Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   		12  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagcaccccgatcagtatgcctcatgctctttctcatctctctgtaccctacgaacccttttctcgaatttgcgtgcgttaaccctagcttctgttctagatctgaaatttccccttaatttgccttaaccttagtactattaacagtttgtttgttcgcgaaaaagGTTTGGGGGTTCAACTGAACCCCCTATGTCCCTCGTTAGATCCGCCCCTGCCCGGCAATGGGCAGCATGGACACGCCAAGAGGAACAAAATTTTTTCAAT

Basic information

species Oryza sativa
transcript LOC_Os03g13790.1
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|88362353|gb|CI608744.1|CI608744
EST:     TTCGCGAGCAGTGGCGCCGTCGTCCGTCCTGCTGCTTCCGCCGCATCCTG                         GTTTGGGGGTTCAACTGAACCCCCTATGTCCCTCGTTAGATCCGCCCCTGC
genomic: TTCGCGAGCAGTGGCGCCGTCGTCCGTCCTGCTGCTTCCGCCGCATCCTGgtgagcaccc ... cgcgaaaaagGTTTGGGGGTTCAACTGAACCCCCTATGTCCCTCGTTAGATCCGCCCCTGC
EST: gi|88328977|gb|CI658625.1|CI658625
EST:     TTCGCGAGCAGTGGCGCCGTCGTCCGTCCTGCTGCTTCCGCCGCATCCTG                         GTTTGGGGGTTCAACTGAACCCCCTATGTCCCTCGTTAGATCCGCCCCTGC
genomic: TTCGCGAGCAGTGGCGCCGTCGTCCGTCCTGCTGCTTCCGCCGCATCCTGgtgagcaccc ... cgcgaaaaagGTTTGGGGGTTCAACTGAACCCCCTATGTCCCTCGTTAGATCCGCCCCTGC
EST: gi|117217875|gb|CT845173.1|CT845173
EST:     TTCGCGAGCAGTGGCGCCGTCGTCCGTCCTGCTGCTTCCGCCG-ATCCTG                         G-TTGGGGGTTCAACTGAACCCCCTATGTCCCTCGTTAGATCCGCCCCTGC
genomic: TTCGCGAGCAGTGGCGCCGTCGTCCGTCCTGCTGCTTCCGCCGCATCCTGgtgagcaccc ... cgcgaaaaagGTTTGGGGGTTCAACTGAACCCCCTATGTCCCTCGTTAGATCCGCCCCTGC
EST: gi|29628330|gb|CB633341.1|CB633341
EST:     TTCGCGAGCAGTGGCGCCGTCGTCCGTCCTGCTGCTTCCGCCGCATCCTG                         GTTTGGGGGTTCAACTGAACCCCCTATGTCCCTCGTTAGATCCGCCCCTGC
genomic: TTCGCGAGCAGTGGCGCCGTCGTCCGTCCTGCTGCTTCCGCCGCATCCTGgtgagcaccc ... cgcgaaaaagGTTTGGGGGTTCAACTGAACCCCCTATGTCCCTCGTTAGATCCGCCCCTGC
EST: gi|88373410|gb|CI614746.1|CI614746
EST:     TTCGCGAGCAGTGGCGCCGTCGTCCGTCCTGCTGCTTCCGGCGCATCCTG                         GTTTGGGGGTTCAACTGAACCCCCTATGTCCCTCGTTAGATCCGCCCCTGC
genomic: TTCGCGAGCAGTGGCGCCGTCGTCCGTCCTGCTGCTTCCGCCGCATCCTGgtgagcaccc ... cgcgaaaaagGTTTGGGGGTTCAACTGAACCCCCTATGTCCCTCGTTAGATCCGCCCCTGC
EST: gi|88351778|gb|CI617503.1|CI617503
EST:     TTCGCGAGCAGTGGCGCCGTCGTCCGTCCTGCTGCTTCCGCCGCATCCTG                         GTTTGGGGGTTCAACTGAACCCCCTATGTCCCTCGTTAGATCCGCCCCTGC
genomic: TTCGCGAGCAGTGGCGCCGTCGTCCGTCCTGCTGCTTCCGCCGCATCCTGgtgagcaccc ... cgcgaaaaagGTTTGGGGGTTCAACTGAACCCCCTATGTCCCTCGTTAGATCCGCCCCTGC
EST: gi|88409790|gb|CI571047.1|CI571047
EST:     TTCGCGAGCAGTGGCGCCGTCGTCCGTCCTGCTGCTTCCGCCGCATCCTG                         GTTTGGGGGTTCAACTGAACCCCCTATGTCCCTCGTTAGATCCGCCCCTGC
genomic: TTCGCGAGCAGTGGCGCCGTCGTCCGTCCTGCTGCTTCCGCCGCATCCTGgtgagcaccc ... cgcgaaaaagGTTTGGGGGTTCAACTGAACCCCCTATGTCCCTCGTTAGATCCGCCCCTGC
EST: gi|88730127|gb|CI753742.1|CI753742
EST:     TTCGCGAGCAGTGGCGCCGTCGTCCGTCCTGCTGCTTCCGCCGCATCCTG                         GTTTGGGGGTTCAACTGAACCCCCTATGTCCCTCGTTAGATCCGCCCCTGC
genomic: TTCGCGAGCAGTGGCGCCGTCGTCCGTCCTGCTGCTTCCGCCGCATCCTGgtgagcaccc ... cgcgaaaaagGTTTGGGGGTTCAACTGAACCCCCTATGTCCCTCGTTAGATCCGCCCCTGC
EST: gi|88351022|gb|CI620682.1|CI620682
EST:     TTCGCGAGCAGTGGCGCCGTCGTCCGTCCTGCTGCTTCCGCCGCATCCTG                         GTTTGGGGGTTCAACTGAACCCCCTATGTCCCTCGTTAGATCCGCCCCTGC
genomic: TTCGCGAGCAGTGGCGCCGTCGTCCGTCCTGCTGCTTCCGCCGCATCCTGgtgagcaccc ... cgcgaaaaagGTTTGGGGGTTCAACTGAACCCCCTATGTCCCTCGTTAGATCCGCCCCTGC
EST: gi|88352611|gb|CI624550.1|CI624550
EST:     TTCGCGAGCAGTGGCGCCGTCGTCCGTCCTGCTGCTTCCGCCGCATCCTG                         GTTTGGGGGTTCAACTGAACCCCCTATGTCCCTCGTTAGATCCGCCCCTGC
genomic: TTCGCGAGCAGTGGCGCCGTCGTCCGTCCTGCTGCTTCCGCCGCATCCTGgtgagcaccc ... cgcgaaaaagGTTTGGGGGTTCAACTGAACCCCCTATGTCCCTCGTTAGATCCGCCCCTGC
EST: gi|29621639|gb|CB626650.1|CB626650
EST:     TTCGCGAGCAGTGGCGCCGTCGTCCGTCCTGCTGCTTCCGCCGCATCCTG                         GTTTGGGGGTTCAACTGAACCCCCTATGTCCCTCGTTAGATCCGCCCCTGC
genomic: TTCGCGAGCAGTGGCGCCGTCGTCCGTCCTGCTGCTTCCGCCGCATCCTGgtgagcaccc ... cgcgaaaaagGTTTGGGGGTTCAACTGAACCCCCTATGTCCCTCGTTAGATCCGCCCCTGC
EST: gi|29630702|gb|CB635711.1|CB635711
EST:     TTCGCGAGCAGTGGCGCCGTCGTCCGTCCTGCTGCTTCCGCCGCATCCTG                         GTTTGGGGGTTCAACTGAACCCCCTATGTCCCTCGTTAGATCCGCCCCTGC
genomic: TTCGCGAGCAGTGGCGCCGTCGTCCGTCCTGCTGCTTCCGCCGCATCCTGgtgagcaccc ... cgcgaaaaagGTTTGGGGGTTCAACTGAACCCCCTATGTCCCTCGTTAGATCCGCCCCTGC
EST: gi|86904162|gb|CI304596.1|CI304596
EST:     TTCGCGAGCAGTGGCGCCGTCGTCCGTCCTGCTGCTTCCGCCGCATCCTG                         GTTTGGGGGTTCAACTGAACCCCCTATGTCCCTCGTTAGATCCGCCCCTGC
genomic: TTCGCGAGCAGTGGCGCCGTCGTCCGTCCTGCTGCTTCCGCCGCATCCTGgtgagcaccc ... cgcgaaaaagGTTTGGGGGTTCAACTGAACCCCCTATGTCCCTCGTTAGATCCGCCCCTGC
EST: gi|88344650|gb|CI637259.1|CI637259
EST:     TTCGCGAGCAGTGGCGCCGTCGTCCGTCCTGCTGCTTCCGCCGCATCCTG                         GTTTGGGGGTTCAACTGAACCCCCTATGTCCCTCGTTAGATCCGCCCCTGC
genomic: TTCGCGAGCAGTGGCGCCGTCGTCCGTCCTGCTGCTTCCGCCGCATCCTGgtgagcaccc ... cgcgaaaaagGTTTGGGGGTTCAACTGAACCCCCTATGTCCCTCGTTAGATCCGCCCCTGC
EST: gi|58612137|gb|CK039849.1|CK039849
EST:     TTCGCGAGCAGTGGCGCCGTCGTCCGTCCTGCTGCTTCCGCCGCATCCTG                         GTTTGGGGGTTCAACTGAACCCCCTATGTCCCTCGTTAGATCCGCCCCTGC
genomic: TTCGCGAGCAGTGGCGCCGTCGTCCGTCCTGCTGCTTCCGCCGCATCCTGgtgagcaccc ... cgcgaaaaagGTTTGGGGGTTCAACTGAACCCCCTATGTCCCTCGTTAGATCCGCCCCTGC
EST: gi|88387482|gb|CI583000.1|CI583000
EST:     TTCGCGAGCAGTGGCGCCGTCGTCCGTCCTGCTGCTTCCGCCGCATCCTG                         GTTTGGGGGTTCAACTGAACCCCCTATGTCCCTCGTTAGATCCGCCCCTGC
genomic: TTCGCGAGCAGTGGCGCCGTCGTCCGTCCTGCTGCTTCCGCCGCATCCTGgtgagcaccc ... cgcgaaaaagGTTTGGGGGTTCAACTGAACCCCCTATGTCCCTCGTTAGATCCGCCCCTGC
EST: gi|87023602|gb|CI286353.1|CI286353
EST:     TTCGCGAGCAGTGGCGCCGTCGTCCGTCCTGCTGCTTCCGCCGCATCCTG                         GTTTGGGGGTTCAACTGAACCCCCTATGTCCCTCGTTAGATCCGCCCCTGC
genomic: TTCGCGAGCAGTGGCGCCGTCGTCCGTCCTGCTGCTTCCGCCGCATCCTGgtgagcaccc ... cgcgaaaaagGTTTGGGGGTTCAACTGAACCCCCTATGTCCCTCGTTAGATCCGCCCCTGC
EST: gi|88573702|gb|CI665471.1|CI665471
EST:     TTCGCGAGCAGTGGCGCCGTCGTCCGTCCTGCTGCTTCCGCCGCATCCTG                         GTTTGGGGGTTCAACTGAACCCCCTATGTCCCTCGTTAGATCCGCCCCTGC
genomic: TTCGCGAGCAGTGGCGCCGTCGTCCGTCCTGCTGCTTCCGCCGCATCCTGgtgagcaccc ... cgcgaaaaagGTTTGGGGGTTCAACTGAACCCCCTATGTCCCTCGTTAGATCCGCCCCTGC
EST: gi|88450057|gb|CI572188.1|CI572188
EST:     TTCGCGAGCAGTGGCGCCGTCGTCCGTCCTGCTGCTTCCGCCGCATCCTG                         GTTTGGGGGTTCAACTGAACCCCCTATGTCCCTCGTTAGATCCGCCCCTGC
genomic: TTCGCGAGCAGTGGCGCCGTCGTCCGTCCTGCTGCTTCCGCCGCATCCTGgtgagcaccc ... cgcgaaaaagGTTTGGGGGTTCAACTGAACCCCCTATGTCCCTCGTTAGATCCGCCCCTGC
EST: gi|88337044|gb|CI628130.1|CI628130
EST:     GTCCGTCCTGCTGCTTCCGCCGCATCCTG                         GTTTGGGGGTTCAACTGAACCCCCTATGTCCCTCGTTAGATCCGCCCCTGC
genomic: GTCCGTCCTGCTGCTTCCGCCGCATCCTGgtgagcaccc ... cgcgaaaaagGTTTGGGGGTTCAACTGAACCCCCTATGTCCCTCGTTAGATCCGCCCCTGC
EST: gi|88412252|gb|CI573528.1|CI573528
EST:     TTCGCGAGCAGTGGCGCCGTCGTCCGTCCTGCTGCTTCCGCCGCATCCTG                         GTTTGGGGGTTCAACTGAACCCCCTATGTCCCTCGTTAGATCCGCCCCTGC
genomic: TTCGCGAGCAGTGGCGCCGTCGTCCGTCCTGCTGCTTCCGCCGCATCCTGgtgagcaccc ... cgcgaaaaagGTTTGGGGGTTCAACTGAACCCCCTATGTCCCTCGTTAGATCCGCCCCTGC
EST: gi|88370989|gb|CI595101.1|CI595101
EST:     TTCGCGAGCAGTGGCGCCGTCGTCCGTCCTGCTGCTTCCGCCGCATCCTG                         GTTTGGGGGTTCAACTGAACCCCCTATGTCCCTCGTTAGATCCGCCCCTGC
genomic: TTCGCGAGCAGTGGCGCCGTCGTCCGTCCTGCTGCTTCCGCCGCATCCTGgtgagcaccc ... cgcgaaaaagGTTTGGGGGTTCAACTGAACCCCCTATGTCCCTCGTTAGATCCGCCCCTGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cccttaatttgccttaaccttagtactattaacagtttgtttgttcgcgaaaaagGTTTGGGGGTTCAACTGAACCCCCTATGTCCCTCGTTAGATCCGCCCCTGCCCGGCAATGGGCAGCATGGACACGCCAAGAGGAACAAAATTTTTTCAAT
                          tattaac  putative branch site (score: 1)
                                       tttgttc  putative PPT
                       tactattaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagcaccccgatcagtatgcctcatgctctttctcatctctctgtaccctacgaacccttttctcgaatttgcgtgcgttaaccctagcttctgttctagatctgaaatttccccttaatttgccttaaccttagtactattaacagtttgtttgttcgcgaaaaagGTTTGGGGGTTCAACTGAACCCCCTATGTCCCTCGTTAGATCCGCCCCTGCCCGGCAATGGGCAGCATGGACACGCCAAGAGGAACAAAATTTTTTCAAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA