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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcttacaaaattcaaaaggaaaagaaatcggtaactagattctatatgttggtcttactgtactagttctagttaaggcaactttttattattttctcagGTGATGTGACATTTAGCCAAGTTGTTATGGAAGTCATGAGGCAGCTTGAAGGAGCCTACGCACTTATCTTTAAAAGCCCACACTACCCCAATGAATTGAT

Basic information

species Oryza sativa
transcript LOC_Os12g03720.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g03720.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G005849_T02 (Zea mays), 3'ss of exon 3
-----tcttacaaaattcaaaaggaaaagaaatcggt--aactagattctatatgttggtcttactgtactagttctagttaaggcaactttttattattttctcagGTGATGTGACATTTAGCCAAGTTGTTATGGAAGTCATGAGGCAGCTTGAAGGAGCCTACGCACTTATCTTTAAAAGCCCACACTACCCCAATGAATTGAT
          ||  ||   |    |||| || ||  |   |||  |  |  ||||    |||   | |   ||| |   |||     | | ||| | | || ||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||| ||||||||||||||
gcagaatagtcattatcgcattacaaaataattcattctgactgaacccattatgact-tctatttatggcagtccc--ttac----attatttttcacttcctcagGTGATGTGACGTTTAGCCAAGTTGTTATGGAAGTCATGAGGCAGCTTGAAGGAGCCTACGCACTTATCTTTAAAAGCCCGCACTATCCCAATGAATTGAT

upper sequence: LOC_Os12g03720.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA18G47860.1 (Glycine max), 3'ss of exon 3
tcttacaaaattcaaaaggaaaagaaatcggtaactagattctatatgttggtcttactgtactagttctagttaaggcaactttttattattttctcagGTGAT------GTGACATTTAGCCAAGTTGTTATGGAAGTCATGAGGCAGCTTGAAGGAGCCTACGCACTTATCTTTAAAAGCCCACACTACCCCAATGAATTGAT
|  ||   ||     |           ||    |   |  |  |||   |  |  |  ||    |  |    || | | |  |||  | |  | |  |||| | |      || || || || ||||||||| | ||||| |||||||| ||||||||||| || || ||||| || ||||| ||||| || || |||||      
ttatatgtaagctgcattttctgcttctcttagatgggtgtgaataacattatggttttgggtgatgttagcttgaagtacatttccaattatcttgcagGAGGTCAGGTTGTTACCTTCAGTCAAGTTGTTCTTGAAGTTATGAGGCATCTTGAAGGAGCTTATGCCCTTATTTTCAAAAGTCCACATTATCCTAATGA------

upper sequence: LOC_Os12g03720.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA09G38460.1 (Glycine max), 3'ss of exon 3
tcttacaaaattcaaaaggaaaagaaatcggtaactagattctatatgttggtcttactgtactagttctagttaaggcaactttttattattttctcagGTGAT------GTGACATTTAGCCAAGTTGTTATGGAAGTCATGAGGCAGCTTGAAGGAGCCTACGCACTTATCTTTAAAAGCCCACACTACCCCAATGAATTGAT
|  ||   ||  |              ||    |   |  |  |||   |  |  |  ||  | |  |    || | | |  |||  | |  | |  |||||| |      || || || |||||||||||| | ||||| |||||||| ||||||||||| || || ||||| || ||||| | ||| || || |||||      
ttatatctaaggcgccttttctgcttctcttagatgggtgtgaataacattatgattttgggcgatcttagcttgaagtacatttccaattatcttgcagGTGGTCAGGTTGTTACCTTCAGCCAAGTTGTTCTTGAAGTTATGAGGCATCTTGAAGGAGCTTATGCCCTTATTTTCAAAAGTCTACATTATCCTAATGA------

upper sequence: LOC_Os12g03720.2 (Oryza sativa), 3'ss of exon 3
lower sequence: EFJ12208 (Selaginella moellendorffii), 3'ss of exon 3
tcttacaaaattcaaaaggaaaagaaatcggtaactagattctatatgttggtcttactgtactagttctagttaaggcaactttttattattttctcagGTGATGTGACATTTAGCCAAGTTGTTATGGAAGTCATGAGGCAGCTTGAAGGAGCCTACGCACTTATCTTTAAAAGCCCACACTACCCCAATGAATTGAT
                              ||||  |  |   |   ||   ||  | |  |   || ||   |     ||||||||   |    |   ||  ||||  | || |  ||||| || |||||||| ||||||||||| || ||||| || ||||| |||||||| || || ||||| ||||||||      
------------------------------gtaagcatctgggactagtc--tcccatttaatgcgtcctctctt---taacttttttgcagAAGCCGCGG--ATGTCTCGTTCACGCAAGTAGTGATGGAAGTTATGAGGCAGCTCGAGGGAGCGTATGCACTCATCTTTAAGAGTCCTCACTATCCCAATGA------

upper sequence: LOC_Os12g03720.2 (Oryza sativa), 3'ss of exon 3
lower sequence: EFJ08214 (Selaginella moellendorffii), 3'ss of exon 3
tcttacaaaattcaaaaggaaaagaaatcggtaactagattctatatgttggtcttactgtactagttctagttaaggcaactttttattattttctcagGTGATGTGACATTTAGCCAAGTTGTTATGGAAGTCATGAGGCAGCTTGAAGGAGCCTACGCACTTATCTTTAAAAGCCCACACTACCCCAATGAATTGAT
                              ||||  |  |   |   ||    | |    | |     ||  ||||        ||| ||       | |  |||||  | || |  ||||| || |||||||| ||||||||||| || ||||| || ||||| |||||||| || || ||||| ||||||||      
------------------------------gtaagcatctgggactagtctcccatttaatgcgtcccctccttaa-------cttttttgcagAAGCCGCGGATGTCTCGTTCACGCAAGTAGTGATGGAAGTTATGAGGCAGCTCGAGGGAGCGTATGCACTCATCTTTAAGAGTCCTCACTATCCCAATGA------


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgttggtcttactgtactagttctagttaaggcaactttttattattttctcagGTGATGTGACATTTAGCCAAGTTGTTATGGAAGTCATGAGGCAGCTTGAAGGAGCCTACGCACTTATCTTTAAAAGCCCACACTACCCCAATGAATTGAT
      gtcttac  putative branch site (score: 3)
                                    ctttttattattttct  putative PPT
                                  aactttttattatttt  TA-rich tract