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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggtttctcaactgcactctgcatgttttaagttatctttcttgacatagcaatgctttttttttttaaagtttacaactcaatgtgcatagcttctccagTGCAGGGCTACAGTGCTGTACTCCCTGAGAAGTTGCAAACTGGAAAGTGGAATGTGTACAG

Basic information

species Oryza sativa
transcript LOC_Os12g04990.1
intron # 1
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|88307649|gb|CI644685.1|CI644685
EST:     CGGCGGCGTTGACCTCGCCGCCAACCCCACCGCCGGCGAGTACGCGCACG                         TGCAGGGCTACAGTGCTGTACTCCCTGAGAAGTGGCAAACTGGAAAGTGGA
genomic: CGGCGGCGTTGACCTCGCCGCCAACCCCACCGCCGGCGAGTACGCGCACGgtacgtacga ... gcttctccagTGCAGGGCTACAGTGCTGTACTCCCTGAGAAGTTGCAAACTGGAAAGTGGA
EST: gi|58590036|gb|CF988344.1|CF988344
EST:     CGGCGGCGTTGACCTCGCCGCCAACCCCACCGCCGGCGAGTACGCGCACG                         TGCAGGGCTACAGTGCTGTACTCCCTGAGAAGTTGCAAACTGGAAAGTGGA
genomic: CGGCGGCGTTGACCTCGCCGCCAACCCCACCGCCGGCGAGTACGCGCACGgtacgtacga ... gcttctccagTGCAGGGCTACAGTGCTGTACTCCCTGAGAAGTTGCAAACTGGAAAGTGGA
EST: gi|88569586|gb|CI660761.1|CI660761
EST:     CGGCGGCGTNGACCTCGCCGCCAACCCCACCGCCGGCGAGTACGCGCACG                         TGCAGGGCTACAGTGCTGTANTCCCTGAGAAGTTGCAAACTGGAAAGTGGA
genomic: CGGCGGCGTTGACCTCGCCGCCAACCCCACCGCCGGCGAGTACGCGCACGgtacgtacga ... gcttctccagTGCAGGGCTACAGTGCTGTACTCCCTGAGAAGTTGCAAACTGGAAAGTGGA
EST: gi|29667939|gb|CB664214.1|CB664214
EST:     CGGCGGCGTTGACCTCGCCGCCAACCCCACCGCCGGCGAGTACGCGCACG                         TGCAGGGCTACAGTGCTGTACTCCCTGAGAAGTTGCAAACTGGAAAGTGGA
genomic: CGGCGGCGTTGACCTCGCCGCCAACCCCACCGCCGGCGAGTACGCGCACGgtacgtacga ... gcttctccagTGCAGGGCTACAGTGCTGTACTCCCTGAGAAGTTGCAAACTGGAAAGTGGA
EST: gi|88294822|gb|CI604694.1|CI604694
EST:     CGGCGGCGTTGACCTCGCCGCCAACCCCACCGCCGGCGAGTACGCGCACG                         TGCAGGGCTACAGTGCTGTACTCCCTGAGAAGTTGCAAACTGGAAAGTGGA
genomic: CGGCGGCGTTGACCTCGCCGCCAACCCCACCGCCGGCGAGTACGCGCACGgtacgtacga ... gcttctccagTGCAGGGCTACAGTGCTGTACTCCCTGAGAAGTTGCAAACTGGAAAGTGGA
EST: gi|87009029|gb|CI304972.1|CI304972
EST:     CGGCGGCGTTGACCTCGCCGCCAACCCCACCGCCGGCGAGTACGCGCACG                         TGCAGGGCTACAGTGCTGTACTCCCTGAGAAGTTGCAAACTGGAAAGTGGA
genomic: CGGCGGCGTTGACCTCGCCGCCAACCCCACCGCCGGCGAGTACGCGCACGgtacgtacga ... gcttctccagTGCAGGGCTACAGTGCTGTACTCCCTGAGAAGTTGCAAACTGGAAAGTGGA
EST: gi|88372758|gb|CI612686.1|CI612686
EST:     CGGCGGCGTTGACCTCGCCGCCAACCCCACCGCCGGCGAGTACGCGCACG                         TGCAGGGCTACAGTGCTGTACTCCCTGAGAAGTTGCAAACTGGAAAGTGGA
genomic: CGGCGGCGTTGACCTCGCCGCCAACCCCACCGCCGGCGAGTACGCGCACGgtacgtacga ... gcttctccagTGCAGGGCTACAGTGCTGTACTCCCTGAGAAGTTGCAAACTGGAAAGTGGA
EST: gi|88288563|gb|CI663352.1|CI663352
EST:     CGGCGGCGTTGACCTCGCCGCCAACCCCACCGCCGGCGAGTACGCGCACG                         TGCAGGGCTACAGTGCTGTACTCCCTGAGAAGTTGCAAACTGGAAAGTGGA
genomic: CGGCGGCGTTGACCTCGCCGCCAACCCCACCGCCGGCGAGTACGCGCACGgtacgtacga ... gcttctccagTGCAGGGCTACAGTGCTGTACTCCCTGAGAAGTTGCAAACTGGAAAGTGGA
EST: gi|29626657|gb|CB631668.1|CB631668
EST:     CGGCGGCGTTGACCTCGCCGCCAACCCCACCGCCGGCGAGTACGCGCACG                         TGCAGGGCTACAGTGCTGTACTCCCTGAGAAGTTGCAAACTGGAAAGTGGA
genomic: CGGCGGCGTTGACCTCGCCGCCAACCCCACCGCCGGCGAGTACGCGCACGgtacgtacga ... gcttctccagTGCAGGGCTACAGTGCTGTACTCCCTGAGAAGTTGCAAACTGGAAAGTGGA
EST: gi|29627108|gb|CB632119.1|CB632119
EST:     CGGCGGCGTTGACCTCGCCGCCAACCCCACCGCCGGCGAGTACGCGCACG                         TGCAGGGCTACAGTGCTGTACTCCCTGAGAAGTTGCAAACTGGAAAGTGGA
genomic: CGGCGGCGTTGACCTCGCCGCCAACCCCACCGCCGGCGAGTACGCGCACGgtacgtacga ... gcttctccagTGCAGGGCTACAGTGCTGTACTCCCTGAGAAGTTGCAAACTGGAAAGTGGA
EST: gi|29630786|gb|CB635795.1|CB635795
EST:     CGGCGGCGTTGACCTCGCCGCCAACCCCACCGCCGGCGAGTACGCGCACG                         TGCAGGGCTACAGTGCTGTACTCCCTGAGAAGTTGCAAACTGGAAAGTGGA
genomic: CGGCGGCGTTGACCTCGCCGCCAACCCCACCGCCGGCGAGTACGCGCACGgtacgtacga ... gcttctccagTGCAGGGCTACAGTGCTGTACTCCCTGAGAAGTTGCAAACTGGAAAGTGGA
EST: gi|29627343|gb|CB632354.1|CB632354
EST:     CGGCGGCGTTGACCTCGCCGCCAACCCCACCGCCGGCGAGTACGCGCACG                         TGCAGGGCTACAGTGCTGTACTCCCTGAGAAGTTGCAAACTGGAAAGTGGA
genomic: CGGCGGCGTTGACCTCGCCGCCAACCCCACCGCCGGCGAGTACGCGCACGgtacgtacga ... gcttctccagTGCAGGGCTACAGTGCTGTACTCCCTGAGAAGTTGCAAACTGGAAAGTGGA
EST: gi|58605691|gb|CK033724.1|CK033724
EST:     CGGCGGCGTTGACCTCGCCGCCAACCCCACCGCCGGCGAGTACGCGCACG                         TGCAGGGCTACAGTGCTGTACTCCCTGAGAAGTTGCAAACTGGAAAGTGGA
genomic: CGGCGGCGTTGACCTCGCCGCCAACCCCACCGCCGGCGAGTACGCGCACGgtacgtacga ... gcttctccagTGCAGGGCTACAGTGCTGTACTCCCTGAGAAGTTGCAAACTGGAAAGTGGA
EST: gi|29674287|gb|CB670562.1|CB670562
EST:     CGGCGGCGTTGACCTCGCCGCCAACCCCACCGCCGGCGAGTACGCGCA--                         --C-GGGCTACAGTGCTGTACTCCCTGAGAAGTTGCAAACTGGAAAGTGGA
genomic: CGGCGGCGTTGACCTCGCCGCCAACCCCACCGCCGGCGAGTACGCGCACGgtacgtacga ... gcttctccagTGCAGGGCTACAGTGCTGTACTCCCTGAGAAGTTGCAAACTGGAAAGTGGA
EST: gi|88574980|gb|CI666749.1|CI666749
EST:     CGGCGGCGTTGACCTCGCCGCCAACCCCACCGCCGGCGAGTACGCGCACG                         TGCAGGGCTACAGTGCTGTACTCCCTGAGAAGTTGCAAACTGGAAAGTGGA
genomic: CGGCGGCGTTGACCTCGCCGCCAACCCCACCGCCGGCGAGTACGCGCACGgtacgtacga ... gcttctccagTGCAGGGCTACAGTGCTGTACTCCCTGAGAAGTTGCAAACTGGAAAGTGGA
EST: gi|33801569|gb|CF326656.1|CF326656
EST:     CGGCGGCGTTGACCTCGCCGCCAACCCCACCGCCGGCGAGTACGCGCACG                         TGCAGGGCTACAGTGCTGTACTCCCTGAGAAGTTGCAAACTGGAAAGTGGA
genomic: CGGCGGCGTTGACCTCGCCGCCAACCCCACCGCCGGCGAGTACGCGCACGgtacgtacga ... gcttctccagTGCAGGGCTACAGTGCTGTACTCCCTGAGAAGTTGCAAACTGGAAAGTGGA
EST: gi|117224882|gb|CT845959.1|CT845959
EST:     CGGCGGCGTTGACCTCGCCGCCAACCCCACCGCCGGCGAGTACGCGCACG                         TGCAGGGCTACAGTGCTGTACTCCCTGAGAAGTTGCAAACTGGAAAGTGGA
genomic: CGGCGGCGTTGACCTCGCCGCCAACCCCACCGCCGGCGAGTACGCGCACGgtacgtacga ... gcttctccagTGCAGGGCTACAGTGCTGTACTCCCTGAGAAGTTGCAAACTGGAAAGTGGA
EST: gi|88356323|gb|CI652760.1|CI652760
EST:     CGGCGGCGTTGACCTCGCCGCCAACCCCACCGCCGGCGAGTACGCGCACG                         TGCAGGGCTACAGTGCTGTACTCCCTGAGAAGTTGCAAACTGGAAAGTGGA
genomic: CGGCGGCGTTGACCTCGCCGCCAACCCCACCGCCGGCGAGTACGCGCACGgtacgtacga ... gcttctccagTGCAGGGCTACAGTGCTGTACTCCCTGAGAAGTTGCAAACTGGAAAGTGGA
EST: gi|88307728|gb|CI644768.1|CI644768
EST:     CGGCGGCGTTGACCTCGCCGCCAACCCCACCGCCGGCGAGTACGCGCACG                         TGCAGGGCTACAGTGCTGTACTCCCTGAGAAGTTGCAAACTGGAAAGTGGA
genomic: CGGCGGCGTTGACCTCGCCGCCAACCCCACCGCCGGCGAGTACGCGCACGgtacgtacga ... gcttctccagTGCAGGGCTACAGTGCTGTACTCCCTGAGAAGTTGCAAACTGGAAAGTGGA

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: 64 (upstream exon), 69 (downstream exon)
Score: 31

CAGCGGCGGCTGCGCGCCGTCTCCGGCCACCTCCAGCCGCCGACGGAGTCCGGCGGCGTTGACCTCGCCGCCAACCCCACCGCCGGCGAGTACGCGCACGgtacgtacga ... gcttctccagTGCAGGGCTACAGTGCTGTACTCCCTGAGAAGTTGCAAACTGGAAAGTGGAATGTGTACAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atagcaatgctttttttttttaaagtttacaactcaatgtgcatagcttctccagTGCAGGGCTACAGTGCTGTACTCCCTGAGAAGTTGCAAACTGGAAAGTGGAATGTGTACAG
                                              cttctcc  CT-rich tract
          tttttttttttaaagt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggtttctcaactgcactctgcatgttttaagttatctttcttgacatagcaatgctttttttttttaaagtttacaactcaatgtgcatagcttctccagTGCAGGGCTACAGTGCTGTACTCCCTGAGAAGTTGCAAACTGGAAAGTGGAATGTGTACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA