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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgttttaccctagggtgctaatagtattccattttttaatatgcatgcctggcacatgagtatttttgttcaaactttaacggtggctgtctgttatcagAAATGCGTCAAGAGAGTTGAGAATGATGATACTGGTCACAAACACTGCACTGGGCAATACTTTGATTACTGGTCATGCATCGACAAATGT

Basic information

species Zea mays
transcript GRMZM2G122039_T07
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G122039_T07 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os11g06340.2 (Oryza sativa), 3'ss of exon 2
-tgttttaccctagggtgctaatagtattccattttttaatatgcatgcctggcacatgagtatttttgttcaaactttaacggtggctgtctg-ttatcagAAATGCGTCAAGAGAGTTGAGAATGATGATACTGGTCACAAACACTGCACTGGGCAATACTTTGATTACTGGTCATGCATCGACAAATGT----------
   ||| |||||||| |  |||||      |   ||   |     ||||       |||| | |    | | |||   ||| ||||  ||| || ||  ||||| |||||||||||||| ||||| ||||||||||| || |||||||||||||||||||| || || || ||||||||||| |||||||||          
ccctttcaccctaggctcataatatcgcgacgacttagcaatgatatgcgctatg-atgaat-tcaacgcttaaatcctaatggtgtttgtatggtttgcagAAGTGCGTCAAGAGAGTGGAGAAGGATGATACTGGGCATAAACACTGCACTGGGCAATATTTCGACTATTGGTCATGCATTGACAAATGTGTAAGTATCT

upper sequence: GRMZM2G122039_T07 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os11g06340.1 (Oryza sativa), 3'ss of exon 2
-tgttttaccctagggtgctaatagtattccattttttaatatgcatgcctggcacatgagtatttttgttcaaactttaacggtggctgtctg-ttatcagAAATGCGTCAAGAGAGTTGAGAATGATGATACTGGTCACAAACACTGCACTGGGCAATACTTTGATTACTGGTCATGCATCGACAAATGT
   ||| |||||||| |  |||||      |   ||   |     ||||       |||| | |    | | |||   ||| ||||  ||| || ||  ||||| |||||||||||||| ||||| ||||||||||| || |||||||||||||||||||| || || || ||||||||||| |||||||||
ccctttcaccctaggctcataatatcgcgacgacttagcaatgatatgcgctatg-atgaat-tcaacgcttaaatcctaatggtgtttgtatggtttgcagAAGTGCGTCAAGAGAGTGGAGAAGGATGATACTGGGCATAAACACTGCACTGGGCAATATTTCGACTATTGGTCATGCATTGACAAATGT

upper sequence: GRMZM2G122039_T07 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA08G19380.1 (Glycine max), 3'ss of exon 2
tgttttaccctagggtgctaa--tagtattccatttt-ttaatatgcatgcctggcacatgagtatttttgttcaaactttaacggtggctgtctg--ttat--cagAAATGCGTCAAGAGAGTTGAGAATGATGATACTGGTCACAAACACTGCACTGGGCAATACTTTGATTACTGGTCATGCATCGACAAATGT
          ||   ||| ||  |  | |||    || || || |  ||  ||   |  | ||  || ||| |    |   ||  ||   ||| |   ||    |||   ||| | || ||  |  |   ||||||  |||| || |||||||||||||| ||||| |||||||| ||||| || || |||||||||
-----agtgataaattgccaaatttttgttctgccttatttatttttatttcttcaaattaag--ttcttgcttggccgagaaaagtaattgtttaaattgctacagGCGTGCATTAAAAGGATACATGGTGATGAATCTGGGCAGAAACACTGCACTGGACAATATTTTGATTATTGGTCTTGTATTGACAAATGT

upper sequence: GRMZM2G122039_T07 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA15G05620.1 (Glycine max), 3'ss of exon 2
tgttttaccctagggtgctaatagtattccattttttaatatgcatgcctggcacatgagtatttttgttcaaactttaacggtggctgtctg--ttat--cagAAATGCGTCAAGAGAGTTGAGAATGATGATACTGGTCACAAACACTGCACTGGGCAATACTTTGATTACTGGTCATGCATCGACAAATGT
   |      ||   ||  ||   | |   ||   ||||| |          || || |   || ||| |    |   ||  ||   ||| ||  ||    |||   ||| | || ||  |  |   ||||||| |||| || |||||||||||||| ||||| |||||||| ||||| || || |||||||||
---tgagtgataaattgtcaaatttttgttatgccttaattttttatttcttcaaattaa-gttcttgcttggccgagaaaagtaattgtttgaattgctacagGCGTGCATTAAAAGGATACATGGTGATGATTCTGGGCAGAAACACTGCACTGGACAATATTTTGATTATTGGTCTTGTATTGACAAATGT

upper sequence: GRMZM2G122039_T07 (Zea mays), 3'ss of exon 2
lower sequence: AT2G01090.2 (Arabidopsis thaliana), 3'ss of exon 3
-----------------------------------------------------tgttttaccctagggtgctaatagtattccattttttaatatgcatgcctggcacatga----gtatttttgttca----aactttaacg----gtggctgtctgttat-cagAAATGCGTCAAGAGAGTTGAGAATGATGATACTGGTCACAAACACTGCACTGGGCAATACTTTGATTACTGGTCATGCATCGACAAATGT----------
                                                     |  |||  | ||| | |  | | | ||| | ||   |  |    ||   |  ||||| |    |  | || || |     |  ||||||     || | |||  ||  | |||   || ||||||||  |  |  |||||||  |||| |||||||| |||||||||||||| ||||||||||||   ||  | |||||||||          
gtgaatacgacttgagctgtcactggtcataaccttgttttgcattatacgagtcatttgacatagagagagagttg-attgctttcggtgctgcttatctatctcacatcacatggcttcttagtgctgctcagttttaacatcttgttgttgtgggtggttcagGCGTGTGTCAAGAGGATCCAAGATGATGAGTCTGGCCACAAACATTGCACTGGGCAATATTTTGATTACTGGCATTGTGTTGACAAATGTGTAAGTGTGT

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|211526997|gb|FL156384.1|FL156384
EST:     TTGAGGAACGATGCAAGCCGCAATGTGTAAAATCACTTTACGAATATGAG                         AAATGCGTCAAGAGAGTTGAGAATGATGATACTGGTCACAAACACTGCACT
genomic: TTGAGGAACGATGCAAGCCGCAATGTGTAAAATCACTTTACGAATATGAGgtctgcctcc ... ctgttatcagAAATGCGTCAAGAGAGTTGAGAATGATGATACTGGTCACAAACACTGCACT
EST: gi|74035153|gb|DT535643.1|DT535643
EST:     TTGAGGAACGATGCNAGCCGCAATGTGTAAAATCACTTTACGAATATGAG                         AAATGCGTCAAGAGAGTTGAGAATGATGATACTGGTCACAAACACTGCACT
genomic: TTGAGGAACGATGCAAGCCGCAATGTGTAAAATCACTTTACGAATATGAGgtctgcctcc ... ctgttatcagAAATGCGTCAAGAGAGTTGAGAATGATGATACTGGTCACAAACACTGCACT
EST: gi|211523994|gb|FL156376.1|FL156376
EST:     TTGAGGAACGATGCAAGCCGCAATGTGTAAAATCACTTTACGAATATGAG                         AAATGCGTCAAGAGAGTTGAGAATGATGATACTGGTCACAAACACTGCACT
genomic: TTGAGGAACGATGCAAGCCGCAATGTGTAAAATCACTTTACGAATATGAGgtctgcctcc ... ctgttatcagAAATGCGTCAAGAGAGTTGAGAATGATGATACTGGTCACAAACACTGCACT
EST: gi|211526993|gb|FL156380.1|FL156380
EST:     TTGAGGAACGATGCAAGCCGCAATGTGTAAAATCACTTTACGAATATGAG                         AAATGCGTCAAGAGAGTTGAGAATGATGATACTGGTCACAAACACTGCACT
genomic: TTGAGGAACGATGCAAGCCGCAATGTGTAAAATCACTTTACGAATATGAGgtctgcctcc ... ctgttatcagAAATGCGTCAAGAGAGTTGAGAATGATGATACTGGTCACAAACACTGCACT
EST: gi|211523996|gb|FL156378.1|FL156378
EST:     TTGAGGAACGATGCAAGCCGCAATGTGTAAAATCACTTTACGAATATGAG                         AAATGCGTCAAGAGAGTTGAGAATGATGATACTGGTCACAAACACTGCACT
genomic: TTGAGGAACGATGCAAGCCGCAATGTGTAAAATCACTTTACGAATATGAGgtctgcctcc ... ctgttatcagAAATGCGTCAAGAGAGTTGAGAATGATGATACTGGTCACAAACACTGCACT
EST: gi|211523991|gb|FL156373.1|FL156373
EST:     TTGAGGAACGATGCAAGCCGCAATGTGTAAAATCACTTTACGAATATGAG                         AAATGCGTCAAGAGAGTTGAGAATGATGATACTGGTCACAAACACTGCACT
genomic: TTGAGGAACGATGCAAGCCGCAATGTGTAAAATCACTTTACGAATATGAGgtctgcctcc ... ctgttatcagAAATGCGTCAAGAGAGTTGAGAATGATGATACTGGTCACAAACACTGCACT
EST: gi|211523992|gb|FL156374.1|FL156374
EST:     TTGAGGAACGATGCAAGCCGCAATGTGTAAAATCACTTTACGAATATGAG                         AAATGCGTCAAGAGAGTTGAGAATGATGATACTGGTCACAAACACTGCACT
genomic: TTGAGGAACGATGCAAGCCGCAATGTGTAAAATCACTTTACGAATATGAGgtctgcctcc ... ctgttatcagAAATGCGTCAAGAGAGTTGAGAATGATGATACTGGTCACAAACACTGCACT
EST: gi|211526998|gb|FL156385.1|FL156385
EST:     TTGAGGAACGATGCAAGCCGCAATGTGTAAAATCACTTTACGAATATGAG                         AAATGCGTCAAGAGAGTTGAGAATGATGATACTGGTCACAAACACTGCACT
genomic: TTGAGGAACGATGCAAGCCGCAATGTGTAAAATCACTTTACGAATATGAGgtctgcctcc ... ctgttatcagAAATGCGTCAAGAGAGTTGAGAATGATGATACTGGTCACAAACACTGCACT
EST: gi|32808494|gb|CD960728.1|CD960728
EST:     TTGAGGAACGATGCAAGCCGCAATGTGTAAAATCACTTTGCGAATATGAG                         AAATGCGTCAAGAGAGTTGAGAATGATGATACTGGTCACAAACACTGCACT
genomic: TTGAGGAACGATGCAAGCCGCAATGTGTAAAATCACTTTACGAATATGAGgtctgcctcc ... ctgttatcagAAATGCGTCAAGAGAGTTGAGAATGATGATACTGGTCACAAACACTGCACT
EST: gi|211526996|gb|FL156383.1|FL156383
EST:     TTGAGGAACGATGCAAGCCGCAATGTGTAAAATCACTTTACGAATATGAG                         AAATGCGTCAAGAGAGTTGAGAATGATGATACTGGTCACAAACACTGCACT
genomic: TTGAGGAACGATGCAAGCCGCAATGTGTAAAATCACTTTACGAATATGAGgtctgcctcc ... ctgttatcagAAATGCGTCAAGAGAGTTGAGAATGATGATACTGGTCACAAACACTGCACT
EST: gi|211526994|gb|FL156381.1|FL156381
EST:     TTGAGGAACGATGCAAGCCGCAATGTGTAAAATCACTTTACGAATATGAG                         AAATGCGTCAAGAGAGTTGAGAATGATGATACTGGTCACAAACACTGCACT
genomic: TTGAGGAACGATGCAAGCCGCAATGTGTAAAATCACTTTACGAATATGAGgtctgcctcc ... ctgttatcagAAATGCGTCAAGAGAGTTGAGAATGATGATACTGGTCACAAACACTGCACT
EST: gi|33092405|gb|CF052399.1|CF052399
EST:     TTGAGGAACGATGCAAGCCGCAATGTGTAAAATCACTTTACGAATATGAG                         AAATGCGTCAAGAGAGTTGAGAATGATGATACTGGTCACAAACACTGCACT
genomic: TTGAGGAACGATGCAAGCCGCAATGTGTAAAATCACTTTACGAATATGAGgtctgcctcc ... ctgttatcagAAATGCGTCAAGAGAGTTGAGAATGATGATACTGGTCACAAACACTGCACT
EST: gi|37395178|gb|CF634869.1|CF634869
EST:     TTGAGGAACGATGCAAGCCGCAATGTGTAAAATCACTTTACGAATATGAG                         AAATGCGTCAAGAGAGTTGAGAATGATGATACTGGTCACAAACACTGCACT
genomic: TTGAGGAACGATGCAAGCCGCAATGTGTAAAATCACTTTACGAATATGAGgtctgcctcc ... ctgttatcagAAATGCGTCAAGAGAGTTGAGAATGATGATACTGGTCACAAACACTGCACT
EST: gi|211523997|gb|FL156379.1|FL156379
EST:     TTGAGGAACGATGCAAGCCGCAATGTGTAAAATCACTTTACGAATATGAG                         AAATGCGTCAAGAGAGTTGAGAATGATGATACTGGTCACAAACACTGCACT
genomic: TTGAGGAACGATGCAAGCCGCAATGTGTAAAATCACTTTACGAATATGAGgtctgcctcc ... ctgttatcagAAATGCGTCAAGAGAGTTGAGAATGATGATACTGGTCACAAACACTGCACT
EST: gi|78026630|gb|DV495017.1|DV495017
EST:     TTGAGGAACGATGCAAGCCGCAATGTGTAAAATCACTTTACGAATATGAG                         AAATGCGTCAAGAGAGTTGAGAATGATGATACTGGTCACAAACACTGCACT
genomic: TTGAGGAACGATGCAAGCCGCAATGTGTAAAATCACTTTACGAATATGAGgtctgcctcc ... ctgttatcagAAATGCGTCAAGAGAGTTGAGAATGATGATACTGGTCACAAACACTGCACT
EST: gi|211523990|gb|FL156372.1|FL156372
EST:     TTGAGGAACGATGCAAGCCGCAATGTGTAAAATCACTTTACGAATATGAG                         AAATGCGTCAAGAGAGTTGAGAATGATGATACTGGTCACAAACACTGCACT
genomic: TTGAGGAACGATGCAAGCCGCAATGTGTAAAATCACTTTACGAATATGAGgtctgcctcc ... ctgttatcagAAATGCGTCAAGAGAGTTGAGAATGATGATACTGGTCACAAACACTGCACT
EST: gi|6671465|gb|AW282244.1|AW282244
EST:     TTGAGGAACGATGCAAGCCGCAATGTGTAAAATCACTTTACGAATATGAG                         AAATGCGTCAAGAGAGTTGAGAATGATGATACTGGTCACAAACACTGCACT
genomic: TTGAGGAACGATGCAAGCCGCAATGTGTAAAATCACTTTACGAATATGAGgtctgcctcc ... ctgttatcagAAATGCGTCAAGAGAGTTGAGAATGATGATACTGGTCACAAACACTGCACT
EST: gi|211526995|gb|FL156382.1|FL156382
EST:     TTGAGGAACGATGCAAGCCGCAATGTGTAAAATCACTTTACGAATATGAG                         AAATGCGTCAAGAGAGTTGAGAATGATGATACTGGTCACAAACACTGCACT
genomic: TTGAGGAACGATGCAAGCCGCAATGTGTAAAATCACTTTACGAATATGAGgtctgcctcc ... ctgttatcagAAATGCGTCAAGAGAGTTGAGAATGATGATACTGGTCACAAACACTGCACT
EST: gi|211526999|gb|FL156386.1|FL156386
EST:     TTGAGGA-CGATGCAAGCCGCAATGTGTAAAATCACTTTACGAATATGAG                         AAAATGCGTCAAGAGAGTTGAGAATGATGATACTGGTCACAAACACTGCAC
genomic: TTGAGGAACGATGCAAGCCGCAATGTGTAAAATCACTTTACGAATATGAGgtctgcctcc ... ctgttatcagAAA-TGCGTCAAGAGAGTTGAGAATGATGATACTGGTCACAAACACTGCAC
EST: gi|211523995|gb|FL156377.1|FL156377
EST:     TTGAGGAACGATGCAAGCCGCAATGTGTAAAATCACTTTACGAATATGAG                         AAATGCGTCAAGAGAGTTGAGAATGATGATACTGGTCACAAACACTGCACT
genomic: TTGAGGAACGATGCAAGCCGCAATGTGTAAAATCACTTTACGAATATGAGgtctgcctcc ... ctgttatcagAAATGCGTCAAGAGAGTTGAGAATGATGATACTGGTCACAAACACTGCACT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcctggcacatgagtatttttgttcaaactttaacggtggctgtctgttatcagAAATGCGTCAAGAGAGTTGAGAATGATGATACTGGTCACAAACACTGCACTGGGCAATACTTTGATTACTGGTCATGCATCGACAAATGT
                             ctttaac  putative branch site (score: 3)
               tatttttgttcaaa  TA-rich tract