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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_T06
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|37395178|gb|CF634869.1|CF634869
EST:     TTGAGGAACGATGCAAGCCGCAATGTGTAAAATCACTTTACGAATATGAG                         AAATGCGTCAAGAGAGTTGAGAATGATGATACTGGTCACAAACACTGCACT
genomic: TTGAGGAACGATGCAAGCCGCAATGTGTAAAATCACTTTACGAATATGAGgtctgcctcc ... ctgttatcagAAATGCGTCAAGAGAGTTGAGAATGATGATACTGGTCACAAACACTGCACT
EST: gi|15499626|gb|BI596139.1|BI596139
EST:     TTGAGGAACGATGCAAGCCGCAATGTGTAAAATCACTTTACGAATATGAG                         AAATGCGTCAAGAGAGTTGAGAATGATGATACTGGTCACAAACACTGCACT
genomic: TTGAGGAACGATGCAAGCCGCAATGTGTAAAATCACTTTACGAATATGAGgtctgcctcc ... ctgttatcagAAATGCGTCAAGAGAGTTGAGAATGATGATACTGGTCACAAACACTGCACT
EST: gi|15312761|gb|BI478359.1|BI478359
EST:     TTGAGGAACGATGCAAGCCGCAATGTGT-AAATCACTTTACGAATATGAG                         AAATGCGTCAAGAGAGTTGAGAATGATGATACTGGTCACAAACACTGCACT
genomic: TTGAGGAACGATGCAAGCCGCAATGTGTAAAATCACTTTACGAATATGAGgtctgcctcc ... ctgttatcagAAATGCGTCAAGAGAGTTGAGAATGATGATACTGGTCACAAACACTGCACT
EST: gi|211526993|gb|FL156380.1|FL156380
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|211523994|gb|FL156376.1|FL156376
EST:     TTGAGGAACGATGCAAGCCGCAATGTGTAAAATCACTTTACGAATATGAG                         AAATGCGTCAAGAGAGTTGAGAATGATGATACTGGTCACAAACACTGCACT
genomic: TTGAGGAACGATGCAAGCCGCAATGTGTAAAATCACTTTACGAATATGAGgtctgcctcc ... ctgttatcagAAATGCGTCAAGAGAGTTGAGAATGATGATACTGGTCACAAACACTGCACT
EST: gi|211523996|gb|FL156378.1|FL156378
EST:     TTGAGGAACGATGCAAGCCGCAATGTGTAAAATCACTTTACGAATATGAG                         AAATGCGTCAAGAGAGTTGAGAATGATGATACTGGTCACAAACACTGCACT
genomic: TTGAGGAACGATGCAAGCCGCAATGTGTAAAATCACTTTACGAATATGAGgtctgcctcc ... ctgttatcagAAATGCGTCAAGAGAGTTGAGAATGATGATACTGGTCACAAACACTGCACT
EST: gi|74035153|gb|DT535643.1|DT535643
EST:     TTGAGGAACGATGCNAGCCGCAATGTGTAAAATCACTTTACGAATATGAG                         AAATGCGTCAAGAGAGTTGAGAATGATGATACTGGTCACAAACACTGCACT
genomic: TTGAGGAACGATGCAAGCCGCAATGTGTAAAATCACTTTACGAATATGAGgtctgcctcc ... ctgttatcagAAATGCGTCAAGAGAGTTGAGAATGATGATACTGGTCACAAACACTGCACT
EST: gi|33092405|gb|CF052399.1|CF052399
EST:     TTGAGGAACGATGCAAGCCGCAATGTGTAAAATCACTTTACGAATATGAG                         AAATGCGTCAAGAGAGTTGAGAATGATGATACTGGTCACAAACACTGCACT
genomic: TTGAGGAACGATGCAAGCCGCAATGTGTAAAATCACTTTACGAATATGAGgtctgcctcc ... ctgttatcagAAATGCGTCAAGAGAGTTGAGAATGATGATACTGGTCACAAACACTGCACT
EST: gi|211523997|gb|FL156379.1|FL156379
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|211526998|gb|FL156385.1|FL156385
EST:     TTGAGGAACGATGCAAGCCGCAATGTGTAAAATCACTTTACGAATATGAG                         AAATGCGTCAAGAGAGTTGAGAATGATGATACTGGTCACAAACACTGCACT
genomic: TTGAGGAACGATGCAAGCCGCAATGTGTAAAATCACTTTACGAATATGAGgtctgcctcc ... ctgttatcagAAATGCGTCAAGAGAGTTGAGAATGATGATACTGGTCACAAACACTGCACT
EST: gi|211526996|gb|FL156383.1|FL156383
EST:     TTGAGGAACGATGCAAGCCGCAATGTGTAAAATCACTTTACGAATATGAG                         AAATGCGTCAAGAGAGTTGAGAATGATGATACTGGTCACAAACACTGCACT
genomic: TTGAGGAACGATGCAAGCCGCAATGTGTAAAATCACTTTACGAATATGAGgtctgcctcc ... ctgttatcagAAATGCGTCAAGAGAGTTGAGAATGATGATACTGGTCACAAACACTGCACT
EST: gi|78026630|gb|DV495017.1|DV495017
EST:     TTGAGGAACGATGCAAGCCGCAATGTGTAAAATCACTTTACGAATATGAG                         AAATGCGTCAAGAGAGTTGAGAATGATGATACTGGTCACAAACACTGCACT
genomic: TTGAGGAACGATGCAAGCCGCAATGTGTAAAATCACTTTACGAATATGAGgtctgcctcc ... ctgttatcagAAATGCGTCAAGAGAGTTGAGAATGATGATACTGGTCACAAACACTGCACT
EST: gi|211526994|gb|FL156381.1|FL156381
EST:     TTGAGGAACGATGCAAGCCGCAATGTGTAAAATCACTTTACGAATATGAG                         AAATGCGTCAAGAGAGTTGAGAATGATGATACTGGTCACAAACACTGCACT
genomic: TTGAGGAACGATGCAAGCCGCAATGTGTAAAATCACTTTACGAATATGAGgtctgcctcc ... ctgttatcagAAATGCGTCAAGAGAGTTGAGAATGATGATACTGGTCACAAACACTGCACT
EST: gi|211523990|gb|FL156372.1|FL156372
EST:     TTGAGGAACGATGCAAGCCGCAATGTGTAAAATCACTTTACGAATATGAG                         AAATGCGTCAAGAGAGTTGAGAATGATGATACTGGTCACAAACACTGCACT
genomic: TTGAGGAACGATGCAAGCCGCAATGTGTAAAATCACTTTACGAATATGAGgtctgcctcc ... ctgttatcagAAATGCGTCAAGAGAGTTGAGAATGATGATACTGGTCACAAACACTGCACT
EST: gi|95107584|gb|EB739813.1|EB739813
EST:     TTGAGGAACGATGCAAGCCGCAATGTGTAAAATCACTTTACGAATATGAG                         AAATGCGTCAAGAGAGTTGAGAATGATGATACTGGTCACAAACACTGCACT
genomic: TTGAGGAACGATGCAAGCCGCAATGTGTAAAATCACTTTACGAATATGAGgtctgcctcc ... ctgttatcagAAATGCGTCAAGAGAGTTGAGAATGATGATACTGGTCACAAACACTGCACT
EST: gi|211526997|gb|FL156384.1|FL156384
EST:     TTGAGGAACGATGCAAGCCGCAATGTGTAAAATCACTTTACGAATATGAG                         AAATGCGTCAAGAGAGTTGAGAATGATGATACTGGTCACAAACACTGCACT
genomic: TTGAGGAACGATGCAAGCCGCAATGTGTAAAATCACTTTACGAATATGAGgtctgcctcc ... ctgttatcagAAATGCGTCAAGAGAGTTGAGAATGATGATACTGGTCACAAACACTGCACT
EST: gi|32808494|gb|CD960728.1|CD960728
EST:     TTGAGGAACGATGCAAGCCGCAATGTGTAAAATCACTTTGCGAATATGAG                         AAATGCGTCAAGAGAGTTGAGAATGATGATACTGGTCACAAACACTGCACT
genomic: TTGAGGAACGATGCAAGCCGCAATGTGTAAAATCACTTTACGAATATGAGgtctgcctcc ... ctgttatcagAAATGCGTCAAGAGAGTTGAGAATGATGATACTGGTCACAAACACTGCACT
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
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgttttaccctagggtgctaatagtattccattttttaatatgcatgcctggcacatgagtatttttgttcaaactttaacggtggctgtctgttatcagAAATGCGTCAAGAGAGTTGAGAATGATGATACTGGTCACAAACACTGCACTGGGCAATACTTTGATTACTGGTCATGCATCGACAAATGT

- - - - - - -ggtgcta
- - - - - - - - - - - - - - - - - - - - -tgcatgc
- - - - - - - - - - - - - - - - - - - - - - - - - - cacatga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gtggctg