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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgtctttttttttgttatttatagaacaaaaactcttcttacttagcactgctcagagttctggtgaagtgcatctgactttgattttctgtcactgcagGCGTGACGACCGTCGGCATCGACGCTAGACACATGGTCGAGGGTTTTAGCATGAACCGGATCGTTTGGTGTTTCAATTCAGAGGTTCATGTGGGAAAGAT

Basic information

species Oryza sativa
transcript LOC_Os02g39300.1
intron # 12
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|88274911|gb|CI388369.1|CI388369
EST:     CGAAGGTCACGCTCCCCTAGGGACCGTTCCAGAGACTATGATCGATACGG                         GCGTGACGACCGTCGGCATCGACGCTAGACACATGGTCGAGGGTTTTAGCA
genomic: CGAAGGTCACGCTCCCCTAGGGACCGTTCCAGAGACTATGATCGATACGGgtatgcttac ... gtcactgcagGCGTGACGACCGTCGGCATCGACGCTAGACACATGGTCGAGGGTTTTAGCA
EST: gi|88486736|gb|CI424007.1|CI424007
EST:     CGAAGGTCACGCTCCCCTAGGGACCGTTCCAGAGACTATGATCGATACGG                         GCGTGACGACCGTCGGCATCGACGCTAGACACATGGTCGAGGGTTTTAGCA
genomic: CGAAGGTCACGCTCCCCTAGGGACCGTTCCAGAGACTATGATCGATACGGgtatgcttac ... gtcactgcagGCGTGACGACCGTCGGCATCGACGCTAGACACATGGTCGAGGGTTTTAGCA
EST: gi|15854643|gb|BI807455.1|BI807455
EST:     CGAAGGTCACGCTCCCCTAGGGACCGTTCCAGAGACTATGATCGATACGG                         GCGTGACGACCGTCGGCATCGACGCTAGACACATGGTCGAGGGTTTTAGCA
genomic: CGAAGGTCACGCTCCCCTAGGGACCGTTCCAGAGACTATGATCGATACGGgtatgcttac ... gtcactgcagGCGTGACGACCGTCGGCATCGACGCTAGACACATGGTCGAGGGTTTTAGCA
EST: gi|10931057|gb|AU161331.1|AU161331
EST:     CGAAGGTCACGCTCCCCTAGGGACCGTTCCAGAGACTATGATCGATACGG                         GCGTGACGACCGTCGGCATCGACGCTAGACACATGGTCGAGGGTTTTAGCA
genomic: CGAAGGTCACGCTCCCCTAGGGACCGTTCCAGAGACTATGATCGATACGGgtatgcttac ... gtcactgcagGCGTGACGACCGTCGGCATCGACGCTAGACACATGGTCGAGGGTTTTAGCA
EST: gi|29632666|gb|CB637675.1|CB637675
EST:     CGAAGGTCACGCTCCCCTAGGGACCGTTCCAGAGACTATGATCGATACGG                         GCGTGACGACCGTCGGCATTGACGCTAGACACATGGTCGAGGGTTTTAGCA
genomic: CGAAGGTCACGCTCCCCTAGGGACCGTTCCAGAGACTATGATCGATACGGgtatgcttac ... gtcactgcagGCGTGACGACCGTCGGCATCGACGCTAGACACATGGTCGAGGGTTTTAGCA
EST: gi|29666474|gb|CB662749.1|CB662749
EST:     CGAAGGTCACGCTCCCCTAGGGACCGTTCCAGAGACTATGATCGATACGG                         GCGTGACGACCGTCGGCATCGACGCTAGACACATGGTCGAGGGTTTTAGCA
genomic: CGAAGGTCACGCTCCCCTAGGGACCGTTCCAGAGACTATGATCGATACGGgtatgcttac ... gtcactgcagGCGTGACGACCGTCGGCATCGACGCTAGACACATGGTCGAGGGTTTTAGCA
EST: gi|29673663|gb|CB669938.1|CB669938
EST:     CGAAGGTCACGCTCCCCTAGGGACCGTTCCAGAGACTATGATCGATACGG                         GCGTGACGACCGTCGGCATCGACGCTAGACACATGGTCGAGGGTTTTAGCA
genomic: CGAAGGTCACGCTCCCCTAGGGACCGTTCCAGAGACTATGATCGATACGGgtatgcttac ... gtcactgcagGCGTGACGACCGTCGGCATCGACGCTAGACACATGGTCGAGGGTTTTAGCA
EST: gi|29666475|gb|CB662750.1|CB662750
EST:     CGAAGGTCACGCTCCCCTAGGGACCGTTCCAGAGACTATGATCGATACGG                         GCGTGACGACCGTCGGCATTGACGCTAGACACATGGTTGAGGGTTTTAGCA
genomic: CGAAGGTCACGCTCCCCTAGGGACCGTTCCAGAGACTATGATCGATACGGgtatgcttac ... gtcactgcagGCGTGACGACCGTCGGCATCGACGCTAGACACATGGTCGAGGGTTTTAGCA
EST: gi|89188687|gb|CI115936.1|CI115936
EST:     CGAAGGTCACGCTCCCCTAGGGACCGTTCCAGAGACTATGATCGATACGG                         GCGTGACGACCGTCGGCATCGACGCTAGACACATGGTCGAGGGTTTTAGCA
genomic: CGAAGGTCACGCTCCCCTAGGGACCGTTCCAGAGACTATGATCGATACGGgtatgcttac ... gtcactgcagGCGTGACGACCGTCGGCATCGACGCTAGACACATGGTCGAGGGTTTTAGCA
EST: gi|88274571|gb|CI394977.1|CI394977
EST:     CGAAGGTCACGCTCCCCTAGGGACCGTTCCAGAGACTATGATCGATACGG                         GCGTGACGACCGTCGGCATCGACGCTAGACACATGGTCGAGGGTTTTAGCA
genomic: CGAAGGTCACGCTCCCCTAGGGACCGTTCCAGAGACTATGATCGATACGGgtatgcttac ... gtcactgcagGCGTGACGACCGTCGGCATCGACGCTAGACACATGGTCGAGGGTTTTAGCA
EST: gi|86601880|gb|CI258556.1|CI258556
EST:     CGAAGGTCACGCTCCCCTAGGGACCGTTCCAGAGACTATGATCGATACGG                         GCGTGACGACCGTCGGCATCGACGCTAGACACATGGTCGAGGGTTTTAGCA
genomic: CGAAGGTCACGCTCCCCTAGGGACCGTTCCAGAGACTATGATCGATACGGgtatgcttac ... gtcactgcagGCGTGACGACCGTCGGCATCGACGCTAGACACATGGTCGAGGGTTTTAGCA
EST: gi|86427884|gb|CI072981.1|CI072981
EST:     CGAAGGTCACGCTCCCCTAGGGACCGTTCCAGAGACTATGATCGATACGG                         GCGTGACGACCGTCGGCATCGACGCTAGACACATGGTCGAGGGTTTTAGCA
genomic: CGAAGGTCACGCTCCCCTAGGGACCGTTCCAGAGACTATGATCGATACGGgtatgcttac ... gtcactgcagGCGTGACGACCGTCGGCATCGACGCTAGACACATGGTCGAGGGTTTTAGCA
EST: gi|86889989|gb|CI319978.1|CI319978
EST:     CGAAGGTCACGCTCCCCTAGGGACCGTTCCAGAGACTATGATCGATACGG                         GCGTGACGACCGTCGGCATCGACGCTAGACACATGGTCGAGGGTTTTAGCA
genomic: CGAAGGTCACGCTCCCCTAGGGACCGTTCCAGAGACTATGATCGATACGGgtatgcttac ... gtcactgcagGCGTGACGACCGTCGGCATCGACGCTAGACACATGGTCGAGGGTTTTAGCA
EST: gi|218503772|gb|FG969027.1|FG969027
EST:     CGAAGGTCACGCTCCCCTAGGGACCGTTCCAGAGACTATGATCGATACGG                         GCGTGACGACCGTCGGCATCGACGCTAGACACATGGTCGAGGGTTTTAGCA
genomic: CGAAGGTCACGCTCCCCTAGGGACCGTTCCAGAGACTATGATCGATACGGgtatgcttac ... gtcactgcagGCGTGACGACCGTCGGCATCGACGCTAGACACATGGTCGAGGGTTTTAGCA

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: 75 (upstream exon), 75 (downstream exon)
Score: 17

ACAAGGACAGAGAATCAGGGAGATCCCATAGTTATGATTCAAGGGGCTACCGAAGGTCACGCTCCCCTAGGGACCGTTCCAGAGACTATGATCGATACGGgtatgcttac ... gtcactgcagGCGTGACGACCGTCGGCATCGACGCTAGACACATGGTCGAGGGTTTTAGCATGAACCGGATCGTTTGGTGTTTCAATTCAGAGGTTCATGTGGGAAAGAT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcactgctcagagttctggtgaagtgcatctgactttgattttctgtcactgcagGCGTGACGACCGTCGGCATCGACGCTAGACACATGGTCGAGGGTTTTAGCATGAACCGGATCGTTTGGTGTTTCAATTCAGAGGTTCATGTGGGAAAGAT
                                       ttttctgtc  CT-rich tract
                                  tttgatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgtctttttttttgttatttatagaacaaaaactcttcttacttagcactgctcagagttctggtgaagtgcatctgactttgattttctgtcactgcagGCGTGACGACCGTCGGCATCGACGCTAGACACATGGTCGAGGGTTTTAGCATGAACCGGATCGTTTGGTGTTTCAATTCAGAGGTTCATGTGGGAAAGAT

- - - - - - - - - - - -gaacaaa
- - - - - - - - - - - - - - - - - - - - - - - cactgct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctggtga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gtgcatc