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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AACGCCCAAGCTAGATTACATAACATGAATGCAGGATTCAGCCCACAGATCTTGGCGCAGAAGCTTTTGAAGCTCAATAATTCACGACAAAGTATAGAGAgtatccttccagagtgtgatcctacaactttctccatcattaacttagtgacgtcctttctaatgtggtttagcgtaattgtcgcatagctattgttctt...

Basic information

species Oryza sativa
transcript LOC_Os01g70060.1
intron # 2
splice site 5'
intron type U12 (go to U12 genes for details)

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|88390733|gb|CI610959.1|CI610959
EST:     CTTGGCGCAGAAGCTTTTGAAGCTCAATAATTCACGACAAAGTATAGAGA                         CTTTGTCACATTGGTGTGTCTTTCATTATCGACACTGCCGACAAGTTGTTG
genomic: CTTGGCGCAGAAGCTTTTGAAGCTCAATAATTCACGACAAAGTATAGAGAgtatccttcc ... aaaagaaaagCTTTGTCACATTGGTGTGTCTTTCATTATCGACACTGCCGACAAGTTGTTG
EST: gi|88401664|gb|CI588605.1|CI588605
EST:     CTTGGCGCAGAAGCTTTTGAAGCTCAATAATTCACGACAAAGTATAGAGA                         CTTTGTCACATTGGTGTGTCTTTCATTATCGACACTGCCGACAAGTTGTTG
genomic: CTTGGCGCAGAAGCTTTTGAAGCTCAATAATTCACGACAAAGTATAGAGAgtatccttcc ... aaaagaaaagCTTTGTCACATTGGTGTGTCTTTCATTATCGACACTGCCGACAAGTTGTTG
EST: gi|88694292|gb|CI738330.1|CI738330
EST:     CTTGGCGCAGAAGCTTTTGAAGCTCAATAATTCACGACAAAGTATAGAGA                         CTTTGTCACATTGGTGTGTCTTTCATTATCGACACTGCCGACAAGTTGTTG
genomic: CTTGGCGCAGAAGCTTTTGAAGCTCAATAATTCACGACAAAGTATAGAGAgtatccttcc ... aaaagaaaagCTTTGTCACATTGGTGTGTCTTTCATTATCGACACTGCCGACAAGTTGTTG
EST: gi|29638160|gb|CB643169.1|CB643169
EST:     CTTGGCGCAGAAGCTTTTGAAGCTCAATAATTCACGACAAAGTATAGAGA                         CTTTGTCACATTGGTGTGTCTTTCATTATCGACACTGCCGACAAGTTGTTG
genomic: CTTGGCGCAGAAGCTTTTGAAGCTCAATAATTCACGACAAAGTATAGAGAgtatccttcc ... aaaagaaaagCTTTGTCACATTGGTGTGTCTTTCATTATCGACACTGCCGACAAGTTGTTG
EST: gi|87008922|gb|CI304865.1|CI304865
EST:     CTTGGCGCAGAAGCTTTTGAAGCTCAATAATTCACGACAAAGTATAGAGA                         CTTTGTCACATTGGTGTGTCTTTCATTATCGACACTGCCGACAAGTTGTTG
genomic: CTTGGCGCAGAAGCTTTTGAAGCTCAATAATTCACGACAAAGTATAGAGAgtatccttcc ... aaaagaaaagCTTTGTCACATTGGTGTGTCTTTCATTATCGACACTGCCGACAAGTTGTTG
EST: gi|88312139|gb|CI580304.1|CI580304
EST:     CTTGGCGCAGAAGCTTTTGAAGCTCAATAATTCACGACAAAGTATAGAGA                         CTTTGTCACATTGGTGTGTCTTTCATTATCGACACTGCCGACAAGTTGTTG
genomic: CTTGGCGCAGAAGCTTTTGAAGCTCAATAATTCACGACAAAGTATAGAGAgtatccttcc ... aaaagaaaagCTTTGTCACATTGGTGTGTCTTTCATTATCGACACTGCCGACAAGTTGTTG
EST: gi|58612604|gb|CK040316.1|CK040316
EST:     CTTGGCGCAGAAGCTTTTGAAGCTCAATAATTCACGACAAAGTATAGAGA                         CTTTGTCACATTGGTGTGTCTTTCATTATCGACACTGCCGACAAGTTGTTG
genomic: CTTGGCGCAGAAGCTTTTGAAGCTCAATAATTCACGACAAAGTATAGAGAgtatccttcc ... aaaagaaaagCTTTGTCACATTGGTGTGTCTTTCATTATCGACACTGCCGACAAGTTGTTG
EST: gi|58671318|gb|CK060004.1|CK060004
EST:     CTTGGCGCAGAAGCTTTTGAAGCTCAATAATTCACGACAAAGTATAGAGA                         CTTTGTCACATTGGTGTGTCTTTCATTATCGACACTGCCGACAAGTTGTTG
genomic: CTTGGCGCAGAAGCTTTTGAAGCTCAATAATTCACGACAAAGTATAGAGAgtatccttcc ... aaaagaaaagCTTTGTCACATTGGTGTGTCTTTCATTATCGACACTGCCGACAAGTTGTTG
EST: gi|58659612|gb|CK048292.1|CK048292
EST:     CTTGGCGCAGAAGCTTTTGAAGCTCAATAATTCACGACAAAGTATAGAGA                         CTTTGTCACATTGGTGTGTCTTTCATTATCGACACTGCCGACAAGTTGTTG
genomic: CTTGGCGCAGAAGCTTTTGAAGCTCAATAATTCACGACAAAGTATAGAGAgtatccttcc ... aaaagaaaagCTTTGTCACATTGGTGTGTCTTTCATTATCGACACTGCCGACAAGTTGTTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AACGCCCAAGCTAGATTACATAACATGAATGCAGGATTCAGCCCACAGATCTTGGCGCAGAAGCTTTTGAAGCTCAATAATTCACGACAAAGTATAGAGAgtatccttccagagtgtgatcctacaactttctccatcattaacttagtgacgtcctttctaatgtggtttagcgtaattgtcgcatagctattgttctt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA