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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatatccaagccctttttcatattaaattatgctatctgatgagtgatgataacttgaatatgtggcacttttaactctttacttttgctgctatgcagCCACCTCTAAAGACTCTTCCCAAGCAGATGGCTTAGCGTATGCCAGCAGCCGGGAGTATGGAAGTGCCTTCAATAATTCTTGGAATACATCAAATTCCAC

Basic information

species Oryza sativa
transcript LOC_Os01g68380.1
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|29644363|gb|CB649370.1|CB649370
EST:     GCAAAGTCAGGGTTACTCTGCAAACAATGATATCTTTGGTCGGTTCCGAG                         CCACCTCTAAAGACTCTTCCCAAGCAGATGGCTTAGCGTATGCCAGCAGCC
genomic: GCAAAGTCAGGGTTACTCTGCAAACAATGATATCTTTGGTCGGTTCCGAGgtatatccaa ... tgctatgcagCCACCTCTAAAGACTCTTCCCAAGCAGATGGCTTAGCGTATGCCAGCAGCC
EST: gi|29672334|gb|CB668609.1|CB668609
EST:     GCAAAGTCAGGGTTACTCTGCAAACAATGATATCTTTGGTCGGTTCCGAG                         CCACCTCTAAAGACTCTTCCCAAGCAGATGGCTTAGCGTATGCCAGCAGCC
genomic: GCAAAGTCAGGGTTACTCTGCAAACAATGATATCTTTGGTCGGTTCCGAGgtatatccaa ... tgctatgcagCCACCTCTAAAGACTCTTCCCAAGCAGATGGCTTAGCGTATGCCAGCAGCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgatgataacttgaatatgtggcacttttaactctttacttttgctgctatgcagCCACCTCTAAAGACTCTTCCCAAGCAGATGGCTTAGCGTATGCCAGCAGCCGGGAGTATGGAAGTGCCTTCAATAATTCTTGGAATACATCAAATTCCAC
                         ttttaac  putative branch site (score: 2)
                               ctctttacttttgct  CT-rich tract
                                  tttactttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatatccaagccctttttcatattaaattatgctatctgatgagtgatgataacttgaatatgtggcacttttaactctttacttttgctgctatgcagCCACCTCTAAAGACTCTTCCCAAGCAGATGGCTTAGCGTATGCCAGCAGCCGGGAGTATGGAAGTGCCTTCAATAATTCTTGGAATACATCAAATTCCAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG