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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gttttaccgttcctagggctaatggttggaggtcactgttattgtgtgggtactaaccaaatatttaccgcatttcatgacttgacctccctatgttcagGTTAAAAGGAAGAAAGCTAAACATGCCGGGATGTTTGATATTGCCAAGACAGCAAATAGACCCATGATACATATAGGTGGCTGAGGTATCCTCTTATCAA

Basic information

species Zea mays
transcript GRMZM2G135816_T03
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G135816_T03 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os02g15870.3 (Oryza sativa), 3'ss of exon 6
gttttaccgttcctagggctaatggttggaggtcactgttatt-gtgtgggtactaaccaaatat-ttaccgcatttcatgacttgacctccctatgttcagGTTAAAAGGAAGAAAGCTAAACATGCCGGGATGTTTGATATTGCCAAGACAGCAAATAGACCCATGATACATATAGGTGGCTGAGGTATCCTCTTATCAA
  ||  || |    |  ||||    | |        ||  |   |  | |    | |  |  ||| ||| |   |||  |  |   | ||  || |   ||||||||||||||||||||||||||||| ||||||||||||||||| ||||| ||||||||||| ||||| || || ||||||||||               
acttgtccatgttcatagctagaaatagctacattttgggacgagcatagcatatcattagttatattatcatgtttagtcgcc--aacttactttacccagGTTAAAAGGAAGAAAGCTAAACATGCTGGGATGTTTGATATTGCTAAGACGGCAAATAGACCTATGATTCACATTGGTGGCTGAG---------------

upper sequence: GRMZM2G135816_T03 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os12g32230.1 (Oryza sativa), 3'ss of exon 6
---gttttaccgttcctaggg--ctaatggttggaggtcactgttattgtgtgggtactaaccaaatatttaccgcatttcatgacttgacctccctatgttcagGTTAAAAGGAAGAAAGCTAAACATGCCGGGATGTTTGATATTGCCAAGACAGCAAATAGACCCATGATACATATAGGTGGCTGAGGTATCCTCTTATCAA
   |    ||    | ||| |    | | |||  |    |     | ||| ||  ||||| ||   | |||| |     | ||  |   | ||   | |   |||||||||||||||||||||||||| || ||||||||||||||||| ||||||||||||||||| ||||| || || ||||||||||               
cgggacagacgtaacttagtgtatcattagttatattatagatacaatgtttgcatactagcc---tttttatcatgcgtaatcgcc--aacttattttacccagGTTAAAAGGAAGAAAGCTAAACACGCTGGGATGTTTGATATTGCTAAGACAGCAAATAGACCTATGATTCACATTGGTGGCTGAG---------------

upper sequence: GRMZM2G135816_T03 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA08G16780.1 (Glycine max), 3'ss of exon 5
gttttaccgttcctagggctaatggttggaggtcactgttattgtgtgggtac-taaccaaatatttaccgcatttcatgac-ttgacctccctatgttc-agGTTAAAAGGAAGAAAGCTAAACATGCCGGGATGTTTGATATTGCCAAGACAGCAAATAGACCCATGATACATATAGGTGGCTGAGGTATCCTCTTATCAA
||  ||   | | |     |     |||         ||||   | |   ||      |   || | | |   |||| | |  ||| | | | | ||| | |||| || ||||||||||||  |||||| || ||||| || || || ||||| |||||||| || ||||||||||| ||||| | ||               
gtcatagactacttgaaattg--tattgccaactttagttaagctatttttatgcggtcttgtaat-atcatgtttcttaatgttgcctttcttttgtcctagGTGAAGAGGAAGAAAGCTTCACATGCTGGTATGTTCGACATAGCAAAGACTGCAAATAGGCCTATGATACATATTGGTGGATAAG---------------

upper sequence: GRMZM2G135816_T03 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA15G42290.1 (Glycine max), 3'ss of exon 5
gttttaccgttcctagggcta-atggttggaggtcact---gttattgtgtgggtactaaccaaatatttaccgcatttcatgac-ttgacctccctatgttc-agGTTAAAAGGAAGAAAGCTAAACATGCCGGGATGTTTGATATTGCCAAGACAGCAAATAGACCCATGATACATATAGGTGGCTGAGGTATCCTCTTATCAA
||  ||   | | |     |  ||      |  | | |   | |||| | ||||  ||           || |  ||||| | |  ||| | | ||| ||||| |||| || ||||||||||||  |||||| || |||||||| || || ||||| |||||||| |||||||||||||| ||||| | ||               
gtcatagactacttgaaattgtataagcaaactttagttaagctattttatggggtcttgta------ctatcatatttcttaatgttgtctttcctttgttctagGTGAAGAGGAAGAAAGCTTCACATGCTGGTATGTTTGACATAGCAAAGACTGCAAATAGGCCCATGATACATATTGGTGGATAAG---------------

upper sequence: GRMZM2G135816_T03 (Zea mays), 3'ss of exon 5
lower sequence: Vv13s0156g00170.t01 (Vitis vinifera), 3'ss of exon 7
-----gttttaccgttcctagggctaatggttggaggtcactgttattgtgtgggtactaaccaa-atatttaccgcatttcatgacttgacctccctatgttcagGTTAAAAGGAAGAAAGCTAAACATGCCGGGATGTTTGATATTGCCAAGACAGCAAATAGACCCATGATACATATAGGTGGCTGAGGTATCCTCTTATCAA
        | |  |  |||     | |     |      | |||  |||| |||    |  | || |  |||  |  |||||     |||  ||   |   | ||||| || ||||||||||||   ||||| || |||||||| ||||| ||||| |||||||| |||||||||||||| ||||||| ||               
ggccaagatcattgc-cctgaaattcacttcagctttcaagtgtccttgtctggtctttgcctaatacgtttttcatatttc-----ttgttcttgttggctgcagGTCAAGAGGAAGAAAGCTTCTCATGCTGGAATGTTTGACATTGCAAAGACCGCAAATAGGCCCATGATACATATTGGTGGCTAAG---------------

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|6020607|gb|AW065640.1|AW065640
EST:     TCCGTACTGGTGTTGATGACGCTGGACTGAAGGAGATAATTGGTGCCGCG                         GTGAAAAGGAAGAAAGCTAAACATGCTGGGATGTTTGATATTGCCAAGACA
genomic: TCCGTACTGGTGTTGATGACGCTGGACTGAAGGAGATAATTGGTGCCGCGgtatgtaaat ... ctatgttcagGTTAAAAGGAAGAAAGCTAAACATGCCGGGATGTTTGATATTGCCAAGACA
EST: gi|6194756|gb|AW146860.1|AW146860
EST:     TCCGTACTGGTGTTGATGACGCTGGACTGAAGGAGATAATTGGTGCCGCG                         GTGAAAAGGAAGAAAGCTAAACATGCTGGGATGTTTGATATTGCCAAGACA
genomic: TCCGTACTGGTGTTGATGACGCTGGACTGAAGGAGATAATTGGTGCCGCGgtatgtaaat ... ctatgttcagGTTAAAAGGAAGAAAGCTAAACATGCCGGGATGTTTGATATTGCCAAGACA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgggtactaaccaaatatttaccgcatttcatgacttgacctccctatgttcagGTTAAAAGGAAGAAAGCTAAACATGCCGGGATGTTTGATATTGCCAAGACAGCAAATAGACCCATGATACATATAGGTGGCTGAGGTATCCTCTTATCAA
                                        cctccctat  CT-rich tract
        taaccaaatattta  TA-rich tract