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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCCGCCCACACTCCCCTTCTCCCTCAAGAAGCCGCCGCCCATGCCGGTGTACAAGGACCTGCACTTCAACCGCGACCTCTCCGCCACCAAGAAGCTGCAGgtaagcaaatcatcgaacagcttgcctacccccggggcgcgcctgaaatctatctggcccttctctgagatttgttgctcgccgaattcctctctttgtgcaag

Basic information

species Oryza sativa
transcript 13113.m00214
intron # 1
splice site 5'
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|58607174|gb|CK035207.1|CK035207
EST:     ACAAGGACCTGCACTTCAACCGCGACCTCTCCGCCACCAAGAAGCTGCAG                         GCCGGCGTGGACCTGGTGGCACGGCTGGTCGGGGTGACGCTGGGGCCCAAG
genomic: ACAAGGACCTGCACTTCAACCGCGACCTCTCCGCCACCAAGAAGCTGCAGgtaagcaaat ... tttgtgcaagGCCGGCGTGGACCTGGTGGCACGGCTGGTCGGGGTGACGCTGGGGCCCAAG
EST: gi|58696091|gb|CK084778.1|CK084778
EST:     ACAA-GA-CTGCACTTCAACCGCGA-CTCTCCGCCACCAAGAAGCTGCAG                         GCCGGCGTGGACCTGGTGGCACGGCTGGTCGGGGTGACGCTGGGGCCCAAG
genomic: ACAAGGACCTGCACTTCAACCGCGACCTCTCCGCCACCAAGAAGCTGCAGgtaagcaaat ... tttgtgcaagGCCGGCGTGGACCTGGTGGCACGGCTGGTCGGGGTGACGCTGGGGCCCAAG
EST: gi|58693133|gb|CK081820.1|CK081820
EST:     ACAAGGACCTGCACTTCAACCGCGACCTCTCCGCCACCAAGAAGCTGCAG                         GCCGGCGTGGACCTGGTGGCACGGCTGGTCGGGGTGACGCTGGGGCCCAAG
genomic: ACAAGGACCTGCACTTCAACCGCGACCTCTCCGCCACCAAGAAGCTGCAGgtaagcaaat ... tttgtgcaagGCCGGCGTGGACCTGGTGGCACGGCTGGTCGGGGTGACGCTGGGGCCCAAG
EST: gi|58695701|gb|CK084388.1|CK084388
EST:     ACAAGGACCTGCACTTCAACCGCGACCTCTCCGCCACCAAGAAGCTGCAG                         GCCGGCGTGGACCTGGTGGCACGGCTGGTCGGGGTGACGCTGGGGCCCAAG
genomic: ACAAGGACCTGCACTTCAACCGCGACCTCTCCGCCACCAAGAAGCTGCAGgtaagcaaat ... tttgtgcaagGCCGGCGTGGACCTGGTGGCACGGCTGGTCGGGGTGACGCTGGGGCCCAAG
EST: gi|29668478|gb|CB664753.1|CB664753
EST:     ACAAGGACCTGCACTTCAACCGCGACCTCTCCGCCACCAAGAAGCTGCAG                         GCCGGCGTGGACCTGGTGGCACGGCTGGTCGGGGTGACGCTGGGGCCCAAG
genomic: ACAAGGACCTGCACTTCAACCGCGACCTCTCCGCCACCAAGAAGCTGCAGgtaagcaaat ... tttgtgcaagGCCGGCGTGGACCTGGTGGCACGGCTGGTCGGGGTGACGCTGGGGCCCAAG
EST: gi|58612235|gb|CK039947.1|CK039947
EST:     ACAAGGACCTGCACTTCAACCGCGACCTCTCCGCCACCAAGAAGCTGCAG                         GCCGGCGTGGACCTGGTGGCACGGCTGGTCGGGGTGACGGTGGGGCCCAAG
genomic: ACAAGGACCTGCACTTCAACCGCGACCTCTCCGCCACCAAGAAGCTGCAGgtaagcaaat ... tttgtgcaagGCCGGCGTGGACCTGGTGGCACGGCTGGTCGGGGTGACGCTGGGGCCCAAG
EST: gi|29633815|gb|CB638824.1|CB638824
EST:     ACAAGGACCTGCACTTCAACCGCGACCTCTCCGCCACCAAGAAGCTGCAG                         GCCGGCGTGGACCTGGTGGCACGGCTGGTCGGGGTGACGCTGGGGCCCAAG
genomic: ACAAGGACCTGCACTTCAACCGCGACCTCTCCGCCACCAAGAAGCTGCAGgtaagcaaat ... tttgtgcaagGCCGGCGTGGACCTGGTGGCACGGCTGGTCGGGGTGACGCTGGGGCCCAAG
EST: gi|58612432|gb|CK040144.1|CK040144
EST:     ACAAGGACCTGCACTTCAACCGCGACCTCTCCGCCACCAAGAAGCTGCAG                         GCCGGCGTGGATCTGGTGGCACGGCTGGTCGGGGTGACGCTGGGGCCCAAG
genomic: ACAAGGACCTGCACTTCAACCGCGACCTCTCCGCCACCAAGAAGCTGCAGgtaagcaaat ... tttgtgcaagGCCGGCGTGGACCTGGTGGCACGGCTGGTCGGGGTGACGCTGGGGCCCAAG
EST: gi|29625035|gb|CB630046.1|CB630046
