTGTCGCCAAG                         GCGAAAGAGATCAGAAGACTCGCGGATAATATGGTGCAGCTTGGAAAGGAG
genomic: TGGTCTCGCAGTTGGTGAAGCACGAGCGCATCGAAACTACTGTCGCCAAGgtacgagtca ... ttgatcgcagGCGAAAGAGATCAGAAGACTCGCGGATAATATGGTGCAGCTTGGAAAGGAG
EST: gi|192311622|gb|FK003105.1|FK003105
EST:     TGGTCTCGCAGTTGGTGAAGCACGAGCGCATCGAAACTACTGTCGCCAAG                         GCGAAAGAGATCAGAAGACTCGCGGATAATATGGTGCAGCTTGGAAAGGAG
genomic: TGGTCTCGCAGTTGGTGAAGCACGAGCGCATCGAAACTACTGTCGCCAAGgtacgagtca ... ttgatcgcagGCGAAAGAGATCAGAAGACTCGCGGATAATATGGTGCAGCTTGGAAAGGAG
EST: gi|7587908|gb|AW703714.1|AW703714
EST:     TGGTCTCGCAGTTGGTGAAGCACGAGCGCATCGAAACTACTGTCGCCAAG                         GCGAAAGAGATCAGAAGACTCGCGGATAATATGGTGCAGCTTGGAAAGGAG
genomic: TGGTCTCGCAGTTGGTGAAGCACGAGCGCATCGAAACTACTGTCGCCAAGgtacgagtca ... ttgatcgcagGCGAAAGAGATCAGAAGACTCGCGGATAATATGGTGCAGCTTGGAAAGGAG
EST: gi|298174461|gb|HO014606.1|HO014606
EST:     TGGTCTCGCAGTTGGTGAAGCACGAGCGCATCGAAACTACTGTCGCCAAG                         GCGAAAGAGATCAGAAGACTCGCGGATAATATGGTGCAGCTTGGAAAGGAG
genomic: TGGTCTCGCAGTTGGTGAAGCACGAGCGCATCGAAACTACTGTCGCCAAGgtacgagtca ... ttgatcgcagGCGAAAGAGATCAGAAGACTCGCGGATAATATGGTGCAGCTTGGAAAGGAG
EST: gi|23064422|gb|BU579195.1|BU579195
EST:     TGGTCTCGCAGTTGGTGAAGCACGAGCGCATCGAAACTACTGTCGCCAAG                         GCGAAAGAGATCAGAAGACTCGCGGATAATATGGTGCAGCTTGGAAAGGAG
genomic: TGGTCTCGCAGTTGGTGAAGCACGAGCGCATCGAAACTACTGTCGCCAAGgtacgagtca ... ttgatcgcagGCGAAAGAGATCAGAAGACTCGCGGATAATATGGTGCAGCTTGGAAAGGAG
EST: gi|298189819|gb|HO038222.1|HO038222
EST:     TGGTCTCGCAGTTGGTGAAGCACGAGCGCATCGAAACTACTGTCGCCAAG                         GCGAAAGAGATCAGAAGACTCGCGGATAATATGGTGCAGCTTGGAAAGGAG
genomic: TGGTCTCGCAGTTGGTGAAGCACGAGCGCATCGAAACTACTGTCGCCAAGgtacgagtca ... ttgatcgcagGCGAAAGAGATCAGAAGACTCGCGGATAATATGGTGCAGCTTGGAAAGGAG
EST: gi|14009072|gb|BG725667.1|BG725667
EST:     TGGTCTCGCAGTTGGTGAAGCACGAGCGCATCGAAACTACTGTCGCCAAG                         GCGAAAGAGATCAGAAGACTCGCGGATAATATGGTGCAGCTTGGAAAGGAG
genomic: TGGTCTCGCAGTTGGTGAAGCACGAGCGCATCGAAACTACTGTCGCCAAGgtacgagtca ... ttgatcgcagGCGAAAGAGATCAGAAGACTCGCGGATAATATGGTGCAGCTTGGAAAGGAG
EST: gi|16343728|gb|BI969323.1|BI969323
EST:     TGGTCTCGCAGTTGGTGAAGCACGAGCGCATCGAAACTACTGTCGCCAAG                         GCGAAAGAGATCAGAAGACTCGCGGATAATATGGTGCAGCTTGGAAAGGAG
genomic: TGGTCTCGCAGTTGGTGAAGCACGAGCGCATCGAAACTACTGTCGCCAAGgtacgagtca ... ttgatcgcagGCGAAAGAGATCAGAAGACTCGCGGATAATATGGTGCAGCTTGGAAAGGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttacgaccctgtgaatttcagattgtacttaacgtgtttgtaatttgatcgcagGCGAAAGAGATCAGAAGACTCGCGGATAATATGGTGCAGCTTGGAAAGGAG
                                     tttgtaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacgagtcatggcgacgtcgtttacgaccctgtgaatttcagattgtacttaacgtgtttgtaatttgatcgcagGCGAAAGAGATCAGAAGACTCGCGGATAATATGGTGCAGCTTGGAAAGGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG