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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gcaagtgatcagttaagctagcttaattttgcgtgaatttttactacttgtactgcatgatgctactcgtgttggtttgttcttcagGGTCAGGAAGCTGTCGGAGATGACGGAGAAGATGAGCCAGTCGTTGCTCGACACGGTCATCGCGGTGACGGGGTCCATGGCCGCGCCGCTGCTTCGTTCG

Basic information

species Oryza sativa
transcript LOC_Os01g52480.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g52480.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G151245_T01 (Zea mays), 3'ss of exon 2
-----gcaagtgatcagttaagctagctta-attttgcgtgaatttttactacttgtactg-catgatgctactcgtgttggtttgttc--ttcagGGTCAGGAAGCTGTCGGAGATGACGGAGAAGATGAGCCAGTCGTTGCTCGACACGGTCATCGCGGTGACGGGGTCCATGGCCGCGCCGCTGCTTCGTTCG
      ||||     |   | |||  |||   |  ||| |  | | |   | ||  |  |   |  | |||   |   |||  ||| ||  ||||||||||||||||||||||||||||| |||||||||||||||||| ||||||||||||||||| ||||||| ||||||||||| ||||||||| | || || 
gtaactcaagaacctatgcatgctttcttttgtcctgcatctactgtctatgctcatgttaatagcaagctttgctgattgcgttgatcaattcagGGTCAGGAAGCTGTCGGAGATGACCGAGAAGATGAGCCAGTCGCTGCTCGACACGGTCATCTCGGTGACCGGGTCCATGGCGGCGCCGCTGATCCGCTCC
















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|87021599|gb|CI275998.1|CI275998
EST:     ACCGCCCAACCGAACGCGAAGCGCGGAGGAGTCAACAAGAGCCTCAAGAG                         GGTCAGGAAGCTGTCGGAGATGACGGAGAAGATGAGCCAGTCGTTGCTCGA
genomic: ACCGGCCAACCGGACGCGAAGCGCGGAGGAGTCAACAAGAGCCTCAAGAGgcaagtgatc ... tgttcttcagGGTCAGGAAGCTGTCGGAGATGACGGAGAAGATGAGCCAGTCGTTGCTCGA
EST: gi|86597874|gb|CI276660.1|CI276660
EST:     GCCAACCGGACGCGAAGCGCGGAGGAGTCAACAAGAGCCTCAAGAG                         GGTCAGGAAGCTGTCGGAGATGACGGAGAAGATGAGCCAGTCGTTGCTCGA
genomic: GCCAACCGGACGCGAAGCGCGGAGGAGTCAACAAGAGCCTCAAGAGgcaagtgatc ... tgttcttcagGGTCAGGAAGCTGTCGGAGATGACGGAGAAGATGAGCCAGTCGTTGCTCGA
EST: gi|86501629|gb|CI144262.1|CI144262
EST:     GACGCGAAGCGCGGAGGAGTCAACAAGAGCCTCAAGAG                         GGTCAGGAAGCTGTCCGGAGATGACGGAGAAGATGAGCCAGTCGTTGCTCG
genomic: GACGCGAAGCGCGGAGGAGTCAACAAGAGCCTCAAGAGgcaagtgatc ... tgttcttcagGGTCAGGAAGCTGT-CGGAGATGACGGAGAAGATGAGCCAGTCGTTGCTCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgaatttttactacttgtactgcatgatgctactcgtgttggtttgttcttcagGGTCAGGAAGCTGTCGGAGATGACGGAGAAGATGAGCCAGTCGTTGCTCGACACGGTCATCGCGGTGACGGGGTCCATGGCCGCGCCGCTGCTTCGTTCG
                                           tttgttcttc  CT-rich tract
     tttttacta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcaagtgatcagttaagctagcttaattttgcgtgaatttttactacttgtactgcatgatgctactcgtgttggtttgttcttcagGGTCAGGAAGCTGTCGGAGATGACGGAGAAGATGAGCCAGTCGTTGCTCGACACGGTCATCGCGGTGACGGGGTCCATGGCCGCGCCGCTGCTTCGTTCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT