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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...catggctagttcttagagttctagggacaagtacaactattgttaaatagcacgaattcaaggttctgagtatgatttctgtacttcttttgatggacagGCAAAACATCCATCTGATTTATCTTGCGAATTGGATTGCTTAACCTAATCTGGGAATTCAAGTCAGTACGTACGATATGCCGGCACCATCGGCATCCATC

Basic information

species Oryza sativa
transcript LOC_Os01g49820.1
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|33687572|gb|CF315811.1|CF315811
EST:     GTCCGGGCGGCAAGCCAAGGCGGCCGTTCTTTCCGTCGTGAACGCTTCGTGT                        
genomic: GTCCGGGCGGCAAGCCAAGGCGGCCGTTCTTTCCGTCGTGAACGCTTC--GTgtaaggttcg ... tgatggaca
EST: gi|33687572|gb|CF315811.1|CF315811
EST:     GTCCGGGCGGCAAGCCAAGGCGGCCGTTCTTTCCGTCGTGAACGCTTCGTGT                        
genomic: GTCCGGGCGGCAAGCCAAGGCGGCCGTTCTTTCCGTCGTGAACGCTTC--GTgtaaggttcg ... tgatggaca
EST: gi|33687572|gb|CF315811.1|CF315811
EST:     GTCCGGGCGGCAAGCCAAGGCGGCCGTTCTTTCCGTCGTGAACGCTTCGTGT                        
genomic: GTCCGGGCGGCAAGCCAAGGCGGCCGTTCTTTCCGTCGTGAACGCTTC--GTgtaaggttcg ... tgatggaca
EST: gi|33687572|gb|CF315811.1|CF315811
EST:     GTCCGGGCGGCAAGCCAAGGCGGCCGTTCTTTCCGTCGTGAACGCTTCGTGT                        
genomic: GTCCGGGCGGCAAGCCAAGGCGGCCGTTCTTTCCGTCGTGAACGCTTC--GTgtaaggttcg ... tgatggaca
EST: gi|88390513|gb|CI607549.1|CI607549
EST:     GTCCGGGCGGCAAGCCAAGGCGGCCGTTCTTTCCGTCGTGAACGCTTCGT                         GCAAAACATCCATCTGATTTATCTTGCGAATTGGATTGCTTAACCTAATCT
genomic: GTCCGGGCGGCAAGCCAAGGCGGCCGTTCTTTCCGTCGTGAACGCTTCGTgtaaggttcg ... tgatggacagGCAAAACATCCATCTGATTTATCTTGCGAATTGGATTGCTTAACCTAATCT
EST: gi|88294170|gb|CI667144.1|CI667144
EST:     GTCCGGGCGGCAAGCCAAGGCGGCCGTTCTTTCCGTCGTGAACGCTTCGT                         GCAAAACATCCATCTGATTTATCTTGCGAATTGGATTGCTTAACCTAATCT
genomic: GTCCGGGCGGCAAGCCAAGGCGGCCGTTCTTTCCGTCGTGAACGCTTCGTgtaaggttcg ... tgatggacagGCAAAACATCCATCTGATTTATCTTGCGAATTGGATTGCTTAACCTAATCT
EST: gi|88343234|gb|CI627194.1|CI627194
EST:     GTCCGGGCGGCAAGCCAAGGCGGCCGTTCTTTCCGTCGTGAACGCTTCGTGT                        
genomic: GTCCGGGCGGCAAGCCAAGGCGGCCGTTCTTTCCGTCGTGAACGCTTC--GTgtaaggttcg ... tgatggaca
EST: gi|88343234|gb|CI627194.1|CI627194
EST:     GTCCGGGCGGCAAGCCAAGGCGGCCGTTCTTTCCGTCGTGAACGCTTCGTGT                        
genomic: GTCCGGGCGGCAAGCCAAGGCGGCCGTTCTTTCCGTCGTGAACGCTTC--GTgtaaggttcg ... tgatggaca
EST: gi|88343234|gb|CI627194.1|CI627194
EST:     GTCCGGGCGGCAAGCCAAGGCGGCCGTTCTTTCCGTCGTGAACGCTTCGTGT                        
genomic: GTCCGGGCGGCAAGCCAAGGCGGCCGTTCTTTCCGTCGTGAACGCTTC--GTgtaaggttcg ... tgatggaca
EST: gi|88343234|gb|CI627194.1|CI627194
EST:     GTCCGGGCGGCAAGCCAAGGCGGCCGTTCTTTCCGTCGTGAACGCTTCGTGT                        
genomic: GTCCGGGCGGCAAGCCAAGGCGGCCGTTCTTTCCGTCGTGAACGCTTC--GTgtaaggttcg ... tgatggaca
EST: gi|88351936|gb|CI625936.1|CI625936
EST:     GTCCGGGCGGCAAGCCAAGGCGGCCGTTCTTTCCGTCGTGAACGCTTCGT                         GCAAAACATCCATCTGATTTATCTTGCGAATTGGATTGCTTAACCTAATCT
genomic: GTCCGGGCGGCAAGCCAAGGCGGCCGTTCTTTCCGTCGTGAACGCTTCGTgtaaggttcg ... tgatggacagGCAAAACATCCATCTGATTTATCTTGCGAATTGGATTGCTTAACCTAATCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatagcacgaattcaaggttctgagtatgatttctgtacttcttttgatggacagGCAAAACATCCATCTGATTTATCTTGCGAATTGGATTGCTTAACCTAATCTGGGAATTCAAGTCAGTACGTACGATATGCCGGCACCATCGGCATCCATC
                                          ttttgat  putative branch site (score: 4)
                              tttctgtacttctttt  CT-rich tract
                         tatgattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
catggctagttcttagagttctagggacaagtacaactattgttaaatagcacgaattcaaggttctgagtatgatttctgtacttcttttgatggacagGCAAAACATCCATCTGATTTATCTTGCGAATTGGATTGCTTAACCTAATCTGGGAATTCAAGTCAGTACGTACGATATGCCGGCACCATCGGCATCCATC

catggct
- - - - - - - - - - - - - - aagtacaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggttctg