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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtatttcaatactatagtattataatatatataaattctaatattttgcttttcctcttaacattttccaacattttcttatgatcctacattaccagGTTTGGCCAGCCAATAAAAGTCAATTGGGCATATGCAAGTACTCAAAGAGAGGATACATCAG

Basic information

species Oryza sativa
transcript LOC_Os11g40510.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g40510.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G008611_T01 (Zea mays), 3'ss of exon 5
-gtaagtattt-caatactatagtattataatatatataaattctaatattttgcttttcctcttaacattttccaacattttcttatgatcctacattaccagGTTTGGCCAGCCAATAAAAGTCAATTGGGCATATGCAAGTACTCAAAGAGAGGATACATCAG
   || || || || | | | ||       ||    ||   |  ||| |||   ||| |  |      | |||   | ||     ||  | || | |||  ||||| ||| ||||| || |||||||||||||||||| |||||||||  || ||||  |||||||
taaaattacttacagttcgaaagggactacatgctaattcctattaacattggccttgttttggctctaattttgta-ataccactacca-ccaaaatt--cagGTATGGTCAGCCGATTAAAGTCAATTGGGCATATACAAGTACTCCGAGGGAGGGCACATCAG

upper sequence: LOC_Os11g40510.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM5G835213_T02 (Zea mays), 3'ss of exon 4
gtaagtatttcaatactatagtattataatatatataaattctaata--ttttgcttttcctcttaacattttccaacattttcttatgatcctacattaccagGTTTGGCCAGCCAATAAAAGTCAATTGGGCATATGCAAGTACTCAAAGAGAGGATACATCAG
  ||       |||    ||   ||  ||      ||  | |||||   | ||    || | |||    ||  |    ||||| | ||    | | | |  ||||| ||| ||||| || |||||||||||||||||| |||||||||  || ||||| |||||||
--aaaagccaaaattacttacagttcaaaagggagtacgtgctaattcctcttaacattgcccttgtt-ttggctctgattttttaataccaccaaaat-tcagGTATGGTCAGCCGATTAAAGTCAATTGGGCATATACAAGTACTCCGAGGGAGGACACATCAG

upper sequence: LOC_Os11g40510.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA07G04640.1 (Glycine max), 3'ss of exon 4
gtaagtatttcaatactatagtattataatatatataaattctaatattttgcttttcctcttaacattttccaacattttcttatgatcctacattac-cagGTTTGGCCAGCCAATAAAAGTCAATTGGGCATATGCAAGTACTCAAAGAGAGGATACATCAG
                             ||  | |   |  ||| ||||   ||    |  |  ||||||      |    || | || | |   |   ||| ||||| ||||| || ||||| |||||||||||||| |||  ||| ||||||||||| ||||
----------------------------gtaagtgttgctgttaagatttatgttaaattgatttcattttgtg--ttcaaattctaattcaatgctttgcagATTTGGGCAGCCTATCAAAGTTAATTGGGCATATGCTAGTGGTCAGAGAGAGGATACGTCAG

upper sequence: LOC_Os11g40510.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA16G01230.1 (Glycine max), 3'ss of exon 4
gtaagtatttcaatactatagtattataatatatataaattctaatattttgcttttcctcttaacattttccaacattttcttatgatcctacattaccagGTTTGGCCAGCCAATAAAAGTCAATTGGGCATATGCAAGTACTCAAAGAGAGGATACATCAG
                             ||  | |   |  | | ||||   ||    |  |  ||||||  |   |  | |||      | | || | || ||||| ||||| || ||||| |||||||||||||| |||  ||| ||||||||||| ||||
----------------------------gtaagtgttgctctttagatttatgttaaattgatttcattttgtattctaattttaattcaatgctttgc-agATTTGGGCAGCCTATCAAAGTTAATTGGGCATATGCGAGTGGTCAGAGAGAGGATACGTCAG

upper sequence: LOC_Os11g40510.1 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv11s0016g00700.t01 (Vitis vinifera), 3'ss of exon 4
gtaagtatttcaatactatagtattataatatatataaattctaatattttgcttttcctcttaacattttccaacatttt--cttatgatcctacattaccagGTTTGGCCAGCCAATAAAAGTCAATTGGGCATATGCAAGTACTCAAAGAGAGGATACATCAG
                                   ||| |   |||    |   ||||    | || |||||||    | |  ||||  ||  ||  ||  ||||||||| |||||||| ||||| |||||||||||||| |||| ||| ||||||||||||||||
----------------------------------gtaagtagaaatccgatagatttctaactgactttttccactcctgtatcttaacatgtta-gtttgcagGTTTGGTCAGCCAATCAAAGTTAATTGGGCATATGCTAGTAGTCAGAGAGAGGATACATCAG

upper sequence: LOC_Os11g40510.1 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv09s0002g00880.t01 (Vitis vinifera), 3'ss of exon 4
gtaagtatttcaatactatagtattataatatatataaattctaatattttgcttttcctcttaacattttccaacattttcttatgatcctacattaccagGTTTGGCCAGCCAATAAAAGTCAATTGGGCATATGCAAGTACTCAAAGAGAGGATACATCAG
                       | | || |    |  ||| | ||   ||   || | | ||   ||||     |  || || ||  |     |||  ||||||||| ||||| || ||||| |||||||||||||| |||  |||||| ||||| |||||||
----------------------gtaagaagaacccttgatttttat---ttatgttacatgttgggatttgttt-ctgttgctcat--tttgtaatttgcagGTTTGGGCAGCCTATCAAAGTTAATTGGGCATATGCTAGTGGTCAAAGGGAGGACACATCAG

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|58688359|gb|CK077046.1|CK077046
EST:     GACCGTAGATCTGCTGCAATTGCAATTGTATCACTCAACGGTAGACAATT                         GTTTGGCCAGCCAATAAAAGTCAATTGGGCATATGCAAGTACTCAAAGAGA
genomic: GACCGTAGATCTGCTGCAATTGCAATTGTATCACTCAACGGTAGACAATTgtaagtattt ... acattaccagGTTTGGCCAGCCAATAAAAGTCAATTGGGCATATGCAAGTACTCAAAGAGA
EST: gi|86897973|gb|CI290697.1|CI290697
EST:     GACCGTAGATCTGCTGCAATTGCAATTGTATCACTCAACGGTAGACAATT                         GTTTGGCCAGCCAATAAAAGTCAATTGGGCATATGCAAGTACTCAAAGAGA
genomic: GACCGTAGATCTGCTGCAATTGCAATTGTATCACTCAACGGTAGACAATTgtaagtattt ... acattaccagGTTTGGCCAGCCAATAAAAGTCAATTGGGCATATGCAAGTACTCAAAGAGA
EST: gi|87012285|gb|CI293335.1|CI293335
EST:     GACCGTAGATCTGCTGCAATTGCAATTGTATCACTCAACGGTAGACAATT                         GTTTGGCCAGCCAATAAAAGTCAATTGGGCATATGCAAGTACTCAAAGAGA
genomic: GACCGTAGATCTGCTGCAATTGCAATTGTATCACTCAACGGTAGACAATTgtaagtattt ... acattaccagGTTTGGCCAGCCAATAAAAGTCAATTGGGCATATGCAAGTACTCAAAGAGA
EST: gi|58602505|gb|CK013033.1|CK013033
EST:     GACCGTAGATCTGCTGCAATTGCAATTGTATCACTCAACGGTAGACAATT                         GTTTGGCCAGCCAATAAAAGTCAATTGGGCATATGCAAGTACTCAAAGAGA
genomic: GACCGTAGATCTGCTGCAATTGCAATTGTATCACTCAACGGTAGACAATTgtaagtattt ... acattaccagGTTTGGCCAGCCAATAAAAGTCAATTGGGCATATGCAAGTACTCAAAGAGA
EST: gi|58681227|gb|CK069914.1|CK069914
EST:     GACCGTAGATCTGCTGCAATTGCAATTGTATCACTCAACGGTAGACAATT                         GTTTGGCCAGCCAATAAAAGTCAAGTGGGCATATGCAAGTACTCAAAGAGA
genomic: GACCGTAGATCTGCTGCAATTGCAATTGTATCACTCAACGGTAGACAATTgtaagtattt ... acattaccagGTTTGGCCAGCCAATAAAAGTCAATTGGGCATATGCAAGTACTCAAAGAGA
EST: gi|88321854|gb|CI672999.1|CI672999
EST:     GACCGTAGATCTGCTGCAATTGCAATTGTATCACTCAACGGTAGACAATT                         GTTTGGCCAGCCAATAAAAGTCAATTGGGCATATGCAAGTACTCAAAGAGA
genomic: GACCGTAGATCTGCTGCAATTGCAATTGTATCACTCAACGGTAGACAATTgtaagtattt ... acattaccagGTTTGGCCAGCCAATAAAAGTCAATTGGGCATATGCAAGTACTCAAAGAGA
EST: gi|58678674|gb|CK067361.1|CK067361
EST:     GACCGTAGATCTGCTGCAATTGCAATTGTATCACTCAACGGTAGACAATT                         GTTTGGCCAGCCAATAAAAGTCAATTGGGCATATGCAAGTACTCAAAGAGA
genomic: GACCGTAGATCTGCTGCAATTGCAATTGTATCACTCAACGGTAGACAATTgtaagtattt ... acattaccagGTTTGGCCAGCCAATAAAAGTCAATTGGGCATATGCAAGTACTCAAAGAGA
EST: gi|58690866|gb|CK079553.1|CK079553
EST:     GACCGTAGATCTGCTGCAATTGCAATTGTATCACTCAACGGTAGACAATT                         GTTTGGCCAGCCAATAAAAGTCAATTGGGCATATGCAAGTACTCAAAGAGA
genomic: GACCGTAGATCTGCTGCAATTGCAATTGTATCACTCAACGGTAGACAATTgtaagtattt ... acattaccagGTTTGGCCAGCCAATAAAAGTCAATTGGGCATATGCAAGTACTCAAAGAGA
EST: gi|87022688|gb|CI293578.1|CI293578
EST:     GACCGTAGATCTGCTGCAATTGCAATTGTATCACTCAACGGTAGACAATT                         GTTTGGCCAGCCAATAAAAGTCAATTGGGCATATGCAAGTACTCAAAGAGA
genomic: GACCGTAGATCTGCTGCAATTGCAATTGTATCACTCAACGGTAGACAATTgtaagtattt ... acattaccagGTTTGGCCAGCCAATAAAAGTCAATTGGGCATATGCAAGTACTCAAAGAGA
EST: gi|58694246|gb|CK082933.1|CK082933
EST:     GACCGTAGATCTGCTGCAATTGCAATTGTATCACTCAACGGTAGACAATT                         GTTTGGCCAGCCAATAAAAGTCAATTGGGCATATGCAAGTACTCAAAGAGA
genomic: GACCGTAGATCTGCTGCAATTGCAATTGTATCACTCAACGGTAGACAATTgtaagtattt ... acattaccagGTTTGGCCAGCCAATAAAAGTCAATTGGGCATATGCAAGTACTCAAAGAGA
EST: gi|25797088|gb|CA753049.1|CA753049
EST:     GACCGTAGATCTGCTGCAATTGCAATTGTATCACTCAACGGTAGACAATT                         GTTTGGCCAGCCATTTAAAGTCAATTGGGCATATGCAAGTACTCAAAGAGA
genomic: GACCGTAGATCTGCTGCAATTGCAATTGTATCACTCAACGGTAGACAATTgtaagtattt ... acattaccagGTTTGGCCAGCCAATAAAAGTCAATTGGGCATATGCAAGTACTCAAAGAGA
EST: gi|58606512|gb|CK034545.1|CK034545
EST:     TTGCAA-TGTATCACTCAACGGTAGACAATT                         GTTTGGCCAGCCAATAAAAGTCAATTGGGCATATGCAAGTACTCAAAGAGA
genomic: TTGCAATTGTATCACTCAACGGTAGACAATTgtaagtattt ... acattaccagGTTTGGCCAGCCAATAAAAGTCAATTGGGCATATGCAAGTACTCAAAGAGA
EST: gi|58666336|gb|CK055022.1|CK055022
EST:     GACCGTAGATCTGCTGCAATTGCAATTGTATCACTCAACGGTAGACAATT                         GTTTGGCCAGCCAATAAAAGTCAATTGGGCATATGCAAGTACT
genomic: GACCGTAGATCTGCTGCAATTGCAATTGTATCACTCAACGGTAGACAATTgtaagtattt ... acattaccagGTTTGGCCAGCCAATAAAAGTCAATTGGGCATATGCAAGTACT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttgcttttcctcttaacattttccaacattttcttatgatcctacattaccagGTTTGGCCAGCCAATAAAAGTCAATTGGGCATATGCAAGTACTCAAAGAGAGGATACATCAG
            tcttaac  putative branch site (score: 2)
              ttaacatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtatttcaatactatagtattataatatatataaattctaatattttgcttttcctcttaacattttccaacattttcttatgatcctacattaccagGTTTGGCCAGCCAATAAAAGTCAATTGGGCATATGCAAGTACTCAAAGAGAGGATACATCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT