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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agttccactgctctagtgatatatgtagtctgtagttttactatataaatcttttctacctatctctcttcatagtctgacatatactttcgttctgcagCATTCTCACGGGCCTCCTTTCATTCATG

Basic information

species Oryza sativa
transcript LOC_Os06g09330.1
intron # 6
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|87015788|gb|CI279540.1|CI279540
EST:     TTCATCCGGAATCTTGGAATCCTATGTGGTCTGTGGCAAG                         CATTCTCACGGGCCTCCTTTCATTCATG
genomic: TTCATCCGGAATCTTGGAATCCTATGTGGTCTGTGGCAAGgtatgtacaa ... cgttctgcagCATTCTCACGGGCCTCCTTTCATTCATG
EST: gi|87010686|gb|CI312378.1|CI312378
EST:     TTCATCCGGAATCTTGGAATCCTATGTGGTCTGTGGCAAG                         CATTCTCACGGGCCTCCTTTCATTCATG
genomic: TTCATCCGGAATCTTGGAATCCTATGTGGTCTGTGGCAAGgtatgtacaa ... cgttctgcagCATTCTCACGGGCCTCCTTTCATTCATG
EST: gi|86599367|gb|CI251325.1|CI251325
EST:     TTCATCCGGAATCTTGGAATCCTATGTGGTCTGTGGCAAG                         CATTCTCACGGGCCTCCTTTCATTCATG
genomic: TTCATCCGGAATCTTGGAATCCTATGTGGTCTGTGGCAAGgtatgtacaa ... cgttctgcagCATTCTCACGGGCCTCCTTTCATTCATG
EST: gi|86514651|gb|CI157284.1|CI157284
EST:     TTCATCCGGAATCTTGGAATCCTATGTGGTCTGTGGCAAG                         CATTCTCACGGGCCTCCTTTCATTCATG
genomic: TTCATCCGGAATCTTGGAATCCTATGTGGTCTGTGGCAAGgtatgtacaa ... cgttctgcagCATTCTCACGGGCCTCCTTTCATTCATG
EST: gi|86855623|gb|CI268950.1|CI268950
EST:     ATGTGGTCTGTGGCAAG                         CATTCTCACGGGCCTCCTTTCATTCATG
genomic: ATGTGGTCTGTGGCAAGgtatgtacaa ... cgttctgcagCATTCTCACGGGCCTCCTTTCATTCATG
EST: gi|87035496|gb|CI190118.1|CI190118
EST:     TTCATCCGGAATCTTGGAATCCTATGTGGTCTGTGGCAAG                         CATTCTCACGGGCCTCCTTTCATTCATG
genomic: TTCATCCGGAATCTTGGAATCCTATGTGGTCTGTGGCAAGgtatgtacaa ... cgttctgcagCATTCTCACGGGCCTCCTTTCATTCATG
EST: gi|88206366|gb|CI206215.1|CI206215
EST:     TTCATCCGGAATCTTGGAATCCTATGTGGTCTGTGGCAAG                         CATTCTCACGGGCCTCCTTTCATTCATG
genomic: TTCATCCGGAATCTTGGAATCCTATGTGGTCTGTGGCAAGgtatgtacaa ... cgttctgcagCATTCTCACGGGCCTCCTTTCATTCATG
EST: gi|86495662|gb|CI138295.1|CI138295
EST:     TTCATCCGGAATCTTGGAATCCTATGTGGTCTGTGGCAAG                         CATTCTCACGGGCCTCCTTTCATTCATG
genomic: TTCATCCGGAATCTTGGAATCCTATGTGGTCTGTGGCAAGgtatgtacaa ... cgttctgcagCATTCTCACGGGCCTCCTTTCATTCATG
EST: gi|8956608|gb|BE230283.1|BE230283
EST:     TTCATCCGGAATCTTGGAATCCTATGTGGTCTGTGGCAAG                         CATTCTCACGGGCCTCCTTTCATTCATG
genomic: TTCATCCGGAATCTTGGAATCCTATGTGGTCTGTGGCAAGgtatgtacaa ... cgttctgcagCATTCTCACGGGCCTCCTTTCATTCATG
EST: gi|87035120|gb|CI189743.1|CI189743
EST:     AGTGACTTTCATCCGGAATCTTGGAATCCTATGTGGTCTGTGGCAAG                         CATTCTCACGGGCCTCCTTTCATTCATG
genomic: AGTGACTTTCATCCGGAATCTTGGAATCCTATGTGGTCTGTGGCAAGgtatgtacaa ... cgttctgcagCATTCTCACGGGCCTCCTTTCATTCATG
EST: gi|7134934|gb|AU082746.1|AU082746
EST:     TTCATCCGGAATCTTGGAATCCTATGTGGTCTGTGGCAAG                         CATTCTCACGGGCCTCCTTTCATTCATG
genomic: TTCATCCGGAATCTTGGAATCCTATGTGGTCTGTGGCAAGgtatgtacaa ... cgttctgcagCATTCTCACGGGCCTCCTTTCATTCATG
EST: gi|218487817|gb|FG955497.1|FG955497
EST:     TTCATCCGGAATCTTGGAATCCTATGTGGTCTGTGGCAAG                         CATTCTCACGGGCCTCCTTTCATTCATG
genomic: TTCATCCGGAATCTTGGAATCCTATGTGGTCTGTGGCAAGgtatgtacaa ... cgttctgcagCATTCTCACGGGCCTCCTTTCATTCATG
EST: gi|218490255|gb|FG953556.1|FG953556
EST:     TTCATCCGGAATCTTGGAATCCTATGTGGTCTGTGGCAAG                         CATTCTCACGGGCCTCCTTTCATTCATG
genomic: TTCATCCGGAATCTTGGAATCCTATGTGGTCTGTGGCAAGgtatgtacaa ... cgttctgcagCATTCTCACGGGCCTCCTTTCATTCATG
EST: gi|218494998|gb|FG948724.1|FG948724
EST:     TTCATCCGGAATCTTGGAATCCTATGTGGTCTGTGGCAAG                         CATTCTCACGGGCCTCCTTTCATTCATG
genomic: TTCATCCGGAATCTTGGAATCCTATGTGGTCTGTGGCAAGgtatgtacaa ... cgttctgcagCATTCTCACGGGCCTCCTTTCATTCATG

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), 39 (downstream exon)
Score: 72

TTCATCCGGAATCTTGGAATCCTATGTGGTCTGTGGCAAGgtatgtacaa ... cgttctgcagCATTCTCACGGGCCTCCTTTCATTCATG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taaatcttttctacctatctctcttcatagtctgacatatactttcgttctgcagCATTCTCACGGGCCTCCTTTCATTCATG
                             gtctgac  putative branch site (score: 72)
                                         ctttcgttct  putative PPT
                                    atatacttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agttccactgctctagtgatatatgtagtctgtagttttactatataaatcttttctacctatctctcttcatagtctgacatatactttcgttctgcagCATTCTCACGGGCCTCCTTTCATTCATG

- - -cactgct
- - - - - - - - - - atatgta