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

gtgaagagatgctggcgcttttgcagttcatgagctgcttgtcggagtacgattttttttttgatattttctgtggtctttctgttgcatacagAGCGAACTGCTCCAGGTGGTGCAGCCGTTCGGCACTGTCGCCAAGCTCGTCATGCTGCGTGCTAAGAACCAG

Basic information

species Oryza sativa
transcript LOC_Os01g64770.5
intron # 2
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|29656748|gb|CB653023.1|CB653023
EST:     AGCCCTCCAAGGTGATCCACATACGGAACGTCGGGCATGAGATCTCCGAG                         AGCGAACTGCTCCAGGTGGTGCAGCCGTTCGGCACTGTCGCCAAGCTCGTC
genomic: AGCCCTCCAAGGTGATCCACATACGGAACGTCGGGCATGAGATCTCCGAGgtgaagagat ... ttgcatacagAGCGAACTGCTCCAGGTGGTGCAGCCGTTCGGCACTGTCGCCAAGCTCGTC
EST: gi|88585290|gb|CI702911.1|CI702911
EST:     AGCCCTCCAAGGTGATCCACATACGGAACGTCGGGCATGAGATCTCCGAG                         AGCGAACTGCTCCAGGTGGTGCAGCCGTTCGGCACTGTCGCCAAGCTCGTC
genomic: AGCCCTCCAAGGTGATCCACATACGGAACGTCGGGCATGAGATCTCCGAGgtgaagagat ... ttgcatacagAGCGAACTGCTCCAGGTGGTGCAGCCGTTCGGCACTGTCGCCAAGCTCGTC
EST: gi|88344519|gb|CI677575.1|CI677575
EST:     AGCCCTCCAAGGTGATCCACATACGGAACGTCGGGCATGAGATCTCCGAG                         AGCGAACTGCTCCAGGTGGTGCAGCCGTTCGGCACTGTCGCCAAGCTCGTC
genomic: AGCCCTCCAAGGTGATCCACATACGGAACGTCGGGCATGAGATCTCCGAGgtgaagagat ... ttgcatacagAGCGAACTGCTCCAGGTGGTGCAGCCGTTCGGCACTGTCGCCAAGCTCGTC
EST: gi|88722525|gb|CI746035.1|CI746035
EST:     GCCCTCCAAGGTGATCCAAATACGGAAACGTCGGGCATGAGATCTCCGAG                         AGCGAACTGCTCCAGGTGGTGCAGCCGTTCGGCACTGTCGCCCAAGCTCGT
genomic: GCCCTCCAAGGTGATCCACATACGGAA-CGTCGGGCATGAGATCTCCGAGgtgaagagat ... ttgcatacagAGCGAACTGCTCCAGGTGGTGCAGCCGTTCGGCACTGTCGCC-AAGCTCGT
EST: gi|88590878|gb|CI707773.1|CI707773
EST:     AGCCCTCCAAGGTGATCCACATACGGAACGTCGGGCATGAGATCTCCGAG                         AGCGAACTGCTCCAGGTGGTGCAGCCGTTCGGCACTGTCGCCAAGCTCGTC
genomic: AGCCCTCCAAGGTGATCCACATACGGAACGTCGGGCATGAGATCTCCGAGgtgaagagat ... ttgcatacagAGCGAACTGCTCCAGGTGGTGCAGCCGTTCGGCACTGTCGCCAAGCTCGTC
EST: gi|88334859|gb|CI648634.1|CI648634
EST:     AGCNCTCCAAGGTGATCCACATACGGAACGTCGGGCATGAGATCTCCGAG                         AGCGAACTGCTCCAGGTGGTGCAGCCGTTCGGCACTGTCGCCAAGCTCGTC
genomic: AGCCCTCCAAGGTGATCCACATACGGAACGTCGGGCATGAGATCTCCGAGgtgaagagat ... ttgcatacagAGCGAACTGCTCCAGGTGGTGCAGCCGTTCGGCACTGTCGCCAAGCTCGTC
EST: gi|33798640|gb|CF325178.1|CF325178
EST:     AGCCCTCCAAGGTGATCCACATACGGAACGTCGGGCATGAGATCTCCGAG                         AGCGAACTGCTCCAGGTGGTGCAGCCGTTCGGCACTGTCGCCAAGCTCGTC
genomic: AGCCCTCCAAGGTGATCCACATACGGAACGTCGGGCATGAGATCTCCGAGgtgaagagat ... ttgcatacagAGCGAACTGCTCCAGGTGGTGCAGCCGTTCGGCACTGTCGCCAAGCTCGTC
EST: gi|88355035|gb|CI615916.1|CI615916
EST:     AGCCCTCCAAGGTGATCCACATACGGAACGTCGGGCATGAGATCTCCGAG                         AGCGAACTGCTCCAGGTGGTGCAGCCGTTCGGCACTGTCGCCAAGCTCGTC
genomic: AGCCCTCCAAGGTGATCCACATACGGAACGTCGGGCATGAGATCTCCGAGgtgaagagat ... ttgcatacagAGCGAACTGCTCCAGGTGGTGCAGCCGTTCGGCACTGTCGCCAAGCTCGTC
EST: gi|88362576|gb|CI607334.1|CI607334
EST:     AGCCCTCCAAGGTGATCCACATACGGAACGTCGGGCATGAGATCTCCGAG                         AGCGAACTGCTCCAGGTGGTGCAGCCGTTCGGCACTGTCGCCAAGCTCGTC
genomic: AGCCCTCCAAGGTGATCCACATACGGAACGTCGGGCATGAGATCTCCGAGgtgaagagat ... ttgcatacagAGCGAACTGCTCCAGGTGGTGCAGCCGTTCGGCACTGTCGCCAAGCTCGTC
EST: gi|88426086|gb|CI604375.1|CI604375
EST:     AGCCCTCCAAGGTGATCCACATACGGAACGTCGGGCATGAGATCTCCGAG                         AGCGAACTGCTCCAGGTGGTGCAGCCGTTCGGCACTGTCGCCAAGCTCGTC
genomic: AGCCCTCCAAGGTGATCCACATACGGAACGTCGGGCATGAGATCTCCGAGgtgaagagat ... ttgcatacagAGCGAACTGCTCCAGGTGGTGCAGCCGTTCGGCACTGTCGCCAAGCTCGTC
EST: gi|88309155|gb|CI654774.1|CI654774
EST:     AGCCCTCCAAGGTGATCCACATACGGAACGTCGGGCATGAGATCTCCGAG                         AGCGAACTGCTCCAGGTGGTGCAGCCGTTCGGCACTGTCGCCAAGCTCGTC
genomic: AGCCCTCCAAGGTGATCCACATACGGAACGTCGGGCATGAGATCTCCGAGgtgaagagat ... ttgcatacagAGCGAACTGCTCCAGGTGGTGCAGCCGTTCGGCACTGTCGCCAAGCTCGTC
EST: gi|88730907|gb|CI754520.1|CI754520
EST:     AGCCCTCCAAGGTGATCCACATACGGAACGTCGGGCATGAGATCTCCGAG                         AGCGAACTGCTCCAGGTGGTGCAGCCGTTCG
genomic: AGCCCTCCAAGGTGATCCACATACGGAACGTCGGGCATGAGATCTCCGAGgtgaagagat ... ttgcatacagAGCGAACTGCTCCAGGTGGTGCAGCCGTTCG
EST: gi|88348634|gb|CI634229.1|CI634229
EST:     AGCCCTCCAAGGTGATCCACATACGGAACGTCGGGCATGAGATCTCCGAG                         AGCGAACTGCTCCAGGTGGTGCAGCCGTTCGGCACTGTCGCCAAGCTCGTC
genomic: AGCCCTCCAAGGTGATCCACATACGGAACGTCGGGCATGAGATCTCCGAGgtgaagagat ... ttgcatacagAGCGAACTGCTCCAGGTGGTGCAGCCGTTCGGCACTGTCGCCAAGCTCGTC
EST: gi|88308532|gb|CI650941.1|CI650941
EST:     AGCCCTCCAAGGTGATCCACATACGGAACGTCGGGCATGAGATCTCCGAG                         AGCGAACTGCTCCAGGTGGTGCAGCCGTTCGGCACTGTCGCCCAAGCTCGT
genomic: AGCCCTCCAAGGTGATCCACATACGGAACGTCGGGCATGAGATCTCCGAGgtgaagagat ... ttgcatacagAGCGAACTGCTCCAGGTGGTGCAGCCGTTCGGCACTGTCGCC-AAGCTCGT
EST: gi|88739105|gb|CI762613.1|CI762613
EST:     AGCCCTCCAAGGTGATCCACATACGGAACGTCGGGCATGAGATCTCCGAG                         AGCGAACTGCTCCAGGTGGTGCAGCCGTTCGGCACTGTCGCCAAGCTCGTC
genomic: AGCCCTCCAAGGTGATCCACATACGGAACGTCGGGCATGAGATCTCCGAGgtgaagagat ... ttgcatacagAGCGAACTGCTCCAGGTGGTGCAGCCGTTCGGCACTGTCGCCAAGCTCGTC
