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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattaaagcaagaaacattatccactcagctttcattgtcattcctaaacagtctcgttccttccttttctgtaacattgaactgataaatatacaatgtctatattatcttccttttacagAAGACGGTTCTACTGACAAAGAAGCAAATG

Basic information

species Oryza sativa
transcript LOC_Os01g64000.1
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|25806940|gb|CA762901.1|CA762901
EST:     CTGAACTGAACTATCTCAAGCAGGAGAACGCTCGTCTCAAAGAGGCAGAG                         AAGACGGTTCTACTGACAAAGAAGCAAATG
genomic: CTGAACTGAACTATCTCAAGCAGGAGAACGCTCGTCTCAAAGAGGCAGAGgtattaaagc ... ccttttacagAAGACGGTTCTACTGACAAAGAAGCAAATG
EST: gi|86492277|gb|CI134910.1|CI134910
EST:     CTGAACTGAACTATCTCAAGCAGGAGAACGCTCGTCTCAAAGAGGCAGAG                         AAGACGGTTCTACTGACAAAGAAGCAAATG
genomic: CTGAACTGAACTATCTCAAGCAGGAGAACGCTCGTCTCAAAGAGGCAGAGgtattaaagc ... ccttttacagAAGACGGTTCTACTGACAAAGAAGCAAATG
EST: gi|5701698|gb|AU063505.2|AU063505
EST:     CTGAACTGAACTATCTCAAGCAGGAGAACGCTCGTCTCAAAGAGGCAGAG                         AAGACGGTTCTACTGACAAAGAAGCAAATG
genomic: CTGAACTGAACTATCTCAAGCAGGAGAACGCTCGTCTCAAAGAGGCAGAGgtattaaagc ... ccttttacagAAGACGGTTCTACTGACAAAGAAGCAAATG
EST: gi|86497616|gb|CI140249.1|CI140249
EST:     TGAACTGAACTATCTCAAGCCAGGAGAACGCTCGTCTCAAAGAGGCAGAG                         AAGACGGTTCTACTGACAAAGAAGCAAATG
genomic: TGAACTGAACTATCTCAAG-CAGGAGAACGCTCGTCTCAAAGAGGCAGAGgtattaaagc ... ccttttacagAAGACGGTTCTACTGACAAAGAAGCAAATG
EST: gi|88964713|gb|CI070059.1|CI070059
EST:     CTGAACTGAACTATCTCAAGCAGGAGAACGCTCGTCTCAAAGAGGCAGAG                         AAGACGGTTCTACTGACAAAGAAGCAAATG
genomic: CTGAACTGAACTATCTCAAGCAGGAGAACGCTCGTCTCAAAGAGGCAGAGgtattaaagc ... ccttttacagAAGACGGTTCTACTGACAAAGAAGCAAATG
EST: gi|89189330|gb|CI048869.1|CI048869
EST:     AAAGAGGCAGAG                         AAGACGGTTCTACTGACAAAGAAGCAAATG
genomic: AAAGAGGCAGAGgtattaaagc ... ccttttacagAAGACGGTTCTACTGACAAAGAAGCAAATG
EST: gi|27548974|gb|CA766860.2|CA766860
EST:     CTGAACTGAACTATCTCAAGCAGGAGAACGCTCGTCTCAAAGAGGCAGAG                         AAGACGGTTCTACTGACAAAGAAGCAAATG
genomic: CTGAACTGAACTATCTCAAGCAGGAGAACGCTCGTCTCAAAGAGGCAGAGgtattaaagc ... ccttttacagAAGACGGTTCTACTGACAAAGAAGCAAATG
EST: gi|86601832|gb|CI258508.1|CI258508
EST:     CTGAACTGAACTATCTCAAGCAGGAGAACGCTCGTCTCAAAGAGGCAGAG                         AAGACGGTTCTACTGACAAAGAAGCAAATG
genomic: CTGAACTGAACTATCTCAAGCAGGAGAACGCTCGTCTCAAAGAGGCAGAGgtattaaagc ... ccttttacagAAGACGGTTCTACTGACAAAGAAGCAAATG
EST: gi|88481991|gb|CI419262.1|CI419262
EST:     AGCAGGAGAACGCTCGTCTCAAAGAGGCAGAG                         AAGACGGTTCTACTGACAAAGAAGCAAATG
genomic: AGCAGGAGAACGCTCGTCTCAAAGAGGCAGAGgtattaaagc ... ccttttacagAAGACGGTTCTACTGACAAAGAAGCAAATG
EST: gi|88841546|gb|CI080802.1|CI080802
EST:     CTGAACTGAACTATCTCAAGCAGGAGAACGCTCGTCTCAAAGAGGCAGAG                         AAGACGGTTCTACTGACAAAGAAGCAAATG
genomic: CTGAACTGAACTATCTCAAGCAGGAGAACGCTCGTCTCAAAGAGGCAGAGgtattaaagc ... ccttttacagAAGACGGTTCTACTGACAAAGAAGCAAATG
EST: gi|9457318|gb|AU063339.2|AU063339
EST:     CTGAACTGAACTATCTCAAGCAGGAGAACGCTCGTCTCAAAGAGGCAGAG                         AAGACGGTTCTACTGACAAAGAAGCAAATG
genomic: CTGAACTGAACTATCTCAAGCAGGAGAACGCTCGTCTCAAAGAGGCAGAGgtattaaagc ... ccttttacagAAGACGGTTCTACTGACAAAGAAGCAAATG
EST: gi|88842196|gb|CI081452.1|CI081452
EST:     CTGAACTGAACTATCTCAAGCAGGAGAACGCTCGTCTCAAAGAGGCAGAG                         AAGACGGTTCTACTGACAAAGAAGCAAATG
genomic: CTGAACTGAACTATCTCAAGCAGGAGAACGCTCGTCTCAAAGAGGCAGAGgtattaaagc ... ccttttacagAAGACGGTTCTACTGACAAAGAAGCAAATG
EST: gi|8527686|gb|AU092501.1|AU092501
EST:     CTGAACTGAACTATCTCAAGCAGGAGAACGCTCGTCTCAAAGAGGCAGAG                         AAGACGGTTCTACTGACAAAGAAGCAAATG
genomic: CTGAACTGAACTATCTCAAGCAGGAGAACGCTCGTCTCAAAGAGGCAGAGgtattaaagc ... ccttttacagAAGACGGTTCTACTGACAAAGAAGCAAATG
EST: gi|8528101|gb|AU092916.1|AU092916
EST:     CTGAACTGAACTATCTCAAGCAGGAGAACGCTCGTCTCAAAGAGGCAGAG                         AAGACGGTTCTACTGACAAAGAAGCAAATG
genomic: CTGAACTGAACTATCTCAAGCAGGAGAACGCTCGTCTCAAAGAGGCAGAGgtattaaagc ... ccttttacagAAGACGGTTCTACTGACAAAGAAGCAAATG
EST: gi|86522773|gb|CI162979.1|CI162979
EST:     CTGAACTGAACTATCTCAAGCAGGAGAACGCTCGTCTCAAAGAGGCAGAG                         AAGACGGTTCTACTGACAAAGAAGCAAATG
genomic: CTGAACTGAACTATCTCAAGCAGGAGAACGCTCGTCTCAAAGAGGCAGAGgtattaaagc ... ccttttacagAAGACGGTTCTACTGACAAAGAAGCAAATG
EST: gi|8528266|gb|AU093081.1|AU093081
EST:     CTGAACTGAACTATCTCAAGCAGGAGAACGCTCGTCTCAAAGAGGCAGAG                         AAGACGGTTCTACTGACAAAGAAGCAAATG
genomic: CTGAACTGAACTATCTCAAGCAGGAGAACGCTCGTCTCAAAGAGGCAGAGgtattaaagc ... ccttttacagAAGACGGTTCTACTGACAAAGAAGCAAATG
EST: gi|86435385|gb|CI106618.1|CI106618
EST:     CTGAACTGAACTATCTCAAGCAGGAGAACGCTCGTCTCAAAGAGGCAGAG                         AAGACGGTTCTACTGACAAAGAAGCAAATG
genomic: CTGAACTGAACTATCTCAAGCAGGAGAACGCTCGTCTCAAAGAGGCAGAGgtattaaagc ... ccttttacagAAGACGGTTCTACTGACAAAGAAGCAAATG
EST: gi|87029252|gb|CI276520.1|CI276520
EST:     CTGAACTGAACTATCTCAAGCAGGAGAACGCTCGTCTCAAAGAGGCAGAG                         AAGACGGTTCTACTGACAAAGAAGCAAATG
genomic: CTGAACTGAACTATCTCAAGCAGGAGAACGCTCGTCTCAAAGAGGCAGAGgtattaaagc ... ccttttacagAAGACGGTTCTACTGACAAAGAAGCAAATG

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 72 (upstream exon), 30 (downstream exon)
Score: 15

GCTTATACGGTGGAGCTCGAAGCTGAACTGAACTATCTCAAGCAGGAGAACGCTCGTCTCAAAGAGGCAGAGgtattaaagc ... ccttttacagAAGACGGTTCTACTGACAAAGAAGCAAATG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttctgtaacattgaactgataaatatacaatgtctatattatcttccttttacagAAGACGGTTCTACTGACAAAGAAGCAAATG
             aactgat  putative branch site (score: 15)
                                    tattatcttcctttt  putative PPT
                  ataaatatacaatgtc  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtattaaagcaagaaacattatccactcagctttcattgtcattcctaaacagtctcgttccttccttttctgtaacattgaactgataaatatacaatgtctatattatcttccttttacagAAGACGGTTCTACTGACAAAGAAGCAAATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA