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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTCCCTTTCTTTTGCAGTGACCGTGAATACATTTTTGGGCGGCGGATATGGGAATCTGGGAAAACTTACTATTGTGTTACAAAGgtatttctaccacaaggttccagtattactattttcacaagacatttttatgatatgctaacctggctttggctgatgttctcatatggatatctaactt...

Basic information

species Oryza sativa
transcript LOC_Os07g08760.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g08760.2 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G124965_T01 (Zea mays), 5'ss of exon 4
TTCCCTTTCTTTTGCAGTGACCGTGAATACATTTTTGGGCGGCGGATATGGGAATCTGGGAAAACTTACTATTGTGTTACAAAGgtatttctaccacaaggttccagtattactattttcacaagac---atttttatgatatgctaacctggctttggctgatgttctcatatggatatctaactt-
||||| |||||||||||||||||||||||||| |||||  | || ||||||||||||||||| ||||||||||||||||||||||||| | ||  |||  |||  | |   |  |     |   |       | || |  |     || |||   |  ||| |||  | |||| | | |  | |  | 
TTCCCATTCTTTTGCAGTGACCGTGAATACATCTTTGGAGGACGCATATGGGAATCTGGGAAGACTTACTATTGTGTTACAAAGgtatgtttat-acagtgttttattcagataagccctatttggttgagctgttgtatttgaaaaagctgatgtgagct-atgagc-cata-gaaaagttgatgtg

upper sequence: LOC_Os07g08760.2 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G121223_T02 (Zea mays), 5'ss of exon 5
TTCCCTTTCTTTTGCAGTGACCGTGAATACATTTTTGGGCGGCGGATATGGGAATCTGGGAAAACTTACTATTGTGTTACAAAGgtatttctaccacaaggttccagta-ttactattttcacaagacatttttatgatatgctaacctggctttggctgatgttctcatatggatatctaactt--
||||| |||||||||||||||||||||||||| |||||  | || ||||||||||||||||| ||||||||||||||||| ||||||  | ||| | |  |||  | ||     || ||  ||   |  |  |  | ||   |   ||    | ||    | |   ||||||   | | |||||   
TTCCCGTTCTTTTGCAGTGACCGTGAATACATCTTTGGAGGACGCATATGGGAATCTGGGAAGACTTACTATTGTGTTACTAAGgtacatgtac-atagtgttttattaaccgatacttctactc-atgtaatgttaatgctccctccattatctgaa-aaagaattcatataattttataactgac
















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|29659937|gb|CB656212.1|CB656212
EST:     TTGGGCGGCGGATATGGGAATCTGGGAAAACTTACTATTGTGTTACAAAG                         GGAGTTCCTTATCCAGCTTTGCCTAAGAAGGAAAAACCAAGGCGTGTGGAA
genomic: TTGGGCGGCGGATATGGGAATCTGGGAAAACTTACTATTGTGTTACAAAGgtatttctac ... ccatttgcagGGAGTTCCTTATCCAGCTTTGCCTAAGAAGGAAAAACCAAGGCGTGTGGAA
EST: gi|86495790|gb|CI138423.1|CI138423
EST:     TTGGGCGCCGGATATGGGAATCTGGGAAAACTTACTATTGTGTTACAAAG                         GGAGTTCCTTATCCAGCTTTGCCTAAGAAGGAAAAACCAAGGCGTGTGGAA
genomic: TTGGGCGGCGGATATGGGAATCTGGGAAAACTTACTATTGTGTTACAAAGgtatttctac ... ccatttgcagGGAGTTCCTTATCCAGCTTTGCCTAAGAAGGAAAAACCAAGGCGTGTGGAA
EST: gi|86494162|gb|CI136795.1|CI136795
EST:     TTGGCCGGCGGATATGGGAATCTGGGAAAACTTACTATTGTGTTACAAAG                         GGAGTTCCTTATCCAGCTTTGCCTAAGAAGGAAAAACCAAGGCGTGTGGAA
genomic: TTGGGCGGCGGATATGGGAATCTGGGAAAACTTACTATTGTGTTACAAAGgtatttctac ... ccatttgcagGGAGTTCCTTATCCAGCTTTGCCTAAGAAGGAAAAACCAAGGCGTGTGGAA
EST: gi|30226837|gb|CB964729.1|CB964729
EST:     TTGGGCGGCGGATATGGGAATCTGGGAAAACTTACTATTGTGTTACAAAG                         GGAGTTCCTTATCCAGCTTTGCCTAAGAAGGAAAAACCAAGGCGTGTGGAA
genomic: TTGGGCGGCGGATATGGGAATCTGGGAAAACTTACTATTGTGTTACAAAGgtatttctac ... ccatttgcagGGAGTTCCTTATCCAGCTTTGCCTAAGAAGGAAAAACCAAGGCGTGTGGAA
EST: gi|14981939|gb|BI306617.1|BI306617
EST:     TTGGGCGGCGGATATGGGAATCTGGGAAAACTTACTATTGTGTTACAAAG                         GGAGTTCCTTATCCAGCTTTGCCTAAGAAGGAAAAACCAAGGCGTGTGGAA
genomic: TTGGGCGGCGGATATGGGAATCTGGGAAAACTTACTATTGTGTTACAAAGgtatttctac ... ccatttgcagGGAGTTCCTTATCCAGCTTTGCCTAAGAAGGAAAAACCAAGGCGTGTGGAA
EST: gi|86503157|gb|CI145790.1|CI145790
EST:     TTGGNCGNCGGATATGGGAATCTGGGAAAACTTACTATTGTGTTACAAAG                         GGAGTTCCTTATCCAGCTTTGCCTAAGAAGGAAAAACCAAGGCGTGTGGAA
genomic: TTGGGCGGCGGATATGGGAATCTGGGAAAACTTACTATTGTGTTACAAAGgtatttctac ... ccatttgcagGGAGTTCCTTATCCAGCTTTGCCTAAGAAGGAAAAACCAAGGCGTGTGGAA
EST: gi|29659876|gb|CB656151.1|CB656151
EST:     TTGGGCGGCGGATATGGGAATCTGGGAAAACTTACTATTGTGTTACAAAG                         GGAGTTCCTTATCCAGCTTTGCCTAAGAAGGAAAAACCAAGGCGTGTGGAA
genomic: TTGGGCGGCGGATATGGGAATCTGGGAAAACTTACTATTGTGTTACAAAGgtatttctac ... ccatttgcagGGAGTTCCTTATCCAGCTTTGCCTAAGAAGGAAAAACCAAGGCGTGTGGAA
EST: gi|30228065|gb|CB965957.1|CB965957
EST:     TTGGGCGGCGGATATGGGAATCTGGGAAAACTTACTATTGTGTTACAAAG                         GGAGTTCCTTATCCAGCTTTGCCTAAGAAGGAAAAACCAAGGCGTGTGGAA
genomic: TTGGGCGGCGGATATGGGAATCTGGGAAAACTTACTATTGTGTTACAAAGgtatttctac ... ccatttgcagGGAGTTCCTTATCCAGCTTTGCCTAAGAAGGAAAAACCAAGGCGTGTGGAA
EST: gi|23512848|gb|BU672864.1|BU672864
EST:     TTGGGCGGCGGATATGGGAATCTGGGAAAACTTACTATTGTGTTACAAAG                         GGAGTTCCTTATCCAGCTTTGCCTAAGAAGGAAAAACCAAGGCGTGTGGAA
genomic: TTGGGCGGCGGATATGGGAATCTGGGAAAACTTACTATTGTGTTACAAAGgtatttctac ... ccatttgcagGGAGTTCCTTATCCAGCTTTGCCTAAGAAGGAAAAACCAAGGCGTGTGGAA
EST: gi|30228719|gb|CB966609.1|CB966609
EST:     TTGGGCGGCGGATATGGGAATCTGGGAAAACTTACTATTGTGTTACAAAG                         GGAGTTCCTTATCCAGCTTTGCCTAAGAAGGAAAAACCAAGGCGTGTGGAA
genomic: TTGGGCGGCGGATATGGGAATCTGGGAAAACTTACTATTGTGTTACAAAGgtatttctac ... ccatttgcagGGAGTTCCTTATCCAGCTTTGCCTAAGAAGGAAAAACCAAGGCGTGTGGAA

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: 71 (upstream exon), 74 (downstream exon)
Score: 35

TTCCCTTTCTTTTGCAGTGACCGTGAATACATTTTTGGGCGGCGGATATGGGAATCTGGGAAAACTTACTATTGTGTTACAAAGgtatttctac ... ccatttgcagGGAGTTCCTTATCCAGCTTTGCCTAAGAAGGAAAAACCAAGGCGTGTGGAACTGTATTTCTCAAGTTGGCGTATTAGAGCAG




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