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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgcgtaacctttttttctttttttgattcctttgtgtttgggtttcgttctgaatttctgatgattgagtctgatggtgttttttttacgctgtgcagGGCGTAATGTGGATGGGAGGAACATCATGGTGCAGTTTGCCAAGTATGGGCCCAATGCGGAGCCAAT

Basic information

species Oryza sativa
transcript LOC_Os08g37960.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g37960.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G016296_T06 (Zea mays), 3'ss of exon 3
--gtgcgtaacctttttttcttttt--ttgattcctttgtgtttgggtttcgttctgaatttctgatgattgagtctga-tggtgttttttttacgctgtgcagGGCGTAATGTGGATGGGAGGAACATCATGGTGCAGTTTGCCAAGTATGGGCCCAATGCGGAGCCAAT
  | || |  |||| |||| ||| |    |  |      |||  || ||| || ||    |  | || | ||   |||| |   |||| ||||  |    ||||| ||| ||||||||||||| |||||||||||||||||||| ||||| || |||||||| ||||||||
gtgggcttcgccttattttttttgtaaccgtctttcccctgtggggattttgtgctt--ctattcataactgcacctgaatttcgtttgttttttg----gcagGCCGTGATGTGGATGGGAGAAACATCATGGTGCAGTTTGCAAAGTACGGCCCCAATGCTGAGCCAAT

upper sequence: LOC_Os08g37960.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G110143_T02 (Zea mays), 3'ss of exon 3
gtgcgtaacctttttttctttttttgattcctttgtgtttgggtttcgttctgaatttctgatgattgagtctgatggtgttttttttacgctgtgcagGGCGTAATGTGGATGGGAGGAACATCATGGTGCAGTTTGCCAAGTATGGGCCCAATGCGGAGCCAAT
    ||    |||||||     | || | |   ||||   || ||| |    ||  |||| ||  ||||   | || ||   ||||||     ||||||| |||||||||||||||||||||||||||||||||||||| ||||| || |||||||| | ||||||
----gtggttttttttttcgactgtgctccacatgtgg--ggattttg----gagcttct-atttttga---taattgtagattttttgg---gtgcagGCCGTAATGTGGATGGGAGGAACATCATGGTGCAGTTTGCAAAGTACGGCCCCAATGCTGTGCCAAT

upper sequence: LOC_Os08g37960.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G110143_T01 (Zea mays), 3'ss of exon 3
gtgcgtaacctttttttctttttttgattcctttgtgtttgggtttcgttctgaatttctgatgattgagtctgatggtgttttttttacgctgtgcagGGCGTAATGTGGATGGGAGGAACATCATGGTGCAGTTTGCCAAGTATGGGCCCAATGCGGAGCCAAT
    ||    |||||||     | || | |   ||||   || ||| |    ||  |||| ||  ||||   | || ||   ||||||     ||||||| |||||||||||||||||||||||||||||||||||||| ||                        
----gtggttttttttttcgactgtgctccacatgtgg--ggattttg----gagcttct-atttttga---taattgtagattttttgg---gtgcagGCCGTAATGTGGATGGGAGGAACATCATGGTGCAGTTTGCAAA------------------------

upper sequence: LOC_Os08g37960.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G110143_T05 (Zea mays), 3'ss of exon 3
gtgcgtaacctttttttctttttttgattcctttgtgtttgggtttcgttctgaatttctgatgattgagtctgatggtgttttttttacgctgtgcagGGCGTAATGTGGATGGGAGGAACATCATGGTGCAGTTTGCCAAGTATGGGCCCAATGCGGAGCCAAT
           |||||| ||    ||    |    |||  || ||| |    ||  |||| ||  ||||   | || ||   ||||||     ||||||| ||||||||||||||||||||||                                           
-----------tTTTTTTTTCGACTGTGCTCCACATGTGGGGATTTTG----GAGCTTCT-ATTTTTGA---TAATTGTAGATTTTTTGG---GTGCAGGCCGTAATGTGGATGGGAGGAACA-------------------------------------------

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|88726297|gb|CI749952.1|CI749952
EST:     GCGCTACAAGTACGCTGAAGAGGCGCAGAAGGCTATAGATCGGCTTGATG                         GGCGTAATGTGGATGGGAGGAACATCATGGTGCAGTTTGCCAAGTATGGGC
genomic: GCGCTACAAGTACGCTGAAGAGGCGCAGAAGGCTATAGATCGGCTTGATGgtgcgtaacc ... cgctgtgcagGGCGTAATGTGGATGGGAGGAACATCATGGTGCAGTTTGCCAAGTATGGGC
EST: gi|33794171|gb|CF322976.1|CF322976
EST:     GCGCTACAAGTACGCTGAAGAGGCGCAGAAGGCTATAGATCGGCTTGATG                         GGCGTAATGTGGATGGGAGGAACATCATGGTGCAGTTTGCCAAGTATGGGC
genomic: GCGCTACAAGTACGCTGAAGAGGCGCAGAAGGCTATAGATCGGCTTGATGgtgcgtaacc ... cgctgtgcagGGCGTAATGTGGATGGGAGGAACATCATGGTGCAGTTTGCCAAGTATGGGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcgttctgaatttctgatgattgagtctgatggtgttttttttacgctgtgcagGGCGTAATGTGGATGGGAGGAACATCATGGTGCAGTTTGCCAAGTATGGGCCCAATGCGGAGCCAAT
                                    ttttttttac  CT-rich tract
                                  tgtttttttta  TA-rich tract