EST:     ACAAGGACCTGCACTTCAACCGCGACCTCTCCGCCACCAAGAAGCTGAAG                         GCCGGCGTGGACCTGGTGGCACGGCTGGTCGGGGTGACGCTGGGGCCCAAG
genomic: ACAAGGACCTGCACTTCAACCGCGACCTCTCCGCCACCAAGAAGCTGCAGgtaagcaaat ... tttgtgcaagGCCGGCGTGGACCTGGTGGCACGGCTGGTCGGGGTGACGCTGGGGCCCAAG
EST: gi|29665658|gb|CB661933.1|CB661933
EST:     ACAAGGACCTGCACTTCAACCGCGACCTCTCCGCCACCAAGAAGCTGCAG                         GCCGGCGTGGACCTGGTGGCACGGCTGGTCGGGGTGACGCTGGGGCCCAAG
genomic: ACAAGGACCTGCACTTCAACCGCGACCTCTCCGCCACCAAGAAGCTGCAGgtaagcaaat ... tttgtgcaagGCCGGCGTGGACCTGGTGGCACGGCTGGTCGGGGTGACGCTGGGGCCCAAG
EST: gi|29644239|gb|CB649246.1|CB649246
EST:     ACAAGGACCTGCACTTCAACCGCGACCTCTCCGCCACCAAGAAGCTGCAG                         GCCGGCGTGGACCTGGTGGCACGGCTGGTCGGGGTGACGCTGGGGCCCAAG
genomic: ACAAGGACCTGCACTTCAACCGCGACCTCTCCGCCACCAAGAAGCTGCAGgtaagcaaat ... tttgtgcaagGCCGGCGTGGACCTGGTGGCACGGCTGGTCGGGGTGACGCTGGGGCCCAAG
EST: gi|58688240|gb|CK076927.1|CK076927
EST:     ACAAGGACCTGCACTTCAACCGCGA-CTCTCCGCCACCAAGAAGCTGCAG                         GCCGGCGTGGACCTGGTGGCACGGCTGGTCGGGGTGACGCTGGGGCCCAAG
genomic: ACAAGGACCTGCACTTCAACCGCGACCTCTCCGCCACCAAGAAGCTGCAGgtaagcaaat ... tttgtgcaagGCCGGCGTGGACCTGGTGGCACGGCTGGTCGGGGTGACGCTGGGGCCCAAG
EST: gi|58689779|gb|CK078466.1|CK078466
EST:     CTCTCCGCCACCAAGAAGCTGCAG                         GCCGGCGTGGACCTGGTGGCACGGCTGGTCGGGGTGACGCTGGGGCCCAAG
genomic: CTCTCCGCCACCAAGAAGCTGCAGgtaagcaaat ... tttgtgcaagGCCGGCGTGGACCTGGTGGCACGGCTGGTCGGGGTGACGCTGGGGCCCAAG
EST: gi|58695960|gb|CK084647.1|CK084647
EST:     ACAAGGACCTGCACTTCAACCGCGACCTCTCCGCCACCAAGAAGCTGCAG                         GCCGGCGTGGACCTGGTGGCACGGCTGGTCGGGGTGACGCTGGGGCCCAAG
genomic: ACAAGGACCTGCACTTCAACCGCGACCTCTCCGCCACCAAGAAGCTGCAGgtaagcaaat ... tttgtgcaagGCCGGCGTGGACCTGGTGGCACGGCTGGTCGGGGTGACGCTGGGGCCCAAG
EST: gi|58605670|gb|CK033703.1|CK033703
EST:     ACAAGGACCTGCACTTCAACCGCGACCTCTCCGCCACCAAGAAGCTGCAG                         GCCGGCGTGGACCTGGTGGCACGGCTGGTCGGGGTGACGCTGGGGCCCAAG
genomic: ACAAGGACCTGCACTTCAACCGCGACCTCTCCGCCACCAAGAAGCTGCAGgtaagcaaat ... tttgtgcaagGCCGGCGTGGACCTGGTGGCACGGCTGGTCGGGGTGACGCTGGGGCCCAAG
EST: gi|58691857|gb|CK080544.1|CK080544
EST:     CGCGA-CTCTCCGCCACCAAGAAGCTGCAG                         GCCGGCGTGGACCTGGTGGCACGGCTGGTCGGGGTGACGCTGGGGCCCAAG
genomic: CGCGACCTCTCCGCCACCAAGAAGCTGCAGgtaagcaaat ... tttgtgcaagGCCGGCGTGGACCTGGTGGCACGGCTGGTCGGGGTGACGCTGGGGCCCAAG

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 73 (upstream exon), 68 (downstream exon)
Score: 13

GCCGCCCACACTCCCCTTCTCCCTCAAGAAGCCGCCGCCCATGCCGGTGTACAAGGACCTGCACTTCAACCGCGACCTCTCCGCCACCAAGAAGCTGCAGgtaagcaaat ... tttgtgcaagGCCGGCGTGGACCTGGTGGCACGGCTGGTCGGGGTGACGCTGGGGCCCAAGGGGAGGAACGTGGTGCTGAGCAACAAGTACGGCCCTCCCAAGATCGTCA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCCGCCCACACTCCCCTTCTCCCTCAAGAAGCCGCCGCCCATGCCGGTGTACAAGGACCTGCACTTCAACCGCGACCTCTCCGCCACCAAGAAGCTGCAGgtaagcaaatcatcgaacagcttgcctacccccggggcgcgcctgaaatctatctggcccttctctgagatttgttgctcgccgaattcctctctttgtgcaag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG