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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gagaaaggatagttgagtgctccagctgctctcgcagttctgtgcaaccaacggcttgttcttaacccccttctctgccaccaaaaccgatctatttcagGCAGGAGATTCGCTCTGCCACGAGCTCGATGACTTCGGTTCCAAAGCCACTGAAATTCCTCCGCCCACACTTTGGAACTCTCAAGTCCTATTTCGAAACA

Basic information

species Zea mays
transcript GRMZM2G155384_T02
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G155384_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os02g05340.1 (Oryza sativa), 3'ss of exon 2
gagaaaggatagttgagtgctccagctgctctcgcagttctgtgcaaccaacggct--tgttcttaacccccttctctgccaccaaaa--ccgatctatttc--agGCAGGAGATTCGCTCTGCCACGAGCTCGATGACTTCGGTTCCAAAGCCACTGAAATTCCTCCGCCCACACTTTGGAACTCTCAAGTCCTATTTCGAAACA
      |  || ||   | | |||           | ||   |   |||||    |  || | | |   || |  |||| ||| ||||   |   ||   |   |||||||||||||| || ||||| ||||| ||||| || || ||||||||||||||||||||||| ||||||| |||||| |||||||| || || ||||| 
------gtttattttgatccaccatagttagatttacttggttaagaccaaattttgttgctttgatttccatcttctgtcactaaaatatcatcctccctaaaagGCAGGAGATTCGTTCCGCCACAAGCTCAATGACATCTGTACCAAAGCCACTGAAATTCCTCCGGCCACACTATGGAACACTCAAGTCTTACTTTGAAACC

upper sequence: GRMZM2G155384_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA06G44340.1 (Glycine max), 3'ss of exon 2
gagaaaggatagttgagtgctccagctgctctcgc----agttctgtgcaa----ccaacggcttgttcttaacccc----cttctctgccaccaaaaccgatc------tatttcagGCAGGAGATTCGCTCTGCCACGAGCTCGATGACTTCGGTTCCAAAGCCACTGAAATTCCTCCGCCCACACTTTGGAACTCTCAAGTCCTATTTCGAAACA
  | ||   |||||   ||||| | |||  | |      | ||   ||  |        |   || ||||           | | | ||  |    ||    |       | || |||||| || |||||  || |||||||||| |||||||||||||| |||||| |||| ||||| || || || | ||| ||||| ||| ||||||  ||||| 
--gtaaacctagttttatgctcgaactgaacacattttgatttgaatgggaatttttggctatttattctagttttgaatgcatgtttgaaattggaatttgtggttgtgtgttgcagGCAAGAAATTCGAACTTCCACGAGCTCTATGACTTCGGTTCCTAAGCCATTGAAGTTCCTTCGTCCGCATTATGGCACTCTTAAGACCTATTATGAAACT

upper sequence: GRMZM2G155384_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA12G13410.1 (Glycine max), 3'ss of exon 2
gagaaaggatagttgagtgctccagctgctc----tcgcagttctgtgcaaccaacggcttgttcttaacccccttctctgccaccaaaaccga----------tctatttcagGCAGGAGATTCGCTCTGCCACGAGCTCGATGACTTCGGTTCCAAAGCCACTGAAATTCCTCCGCCCACACTTTGGAACTCTCAAGTCCTATTTCGAAACA
  | ||   |||||   ||||| |   |  |    |   | ||   || |          | || ||       || | ||      |||  |           | | ||  ||||| || |||||  || |||||||||| |||||||||||||| |||||  |||| ||||| ||||| || | ||| ||||| ||  | ||||  ||||| 
--gtaaacctagttttatgctcgaaaggaacaaattttgatttgaatggacatttttaactattttttttagttttatttgtgtttgaaattggaatgtgtggttgtgttctagGCAAGAAATTCGAACTTCCACGAGCTCTATGACTTCGGTTCCTAAGCCGTTGAAGTTCCTTCGCCCTCATTATGGCACTCTTAAAACGTATTATGAAACT

upper sequence: GRMZM2G155384_T01 (Zea mays), 3'ss of exon 2
lower sequence: EFJ26022 (Selaginella moellendorffii), 3'ss of exon 2
gagaaaggatagttgagtgctccagctgctctcgcagttctgtgcaaccaacggcttgttcttaacccccttctctgccaccaaaaccgatctattt---cagGCAGGAGATTCGCTCTGCCACGAGCTCGATGACTTCGGTTCCAAAGCCACTGAAATTCCTCCGCCCACACTTTGGAACTCTCAAGTCCTATTTCGAAACA
                                        |  || |  |   | ||  || |            ||     |  | |  | | | |   |||||| ||||||||   ||| || ||||| |||||||| || || ||||| ||||||||||||||||| || | ||| ||| | ||| | |  ||| | | |
---------------------------------------gtacgcgagtaggagtttaatcgt---------tcgtgttgtgaggagctgtgtgtatgcgcagGCAAGAGATTCGGAGTGCTACAAGCTCCATGACTTCCGTGCCCAAGCCGCTGAAATTCCTCCGCCCGCATTATGGGACTTTGAAGGCGTTCTTCCAGAAA

upper sequence: GRMZM2G155384_T01 (Zea mays), 3'ss of exon 2
lower sequence: EFJ14427 (Selaginella moellendorffii), 3'ss of exon 2
gagaaaggatagttgagtgctccagctgctctcgcagttctgtgcaaccaacggcttgttcttaacccccttctctgccaccaaaaccgatctattt---cagGCAGGAGATTCGCTCTGCCACGAGCTCGATGACTTCGGTTCCAAAGCCACTGAAATTCCTCCGCCCACACTTTGGAACTCTCAAGTCCTATTTCGAAACA
                                        |  || |  |   | ||  || |          | ||     |  | |  | | | |   |||||| ||||||||   ||| || ||||| |||||||| || || ||||| ||||||||||||||||| || | ||||||| | ||| | |  ||| | | |
---------------------------------------gtacgcgagtaggagtttaatcgt---------ttgtgttgtgaggagctgtgtgtatgcgcagGCAAGAGATTCGGAGTGCTACAAGCTCCATGACTTCCGTGCCCAAGCCGCTGAAATTCCTCCGCCCGCATTATGGAACTTTGAAGGCGTTCTTCCAGAAA

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|18649994|gb|BM498813.1|BM498813
EST:     GCGCAGGACGCGGATCCCGGCGTGCAGTAGCTCGCGCTCGAGAGCATGAG                         GCAGGAGATTC
genomic: GCGCAGGACGCGGATCCCGGCGTGCAGAAGCTCGCGCTCGAGAGCATGAGgtaccgctcg ... tctatttcagGCAGGAGATTC
EST: gi|19822561|gb|BQ048585.1|BQ048585
EST:     GCGCAGGACGCGGATCCCGGCGTGCAGAAGCTCGCGCTCGAGAGCATGAG                         GCAGGAGATTC
genomic: GCGCAGGACGCGGATCCCGGCGTGCAGAAGCTCGCGCTCGAGAGCATGAGgtaccgctcg ... tctatttcagGCAGGAGATTC
EST: gi|86468329|gb|DY234699.1|DY234699
EST:     GCGCAGGACGCGGATCCCGGCGTGCAGAAGCTCGCGCTCGAGAGCATGAG                         GCAGGAGATTCGCTCT
genomic: GCGCAGGACGCGGATCCCGGCGTGCAGAAGCTCGCGCTCGAGAGCATGAGgtaccgctcg ... tctatttcagGCAGGAGATTCGCTCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaccaacggcttgttcttaacccccttctctgccaccaaaaccgatctatttcagGCAGGAGATTCGCTCTGCCACGAGCTCGATGACTTCGGTTCCAAAGCCACTGAAATTCCTCCGCCCACACTTTGGAACTCTCAAGTCCTATTTCGAAACA
              tcttaac  putative branch site (score: 2)
                                             tctatttc  putative PPT
                                            atctattt  TA-rich tract