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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTTTCAGAAGGCAAACTTGGTGTCAAGTTTAAGCCATTCTCAAAGgtatgtaaccacaactttcctttaccttatgtgtaatttattacctatacataatcttttgtagaatagttctgtttgatatggcaagtggttcttcatc...

Basic information

species Oryza sativa
transcript LOC_Os12g34860.1
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g34860.1 (Oryza sativa), 5'ss of exon 7
lower sequence: AC211349.4_FGT001 (Zea mays), 5'ss of exon 7
TTTTCAGAAGGCAAACTTGGTGTCAAGTTTAAGCCATTCTCAAAGgtatg-taaccacaacttt--cctttaccttatgtgtaatttattacctatacataatcttttgtagaatagttctgtttgatatggcaagtggttcttcatc-------------
|| ||||||||||| |||||||||||||| |||||||| ||||||||||  |  | |    | |  |  |||  | ||||  | || |||   |  | | |||  | |  |   | ||   | ||    |  |     |||  |||               
TTCTCAGAAGGCAAGCTTGGTGTCAAGTTCAAGCCATTTTCAAAGgtataatctctatgtttctgtctcttatttaatgtacacttcatttttttgagaaaatagtcttcatcttggtgtcgattatgctcactgacagtttatcactattgtttgtttag

upper sequence: LOC_Os12g34860.1 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM2G078756_T01 (Zea mays), 5'ss of exon 7
TTTTCAGAAGGCAAACTTGGTGTCAAGTTTAAGCCATTCTCAAAGgtatgtaaccacaactttcctttaccttatgtgtaatttattacctat--acataatcttttgtagaatagttctgtttgatatggcaagtggttcttcatc-------
|| ||||||||||| |||||||||||||| |||||||| ||||||||||  || | |    || || |  ||| | |    |  | ||  | |  | | |||  | |  |   | ||     ||    || |     |||  |  |        
TTCTCAGAAGGCAAGCTTGGTGTCAAGTTCAAGCCATTTTCAAAGgtat--aatctctgtgtttctgtttcttgtttaatctacactattttttgagaaaataatcttcatcttggtgtcaattatgctgactgacagtttattgtttgtttag
















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|29629252|gb|CB634263.1|CB634263
EST:     AGAAGGCAAACTTGGTGTCAAGTTTAAGCCATTCTCAAAG                         TTTCCACCTTGCTACAAGGATATGAGTTTTTGGATCAATGAAGAGTTTACA
genomic: AGAAGGCAAACTTGGTGTCAAGTTTAAGCCATTCTCAAAGgtatgtaacc ... tgttctacagTTTCCACCTTGCTACAAGGATATGAGTTTTTGGATCAATGAAGAGTTTACA
EST: gi|58695333|gb|CK084020.1|CK084020
EST:     TTTTCAGAAGGCAAACTTGGTGTCAAGTTTAAGCCATTCTCAAAG                         TTTCCACCTTGCTACAAGGATATGAGTTTTTGGATCAATGAAGAGTTTACA
genomic: TTTTCAGAAGGCAAACTTGGTGTCAAGTTTAAGCCATTCTCAAAGgtatgtaacc ... tgttctacagTTTCCACCTTGCTACAAGGATATGAGTTTTTGGATCAATGAAGAGTTTACA
EST: gi|88221899|gb|CI221855.1|CI221855
EST:     CCCAGTTTTCAGAAGGCAAACTTGGTGTCAAGTGTAAGCCATTCTCAAAG                         TTTCCACCTTGCTACAAGGATATGAGTTTTTGGATCAATGAAGAGTTTACA
genomic: CCCAGTTTTCAGAAGGCAAACTTGGTGTCAAGTTTAAGCCATTCTCAAAGgtatgtaacc ... tgttctacagTTTCCACCTTGCTACAAGGATATGAGTTTTTGGATCAATGAAGAGTTTACA
EST: gi|86493496|gb|CI136129.1|CI136129
EST:     TTTTCAGAAGGCAAACTTGGTGTCAAGTTTAAGCCATTCTCAAAG                         TTTCCACCTTGCTACAAGGATATGAGTTTTTGGATCAATGAAGAGTTTACA
genomic: TTTTCAGAAGGCAAACTTGGTGTCAAGTTTAAGCCATTCTCAAAGgtatgtaacc ... tgttctacagTTTCCACCTTGCTACAAGGATATGAGTTTTTGGATCAATGAAGAGTTTACA
EST: gi|24468878|gb|CA305827.1|CA305827
EST:     TTTTCAGAAGGCAAACTTGGCGTCAAGTTTAAGCCATTCTCAAAG                         TTTCCACCTTGCTACAAGGATATGAGTTTTTGGATCAATGAAGAGTTTACA
genomic: TTTTCAGAAGGCAAACTTGGTGTCAAGTTTAAGCCATTCTCAAAGgtatgtaacc ... tgttctacagTTTCCACCTTGCTACAAGGATATGAGTTTTTGGATCAATGAAGAGTTTACA
EST: gi|29661307|gb|CB657582.1|CB657582
EST:     TTTTCAGAAGGCAAACTTGGTGTCAAGTTTAAGCCATTCTCAAAG                         TTTCCACCTTGCTACAAGGATATGAGTTTTTGGATCAATGAAGAGTTTACA
genomic: TTTTCAGAAGGCAAACTTGGTGTCAAGTTTAAGCCATTCTCAAAGgtatgtaacc ... tgttctacagTTTCCACCTTGCTACAAGGATATGAGTTTTTGGATCAATGAAGAGTTTACA
EST: gi|88202077|gb|CI202432.1|CI202432
EST:     TTTTCAGAAGGCAAACTTGGTGTCAAGTTTAAGCCATTCTCAAAG                         TTTCCACCTTGCTACAAGGATATGAGTTTTTGGATCAATGAAGAGTTTACA
genomic: TTTTCAGAAGGCAAACTTGGTGTCAAGTTTAAGCCATTCTCAAAGgtatgtaacc ... tgttctacagTTTCCACCTTGCTACAAGGATATGAGTTTTTGGATCAATGAAGAGTTTACA
EST: gi|86493622|gb|CI136255.1|CI136255
EST:     TTTTCAGAAGGCAAACTTGGTGTCAAGTTTAAGCCATTCTCAAAG                         TTTCCACCTTGCTACAAGGATATGAGTTTTTGGATCAATGAAGAGTTTACA
genomic: TTTTCAGAAGGCAAACTTGGTGTCAAGTTTAAGCCATTCTCAAAGgtatgtaacc ... tgttctacagTTTCCACCTTGCTACAAGGATATGAGTTTTTGGATCAATGAAGAGTTTACA
EST: gi|29662501|gb|CB658776.1|CB658776
EST:     TTTTCAGAAGGCAAACTTGGTGTCAAGTTTAAGCCATTCTCAAAG                         TTTCCACCTTGCTACAAGGATATGAGTTTTTGGATCAATGAAGAGTTTACA
genomic: TTTTCAGAAGGCAAACTTGGTGTCAAGTTTAAGCCATTCTCAAAGgtatgtaacc ... tgttctacagTTTCCACCTTGCTACAAGGATATGAGTTTTTGGATCAATGAAGAGTTTACA
EST: gi|88223742|gb|CI223591.1|CI223591
EST:     TTTTCAGAAGGCAAACTTGGTGTCAAGTTTAAGCCATTCTCAAAG                         TTTCCACCTTGCTACAAGGATATGAGTTTTTGGATCAATGAAGAGTTTACA
genomic: TTTTCAGAAGGCAAACTTGGTGTCAAGTTTAAGCCATTCTCAAAGgtatgtaacc ... tgttctacagTTTCCACCTTGCTACAAGGATATGAGTTTTTGGATCAATGAAGAGTTTACA
EST: gi|88832351|gb|CI019292.1|CI019292
EST:     TTTTCAGAAGGCAAACTTGGTGTCAAGTTTAAGCCATTCTCAAAG                         TTTCCACCTTGCTACAAGGATATGAGTTTTTGGATCAATGAAGAGTTTACA
genomic: TTTTCAGAAGGCAAACTTGGTGTCAAGTTTAAGCCATTCTCAAAGgtatgtaacc ... tgttctacagTTTCCACCTTGCTACAAGGATATGAGTTTTTGGATCAATGAAGAGTTTACA
EST: gi|86501835|gb|CI144468.1|CI144468
EST:     TTTTCAGAAGGCAAACTTGGTGTCAAGTTTAAGCCATTCTCAAAG                         TTTCCACCTTGCTACAAGGATATGAGTTTTTGGATCAATGAAGAGTTTACA
genomic: TTTTCAGAAGGCAAACTTGGTGTCAAGTTTAAGCCATTCTCAAAGgtatgtaacc ... tgttctacagTTTCCACCTTGCTACAAGGATATGAGTTTTTGGATCAATGAAGAGTTTACA
EST: gi|86541540|gb|CI181746.1|CI181746
EST:     TTTTCAGAAGGCAAACTTGGTGTCAAGTTTAAGCCATTCTCAAAG                         TTTCCACCTTGCTACAAGGATATGAGTTTTTGGATCAATGAAGAGTTTACA
genomic: TTTTCAGAAGGCAAACTTGGTGTCAAGTTTAAGCCATTCTCAAAGgtatgtaacc ... tgttctacagTTTCCACCTTGCTACAAGGATATGAGTTTTTGGATCAATGAAGAGTTTACA
EST: gi|88991649|gb|CI019827.1|CI019827
EST:     TTTTCAGAAGGCAAACTTGGTGTCAAGTTTAAGCCATTCTCAAAG                         TTTCCACCTTGCTACAAGGATATGAGTTTTTGGATCAATGAAGAGTTTACA
genomic: TTTTCAGAAGGCAAACTTGGTGTCAAGTTTAAGCCATTCTCAAAGgtatgtaacc ... tgttctacagTTTCCACCTTGCTACAAGGATATGAGTTTTTGGATCAATGAAGAGTTTACA
EST: gi|86499426|gb|CI142059.1|CI142059
EST:     TTTTCAGAAGGCAAACTTGGTGTCAAGTTTAAGCCATTCTCAAAG                         TGTCCACCTTGCTACAAGGATATGAGTTTTTGGATCAATGAAGAGTTTACA
genomic: TTTTCAGAAGGCAAACTTGGTGTCAAGTTTAAGCCATTCTCAAAGgtatgtaacc ... tgttctacagTTTCCACCTTGCTACAAGGATATGAGTTTTTGGATCAATGAAGAGTTTACA
EST: gi|88961812|gb|CI096965.1|CI096965
EST:     CAAGTTTAAGCCATTCTCAGAG                         TTTCCACCTTGCTACAAGGATATGAGTTTTTGGATCAATGAAGAGTTTACA
genomic: CAAGTTTAAGCCATTCTCAAAGgtatgtaacc ... tgttctacagTTTCCACCTTGCTACAAGGATATGAGTTTTTGGATCAATGAAGAGTTTACA
EST: gi|86434161|gb|CI094504.1|CI094504
EST:     GTGTCAAGTTTAAGCCATTCTCAAAG                         TTTCCACCTTGCTACAAGGATATGAGTTTTTGGATCAATGAAGAGTTTACA
genomic: GTGTCAAGTTTAAGCCATTCTCAAAGgtatgtaacc ... tgttctacagTTTCCACCTTGCTACAAGGATATGAGTTTTTGGATCAATGAAGAGTTTACA
EST: gi|86502413|gb|CI145046.1|CI145046
EST:     TTTTCAGAAGGCAAACTTGGTGTCAAGTTTAAGCCATTCTCAAAG                         TTTCCACCTTGCTACAAGGATATGAGTTTTTGGATCAATGAAGAGTTTACA
genomic: TTTTCAGAAGGCAAACTTGGTGTCAAGTTTAAGCCATTCTCAAAGgtatgtaacc ... tgttctacagTTTCCACCTTGCTACAAGGATATGAGTTTTTGGATCAATGAAGAGTTTACA
EST: gi|86423293|gb|CI060866.1|CI060866
EST:     TTTTCAGAAGGCAAACTTGGTGTCAAGTTTAAGCCATTCTCAAAG                         TTTCCACCTTGCTACAAGGATATGAGTTTTTGGATCAATGAAGAGTTTACA
genomic: TTTTCAGAAGGCAAACTTGGTGTCAAGTTTAAGCCATTCTCAAAGgtatgtaacc ... tgttctacagTTTCCACCTTGCTACAAGGATATGAGTTTTTGGATCAATGAAGAGTTTACA
EST: gi|88248226|gb|CI248075.1|CI248075
EST:     AAGGCAAACTTGGTGTCAAGTTTAAGCCATTCTCAAAG                         TTTCCACCTTGCTACAAGGATATGAGTTTTTGGATCAATGAAGAGTTTACA
genomic: AAGGCAAACTTGGTGTCAAGTTTAAGCCATTCTCAAAGgtatgtaacc ... tgttctacagTTTCCACCTTGCTACAAGGATATGAGTTTTTGGATCAATGAAGAGTTTACA

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: 45 (upstream exon), 66 (downstream exon)
Score: 36

TTTTCAGAAGGCAAACTTGGTGTCAAGTTTAAGCCATTCTCAAAGgtatgtaacc ... tgttctacagTTTCCACCTTGCTACAAGGATATGAGTTTTTGGATCAATGAAGAGTTTACAGAGAACAATTTATGTGAGGTTGTCAGAGGAATTGCTGGAGATCTTGTAG




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