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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gggaggcaacaacagtactagcatgttttgtaattttttagttaactacattttcttaaaagtaatttgtttaactggaacataatacctttttctgtagGTGGAGGTTCTGGAAGGACATAGAGGTGGACCTTGTCTTATGTTGACAACAAGCTATGGAGGATGACCTTGTTTTGGGGGCAAGACAAGGTCATCCTTTT

Basic information

species Oryza sativa
transcript LOC_Os01g29830.1
intron # 5
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|88570773|gb|CI662146.1|CI662146
EST:     ATCAGGGCAAACAAGAGGCCAGGTATCTCCCAATGCGGAG                         GTGGAGGTTCTGGAAG
genomic: ATCAGGGCAAACAAGAGGCCAGGTATCTCCCAATGCGGAGgtattttaca ... ttttctgtagGTGGAGGTTCTGGAAG
EST: gi|88991039|gb|CI108426.1|CI108426
EST:     ATCAGGGCAAACAAGAGGCCAGGTATCTCCCAATGCGGAG                         GTGGAGGTTCTGGAAGGACATAGAGGTGGACCTTGTCTTATGTTGGCAACA
genomic: ATCAGGGCAAACAAGAGGCCAGGTATCTCCCAATGCGGAGgtattttaca ... ttttctgtagGTGGAGGTTCTGGAAGGACATAGAGGTGGACCTTGTCTTATGTTGACAACA
EST: gi|88510689|gb|CI438195.1|CI438195
EST:     ATCAGGGCAAACAAGAGGCCAGGTATCTCCCAATGCGGAG                         GTGGAGGTTCTGGAAGGACATAGAGGTGGACCTTGTCTTATGTTGACAACA
genomic: ATCAGGGCAAACAAGAGGCCAGGTATCTCCCAATGCGGAGgtattttaca ... ttttctgtagGTGGAGGTTCTGGAAGGACATAGAGGTGGACCTTGTCTTATGTTGACAACA
EST: gi|86426398|gb|CI071495.1|CI071495
EST:     ATCAGGGCAAACAAGAGGCCAGGTATCTCCCAATGCGGAG                         GTGGAGGTTCTGGAAGGACATAGAGGTGGACCTTGTCTTATGTTGACAACA
genomic: ATCAGGGCAAACAAGAGGCCAGGTATCTCCCAATGCGGAGgtattttaca ... ttttctgtagGTGGAGGTTCTGGAAGGACATAGAGGTGGACCTTGTCTTATGTTGACAACA
EST: gi|88506084|gb|CI433590.1|CI433590
EST:     ATCAGGGCAAACAAGAGGCCAGGTATCTCCCAATGCGGAG                         GTGGAGGTTCTGGAAGGACATAGAGGTGGACCTTGTCTTATGTTGACAACA
genomic: ATCAGGGCAAACAAGAGGCCAGGTATCTCCCAATGCGGAGgtattttaca ... ttttctgtagGTGGAGGTTCTGGAAGGACATAGAGGTGGACCTTGTCTTATGTTGACAACA
EST: gi|86875673|gb|CI323982.1|CI323982
EST:     ATCAGGGCAAACAAGAGGCCAGGTATCTCCCAATGCGGAG                         GTGGAGGTTCTGGAAGGACATAGAGGTGGACCTTGTCTTATGTTGACAACA
genomic: ATCAGGGCAAACAAGAGGCCAGGTATCTCCCAATGCGGAGgtattttaca ... ttttctgtagGTGGAGGTTCTGGAAGGACATAGAGGTGGACCTTGTCTTATGTTGACAACA
EST: gi|88225672|gb|CI225588.1|CI225588
EST:     ATCAGGGCAAACAAGAGGCCAGGTATCTCCCAATGCGGAG                         GTGGAGGTTCTGGAAGGACATACAGGTGGACCTTGTCTTATGTTGACAACA
genomic: ATCAGGGCAAACAAGAGGCCAGGTATCTCCCAATGCGGAGgtattttaca ... ttttctgtagGTGGAGGTTCTGGAAGGACATAGAGGTGGACCTTGTCTTATGTTGACAACA
EST: gi|66930114|gb|CX116962.1|CX116962
EST:     ATCAGGGCAAACAAGAGGCCAGGTATTTCCCAATGCGGAG                         GTGGAGGTTCTGGAAGGACATAGAGGTGGACCTTGTCTTATGTTGACAACA
genomic: ATCAGGGCAAACAAGAGGCCAGGTATCTCCCAATGCGGAGgtattttaca ... ttttctgtagGTGGAGGTTCTGGAAGGACATAGAGGTGGACCTTGTCTTATGTTGACAACA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctacattttcttaaaagtaatttgtttaactggaacataatacctttttctgtagGTGGAGGTTCTGGAAGGACATAGAGGTGGACCTTGTCTTATGTTGACAACAAGCTATGGAGGATGACCTTGTTTTGGGGGCAAGACAAGGTCATCCTTTT
                       gtttaac  putative branch site (score: 3)
                                        tacctttttct  putative PPT
     ttttcttaaaagtaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gggaggcaacaacagtactagcatgttttgtaattttttagttaactacattttcttaaaagtaatttgtttaactggaacataatacctttttctgtagGTGGAGGTTCTGGAAGGACATAGAGGTGGACCTTGTCTTATGTTGACAACAAGCTATGGAGGATGACCTTGTTTTGGGGGCAAGACAAGGTCATCCTTTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA