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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgttcaatggcacactgtacaggaagtataagttctcttttctcatgatcttttacgttattctttggttaacacgtggtttatgcacccttttgttctttttcagGCTTCCCAGATATTTCAGTCTGTGAAAATTGATATGCTCTCAAGAATGATCCCATTCTTTGACTTTTCTGTTGTTGAGAAGATCTCTGTTGATGCCGTGA

Basic information

species Oryza sativa
transcript LOC_Os01g03070.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g03070.2 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G070487_T04 (Zea mays), 3'ss of exon 4
gtatgttcaatggcacactgtacaggaagtataagttctcttttctcatgatcttttacgttattctttggttaacacgtggtttatgcacccttttgttctttttcagGCTTCCCAGATATTTCAGTCTGTGAAAATTGATATGCTCTCAAGAATGATCCCATTCTTTGACTTTTCTGTTGTTGAGAAGATCTCTGTTGATGCCGTGA
    |||| |   ||   | | |   |  | |  || ||  |||   || ||         ||||  |||   || |     |||  |      |       ||||||||| ||    || || |||||  |||| ||||||||||||||||||||||| || ||||||||||||| |||||| |||||||| ||||||| ||| ||||
----gttcta-atcatgttctgctatatttgtttgtacttattttatataat------tactatttgttg--caataatgacttttagtgtttgtcctcctcttttcagGCCTCTTGTATTTTCCAGTCGATGAAGATTGATATGCTCTCAAGAATGATTCCGTTCTTTGACTTTTTTGTTGTGGAGAAGATTTCTGTTGTTGCTGTGA

upper sequence: LOC_Os01g03070.2 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G093050_T01 (Zea mays), 3'ss of exon 7
gtatgttcaatggcacactgtacaggaagtataagttctcttttctcatgatcttttacgttattctttggttaacacgtggtttatgcacccttttgttctttttcagGCTTCCCAGATATTTCAGTCTGTGAAAATTGATATGCTCTCAAGAATGATCCCATTCTTTGACTTTTCTGTTGTTGAGAAGATCTCTGTTGATGCCGTGA
                  |    | |   |   |  | | |||   ||| | ||| ||  ||  | | || |  |    ||  || |      | |  | |  |||||||| ||    || ||| | ||  | || ||||||||||||||||||||||| |||||||||||||| ||||| || |||||||| ||||||||||| |  |
--------------gtcttaattaagttctgctatatatgtttgtacataa-cttgtaaattgctatatgttgcaataatgacttctagtgtttctcttccaatttcagGCCTCTTGTATTTTTAAATCCATAAAGATTGATATGCTCTCAAGAATGATTCCATTCTTTGACTTCTCTGTCGTGGAGAAGATTTCTGTTGATGCTGCCA
















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|86427691|gb|CI072788.1|CI072788
EST:     AGTACCTTCCTGCTTNGGAGAAGTTAACAACTTTAAGGGTGTTGCAACAG                         GCTTCCCAGATATTTCAGTCTGTGAAAATTGATATGCTCTCAAGAATGATC
genomic: AGTACCTTCCTGCTTTGGAGAAGTTAACAACTTTAAGGGTGTTGCAACAGgtatgttcaa ... tctttttcagGCTTCCCAGATATTTCAGTCTGTGAAAATTGATATGCTCTCAAGAATGATC
EST: gi|88964806|gb|CI084804.1|CI084804
EST:     AGTACCTTCCTGCTTTGGAGAAGTTAACAACTTTAAGGGTGTTGCAACAG                         GCTTCCCAGATATTTCAGTCTGTGAAAATTGATATGCTCTCAAGAATGATC
genomic: AGTACCTTCCTGCTTTGGAGAAGTTAACAACTTTAAGGGTGTTGCAACAGgtatgttcaa ... tctttttcagGCTTCCCAGATATTTCAGTCTGTGAAAATTGATATGCTCTCAAGAATGATC
EST: gi|89192877|gb|CI050175.1|CI050175
EST:     AGTACCTTCCTGCTTTGGAGAAGTTAACAACTTTAAGGGTGTTGCAACAG                         GCTTCCCAGATATTTCAGTCTGTGAAAATTGATATGCTCTCAAGAATGATC
genomic: AGTACCTTCCTGCTTTGGAGAAGTTAACAACTTTAAGGGTGTTGCAACAGgtatgttcaa ... tctttttcagGCTTCCCAGATATTTCAGTCTGTGAAAATTGATATGCTCTCAAGAATGATC
EST: gi|29673992|gb|CB670267.1|CB670267
EST:     AGTACCTTCCTGCTTTGGAGAAGTTAACAACTTTAAGGGTGTTGCAACAC                         GCTTCCCAGATATTTCAGTCTGTGAAAATTGATATGCTCTCAAGAATGATC
genomic: AGTACCTTCCTGCTTTGGAGAAGTTAACAACTTTAAGGGTGTTGCAACAGgtatgttcaa ... tctttttcagGCTTCCCAGATATTTCAGTCTGTGAAAATTGATATGCTCTCAAGAATGATC
EST: gi|86429925|gb|CI082348.1|CI082348
EST:     AGTACCTTCCTGCTTTGGAGAAGTTAACAACTTTAAGGGTGTTGCAACAG                         GCTTCCCAGATATTTCAGTCTGTGAAAATTGATATGCTCTCAAGAATGATC
genomic: AGTACCTTCCTGCTTTGGAGAAGTTAACAACTTTAAGGGTGTTGCAACAGgtatgttcaa ... tctttttcagGCTTCCCAGATATTTCAGTCTGTGAAAATTGATATGCTCTCAAGAATGATC
EST: gi|89185749|gb|CI047618.1|CI047618
EST:     AGTACCTTCCTGCTTTGGAGAAGTTAACAACTTTAAGGGTGTTGCAACAG                         GCTTCCCAGATATTTCAGTCTGTGAAAATTGATATGCTCTCAAGAATGATC
genomic: AGTACCTTCCTGCTTTGGAGAAGTTAACAACTTTAAGGGTGTTGCAACAGgtatgttcaa ... tctttttcagGCTTCCCAGATATTTCAGTCTGTGAAAATTGATATGCTCTCAAGAATGATC
EST: gi|88263846|gb|CI367620.1|CI367620
EST:     AGTACCTTCCTGCTTTGGAGAAGTTAACAACTTTAAGGGTGTTGCAACAG                         GCTTCCCAGATATTTCAGTCTGTGAAAATTGATATGCTCTCAAGAATGATC
genomic: AGTACCTTCCTGCTTTGGAGAAGTTAACAACTTTAAGGGTGTTGCAACAGgtatgttcaa ... tctttttcagGCTTCCCAGATATTTCAGTCTGTGAAAATTGATATGCTCTCAAGAATGATC
EST: gi|58695557|gb|CK084244.1|CK084244
EST:     AGTACCTTCCTGCTTTGGAGAAGTTAACAACTTTAAGGGTGTTGCAACAG                         GCTTCCCAGATATTTCAGTCTGTGAAAATTGATATGCTCTCAAGAATGATC
genomic: AGTACCTTCCTGCTTTGGAGAAGTTAACAACTTTAAGGGTGTTGCAACAGgtatgttcaa ... tctttttcagGCTTCCCAGATATTTCAGTCTGTGAAAATTGATATGCTCTCAAGAATGATC
EST: gi|86432397|gb|CI086008.1|CI086008
EST:     AGTACCTTCCTGCTTTGGAGAAGTTAACAACTTTAAGGGTGTTGCTACAG                         GCTTCCCAGATATTTCAGTCTGTGAAAATTGATATGCTCTCAAGAATGATC
genomic: AGTACCTTCCTGCTTTGGAGAAGTTAACAACTTTAAGGGTGTTGCAACAGgtatgttcaa ... tctttttcagGCTTCCCAGATATTTCAGTCTGTGAAAATTGATATGCTCTCAAGAATGATC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttacgttattctttggttaacacgtggtttatgcacccttttgttctttttcagGCTTCCCAGATATTTCAGTCTGTGAAAATTGATATGCTCTCAAGAATGATCCCATTCTTTGACTTTTCTGTTGTTGAGAAGATCTCTGTTGATGCCGTGA
               ggttaac  putative branch site (score: 3)
                                tgcacccttttgttct  putative PPT
      ttattcttt  TA-rich tract