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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...caatagctcaagagaaacctgcagcatgattttattgtcatttgagcttaccatttcgacagtgaccaatggagctacatatactgcatttttttttcagAGCCTGGATCTTTCAAGGATTGATCGGATCATCCGGCGCTCCCTTGGATCACAAG

Basic information

species Oryza sativa
transcript LOC_Os04g52370.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g52370.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G044629_T03 (Zea mays), 3'ss of exon 1
------------------------caatagctcaagagaaacctgcagcatgattttattgtcatttgagcttac--catttcgacagtgaccaatggagctacatatact-------------gcatttttttttcagAGCCTGGATCTTTCAAGGATTGAT-CGGATCATCCGGCGCTCCCTTGGATCACAAG-----
                        ||  || | |  ||| |  || ||   |   |  | ||   |  |   ||   |  || | ||    |   |  ||||   ||| ||             |   | ||  | |  | |   |   |  ||  |  || |   || |    | ||    || |  || | |      
ggatcatccggcgctcccttggatcacaaggtgagaagagaggtggagggaggaatattcgttgctccaatgtagaacgctttgtcacgtgcatctttagCTGGGTATCCTCAGACAGAGTTATGTGGTGTTCATCCCAATCACAGGCATCCCATTGCCTGCTGTCGAGCCCGTGCCGGAATCTAGTGTCTCCAAGGTGG

upper sequence: LOC_Os04g52370.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G019986_T04 (Zea mays), 3'ss of exon 1
-----caatagctcaagagaaacc-tgcagcatgattttattgtcatttgagcttaccatttcgacagtgacc-aatggagctacatatactgcatttttttttcagAGCCTGGATCTTTCAAGGATTGATCGGATCATCCGGCGCTCCCTTGGATCACAAG
      | |   |||  ||||    | | |||  |||||  | || ||| | || |||  |  ||||||  |  |||   |||   | | ||||||| ||   |||||| || || ||||||||||| ||||||||||||||||||||||||||||| ||||
tgttctattctatcagcagaagtaattctgcagcatttt--tctcctttcatctcacctctctgacagttgctgaatcacgctc--tgtgctgcattctt---tcagAGTCTAGACCTTTCAAGGATCGATCGGATCATCCGGCGCTCCCTTGGATCGCAAG

upper sequence: LOC_Os04g52370.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G044629_T01 (Zea mays), 3'ss of exon 1
-------caatagctcaagagaaacctgcagcatgattttattgtcatttgagcttaccattt-cgacagtgaccaatggagctacatatactgcattttttt-ttcagAGCCTGGATCTTTCAAGGATTGATCGGATCATCCGGCGCTCCCTTGGATCACAAG
       |         |  |||   ||||||||  || |  | |||| |   ||||||| |   ||||||  | ||        ||    ||||  | | || | |||||||| || || |||||||| ||||||||||||||||||||||||||||||||||
tcttatcctgccaacagatggaagtgtgcagcatttttcttctttcatct---cttaccactcgtgacagttgctaaat------cacgctctgcgctgtgttgtccagAGCCTAGACCTCTCAAGGATCGATCGGATCATCCGGCGCTCCCTTGGATCACAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcttaccatttcgacagtgaccaatggagctacatatactgcatttttttttcagAGCCTGGATCTTTCAAGGATTGATCGGATCATCCGGCGCTCCCTTGGATCACAAG
 agcttac  putative branch site (score: 3)
                                      ctgcatttttttttc  putative PPT
                                          atttttttttca  TA-rich tract