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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgagcaatatgaaagcagctcattttaatttgtactccactttatttgattattttgcaatatgaaatattacttaaaactcattttatattctctatagATCTGGGGATTCTCGAGGCTTTGGTTTCTTATCTTTGGAGAAGGATGAGGATGCTGATGCAGCGATTCGTGCTTGTGATGAGACTGAGTGGAACGGTAGG

Basic information

species Oryza sativa
transcript LOC_Os01g26940.1
intron # 3
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|428681|gb|D24833.1|D24833
EST:     TTCTCTAAGTATGGGCGTGTGACAAGTGCACGTGTTGTTCGGGATAAAAG                         ATCTGGGGATTCTCGAGGCTTTGGTTTCTTATCTTTGGAG
genomic: TTCTCTAAGTATGGGCGTGTGACAAGTGCACGTGTTGTTCGGGATAAAAGgtaatttact ... ttctctatagATCTGGGGATTCTCGAGGCTTTGGTTTCTTATCTTTGGAG
EST: gi|29626575|gb|CB631586.1|CB631586
EST:     TTCTCTAAGTATGGGCGTGTGACAAGTGCACGTGTTGTTCGGGATAAAAG                         ATCTGGGGATTCTCGAGGCTTTGGTTTCTTATCTTTGGAGAAGGATGAGGA
genomic: TTCTCTAAGTATGGGCGTGTGACAAGTGCACGTGTTGTTCGGGATAAAAGgtaatttact ... ttctctatagATCTGGGGATTCTCGAGGCTTTGGTTTCTTATCTTTGGAGAAGGATGAGGA
EST: gi|29688129|gb|CB684404.1|CB684404
EST:     TTCTCTAAGTATGGGCGTGTGACAAGTGCACGTGTTGTTCGGGATAAAAG                         ATCTGGGGATTCTCGAGGCTTTGGTTTCTTATCTTTGGAGAAGGATGAGGA
genomic: TTCTCTAAGTATGGGCGTGTGACAAGTGCACGTGTTGTTCGGGATAAAAGgtaatttact ... ttctctatagATCTGGGGATTCTCGAGGCTTTGGTTTCTTATCTTTGGAGAAGGATGAGGA
EST: gi|428680|gb|D24832.1|D24832
EST:     TTCTCTAAGTATGGGCGTGTGACAAGTGCACGTGTTGTTCGGGATAAAAG                         ATCTGGGGATTCTCGAGGCTTTGGTTTCTTATCTTTGGAGAAGGATGAGGA
genomic: TTCTCTAAGTATGGGCGTGTGACAAGTGCACGTGTTGTTCGGGATAAAAGgtaatttact ... ttctctatagATCTGGGGATTCTCGAGGCTTTGGTTTCTTATCTTTGGAGAAGGATGAGGA
EST: gi|29686009|gb|CB682284.1|CB682284
EST:     TTCTCTAAGTATGGGCGTGTGACAAGTGCACGTGTTGTTCGGGATAAAAG                         ATCTGGGGATTCTCGAGGCTTTGGTTTCTTATCTTTGGAGAAGGATGAGGA
genomic: TTCTCTAAGTATGGGCGTGTGACAAGTGCACGTGTTGTTCGGGATAAAAGgtaatttact ... ttctctatagATCTGGGGATTCTCGAGGCTTTGGTTTCTTATCTTTGGAGAAGGATGAGGA
EST: gi|55431162|gb|CV728589.1|CV728589
EST:     TTCTCTAAGTATGGGCGTGTGACAAGTGCACGTGTTGTTCGGGATAAAAG                         ATCTGGGGATTCTCGAGGCTTTGGTTTCTTATCTTTGGAGAAGGATGAGGA
genomic: TTCTCTAAGTATGGGCGTGTGACAAGTGCACGTGTTGTTCGGGATAAAAGgtaatttact ... ttctctatagATCTGGGGATTCTCGAGGCTTTGGTTTCTTATCTTTGGAGAAGGATGAGGA
EST: gi|3767893|gb|AU031920.1|AU031920
EST:     TGACAAGTGCACGTGTTGTTCGGGATAAAAG                         ATCTGGGGATTCTCGAGGCTTTGGTTTCTTATCTTTGGAGAAGGNTGAGGN
genomic: TGACAAGTGCACGTGTTGTTCGGGATAAAAGgtaatttact ... ttctctatagATCTGGGGATTCTCGAGGCTTTGGTTTCTTATCTTTGGAGAAGGATGAGGA

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: 40 (upstream exon), 37 (downstream exon)
Score: 3

TTGTTGCAGGTTTTAGTTATGCCACCACTGAGCGAGATTTGGAAAAGAAATTCTCTAAGTATGGGCGTGTGACAAGTGCACGTGTTGTTCGGGATAAAAGgtaatttact ... ttctctatagATCTGGGGATTCTCGAGGCTTTGGTTTCTTATCTTTGGAGAAGGATGAGGATGCTGATGCAGCGATTCGTGCTTGTGATGAGACTGAGTGGAACGGTAGG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgattattttgcaatatgaaatattacttaaaactcattttatattctctatagATCTGGGGATTCTCGAGGCTTTGGTTTCTTATCTTTGGAGAAGGATGAGGATGCTGATGCAGCGATTCGTGCTTGTGATGAGACTGAGTGGAACGGTAGG
 atttgat  putative branch site (score: 3)
                                           tattctct  putative PPT
             aatatgaaatattact  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgagcaatatgaaagcagctcattttaatttgtactccactttatttgattattttgcaatatgaaatattacttaaaactcattttatattctctatagATCTGGGGATTCTCGAGGCTTTGGTTTCTTATCTTTGGAGAAGGATGAGGATGCTGATGCAGCGATTCGTGCTTGTGATGAGACTGAGTGGAACGGTAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- agcaata
- - - - - - aagcagc
- - - - - - - - - - - - - - - - - - - - - - - - - - ttttgca