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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtctcttctctctactccaatttcactcgccattacttttattcgtttatattatagctcttgatgagtttaaacatgattttgtaatgttgagttgtttttttgtgtttgaagGAAGAGGTGCAGAGATCGAATCGGGAATGGGAATCGTACAAGGAGAAGATACAAGATAATGAGGAGAAAGTTAAACTTAATAAGCAATTGCCCTACCTCG

Basic information

species Glycine max
transcript GLYMA03G39500.1
intron # 1
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|209727631|gb|BW663793.1|BW663793
EST:     ACGTCGTCAGAGCCTCTCGTATTCTCGAAAACGATATTCGCATTCTCAAG                         GAAGAGGTGCAGAGATCGAATCGGGAATGGGAATCGTACAAGGAGAAGATA
genomic: ACGTCGTCAGAGCCTCTCGTATTCTCGAAAACGATATTCGCATTCTCAAGgtctcttctc ... gtgtttgaagGAAGAGGTGCAGAGATCGAATCGGGAATGGGAATCGTACAAGGAGAAGATA
EST: gi|23727048|gb|BU761539.1|BU761539
EST:     ACGTCGTCAGAGCCTCTCGTATTCTCGAAAACGATATTCGCATTCTCAAG                         GAAGAGGTGCAGAGATCGAATCGGGAATGGGAATCGTACAAGGAGAAGATA
genomic: ACGTCGTCAGAGCCTCTCGTATTCTCGAAAACGATATTCGCATTCTCAAGgtctcttctc ... gtgtttgaagGAAGAGGTGCAGAGATCGAATCGGGAATGGGAATCGTACAAGGAGAAGATA
EST: gi|209718165|gb|BW657811.1|BW657811
EST:     ACGTCGTCAGAGCCTCTCGTATTCTCGAAAACGATATTCGCATTCTCAAG                         GAAGAGGTGCAGAGATCGAATCGGGAATGGGAATCGTACAAGGAGAAGATA
genomic: ACGTCGTCAGAGCCTCTCGTATTCTCGAAAACGATATTCGCATTCTCAAGgtctcttctc ... gtgtttgaagGAAGAGGTGCAGAGATCGAATCGGGAATGGGAATCGTACAAGGAGAAGATA
EST: gi|298168340|gb|HO014515.1|HO014515
EST:     ACGTCGTCAGAGCCTCTCGTATTCTCGAAAACGATATTCGCATTCTCAAG                         GAAGAGGTGCAGAGATCGAATCGGGAATGGGAATCGTACAAGGAGAAGATA
genomic: ACGTCGTCAGAGCCTCTCGTATTCTCGAAAACGATATTCGCATTCTCAAGgtctcttctc ... gtgtttgaagGAAGAGGTGCAGAGATCGAATCGGGAATGGGAATCGTACAAGGAGAAGATA
EST: gi|17400340|gb|BM177122.1|BM177122
EST:     ACGTCGTCAGAGCCTCTCGTATTCTCGAAAACGATATTCGCATTCTCAAG                         GAAGAGGTGCAGAGATCGAATCGGGAATGGGAATCGTACAAGGAGAAGATA
genomic: ACGTCGTCAGAGCCTCTCGTATTCTCGAAAACGATATTCGCATTCTCAAGgtctcttctc ... gtgtttgaagGAAGAGGTGCAGAGATCGAATCGGGAATGGGAATCGTACAAGGAGAAGATA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttgatgagtttaaacatgattttgtaatgttgagttgtttttttgtgtttgaagGAAGAGGTGCAGAGATCGAATCGGGAATGGGAATCGTACAAGGAGAAGATACAAGATAATGAGGAGAAAGTTAAACTTAATAAGCAATTGCCCTACCTCG
 tcttgat  putative branch site (score: 4)
                                      tttttttgt  putative PPT
         tttaaacatgatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtctcttctctctactccaatttcactcgccattacttttattcgtttatattatagctcttgatgagtttaaacatgattttgtaatgttgagttgtttttttgtgtttgaagGAAGAGGTGCAGAGATCGAATCGGGAATGGGAATCGTACAAGGAGAAGATACAAGATAATGAGGAGAAAGTTAAACTTAATAAGCAATTGCCCTACCTCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA