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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agagattcagagctaagtgccctgtggttcccaattactgtttcaatcaccccctcttgaagggtcacagttttgtctaatgtatttatgtgtttttcagGTTTCTTACCTCTGGAATTTGGGGGATTCTCAACGCCCAAGCTAGATTACATAACATGAATGCAGGATTCAGCCCACAGATCTTGGCGCAGAAGCTTTTG

Basic information

species Oryza sativa
transcript LOC_Os01g70060.1
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|88390733|gb|CI610959.1|CI610959
EST:     AACCCTAGGATTTTCTCCCCTCCCAATGCTGGAGACGGAGCCGTAGCAAG                         GTTTCTTACCTCTGGAATTTGGGGGATTCTCAACGCCCAAGCTAGATTACA
genomic: AACCCTAGGATTTTCTCCCCTCCCAATGCTGGAGACGGAGCCGTAGCAAGgtctgagatt ... tgtttttcagGTTTCTTACCTCTGGAATTTGGGGGATTCTCAACGCCCAAGCTAGATTACA
EST: gi|88401664|gb|CI588605.1|CI588605
EST:     AACCCTAGGATTTTCTCCCCTCCCAATGCTGGAGACGGAGCCGTAGCAAG                         GTTTCTTACCTCTGGAATTTGGGGGATTCTCAACGCCCAAGCTAGATTACA
genomic: AACCCTAGGATTTTCTCCCCTCCCAATGCTGGAGACGGAGCCGTAGCAAGgtctgagatt ... tgtttttcagGTTTCTTACCTCTGGAATTTGGGGGATTCTCAACGCCCAAGCTAGATTACA
EST: gi|88694292|gb|CI738330.1|CI738330
EST:     AACCCTAGGATTTTCTCCCCTCCCAATGCTGGAGACGGAGCCGTAGCAAG                         GTTTCTTACCTCTGGAATTTGGGGGATTCTCAACGCCCAAGCTAGATTACA
genomic: AACCCTAGGATTTTCTCCCCTCCCAATGCTGGAGACGGAGCCGTAGCAAGgtctgagatt ... tgtttttcagGTTTCTTACCTCTGGAATTTGGGGGATTCTCAACGCCCAAGCTAGATTACA
EST: gi|29638160|gb|CB643169.1|CB643169
EST:     AACCCTAGGATTTTCTCCCCTCCCAATGCTGGAGACGGAGCCGTAGCAAG                         GTTTCTTACCTCTGGAATTTGGGGGATTCTCAACGCCCAAGCTAGATTACA
genomic: AACCCTAGGATTTTCTCCCCTCCCAATGCTGGAGACGGAGCCGTAGCAAGgtctgagatt ... tgtttttcagGTTTCTTACCTCTGGAATTTGGGGGATTCTCAACGCCCAAGCTAGATTACA
EST: gi|87008922|gb|CI304865.1|CI304865
EST:     AATGCTGGAGACGGAGCCGTAGCAAG                         GTTTCTTACCTCTGGAATTTGGGGGATTCTCAACGCCCAAGCTAGATTACA
genomic: AATGCTGGAGACGGAGCCGTAGCAAGgtctgagatt ... tgtttttcagGTTTCTTACCTCTGGAATTTGGGGGATTCTCAACGCCCAAGCTAGATTACA
EST: gi|88312139|gb|CI580304.1|CI580304
EST:     AACCCTAGGATTTTCTCCCCTCCCAATGCTGGAGACGGAGCCGTAGCAAG                         GTTTCTTACCTCTGGAATTTGGGGGATTCTCAACGCCCAAGCTAGATTACA
genomic: AACCCTAGGATTTTCTCCCCTCCCAATGCTGGAGACGGAGCCGTAGCAAGgtctgagatt ... tgtttttcagGTTTCTTACCTCTGGAATTTGGGGGATTCTCAACGCCCAAGCTAGATTACA
EST: gi|58612604|gb|CK040316.1|CK040316
EST:     CTCCCCTCCCAATGCTGGAGACGGAGCCGTAGCAAG                         GTTTCTTACCTCTGGAATTTGGGGGATTCTCAACGCCCAAGCTAGATTACA
genomic: CTCCCCTCCCAATGCTGGAGACGGAGCCGTAGCAAGgtctgagatt ... tgtttttcagGTTTCTTACCTCTGGAATTTGGGGGATTCTCAACGCCCAAGCTAGATTACA
EST: gi|58671318|gb|CK060004.1|CK060004
EST:     AACCCTAGGATTTTCTCCCCTCCCAATGCTGGAGACGGAGCCGTAGCAAG                         GTTTCTTACCTCTGGAATTTGGGGGATTCTCAACGCCCAAGCTAGATTACA
genomic: AACCCTAGGATTTTCTCCCCTCCCAATGCTGGAGACGGAGCCGTAGCAAGgtctgagatt ... tgtttttcagGTTTCTTACCTCTGGAATTTGGGGGATTCTCAACGCCCAAGCTAGATTACA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atcaccccctcttgaagggtcacagttttgtctaatgtatttatgtgtttttcagGTTTCTTACCTCTGGAATTTGGGGGATTCTCAACGCCCAAGCTAGATTACATAACATGAATGCAGGATTCAGCCCACAGATCTTGGCGCAGAAGCTTTTG
                             gtctaat  putative branch site (score: 3)
                                             tgtttttc  putative PPT
                                     tatttatgtgttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agagattcagagctaagtgccctgtggttcccaattactgtttcaatcaccccctcttgaagggtcacagttttgtctaatgtatttatgtgtttttcagGTTTCTTACCTCTGGAATTTGGGGGATTCTCAACGCCCAAGCTAGATTACATAACATGAATGCAGGATTCAGCCCACAGATCTTGGCGCAGAAGCTTTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - -tgccctg
- - - - - - - - - - - - - - - - - - - tgtttca