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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgaggccgggttcctgagctctctttcttttttttttcttaattcatgtcgcttcgtccttccgataacccacgggccacggccattcccagGCCCGTCGAAGAAGGTGAAGCTGGACTGGGACACGAGGCTGAGGATCGCAGTGGGCGCCGCGCAGGGGCTGGCGTACCTCCACCACGACTGCAACCCGCG

Basic information

species Zea mays
transcript GRMZM2G082855_T04
intron # 23
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G082855_T02 (Zea mays), 3'ss of exon 23
lower sequence: LOC_Os06g03970.1 (Oryza sativa), 3'ss of exon 24
gtgaggccgggttcctgagctctctttcttttttttttcttaattcatgtcgcttcgtccttccgataacccacgggccacggccattcccagGCCCGTCGAAGAAGGTGAAGCTGGACTGGGACACGAGGCTGAGGATCGCAGTGGGCGCCGCGCAGGGGCTGGCGTACCTCCACCACGACTGCAACCCGCG
    |   ||| |    | || |   || |   |  ||  | || |||   || ||  ||||   || | | |      | |  | ||  |||| || || ||||| ||||||||  |||||||||| || ||||||||||| || || || || || |||||||| || |||||||| ||||||||||| ||
----gttagggcttgaaacctttggctcatggataatttgttat-cattatgcatctccctt---atgatctata---tatgatccttttcagGTCCATCAAAGAAAGTGAAGCTCAACTGGGACACAAGACTGAGGATCGCGGTCGGAGCTGCACAAGGGCTGGCCTATCTCCACCATGACTGCAACCCTCG

upper sequence: GRMZM2G082855_T02 (Zea mays), 3'ss of exon 23
lower sequence: EFJ16326 (Selaginella moellendorffii), 3'ss of exon 24
gtgaggccgggttcctgagctctctttcttttttttttcttaattcatgtcgcttcgtccttccgataacccacgggccacggccattcccagGCCCGTCGAAGAAGGTGAAGCTGGACTGGGACACGAGGCTGAGGATCGCAGTGGGCGCCGCGCAGGGGCTGGCGTACCTCCACCACGACTGCAACCCGCG
                         |     || |  ||||  ||      |||    | ||   || | |    ||  ||     || ||||| ||   ||  ||||||| ||| ||||||||| || || |||  |||||  ||||||| ||||||||||||| |||||| |||||| |||||| ||| ||
------------------------gtatgacttctcatcttcctttgcaaagctctaacgttttcatgatcttttggaaac-----tttccagGACCAGTGAGAAAGGTGACGCTCGACTGGGACGCGCGGTTGATCATCGCGCTGGGCGCTGCGCAGGGGCTGGAGTACCTGCACCACAACTGCAGCCCCCG

upper sequence: GRMZM2G082855_T02 (Zea mays), 3'ss of exon 23
lower sequence: EFJ17800 (Selaginella moellendorffii), 3'ss of exon 24
gtgaggccgggttcctgagctctctttcttttttttttcttaattcatgtcgcttcgtccttccgataacccacgggccacggcca-ttcccagGCCCGTCGAAGAAGGTGAAGCTGGACTGGGACACGAGGCTGAGGATCGCAGTGGGCGCCGCGCAGGGGCTGGCGTACCTCCACCACGACTGCAACCCGCG
                                            |    || |||| || || | |    | |        ||  | || ||||| ||   ||  ||||||| ||| ||||||||| || || |||  |||||  ||||||| ||||||||||||| ||||||||||||| |||||| ||| ||
-----------------------------------------gtatagcttctcttcttctttgcaaagctctaaatcttgtggaaactttccagGACCAGTGAGAAAGGTGACGCTCGACTGGGACGCGCGGTTGATCATCGCGCTGGGCGCTGCGCAGGGGCTGGAGTACCTCCACCACAACTGCAGCCCCCG

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|78117622|gb|DV536009.1|DV536009
EST:     GCTGTTCTACGACTACATGGAGAACGGCTCCCTGTGGGATCTTCTCCATG                         GCCCGTCGAAGAAGGTGAAGCTGGACTGGGACACGAGGCTGAGGATCGCAG
genomic: GCTGTTCTACGACTACATGGAGAACGGCTCCCTGTGGGATCTTCTCCATGgtgaggccgg ... ccattcccagGCCCGTCGAAGAAGGTGAAGCTGGACTGGGACACGAGGCTGAGGATCGCAG
EST: gi|71775016|gb|DR972894.1|DR972894
EST:     GCTGTTCTACGACTACATGGAGAACGGCTCCCTGTGGGATCTTCTCCATG                         GCCCGTCGAAGAAGGTGAAGCTGGA
genomic: GCTGTTCTACGACTACATGGAGAACGGCTCCCTGTGGGATCTTCTCCATGgtgaggccgg ... ccattcccagGCCCGTCGAAGAAGGTGAAGCTGGA
EST: gi|149088301|gb|EE177395.2|EE177395
EST:     GCTGTTCTACGACTACATGGAGAACGGCTCCCTGTGGGATCTTCTCCATG                         GCCCCGTCGA-GAAGGTGAAGCTGGACTGGGACACGAGGCTGAGGATCGCA
genomic: GCTGTTCTACGACTACATGGAGAACGGCTCCCTGTGGGATCTTCTCCATGgtgaggccgg ... ccattcccagGCCC-GTCGAAGAAGGTGAAGCTGGACTGGGACACGAGGCTGAGGATCGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttaattcatgtcgcttcgtccttccgataacccacgggccacggccattcccagGCCCGTCGAAGAAGGTGAAGCTGGACTGGGACACGAGGCTGAGGATCGCAGTGGGCGCCGCGCAGGGGCTGGCGTACCTCCACCACGACTGCAACCCGCG
                         cgataac  putative branch site (score: 3)
                                             ccattccc  putative PPT