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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agtttggttgtacttgcctatactgtggtatttggtcgtaccatttctttgctcacacttgttttagcacaggatataatacttttcacccttgaaacagATTCATGGAAATTCATTTCAGAAGAAGCTTTCACTTCTTTTCGGAATGCGCTCAGAG

Basic information

species Oryza sativa
transcript LOC_Os03g24220.1
intron # 19
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g24220.2 (Oryza sativa), 3'ss of exon 19
lower sequence: GRMZM2G359566_T01 (Zea mays), 3'ss of exon 4
-----agtttggttgtacttgcctatactgtggtatttggtcgtaccatttctttgctcacacttgttttagcacaggatataatacttttcacccttgaaacagATTCATGGAAATTCATTTCAGAAGAAGCTTTCACTTCTTTTCGGAATGCGCTCAGAG
       |||||  ||||||   | | || || | |  |||   | | ||| ||||  |  | |  ||   | | ||    | |||| | ||| ||||||||||| |||||||||| || ||| ||||||| |||||| |||||||||||||||| ||||||
tactatttttgggcgtacttttgttttctttgct-tgcggt-aaagcttttttttgaacgaaatgcttgcggtaaagc---tgatacgtgtcatccttgaaacagGTTCATGGAAACTCTTTTGAGAAGAAACTTTCAGTTCTTTTCGGAATGCGTTCAGAG
















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|88694289|gb|CI738327.1|CI738327
EST:     AACCATGCTTCTTCAGAACTTACTTCTCCTGGGATAACACAAGATCTGTG                         ATTCATGGAAATTCATTTCAGAAGAAGCTTTCACTTCTTTTCGGAATGCGC
genomic: AACCATGCTTCTTCAGAACTTACTTCTCCTGGGATAACACAAGATCTGTGgtatgctatt ... cttgaaacagATTCATGGAAATTCATTTCAGAAGAAGCTTTCACTTCTTTTCGGAATGCGC
EST: gi|58596217|gb|CK006745.1|CK006745
EST:     AACCATGCTTCTTCAGAACTTACTTCTCCTGGGATAACACAAGATCTGTG                         ATTCATGGAAATTCATTTCAGAAGAAGCTTTCACTTCTTTTCGGAATGCGC
genomic: AACCATGCTTCTTCAGAACTTACTTCTCCTGGGATAACACAAGATCTGTGgtatgctatt ... cttgaaacagATTCATGGAAATTCATTTCAGAAGAAGCTTTCACTTCTTTTCGGAATGCGC
EST: gi|58677092|gb|CK065779.1|CK065779
EST:     AACCATGCTTCTTCAGAACTTACTTCTCCTGGGATAACACAAGATCTGTG                         ATTCATGGAAATTCATTTCAGAAGAAGCTTTCACTTCTTTTCGGAATGCGC
genomic: AACCATGCTTCTTCAGAACTTACTTCTCCTGGGATAACACAAGATCTGTGgtatgctatt ... cttgaaacagATTCATGGAAATTCATTTCAGAAGAAGCTTTCACTTCTTTTCGGAATGCGC
EST: gi|25798468|gb|CA754429.1|CA754429
EST:     AACCATGCTTCTTCAGAACTTACTTCTCCTGNGATAACACAAGATCTGTG                         ATTCATGGAAATTCATTTCAGAAGAAACTTTCACTTCTTTTCGGGATGCGC
genomic: AACCATGCTTCTTCAGAACTTACTTCTCCTGGGATAACACAAGATCTGTGgtatgctatt ... cttgaaacagATTCATGGAAATTCATTTCAGAAGAAGCTTTCACTTCTTTTCGGAATGCGC
EST: gi|396941448|gb|HO188657.1|HO188657
EST:     AACCATGCTTCTTCAGAACTTACTTCTCCTGGGATAACACAAGATCTGTG                         ATTCATGGAAATTCATTTCAGAAGAAGCTTTCACTTCTTTTCGGAATGCGC
genomic: AACCATGCTTCTTCAGAACTTACTTCTCCTGGGATAACACAAGATCTGTGgtatgctatt ... cttgaaacagATTCATGGAAATTCATTTCAGAAGAAGCTTTCACTTCTTTTCGGAATGCGC
EST: gi|88718464|gb|CI741974.1|CI741974
EST:     AACCATGCTTCTTCAGAACTTACTTCTCCTGGGATAACACAAGTTCTGTG                         ATTCATGGAAATTCATTTCAGAAGAAGCTTTCACTTCTTTTCGGAATGCGC
genomic: AACCATGCTTCTTCAGAACTTACTTCTCCTGGGATAACACAAGATCTGTGgtatgctatt ... cttgaaacagATTCATGGAAATTCATTTCAGAAGAAGCTTTCACTTCTTTTCGGAATGCGC
EST: gi|58661440|gb|CK050120.1|CK050120
EST:     AACCATGCTTCTTCAGAACTTACGGCGCCTGGGATAACACAAGATCTGTG                         ATTCATGGAAATTCATTTCAGAAGAAGCTTTCACTTCTTTTCGGAATGCGC
genomic: AACCATGCTTCTTCAGAACTTACTTCTCCTGGGATAACACAAGATCTGTGgtatgctatt ... cttgaaacagATTCATGGAAATTCATTTCAGAAGAAGCTTTCACTTCTTTTCGGAATGCGC
EST: gi|33674859|gb|CF303098.1|CF303098
EST:     AACCATGCTTCTTCAGAACTTACTTCTCCTGNGATAACACAAGATCTGTG                         ATTCATGGAAATTCATTTCAGAAGAAGCTTTCACTTCTTTTCGGAATGCGC
genomic: AACCATGCTTCTTCAGAACTTACTTCTCCTGGGATAACACAAGATCTGTGgtatgctatt ... cttgaaacagATTCATGGAAATTCATTTCAGAAGAAGCTTTCACTTCTTTTCGGAATGCGC
EST: gi|58674368|gb|CK063054.1|CK063054
EST:     AACCATGCTTCTTCAGAACTTACTTCTCCTGGGATAACACAAGATCTGTG                         ATTCATGGAAATTCATTTCAGAAGAAGCTTTCACTTCTTTTCGGAATGCGC
genomic: AACCATGCTTCTTCAGAACTTACTTCTCCTGGGATAACACAAGATCTGTGgtatgctatt ... cttgaaacagATTCATGGAAATTCATTTCAGAAGAAGCTTTCACTTCTTTTCGGAATGCGC
EST: gi|58610643|gb|CK038355.1|CK038355
EST:     AACCATGCTTCTTCAGAACTTACTTCTCCTGGGATAACACAAGATCTGTG                         ATTCATGGAAATTCATTTCAGAAGAAGCTTTCACTTCTTTTCGGAATGCGC
genomic: AACCATGCTTCTTCAGAACTTACTTCTCCTGGGATAACACAAGATCTGTGgtatgctatt ... cttgaaacagATTCATGGAAATTCATTTCAGAAGAAGCTTTCACTTCTTTTCGGAATGCGC
EST: gi|58652740|gb|CK041420.1|CK041420
EST:     AGAACTTACTTCTCCTGGGAT-ACACAAGATCTGTG                         ATTCATGGAAATTCATTTCAGAAGAAGCTTTCACTTCTTTTCGGAATGCGC
genomic: AGAACTTACTTCTCCTGGGATAACACAAGATCTGTGgtatgctatt ... cttgaaacagATTCATGGAAATTCATTTCAGAAGAAGCTTTCACTTCTTTTCGGAATGCGC
EST: gi|56157785|gb|C26501.2|C26501
EST:     ACAAGATCTGTG                         ATTCATGGAAATTCATTTCAGAAGAAGCTTTCACTTCTTTTCGGAATGCGC
genomic: ACAAGATCTGTGgtatgctatt ... cttgaaacagATTCATGGAAATTCATTTCAGAAGAAGCTTTCACTTCTTTTCGGAATGCGC
EST: gi|58652765|gb|CK041445.1|CK041445
EST:     AACCATGCTTCTTCAGAACTTACTTCTCCTGGGATAACACAAGATCTGTG                         ATTCATGGAAATTCATTTCAGAAGAAGCTTTCACTTCTTTTCGGAATGCGC
genomic: AACCATGCTTCTTCAGAACTTACTTCTCCTGGGATAACACAAGATCTGTGgtatgctatt ... cttgaaacagATTCATGGAAATTCATTTCAGAAGAAGCTTTCACTTCTTTTCGGAATGCGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctttgctcacacttgttttagcacaggatataatacttttcacccttgaaacagATTCATGGAAATTCATTTCAGAAGAAGCTTTCACTTCTTTTCGGAATGCGCTCAGAG
    tgctcac  putative branch site (score: 2)
                                  tacttttcaccctt  putative PPT
                            atataatacttttca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agtttggttgtacttgcctatactgtggtatttggtcgtaccatttctttgctcacacttgttttagcacaggatataatacttttcacccttgaaacagATTCATGGAAATTCATTTCAGAAGAAGCTTTCACTTCTTTTCGGAATGCGCTCAGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC