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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtctcgctcttccttaaccatagtagttggtatataggattttgaaatgtttatactattcataattttgcacatcttaactgcagATTATTCCTTTGCGGTAGACTGTGGTAGTAACAGATCTATCAGAGGCTCAGATAATACTATGTATGAATTGGATTTCACAGACCTTGGCAGCTCATCATA

Basic information

species Oryza sativa
transcript LOC_Os08g10320.3
intron # 15
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|29630668|gb|CB635677.1|CB635677
EST:     GCTAAACTGCCTCCAGAAAGACACTCCATGTTTACGAGGTTCTCCAAAAT                         ATTATTCCTTTGCGGTACACTGTGGTAGTAACAGATCTATCACAGGCTCAG
genomic: GCTAAACTGCCTCCAGAAAGACACTCCATGTTTACGAGGTTCTCCAGAATgtatgtctcg ... ttaactgcagATTATTCCTTTGCGGTAGACTGTGGTAGTAACAGATCTATCAGAGGCTCAG
EST: gi|29644124|gb|CB649131.1|CB649131
EST:     GCTAAACTGCCTCCAGAAAGACACTCCATGTTTACGAGGTTCTCCAGAAT                         ATTATTCCTTTGCGGTAGACTGTGGTAGTAACAGATCTATCAGAGGCTCAG
genomic: GCTAAACTGCCTCCAGAAAGACACTCCATGTTTACGAGGTTCTCCAGAATgtatgtctcg ... ttaactgcagATTATTCCTTTGCGGTAGACTGTGGTAGTAACAGATCTATCAGAGGCTCAG
EST: gi|88449939|gb|CI572070.1|CI572070
EST:     GCTAAACTGCCTCCAGAAAGACACTCCATGTTTACGAGGTTCTCCAGAAT                         ATTATTCCTTTGCGGTAGACTGTGGTAGTAACAGATCTATCAGAGGCTCAG
genomic: GCTAAACTGCCTCCAGAAAGACACTCCATGTTTACGAGGTTCTCCAGAATgtatgtctcg ... ttaactgcagATTATTCCTTTGCGGTAGACTGTGGTAGTAACAGATCTATCAGAGGCTCAG
EST: gi|58690195|gb|CK078882.1|CK078882
EST:     GCTAAACTGCCTCCAGAAAGACACTCCATGTTTACGAGGTTCTCCAGAAT                         ATTATTCCTTTGCGGTAGACTGTGGTAGTAACAGATCTATCAGAGGCTCAG
genomic: GCTAAACTGCCTCCAGAAAGACACTCCATGTTTACGAGGTTCTCCAGAATgtatgtctcg ... ttaactgcagATTATTCCTTTGCGGTAGACTGTGGTAGTAACAGATCTATCAGAGGCTCAG
EST: gi|88431028|gb|CI572018.1|CI572018
EST:     GCTAAACTGCCTCCAGAAAGACACTCCATGTTTACGAGGTTCTCCAGAAT                         ATTATTCCTTTGCGGTAGACTGTGGTAGTAACAGATCTATCAGAGGCTCAG
genomic: GCTAAACTGCCTCCAGAAAGACACTCCATGTTTACGAGGTTCTCCAGAATgtatgtctcg ... ttaactgcagATTATTCCTTTGCGGTAGACTGTGGTAGTAACAGATCTATCAGAGGCTCAG
EST: gi|29630383|gb|CB635392.1|CB635392
EST:     GCTAAACTGCCTCCAGAAAGACACTCCATGTTTACGAGGTTCTCCAGAAT                         ATTATTCCTTTGCGGTAGACTGTGGTAGTAACAGATCTATCAGAGGCTCAG
genomic: GCTAAACTGCCTCCAGAAAGACACTCCATGTTTACGAGGTTCTCCAGAATgtatgtctcg ... ttaactgcagATTATTCCTTTGCGGTAGACTGTGGTAGTAACAGATCTATCAGAGGCTCAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atataggattttgaaatgtttatactattcataattttgcacatcttaactgcagATTATTCCTTTGCGGTAGACTGTGGTAGTAACAGATCTATCAGAGGCTCAGATAATACTATGTATGAATTGGATTTCACAGACCTTGGCAGCTCATCATA
                                           tcttaac  putative branch site (score: 2)
       attttgaaatgtttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtctcgctcttccttaaccatagtagttggtatataggattttgaaatgtttatactattcataattttgcacatcttaactgcagATTATTCCTTTGCGGTAGACTGTGGTAGTAACAGATCTATCAGAGGCTCAGATAATACTATGTATGAATTGGATTTCACAGACCTTGGCAGCTCATCATA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA