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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttcagaggagttcttgagattatcctaacaacatttacgagcggttaatttagccttaaccatccgtggtttcttctctccgttgaattctcgcgtgcagTTGAGCTGGACAAACCGTGCTATTGCAATCTCAAGGTGGTGAACAACAGCGAGCATCATGTTGCATTCAAG

Basic information

species Oryza sativa
transcript LOC_Os02g43594.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g43594.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G171406_T02 (Zea mays), 3'ss of exon 2
gtaagttcagaggagttcttgagattatcctaacaacatttacgagcggttaatttagccttaaccatccgtggtttcttctctccgttgaattctcgcgtgcagTTGAGCTGGACAAACCGTGCTATTGCAATCTCAAGGTGGTGAACAACAGCGAGCATCATGTTGCATTCAAG-----------------------------
||||| |  | ||| || |||| ||  || |     ||||  |||  ||||||                     ||||| |||  ||||||||||| ||| | |||||||||||| || ||||||||||||||||||||||||||||||||||||||||||||||| |||||||||                             
gtaagctgtgtggatttattgatatattcgt--tcgcatt-gcgattggttaa--------------------atttctcctccgcgttgaattcttgcgcgtagTTGAGCTGGAGAAGCCGTGCTATTGCAATCTCAAGGTGGTGAACAACAGCGAGCATCATGTCGCATTCAAGGTCCATGTCTTCCCTGTCCCGTGAAGTTC

upper sequence: LOC_Os02g43594.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G171406_T06 (Zea mays), 3'ss of exon 1
gtaagttcagaggagttcttgagattatcctaacaacatttacgagcggttaatttagccttaaccatccgtggtttcttctctccgttgaattctcgcgtgcagTTGAGCTGGACAAACCGTGCTATTGCAATCTCAAGGTGGTGAACAACAGCGAGCATCATGTTGCATTCAAG
||||| |  | ||| || |||| ||  || |     ||||  |||  ||||||                     ||||| |||  ||||||||||| ||| | |||||||||||| || ||||||||||||||||||||||||||||||||||||||||||||||| |||||||||
gtaagctgtgtggatttattgatatattcgt--tcgcatt-gcgattggttaa--------------------atttctcctccgcgttgaattcttgcgcgtagTTGAGCTGGAGAAGCCGTGCTATTGCAATCTCAAGGTGGTGAACAACAGCGAGCATCATGTCGCATTCAAG

upper sequence: LOC_Os02g43594.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G074173_T01 (Zea mays), 3'ss of exon 2
gtaagttcagaggagttcttgagattatcctaacaacatttacgagcggttaatttagccttaaccatccgtggtttcttctctccgttgaattctcgcgtgcagTTGAGCTGGACAAACCGTGCTATTGCAATCTCAAGGTGGTGAACAACAGCGAGCATCATGTTGCATTCAAG
|||||||| | ||| ||||||| ||| || |  |||   |   |   | ||  |  | ||| |  | ||||| |     || |  |||  ||| || ||| |||||||||||||| || ||||||||||||||||||||||||||||||||||||||||| || || |||||||||
gtaagttctgcggatttcttgatattttcgttccaattgtgttg--tgattggtcaaacctca--cttccgttggcatctccccgcgtctaatccttgcgcgcagTTGAGCTGGAGAAGCCGTGCTATTGCAATCTCAAGGTGGTGAACAACAGCGAGCACCACGTCGCATTCAAG

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|88728659|gb|CI752169.1|CI752169
EST:     TGGCGGCGGAACGCTGATCTCCATCTACCCCGAGGACCTCACTTTCCTAT                         TTGAGCTGGACAAACCGTGCTATTGCAATCTCAAGGTGGTGAACAACAGCG
genomic: TGGCGGCGGAACGCTGATCTCCATCTACCCCGAGGACCTCACTTTCCTATgtaagttcag ... tcgcgtgcagTTGAGCTGGACAAACCGTGCTATTGCAATCTCAAGGTGGTGAACAACAGCG
EST: gi|88401755|gb|CI591082.1|CI591082
EST:     TGGCGGGGGAACGCTGATCTCCATCTACCCCGAGGACCTCACTTTCCTAT                         TTGAGCTGGACAAACCGTGCTATTGCAATCTCAAGGTGGTGAACAACAGCG
genomic: TGGCGGCGGAACGCTGATCTCCATCTACCCCGAGGACCTCACTTTCCTATgtaagttcag ... tcgcgtgcagTTGAGCTGGACAAACCGTGCTATTGCAATCTCAAGGTGGTGAACAACAGCG
EST: gi|88389102|gb|CI595336.1|CI595336
EST:     TGGCGGCGGAACGCTGATCTCCATCTACCCCGAGGACCTCACTTTCCTAT                         TTGAGCTGGACAAACCGTGCTATTGCAATCTCAAGGTGGTGAACAACAGCG
genomic: TGGCGGCGGAACGCTGATCTCCATCTACCCCGAGGACCTCACTTTCCTATgtaagttcag ... tcgcgtgcagTTGAGCTGGACAAACCGTGCTATTGCAATCTCAAGGTGGTGAACAACAGCG
EST: gi|88405086|gb|CI685534.1|CI685534
EST:     TGGCGGCGGAACGCTGATCTCCATCTACCCCGAGGACCTCACTTTCCTAT                         TTGAGCTGGACAAACCGTGCTATTGCAATCTCAAGGTGGTGAACAACAGCG
genomic: TGGCGGCGGAACGCTGATCTCCATCTACCCCGAGGACCTCACTTTCCTATgtaagttcag ... tcgcgtgcagTTGAGCTGGACAAACCGTGCTATTGCAATCTCAAGGTGGTGAACAACAGCG
EST: gi|88581198|gb|CI698173.1|CI698173
EST:     TGGCGGCGGAACGCTGATCTCCATCTACCCCGAGGACCTCACTTTCCTAT                         TTGAGCTGGACAAACCGTGCTATTGCAATCTCAAGGTGGTGAACAACAGCG
genomic: TGGCGGCGGAACGCTGATCTCCATCTACCCCGAGGACCTCACTTTCCTATgtaagttcag ... tcgcgtgcagTTGAGCTGGACAAACCGTGCTATTGCAATCTCAAGGTGGTGAACAACAGCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taatttagccttaaccatccgtggtttcttctctccgttgaattctcgcgtgcagTTGAGCTGGACAAACCGTGCTATTGCAATCTCAAGGTGGTGAACAACAGCGAGCATCATGTTGCATTCAAG
        ccttaac  putative branch site (score: 3)
                                          ttctcgc  putative PPT
                                     ttgaatt  TA-rich tract