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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtccgtctctcccctctcggttcgccagtttgccatatgtgcaaatacctagtggtatctgaatatctgcgcgcgcggcgtgcatgcagGCATCATGTTCAACGACATCACGCCGCTGCTGCTGCGCCCGGGGGTGTTCAAGGACGCCGTCGACATCTTCGTCGAGCGCTACCGCGGCATGGCCATCGC

Basic information

species Oryza sativa
transcript LOC_Os02g40010.4
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g40010.4 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G071846_T01 (Zea mays), 3'ss of exon 1
---------------------gtccgtctctcccctctcggttcgccagtt--tgccatatgtgcaaatacctagtggtatctgaatatctgcgcgcgcggcgtg---------ca--------tgcagGCATCATGTTCAACGACATCACGCCGCTGCTGCTGCGCCCGGGGGTGTTCAAGGACGCCGTCGACATCTTCGTCGAGCGCTACCGCGGCATGGCCATCGC
                        || ||| | ||||||    ||||   |  |||||  |||||      | |||     ||   |  ||  ||  ||| |||          ||        |||||||||||||||||||||||||||  ||||||||||||||||  ||||||||||||||||||||||| | |||||||||||||||||||| |||  ||||| 
gtactacgcctttcttcactcactcg-ctcactcctctccacacgccttctgctgccaattgtgccgcccgccagtaacgccttccttgctctgcatgcgccgtcgttgggggccacgggacgctgcagGCATCATGTTCAACGACATCACCACGCTGCTGCTGCGCCCCAGGGTGTTCAAGGACGCCGTCGACCTGTTCGTCGAGCGCTACCGCGGGATGCGCATCGA

upper sequence: LOC_Os02g40010.4 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G179810_T03 (Zea mays), 3'ss of exon 1
---------gtccgt-ctctcccctctcggttcgccagtttgccatatgtgcaaatacctagtggtatc-tgaatatctgcgcgcgcggcgtgcatgcagGCATCATGTTCAACGACATCACGCCGCTGCTGCTGCGCCCGGGGGTGTTCAAGGACGCCGTCGACATCTTCGTCGAGCGCTACCGCGGCATGGCCATCGC
         | |||| || |    | || | |   |    |    | | ||    |   |    | ||| ||  |        | | ||| |||   |||||||||||||||||||||||||  ||||||||||||||||  ||||||||||||||||||||||| | ||||||||||| |||||||| |||| ||||| 
agtaacgctgaccgttcttttttttttctgcttcgcgcgctcttgtgtatgtgtgtgtgtgcatgcatcatgcgtgcgccgttggggggcttgcggtcagGCATCATGTTCAACGACATCACCACGCTGCTGCTGCGCCCCAGGGTGTTCAAGGACGCCGTCGACCTGTTCGTCGAGCGGTACCGCGGGATGGGCATCGA
















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|88211248|gb|CI210888.1|CI210888
EST:     ACGCCATCCGCGTCGTCCCCCACTTCCCCAAGCAAG                         GCATCATGTTTAACGACATCACGCCGCTGCTGCTGCGCCCGGGGGTGTTCA
genomic: ACGCCATCCGCGTCGTCCCCCACTTCCCCAAGCAAGgtccgtctct ... gtgcatgcagGCATCATGTTCAACGACATCACGCCGCTGCTGCTGCGCCCGGGGGTGTTCA
EST: gi|88828038|gb|CI778603.1|CI778603
EST:     TCAGGGCATCTCCGACGCCATCCGCGTCGTCCCCCACTTCCCCAAGCAAG                         GCATCATGTTCAACGACATCACGCCGCTGCTGCTGCGCCCGGGGGTGTTCA
genomic: TCAGGGCATCTCCGACGCCATCCGCGTCGTCCCCCACTTCCCCAAGCAAGgtccgtctct ... gtgcatgcagGCATCATGTTCAACGACATCACGCCGCTGCTGCTGCGCCCGGGGGTGTTCA
EST: gi|88743547|gb|CI767055.1|CI767055
EST:     TCAGGGCATCTCCGACGCCATCCGCGTCGTCCCCCACTTCCCCAAGCAAG                         GCATCATGTTCAACGACATCACGCCGCTGCTGC
genomic: TCAGGGCATCTCCGACGCCATCCGCGTCGTCCCCCACTTCCCCAAGCAAGgtccgtctct ... gtgcatgcagGCATCATGTTCAACGACATCACGCCGCTGCTGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atatgtgcaaatacctagtggtatctgaatatctgcgcgcgcggcgtgcatgcagGCATCATGTTCAACGACATCACGCCGCTGCTGCTGCGCCCGGGGGTGTTCAAGGACGCCGTCGACATCTTCGTCGAGCGCTACCGCGGCATGGCCATCGC
                         tgaatat  TA-rich tract