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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcgtttacatttttactgatcatccatttcttaattttgtggtactttgaattggagactttaatttcattgcattgctattcaacatttccaccaatagGTTAGTCATCATCCAATGCTGATTGCCTGCCACTGTGAAGGCAAGGGCTGGAAATTCTGGGGCGACAGCAATCTCAAATCCAAGTTTTGGGGACAGTCAA

Basic information

species Zea mays
transcript GRMZM2G402653_T03
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G402653_T03 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os08g05870.1 (Oryza sativa), 3'ss of exon 4
-----tcgtttacatttttactgatcatccatttcttaattttgtggtactttgaattggagactttaatttcattgcattgctattcaacatttccaccaatagGTTAGTCATCATCCAATGCTGATTGCCTGCCACTGTGAAGGCAAGGGCTGGAAATTCTGGGGCGACAGCAATCTCAAATCCAAGTTTTGGGGACAGTCAA
     | |  | | ||| ||    | | | |    ||||| |  || || | ||||        ||||||| ||   ||||||| |||  ||||| || || |||||||||||||| || ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||
gacacttgcctccttttctatctgtgaactaaaatttaatatcttgatagtgtgaagca-----tttaattgcaacacattgcttttcgtcattttcatcactagGTTAGTCATCACCCCATGCTGATTGCCTGCCACTGTGAAGGCAAGGGCTGGAAATTCTGGGGCGACAGCAATCTCAAATCCAAGTTTTGGGGGCAGTCAA

upper sequence: GRMZM2G402653_T03 (Zea mays), 3'ss of exon 4
lower sequence: Vv02s0154g00250.t01 (Vitis vinifera), 3'ss of exon 4
tcgtttacatttttactgatcatccatttcttaattttgtggtactttgaattggagactttaatttcattgcattgctattcaacatt-tccacc--aatagGTTAGTCATCATCCAATGCTGATTGCCTGCCACTGTGAAGGCAAGGGCTGGAAATTCTGGGGCGACAGCAATCTCAAATCCAAGTTTTGGGGACAGTCAA
    |    | |  | | |      | ||| | |    |   || |||    ||   | | | |||||||  |     | ||     || |  |    || ||||||||||||| ||||  || ||||||||||| |||||||| || || |||||||||||||  ||||| || ||   | | || ||||||||||  ||||
---ctcttctatcaattaagtcctgaattccttagcaagatttatttttctctgatcattgtcatttcatcaccccctttttttgtgttgtttattgaaacagGTTAGTCATCACCCAACACTCATTGCCTGCCATTGTGAAGGTAAAGGGTGGAAATTCTGGGCTGACAGTAACCTACGAACAAAATTTTGGGGACGATCAA

upper sequence: GRMZM2G402653_T03 (Zea mays), 3'ss of exon 4
lower sequence: Vv02s0154g00240.t01 (Vitis vinifera), 3'ss of exon 6
tcgtttacatttttactgatcatccatttcttaattttgtggtactttgaattggagactttaatttcattgcattgctattcaacatt-tccacc--aatagGTTAGTCATCATCCAATGCTGATTGCCTGCCACTGTGAAGGCAAGGGCTGGAAATTCTGGGGCGACAGCAATCTCAAATCCAAGTTTTGGGGACAGTCAA
    |    | |  | | |      | ||| | |    |   || |||    ||   | | | |||||||  |     | ||     || |  |    || ||||||||||||| ||||  || ||||||||||| |||||||| || || |||||||||||||  ||||| || ||   | | || ||||||||||  ||||
---ctcttctatcaattaagtcctgaattccttagcaagatttatttttctctgagcattgtcatttcatcaccccctttttttgtgttgtttattgaaacagGTTAGTCATCACCCAACACTCATTGCCTGCCATTGTGAAGGTAAAGGGTGGAAATTCTGGGCTGACAGTAACCTACGAACAAAATTTTGGGGACGATCAA

upper sequence: GRMZM2G402653_T03 (Zea mays), 3'ss of exon 4
lower sequence: PP1S67_260V6.1 (Physcomitrella patens), 3'ss of exon 5
tcgtttacatttttactgatcatccatttcttaattttgtggtactttgaattgg--agactttaatttcattgcat-tgctat-tcaacatttccaccaatagGTTAGTCATCATCCAATGCTGATTGCCTGCCACTGTGAAGGCAAGGGCTGGAAATTCTGGGGCGACAGCAATCTCAAATCCAAGTTTTGGGGACAGTCAA
      | || || | |    | |  ||| | |  | | | |  ||||  |||    | |  |||||    |||||| | |||| ||   |  |        |||| ||||||||||||||| |  | || || || || || ||||  ||||||||||||||||| ||||||||| | |||  |||||||||||| |  ||||
----ggagatattaatttgcaacctctttgtcatatctttcgagctttagattaagtaaaagttaatcatcttgcatcttctatctccctacgttgctttgcagGTGAGTCATCATCCAATGATTGTGGCATGTCATTGCGAGGGCAGAGGCTGGAAATTCTGGGGTGACAGCAATTTGAAAAGCAAGTTTTGGGGTCGTTCAA

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|26558450|gb|CA830685.1|CA830685
EST:     CCTATGAAGCTGATTACCCTGACAGAGGAATTCGNNNNNNNGCAGAAAAG                         GTTAGTCATCATCCAATGCTGATTGCCTGCCACTGTGAAGGCAAGGGCTGG
genomic: CCTATGAAGCTGATTACCCTGACAGAGGAATTCGTTTTTTTGCAGAAAAGgttagttaaa ... ccaccaatagGTTAGTCATCATCCAATGCTGATTGCCTGCCACTGTGAAGGCAAGGGCTGG
EST: gi|89106829|gb|DY577046.1|DY577046
EST:     CCTATGAAGCTGATTACCCTGACAGAGGAATTCGNNNNNNNGCAGAAAAG                         GTTAGTCATCATCCAATGCTGATTGCCTGCCACTGTGAAGGCAAGGGCTGG
genomic: CCTATGAAGCTGATTACCCTGACAGAGGAATTCGTTTTTTTGCAGAAAAGgttagttaaa ... ccaccaatagGTTAGTCATCATCCAATGCTGATTGCCTGCCACTGTGAAGGCAAGGGCTGG
EST: gi|26558474|gb|CA830709.1|CA830709
EST:     CCTATGAAGCTGATTACCCTGACAGAGGAATTCGNNNNNNNGCAGAAAAG                         GTTAGTCATCATCCAATGCTGATTGCCTGCCACTGTGAAGGCAAGGGCTGG
genomic: CCTATGAAGCTGATTACCCTGACAGAGGAATTCGTTTTTTTGCAGAAAAGgttagttaaa ... ccaccaatagGTTAGTCATCATCCAATGCTGATTGCCTGCCACTGTGAAGGCAAGGGCTGG
EST: gi|22546239|gb|BU098550.1|BU098550
EST:     CCTATGAAGCTGATTACCCTGACAGAGGAATTCGNNNNNNNGCAGAAAAG                         GTTAGTCATCATCCAATGCTGATTGCCTGCCACTGTGAAGGCAAGGGCTGG
genomic: CCTATGAAGCTGATTACCCTGACAGAGGAATTCGTTTTTTTGCAGAAAAGgttagttaaa ... ccaccaatagGTTAGTCATCATCCAATGCTGATTGCCTGCCACTGTGAAGGCAAGGGCTGG
EST: gi|89106844|gb|DY577061.1|DY577061
EST:     CCTATGAAGCTGATTACCCTGACAGAGGAATTCGNNNNNNNGCAGAAAAG                         GTTAGTCATCATCCAATGCTGATTGCCTGCCACTGTGAAGGCAAGGGCTGG
genomic: CCTATGAAGCTGATTACCCTGACAGAGGAATTCGTTTTTTTGCAGAAAAGgttagttaaa ... ccaccaatagGTTAGTCATCATCCAATGCTGATTGCCTGCCACTGTGAAGGCAAGGGCTGG
EST: gi|22472628|gb|BU037108.1|BU037108
EST:     CCTATGAAGCTGATTACCCTGACAGAGGAATTCGNNNNNNNGCAGAAAAG                         GTTAGTCATCATCCAATGCTGATTGCCTGCCACTGTGAAGGCAAGGGCTGG
genomic: CCTATGAAGCTGATTACCCTGACAGAGGAATTCGTTTTTTTGCAGAAAAGgttagttaaa ... ccaccaatagGTTAGTCATCATCCAATGCTGATTGCCTGCCACTGTGAAGGCAAGGGCTGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgaattggagactttaatttcattgcattgctattcaacatttccaccaatagGTTAGTCATCATCCAATGCTGATTGCCTGCCACTGTGAAGGCAAGGGCTGGAAATTCTGGGGCGACAGCAATCTCAAATCCAAGTTTTGGGGACAGTCAA
             ctttaat  putative branch site (score: 4)
                                          tttccacc  putative PPT
            actttaatttcatt  TA-rich tract