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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCATCCTTTGGTTTTGTTGACTATTATGACCGTAGATCTGCTGCAATTGCAATTGTATCACTCAACGGTAGACAATTgtaagtatttcaatactatagtattataatatatataaattctaatattttgcttttcctcttaacattttccaacattttcttatgatcctacattaccag

Basic information

species Oryza sativa
transcript LOC_Os11g40510.2
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g40510.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM5G835213_T02 (Zea mays), 5'ss of exon 4
TCATCCTTTGGTTTTGTTGACTATTATGACCGTAGATCTGCTGCAATTGCAATTGTATCACTCAACGGTAGACAATTgtaagtatttcaatactatagtattataatatatataaattctaat-attttgcttttcctcttaac-attttccaacattttcttatgatcctacattaccag
||||||||||||||  ||||||| |||||||| |||| ||||||| | |||||| |||| ||||| || |||||| ||||||| ||| | |  | | ||| | |   |    ||| |   | |  |||||  ||| || | | | || |||  || ||||  ||||  |||| |  ||   
TCATCCTTTGGTTTCATTGACTACTATGACCGCAGATATGCTGCACTAGCAATTTTATCTCTCAATGGCAGACAACTgtaagttttttattggttttgtactctc-cactcctaattgtaagtcgttttggcttttctataatctatgttcataccttttactatgtacctagac-aca--

upper sequence: LOC_Os11g40510.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G008611_T01 (Zea mays), 5'ss of exon 5
TCATCCTTTGGTTTTGTTGACTATTATGACCGTAGATCTGCTGCAATTGCAATTGTATCACTCAACGGTAGACAATTgtaagtatttcaatactatagtattataatatatataaattctaat-attttgcttttcc-tcttaacattttccaacattttcttatgatcctacat-taccag
||||||||||||||  |||||||  |||| || |||| ||||||| | |||||| |||| ||||| || |||||| ||||||| ||| | |  | | ||| | |   ||   ||| |   | |  ||| |||||||  | || | |  ||  |  || |   || ||  |    | || |  
TCATCCTTTGGTTTCATTGACTACCATGATCGCAGATATGCTGCACTAGCAATTTTATCTCTCAATGGCAGACAACTgtaagttttttattggt-ttgtactctc-cattcgtaattgtaagtcgtttggcttttctatatttatagcttttactatgtatcta-gacacagtgtatatc--
















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|58666336|gb|CK055022.1|CK055022
EST:     GACCGTAGATCTGCTGCAATTGCAATTGTATCACTCAACGGTAGACAATT                         GTTTGGCCAGCCAATAAAAGTCAATTGGGCATATGCAAGTACT
genomic: GACCGTAGATCTGCTGCAATTGCAATTGTATCACTCAACGGTAGACAATTgtaagtattt ... acattaccagGTTTGGCCAGCCAATAAAAGTCAATTGGGCATATGCAAGTACT
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

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 75 (upstream exon), 31 (downstream exon)
Score: 146

TCATCCTTTGGTTTTGTTGACTATTATGACCGTAGATCTGCTGCAATTGCAATTGTATCACTCAACGGTAGACAATTgtaagtattt ... acattaccagGTTTGGCCAGCCAATAAAAGTCAATTGGGCATATGCAAGTACTCAAAGAGAGGATACATCAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCATCCTTTGGTTTTGTTGACTATTATGACCGTAGATCTGCTGCAATTGCAATTGTATCACTCAACGGTAGACAATTgtaagtatttcaatactatagtattataatatatataaattctaatattttgcttttcctcttaacattttccaacattttcttatgatcctacattaccag

- - - - - - - - - - - - - - - - - - - TGCTGC