EST: gi|88390459|gb|CI607495.1|CI607495
EST:     AGCCCTCCAAGGTGATCCACATACGGAACGTCGGGCATGAGATCTCCGAG                         AGCGAACTGCTCCAGGTGGTGCAGCCGTTCGGCACTGTCGCCAAGCTCGTC
genomic: AGCCCTCCAAGGTGATCCACATACGGAACGTCGGGCATGAGATCTCCGAGgtgaagagat ... ttgcatacagAGCGAACTGCTCCAGGTGGTGCAGCCGTTCGGCACTGTCGCCAAGCTCGTC
EST: gi|88326048|gb|CI651098.1|CI651098
EST:     AGCCCTCCAAGGTGATCCACATACGGAACGTCGGGCATGAGATCTCCGAG                         AGCGAACTGCTCCAGGTGGTGCAGCCGTTCGGCACTGTCGCCAAGCTCGTC
genomic: AGCCCTCCAAGGTGATCCACATACGGAACGTCGGGCATGAGATCTCCGAGgtgaagagat ... ttgcatacagAGCGAACTGCTCCAGGTGGTGCAGCCGTTCGGCACTGTCGCCAAGCTCGTC
EST: gi|88403282|gb|CI571023.1|CI571023
EST:     AGCCCTCCAAGGTGATCCACATACGGAACGTCGGGCATGAGATCTCCGAG                         AGCGAACTGCTCCAGGTGGTGCAGCCGTTCGGCACTGTCGCCAAGCTCGTC
genomic: AGCCCTCCAAGGTGATCCACATACGGAACGTCGGGCATGAGATCTCCGAGgtgaagagat ... ttgcatacagAGCGAACTGCTCCAGGTGGTGCAGCCGTTCGGCACTGTCGCCAAGCTCGTC
EST: gi|88400865|gb|CI616870.1|CI616870
EST:     AGCCCTCCAAGGTGATCCACATACGGAACGTCGGGCATGAGATCTCCGAG                         AGCGAACTGCTCCAGGTGGTGCAGCCGTTCGGCACTGTCGCCAAGCTCGTC
genomic: AGCCCTCCAAGGTGATCCACATACGGAACGTCGGGCATGAGATCTCCGAGgtgaagagat ... ttgcatacagAGCGAACTGCTCCAGGTGGTGCAGCCGTTCGGCACTGTCGCCAAGCTCGTC
EST: gi|88347482|gb|CI637422.1|CI637422
EST:     AGCCCTCCAAGGTGATCCACATACGGAACGTCGGGCATGAGATCTCCGAG                         AGCGAACTGCTCCAGGTGGTGCAGCCGTTCGGCACTGTCGCCAAGCTCGTC
genomic: AGCCCTCCAAGGTGATCCACATACGGAACGTCGGGCATGAGATCTCCGAGgtgaagagat ... ttgcatacagAGCGAACTGCTCCAGGTGGTGCAGCCGTTCGGCACTGTCGCCAAGCTCGTC
EST: gi|33798687|gb|CF325201.1|CF325201
EST:     AGCCCTCCAAGGTGATCCACATACGGAACGTCGGGCATGAGATCTCCGAG                         AGCGAACTGCTCCAGGTGGTGCAGCCGTTCGGCACTGTCGCCAAGCTCGTC
genomic: AGCCCTCCAAGGTGATCCACATACGGAACGTCGGGCATGAGATCTCCGAGgtgaagagat ... ttgcatacagAGCGAACTGCTCCAGGTGGTGCAGCCGTTCGGCACTGTCGCCAAGCTCGTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtcggagtacgattttttttttgatattttctgtggtctttctgttgcatacagAGCGAACTGCTCCAGGTGGTGCAGCCGTTCGGCACTGTCGCCAAGCTCGTCATGCTGCGTGCTAAGAACCAG
                   ttttgat  putative branch site (score: 4)
                                     tctttctgtt  putative PPT
        tacgattttttttttg  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgaagagatgctggcgcttttgcagttcatgagctgcttgtcggagtacgattttttttttgatattttctgtggtctttctgttgcatacagAGCGAACTGCTCCAGGTGGTGCAGCCGTTCGGCACTGTCGCCAAGCTCGTCATGCTGCGTGCTAAGAACCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC