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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tatacactgatgatgaacagctttactgaatgcaggtagccgaaagctagagaacaagctaacaataataccacgtttgtgttcttggtttgtttggcagCGAGATCATGCACGCGATGTGGAAGCCCGCCAAGTTCAAATACATCTACCTGCTGGCGACGCTGTACGTGTTCACGCTGACGCTGCCGTCGTCGGCGGCC

Basic information

species Zea mays
transcript GRMZM2G127949_T03
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G127949_T03 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os01g63770.2 (Oryza sativa), 3'ss of exon 2
-tatacactgatgatgaacagctttactgaatgcaggt-agccgaaagctagagaacaagctaacaataataccacgtttgtgttcttggtttgtttggcagCGAGATCATGCACGCGATGTGGAAGCCCGCCAAGTTCAAATACATCTACCTGCTGGCGACGCTGTACGTGTTCACGCTGACGCTGCCGTCGTCGGCGGCC
  ||   | || |  |    |          ||  | | |       || ||| || ||  |||  |         | | |   | |||| ||| |  |||| ||||||||||||||||||||||| || ||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||| || |||||
gcatgtgccgaggccgttttgtccgttgatttgttgattaataacctgcaagaaaagaaaataatgactgattgggggtggctgttttggattggt--gcagGGAGATCATGCACGCGATGTGGAAACCGGCCAAGTTCAAGTACATCTACCTGCTGGCGACGCTGTACGTGTTCACGCTGACGCTGCCGTCGGCGTCGGCC

upper sequence: GRMZM2G127949_T03 (Zea mays), 3'ss of exon 3
lower sequence: PP1S213_89V6.1 (Physcomitrella patens), 3'ss of exon 5
-----------------------------------------------------tatacactgatgatgaacagctttactgaatgcaggtagccgaaagctagagaacaagctaacaataataccacgtttgtgttcttggtttgt-ttggcagCGAGATCATGCACGCGATGTGGAAGCCCGCCAAGTTCAAATACATCTACCTGCTGGCGACGCTGTACGTGTTCACGCTGACGCTGCCGTCGTCGGCGGCC
                                                      |  |  |  |        | |  |   | |     | | |     ||   |  ||     | || |   || |       ||| |  ||  | ||| ||| |||||||||||||| ||||  || |||  ||||||||| ||| | | |||| ||||||||||||||||||||||||||||  | || ||  | | ||| 
gtaagtaaaaaagggagctcctcctcctgctcctctctcaacggttttcatcccaatcgttcctcgatttttgttccagcaattttgtattgtcactcactgaggctcagagagaaaaaaggccctcaaac---ttcctaattactattgccagGGAGATCATGCACGCCATGTACAAACCCAGCAAGTTCAAGTACGTTTTCCTGTTGGCGACGCTGTACGTGTTCACGCTGACAATCCCCTCCGCAGTGGCA

upper sequence: GRMZM2G127949_T03 (Zea mays), 3'ss of exon 3
lower sequence: EFJ34222 (Selaginella moellendorffii), 3'ss of exon 5
tatacactgatgatgaacagctttactgaatgcaggtagccgaaagctagagaacaagctaacaataataccacgtttgtgttcttggtttgtttggcagCGAGATCATGCACGCGATGTGGAAGCCCGCCAAGTTCAAATACATCTACCTGCTGGCGACGCTGTACGTGTTCACGCTGACGCTGCCGTCGTCGGCGGCC
              | |    ||  ||   |     | || |     |   | |       | |   ||       |  |   ||| | |   ||  ||| |||||||||||||||||||||||||||   |||||||| |   |||| ||  | || ||  | ||||| |||||  |||| || |||||  |  |||| 
--------------gtaagctttcgcttctt-----tcgctg----ttcttgcatggatcgataggcatctt---ctcataaactttgatc--ttcccagGGAGATCATGCACGCGATGTGGAAGCCCCAAAAGTTCAAGTGGGTCTATCTCGTCGCTACCATCTACGTCTTCACCTTGACACTCCCGTCCGCCACGGCA

upper sequence: GRMZM2G127949_T03 (Zea mays), 3'ss of exon 3
lower sequence: EFJ21839 (Selaginella moellendorffii), 3'ss of exon 5
tatacactgatgatgaacagctttactgaatgcaggtagccgaaagctagagaacaagctaacaataataccacgtttgtgttcttggtttg--tttggcagCGAGATCATGCACGCGATGTGGAAGCCCGCCAAGTTCAAATACATCTACCTGCTGGCGACGCTGTACGTGTTCACGCTGACGCTGCCGTCGTCGGCGGCC
                  ||||||      |   | |   |            | | ||||    |  |  ||  |||          ||||   ||  ||| |||||||||||||||||||||||||||   |||||||| |   |||| ||  | || ||  | ||||| |||||  |||| || |||||  |  |||| 
---------------gtaagctttcgcttctttcgctgttcttgcatggatcgataggcta----tgttgtcatcttttctcataaactttgatcttcccagGGAGATCATGCACGCGATGTGGAAGCCCCAAAAGTTCAAGTGGGTCTATCTCGTCGCTACCATCTACGTCTTCACCTTGACACTCCCGTCCGCCACGGCA

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|71442197|gb|DR823247.1|DR823247
EST:     CCCGCAAGGAGAAGGAGGGCGTCAGCTTCAAGAACCACGTCATCCAG                         CGAGATCATGCACGCGATGTGGAAGCCCGCCAAGTTCAAATACATCTACCT
genomic: CCCGCAAGGAGAAGGAGGGCGTCAGCTTCAAGAACCACGTCATCCAGgtatggctct ... tgtttggcagCGAGATCATGCACGCGATGTGGAAGCCCGCCAAGTTCAAATACATCTACCT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gctagagaacaagctaacaataataccacgtttgtgttcttggtttgtttggcagCGAGATCATGCACGCGATGTGGAAGCCCGCCAAGTTCAAATACATCTACCTGCTGGCGACGCTGTACGTGTTCACGCTGACGCTGCCGTCGTCGGCGGCC
           agctaac  putative branch site (score: 2)
                                           tttgttt  putative PPT
              taacaataata  TA-rich tract