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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacaatcattcaaccaatgttgctgccatgccatttaattaagctcgcaaccttggtcagagagattcagagtgaacttgacgacctggctgcagGCGCGTCGAGCGGCATCGGGCTGGAGACGACGCGCGTGTTGGCGCTGCGCGGCGTGCGCGTCGTCATGGCCGTGCGCAACGTCGCCGCCGGGCACAAGGC

Basic information

species Oryza sativa
transcript LOC_Os10g40030.11
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os10g40030.4 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G464885_T01 (Zea mays), 3'ss of exon 1
gtacaatcattcaaccaatgttgctgccatgccattt----aattaagctcgcaaccttggtcagagagattcagagtgaacttgacgacctg---gctgcagGCGCGTCGAGCGGCATCGGGCTGGAGACGACGCGCGTGTTGGCGCTGCGCGGCGTGCGCGTCGTCATGGCCGTGCGCAACGTCGCCGCCGGGCACAAGGC
  || |  || |  |||   | |      |   | |     | ||    | ||| |   ||   |   |  |     |||   |    |||||      ||||| ||||||||||||||||||||||||||| |||| ||  ||||| |||||||||||| ||||||||||||||| ||||||||| ||||||||| ||||||
--accaa-atccggccagcttcgggctagtcggactccgagattttcatttgcagcgaaggaatgccggtgttgagctgagactacgtacctgcgcagcgcagGTGCGTCGAGCGGCATCGGGCTGGAGACGGCGCGTGTCCTGGCGTTGCGCGGCGTGCACGTCGTCATGGCCGTCCGCAACGTCTCCGCCGGGCTCAAGGC

upper sequence: LOC_Os10g40030.4 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G128577_T01 (Zea mays), 3'ss of exon 1
---------gtacaatcattcaacc-aatgttgctgccatgccatttaattaagctcgcaaccttggtcagagagattcagagtgaacttgacgacctggctgcagGCGCGTCGAGCGGCATCGGGCTGGAGACGACGCGCGTGTTGGCGCTGCGCGGCGTGCGCGTCGTCATGGCCGTGCGCAACGTCGCCGCCGGGCACAAGGC
         | |   |    | ||| | | |||  | | || ||||||    |   |    || |         ||  | ||| |    |  ||  ||  ||||||| ||| ||||||||||||||||||||||| |||||||  ||||||||||||| |||||||||||||||||||| ||||||||| | ||||||| || |||
gccggacttgcaagctggaacgacctagttttggagac-tgtcatttacggcaaaacaatgccatatatgagctgagcctgagcg---ctcgcgcgct--ctgcagGTGCGACGAGCGGCATCGGGCTGGAGACGGCGCGCGTTCTGGCGCTGCGCGGTGTGCGCGTCGTCATGGCCGTCCGCAACGTCTCAGCCGGGCTCATGGC

upper sequence: LOC_Os10g40030.4 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G464885_T02 (Zea mays), 3'ss of exon 1
gtacaatcattcaaccaatgttgctgccatgccatttaatt---aagctcgcaaccttggtcagagagattcagagtgaacttga--cgacctggctgc-------agGCGCGTCGAGCGGCATCGGGCTGGAGACGACGCGCGTGTTGGCGCTGCGCGGCGTGCGCGTCGTCATGGCCGTGCGCAACGTCGCCGCCGGGCACAAGGC
   |   ||   || |      ||| |       |   | |   |   |  ||      |  |  ||    | | ||  |  |||  | || |  ||||       ||| ||||||||||||||||||||||||||| |||| ||  ||||| |||||||||||| ||||||||||||||| ||||||||| ||||||||| |     
---cggccaccaaatccggccagcttcgggctagtcggactccgagattttcatttgcagcgaaggaatgccggtgttgagctgagactacgtacctgcgcagCGCAGGTGCGTCGAGCGGCATCGGGCTGGAGACGGCGCGTGTCCTGGCGTTGCGCGGCGTGCACGTCGTCATGGCCGTCCGCAACGTCTCCGCCGGGCTC-----

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|88335213|gb|CI658220.1|CI658220
EST:     GGAGGTCACCGCCGGCGTCGACGCCCGGGGCTTGGCCGCCGTCGTCACAG                         GCGCGTCGAGCGGCATCGGGCTGGAGACGACGCGCGTGTTGGCGCTGCGCG
genomic: GGAGGTCACCGCCGGCGTCGACGCCCGGGGCTTGGCCGCCGTCGTCACAGgtacaatcat ... ctggctgcagGCGCGTCGAGCGGCATCGGGCTGGAGACGACGCGCGTGTTGGCGCTGCGCG
EST: gi|88383988|gb|CI631878.1|CI631878
EST:     GGAGGTCACCGCCGGCGTCGACGCCCGGGGCTTGGCCGCCGTCGTCACAG                         GCGCGTCGAGCGGCATCGGGCTGGAGACGACGCGCGTGTTGGCGCTGCGCG
genomic: GGAGGTCACCGCCGGCGTCGACGCCCGGGGCTTGGCCGCCGTCGTCACAGgtacaatcat ... ctggctgcagGCGCGTCGAGCGGCATCGGGCTGGAGACGACGCGCGTGTTGGCGCTGCGCG
EST: gi|86885823|gb|CI295944.1|CI295944
EST:     GGAGGTCACCGCCGGCGTCGACGCCCGGGGCTTGGCCGCCGTCGTCACAG                         GCGCGTCGAGCGGCATCGGGCTGGAGACGACGCGCGTGTTGGCGCTGCGCG
genomic: GGAGGTCACCGCCGGCGTCGACGCCCGGGGCTTGGCCGCCGTCGTCACAGgtacaatcat ... ctggctgcagGCGCGTCGAGCGGCATCGGGCTGGAGACGACGCGCGTGTTGGCGCTGCGCG
EST: gi|29656760|gb|CB653035.1|CB653035
EST:     GGAGGTCACCGCCGGCGTCGACGCCCGGGGCTTGGCCGCCGTCGTCACAG                         GCGCGTCGAGCGGCATCGGGCTGGAGACGACGCGCGTGTTGGCGCTGCGCG
genomic: GGAGGTCACCGCCGGCGTCGACGCCCGGGGCTTGGCCGCCGTCGTCACAGgtacaatcat ... ctggctgcagGCGCGTCGAGCGGCATCGGGCTGGAGACGACGCGCGTGTTGGCGCTGCGCG
EST: gi|88402445|gb|CI596306.1|CI596306
EST:     GGAGGTCACCGCCGGCGTCGACGCCCGGGGCTTGGCCGCCGTCGTCACAG                         GCGCGTCGAGCGGCATCGGGCTGGAGACGACGCGCGTGTTGGCGCTGCGCG
genomic: GGAGGTCACCGCCGGCGTCGACGCCCGGGGCTTGGCCGCCGTCGTCACAGgtacaatcat ... ctggctgcagGCGCGTCGAGCGGCATCGGGCTGGAGACGACGCGCGTGTTGGCGCTGCGCG
EST: gi|38469273|gb|CF953404.1|CF953404
EST:     GGAGGTCACCGCCGGCGTCGACGCCCGGGGCTTGGCCGCCGTCGTCACAG                         GCGCGTCGAGCGGCATCGGGCTGGAGACGACGCGCGTGTTGGCGCTGCGCG
genomic: GGAGGTCACCGCCGGCGTCGACGCCCGGGGCTTGGCCGCCGTCGTCACAGgtacaatcat ... ctggctgcagGCGCGTCGAGCGGCATCGGGCTGGAGACGACGCGCGTGTTGGCGCTGCGCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aagctcgcaaccttggtcagagagattcagagtgaacttgacgacctggctgcagGCGCGTCGAGCGGCATCGGGCTGGAGACGACGCGCGTGTTGGCGCTGCGCGGCGTGCGCGTCGTCATGGCCGTGCGCAACGTCGCCGCCGGGCACAAGGC
                                   acttgac  putative branch site (score: 4)