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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTGTGCACGCGGCAGCCCCAGGAGACAGGAATTTTTGAAGAAATACGGCATTTTCCAGgttggcaaccatcaaatgttatgccttaaattgtaaaatttcttctttgcgcttgacatgaattactgctgtggcag

Basic information

species Oryza sativa
transcript LOC_Os08g44400.1
intron # 11
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|86899723|gb|CI327545.1|CI327545
EST:     GCGGCAGCCCCAGGAGACAGGAATTTTTGAAGAAATACGGCATTTTCCAG                         GCTCCTTATATCGAAGATCCTAACACAGGGGTCAAGATGTTCGAGAGCGCT
genomic: GCGGCAGCCCCAGGAGACAGGAATTTTTGAAGAAATACGGCATTTTCCAGgttggcaacc ... gctgtggcagGCTCCTTATATCGAAGATCCTAACACAGGGGTCAAGATGTTCGAGAGCGCT
EST: gi|55408882|gb|CV721258.1|CV721258
EST:     GCGGCAGCCCCAGGAGACAGGAATTTTTGAAGAAATACGGCATTTTCCAG                         GCTCCTNTATATCGAAGATCCTAACACAGGGGTCAAGATGTTCGAGAGCGC
genomic: GCGGCAGCCCCAGGAGACAGGAATTTTTGAAGAAATACGGCATTTTCCAGgttggcaacc ... gctgtggcagGCTCCT-TATATCGAAGATCCTAACACAGGGGTCAAGATGTTCGAGAGCGC
EST: gi|86834825|gb|CI345909.1|CI345909
EST:     GCGGCAGCCCCAGGAGACAGGAATTTTTGAAGAAATACGGCATTTTCCAG                         GCTCCTTATATCGAAGATCCTAACACAGGGGTCAAGATGTTCGAGAGCGCT
genomic: GCGGCAGCCCCAGGAGACAGGAATTTTTGAAGAAATACGGCATTTTCCAGgttggcaacc ... gctgtggcagGCTCCTTATATCGAAGATCCTAACACAGGGGTCAAGATGTTCGAGAGCGCT
EST: gi|313084043|gb|HO213826.1|HO213826
EST:     GCGGCAGCCCCAGGAGACAGGAATTTTTGAAGAAATACGGCATTTTCCAG                         GCTCCTTATATCGAAGATCCTAACACAGGGGTCAAGATGTTCGAGAGCGCT
genomic: GCGGCAGCCCCAGGAGACAGGAATTTTTGAAGAAATACGGCATTTTCCAGgttggcaacc ... gctgtggcagGCTCCTTATATCGAAGATCCTAACACAGGGGTCAAGATGTTCGAGAGCGCT
EST: gi|88449108|gb|CI560569.1|CI560569
EST:     GCGGCAGCCCCAGGAGACAGGAATTTTTGAAGAAATACGGCATTTTCCAG                         GCTCCTTATATCGAAGATCCTAACACAGGGGTCAAGATGTTCGAGAGCGCT
genomic: GCGGCAGCCCCAGGAGACAGGAATTTTTGAAGAAATACGGCATTTTCCAGgttggcaacc ... gctgtggcagGCTCCTTATATCGAAGATCCTAACACAGGGGTCAAGATGTTCGAGAGCGCT
EST: gi|88320401|gb|CI523144.1|CI523144
EST:     GAATTTTTGAAGAAATACGGCATTTTCCAG                         GCTCCTTATATCGAAGATCCTAACACAGGGGTCAAGATGTTCGAGAGCGCT
genomic: GAATTTTTGAAGAAATACGGCATTTTCCAGgttggcaacc ... gctgtggcagGCTCCTTATATCGAAGATCCTAACACAGGGGTCAAGATGTTCGAGAGCGCT
EST: gi|86872687|gb|CI341897.1|CI341897
EST:     GCGGCAGCCCCAGGAGACAGGAATTTTTGAAGAAATACGGCATTTTCCAG                         GCTCCTTATATCGAAGATCCTAACACAGGGGTCAAGATGTTCGAGAGCGCT
genomic: GCGGCAGCCCCAGGAGACAGGAATTTTTGAAGAAATACGGCATTTTCCAGgttggcaacc ... gctgtggcagGCTCCTTATATCGAAGATCCTAACACAGGGGTCAAGATGTTCGAGAGCGCT
EST: gi|88459668|gb|CI521928.1|CI521928
EST:     GCGGCAGCCCCAGGAGACATGAATTTTTGAAGAAATACGGCATTTTCCAG                         GCTCCTTATATCGAAGATCCTAACACAGGGGTCAAGATGTTCGAGAGCGCT
genomic: GCGGCAGCCCCAGGAGACAGGAATTTTTGAAGAAATACGGCATTTTCCAGgttggcaacc ... gctgtggcagGCTCCTTATATCGAAGATCCTAACACAGGGGTCAAGATGTTCGAGAGCGCT
EST: gi|86843061|gb|CI342256.1|CI342256
EST:     CCGGCAGCCCCAGGAGACAGGAATTTTTGAAGAAATACGGCATTTTCCAG                         GCTCCTTATATCGAAGATCCTAACACCAGGGGTCAAGATGTTCGAGAGCGC
genomic: GCGGCAGCCCCAGGAGACAGGAATTTTTGAAGAAATACGGCATTTTCCAGgttggcaacc ... gctgtggcagGCTCCTTATATCGAAGATCCTAACA-CAGGGGTCAAGATGTTCGAGAGCGC
EST: gi|33821435|gb|CF336529.1|CF336529
EST:     GCGGCAGCCCCAGGAGACAGGAATTTTTGAAGAAATACGGCATTTTCCAG                         GCTCCTTATATCGAAGATCCTAACACAGGGGTCAAGATGTTCGAGAGCGCT
genomic: GCGGCAGCCCCAGGAGACAGGAATTTTTGAAGAAATACGGCATTTTCCAGgttggcaacc ... gctgtggcagGCTCCTTATATCGAAGATCCTAACACAGGGGTCAAGATGTTCGAGAGCGCT
EST: gi|29687876|gb|CB684151.1|CB684151
EST:     GCGGCAGCCCCAGGAGACAGGAATTTTTGAAGAAATACGGCATTTTCCAG                         GCTCCTTATATCGAAGATCCTAACACAGGGGTCAAGATGTTCGAGAGCGCT
genomic: GCGGCAGCCCCAGGAGACAGGAATTTTTGAAGAAATACGGCATTTTCCAGgttggcaacc ... gctgtggcagGCTCCTTATATCGAAGATCCTAACACAGGGGTCAAGATGTTCGAGAGCGCT
EST: gi|58589659|gb|CF987967.1|CF987967
EST:     GCGGCAGCCCCAGGAGACAGGAATTTTTGAAGAAATACGGCATTTTCCAG                         GGCTCCTTATATCGAAGATCCTAACACAGGGGTCAAGATGTTCGAGAGCGC
genomic: GCGGCAGCCCCAGGAGACAGGAATTTTTGAAGAAATACGGCATTTTCCAGgttggcaacc ... gctgtggcagG-CTCCTTATATCGAAGATCCTAACACAGGGGTCAAGATGTTCGAGAGCGC
EST: gi|38478016|gb|CF962149.1|CF962149
EST:     GCGGCAGCCCCAGGAGACAGGAATTTTTGAAGAAATACGGCATTTTCCAG                         GCTCCTTATATCGAAGATCCTAACACAGGGGTCAAGATGTTCGAGAGCGCT
genomic: GCGGCAGCCCCAGGAGACAGGAATTTTTGAAGAAATACGGCATTTTCCAGgttggcaacc ... gctgtggcagGCTCCTTATATCGAAGATCCTAACACAGGGGTCAAGATGTTCGAGAGCGCT
EST: gi|58593409|gb|CF991717.1|CF991717
EST:     GCGGCAGCCCCAGGAGACAGGAATTTTTGAAGAAATACGGCATTTTCCAG                         GCTCCTTATATCGAAGATCCTAACACAGGGGTCAAGATGTT
genomic: GCGGCAGCCCCAGGAGACAGGAATTTTTGAAGAAATACGGCATTTTCCAGgttggcaacc ... gctgtggcagGCTCCTTATATCGAAGATCCTAACACAGGGGTCAAGATGTT
EST: gi|88527164|gb|CI455292.1|CI455292
EST:     AGACAGGAATTTTTGAAGAAATACGGCATTTTCCAG                         GCTCCTTATATCGAAGATCCTAACACAGGGGTCAAGATGTTCGAGAGCGCT
genomic: AGACAGGAATTTTTGAAGAAATACGGCATTTTCCAGgttggcaacc ... gctgtggcagGCTCCTTATATCGAAGATCCTAACACAGGGGTCAAGATGTTCGAGAGCGCT
EST: gi|38473795|gb|CF957927.1|CF957927
EST:     GCGGCAGCCCCAGGAGACAGGAATTTTTGAAGAAATACGGCATTTTCCAG                         GCTCCTTATATCGAAGATCCTAACACAGGGGTCAAGATGTTCGAGAGCGCT
genomic: GCGGCAGCCCCAGGAGACAGGAATTTTTGAAGAAATACGGCATTTTCCAGgttggcaacc ... gctgtggcagGCTCCTTATATCGAAGATCCTAACACAGGGGTCAAGATGTTCGAGAGCGCT
EST: gi|27577571|gb|CB000266.1|CB000266
EST:     GCGGCAGCCCCAGGAGACAGGAATTTTTGAAGAAATACGGCATTTTCCAG                         GCTCCTTATATCGAAGATCCTAACACAGGGGTCAAGATGTTCGAGAGCGCT
genomic: GCGGCAGCCCCAGGAGACAGGAATTTTTGAAGAAATACGGCATTTTCCAGgttggcaacc ... gctgtggcagGCTCCTTATATCGAAGATCCTAACACAGGGGTCAAGATGTTCGAGAGCGCT
EST: gi|88528036|gb|CI456238.1|CI456238
EST:     GCGGCAGCCCCAGGAGACAGGAATTTTTGAAGAAATACGGCATTTTGCAG                         GCTCCTTATATCGAAGATCCTAACACAGGGTTCAAGATGTTCGAGAGCGCT
genomic: GCGGCAGCCCCAGGAGACAGGAATTTTTGAAGAAATACGGCATTTTCCAGgttggcaacc ... gctgtggcagGCTCCTTATATCGAAGATCCTAACACAGGGGTCAAGATGTTCGAGAGCGCT
EST: gi|88996530|gb|CI260034.1|CI260034
EST:     GCGGCAGCCCCAGGAGACAGGAATTTTTGAAGAAATACGGCATTTTCCAG                         GCTCCTTATATCGAAGATCCTAACACAGGGGTCAAGATGTTCGAGAGCGCT
genomic: GCGGCAGCCCCAGGAGACAGGAATTTTTGAAGAAATACGGCATTTTCCAGgttggcaacc ... gctgtggcagGCTCCTTATATCGAAGATCCTAACACAGGGGTCAAGATGTTCGAGAGCGCT
EST: gi|27548923|gb|CA767585.2|CA767585
EST:     GCGGCAGCCCCAGGAGACAGGAATTTTTGAAGAAATACGGCATTTTCCAG                         GCTCCTTATATCGAAGATCCTAACACAGGGGTCAAGATGTTCGAGAGCGCT
genomic: GCGGCAGCCCCAGGAGACAGGAATTTTTGAAGAAATACGGCATTTTCCAGgttggcaacc ... gctgtggcagGCTCCTTATATCGAAGATCCTAACACAGGGGTCAAGATGTTCGAGAGCGCT
EST: gi|12623212|gb|AU173425.1|AU173425
EST:     GCGGCAGCCCCAGGAGACAGGAATTTTTGAAGAAATACGGCATTTTCCAG                         GCTCCTTATATCGAAGATCCTAACACAGGGGTCAAGATGTTCGAGAGCGCT
genomic: GCGGCAGCCCCAGGAGACAGGAATTTTTGAAGAAATACGGCATTTTCCAGgttggcaacc ... gctgtggcagGCTCCTTATATCGAAGATCCTAACACAGGGGTCAAGATGTTCGAGAGCGCT
EST: gi|29685102|gb|CB681377.1|CB681377
EST:     GCGGCAGCCCCAGGAGACAGGAATTTTTGAAGAAATACGGCATTTTCCAG                         GCTCCTTATATCGAAGATCCTAACACAGGGGTCAAGATGTTCGAGAGCGCT
genomic: GCGGCAGCCCCAGGAGACAGGAATTTTTGAAGAAATACGGCATTTTCCAGgttggcaacc ... gctgtggcagGCTCCTTATATCGAAGATCCTAACACAGGGGTCAAGATGTTCGAGAGCGCT
EST: gi|88993826|gb|CI112730.1|CI112730
EST:     GCGGCAGCCCCAGGAGACAGGAATTTTTGAAGAAATACGGCATTTTCCAG                         GCTCCTTATATCGAAGATCCTAACACAGGGGTCAAGATGTTCGAGAGCGCT
genomic: GCGGCAGCCCCAGGAGACAGGAATTTTTGAAGAAATACGGCATTTTCCAGgttggcaacc ... gctgtggcagGCTCCTTATATCGAAGATCCTAACACAGGGGTCAAGATGTTCGAGAGCGCT
EST: gi|88536787|gb|CI464575.1|CI464575
EST:     GCAGCCCCAGGAGACAGGAATTTTTGAAGAAATACGGCATTTTCCAG                         GCTCCTTATATCGAAGATCCTAACACAGGGGTCAAGATGTTCGAGAGCGCT
genomic: GCAGCCCCAGGAGACAGGAATTTTTGAAGAAATACGGCATTTTCCAGgttggcaacc ... gctgtggcagGCTCCTTATATCGAAGATCCTAACACAGGGGTCAAGATGTTCGAGAGCGCT
EST: gi|33823734|gb|CF337673.1|CF337673
EST:     GCGGCAGCCCCAGGAGACAGGAATTTTTGAAGAAATACGGCATTTTCCAG                         GCTCCTTATATCGAAGATCCTAACACAGGGGTCAAGATGTTCGAGAGCGCT
genomic: GCGGCAGCCCCAGGAGACAGGAATTTTTGAAGAAATACGGCATTTTCCAGgttggcaacc ... gctgtggcagGCTCCTTATATCGAAGATCCTAACACAGGGGTCAAGATGTTCGAGAGCGCT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTGTGCACGCGGCAGCCCCAGGAGACAGGAATTTTTGAAGAAATACGGCATTTTCCAGgttggcaaccatcaaatgttatgccttaaattgtaaaatttcttctttgcgcttgacatgaattactgctgtggcag

- - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - -  AAGAAA