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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagcattgcgcaatagcagcatgtcaatggcgaaaattttcgtcaggaaggcaagtgtgatcaaggaaaacgaacccttttttaactccagttgcttgatcctgtaaacgctttacttttgtagGTCGGCGTGATCCCGGACCGCCCGCTGCCGGCGTCATTCCCCACGGATGAAGACGGCTTCTGCAGCTGCCTCAGGGACTCCAACTCTGCCTGCAATCTTA

Basic information

species Oryza sativa
transcript LOC_Os02g57060.1
intron # 10
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|89189576|gb|CI049115.1|CI049115
EST:     CTGTGACCGTTGCGCGCTATGAAACTCCCGCGCATACTGACATAGACAAG                         GTCGGCGTGATCCCGGACCGCCCGCTGCCGGCGTCATTCCCCACGGATGAA
genomic: CTGTGACCGTTGCGCGCTATGAAACTCCCGCGCATACTGACATAGACAAGgtgagcattg ... acttttgtagGTCGGCGTGATCCCGGACCGCCCGCTGCCGGCGTCATTCCCCACGGATGAA
EST: gi|29679050|gb|CB675325.1|CB675325
EST:     CTGTGACCGTTGCGCGCTATGAAACTCCCGCGCATACTGACATAGACAAG                         GTCGGCGTGATCCCGGACCGCCCGCTGCCGGCGTCATTCCCCACGGATGAA
genomic: CTGTGACCGTTGCGCGCTATGAAACTCCCGCGCATACTGACATAGACAAGgtgagcattg ... acttttgtagGTCGGCGTGATCCCGGACCGCCCGCTGCCGGCGTCATTCCCCACGGATGAA
EST: gi|88473812|gb|CI411083.1|CI411083
EST:     CGCTATGAAACTCCCGCGCATACTGACATAGACAAG                         GTCGGCGTGATCCCGGACCGCCCGCTGCCGGCGTCATTCCCCACGGATGAA
genomic: CGCTATGAAACTCCCGCGCATACTGACATAGACAAGgtgagcattg ... acttttgtagGTCGGCGTGATCCCGGACCGCCCGCTGCCGGCGTCATTCCCCACGGATGAA
EST: gi|86493848|gb|CI136481.1|CI136481
EST:     CTGTGACCGTTGCGCGCTATGAAACTCCCGCGCATACTGACATAGACAAG                         GTCGGCGTGATCCCGGACCGCCCGCTGCCGGCGTCATTCCCCACGGATGAA
genomic: CTGTGACCGTTGCGCGCTATGAAACTCCCGCGCATACTGACATAGACAAGgtgagcattg ... acttttgtagGTCGGCGTGATCCCGGACCGCCCGCTGCCGGCGTCATTCCCCACGGATGAA
EST: gi|88283032|gb|CI404478.1|CI404478
EST:     CTGTGACCGTTGCGCGCTATGAAACTCCCGCGCATACTGACATAGACAAG                         GTCGGCGTGATCCCGGACCGCCCGCTGCCGGCGTCATTCCCCACGGATGAA
genomic: CTGTGACCGTTGCGCGCTATGAAACTCCCGCGCATACTGACATAGACAAGgtgagcattg ... acttttgtagGTCGGCGTGATCCCGGACCGCCCGCTGCCGGCGTCATTCCCCACGGATGAA
EST: gi|88491804|gb|CI429076.1|CI429076
EST:     CTGTGACCGTTGCGCGCTATGAAACTCCCGCGCATACTGACATAGACAAG                         GTCGGCGTGATCCCGGACCGCCCGCTGCCGGCGTCATTCCCCACGGATGAA
genomic: CTGTGACCGTTGCGCGCTATGAAACTCCCGCGCATACTGACATAGACAAGgtgagcattg ... acttttgtagGTCGGCGTGATCCCGGACCGCCCGCTGCCGGCGTCATTCCCCACGGATGAA
EST: gi|29688368|gb|CB684643.1|CB684643
EST:     CTGTGACCGTTGCGCGCTATGAAACTCCCGCGCATACTGACATAGACAAG                         GTCGGCGTGATCCCGGACCGCCCGCTGCCGGCGTCATTCCCCACGGATGAA
genomic: CTGTGACCGTTGCGCGCTATGAAACTCCCGCGCATACTGACATAGACAAGgtgagcattg ... acttttgtagGTCGGCGTGATCCCGGACCGCCCGCTGCCGGCGTCATTCCCCACGGATGAA
EST: gi|88481076|gb|CI418347.1|CI418347
EST:     TGAAACTCCCGCGCATACTGACATAGACAAG                         GTCGGCGTGATCCCGGACCGCCCGCTGCCGGCGTCATTCCCCACGGATGAA
genomic: TGAAACTCCCGCGCATACTGACATAGACAAGgtgagcattg ... acttttgtagGTCGGCGTGATCCCGGACCGCCCGCTGCCGGCGTCATTCCCCACGGATGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acgaacccttttttaactccagttgcttgatcctgtaaacgctttacttttgtagGTCGGCGTGATCCCGGACCGCCCGCTGCCGGCGTCATTCCCCACGGATGAAGACGGCTTCTGCAGCTGCCTCAGGGACTCCAACTCTGCCTGCAATCTTA
                                         ctttactttt  CT-rich tract
        ttttttaact  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagcattgcgcaatagcagcatgtcaatggcgaaaattttcgtcaggaaggcaagtgtgatcaaggaaaacgaacccttttttaactccagttgcttgatcctgtaaacgctttacttttgtagGTCGGCGTGATCCCGGACCGCCCGCTGCCGGCGTCATTCCCCACGGATGAAGACGGCTTCTGCAGCTGCCTCAGGGACTCCAACTCTGCCTGCAATCTTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC