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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGATGGCTTGACAAAGACGAACGACTTGGTATTTGTACTTGCAGCAACAAATTTACCTTGGGAACTGGACGCAGCTATGCTCCGCCGGCTTGAGAAACGGgtacattttttttacattccggtactatagtccaataagtaggggcgggattaaatttgtaaatcttctttgtaatagtcatttgagctttgccttggat...

Basic information

species Oryza sativa
transcript LOC_Os01g55260.1
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g55260.2 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM2G022777_T01 (Zea mays), 5'ss of exon 9
GGATGGCTTGACAAAGACGAACGACTTGGTATTTGTACTTGCAGCAACAAATTTACCTTGGGAACTGGACGCAGCTATGCTCCGCCGGCTTGAGAAACGGgtacattttttttacattccggtactatagtccaataagtaggggcg-ggattaaatttgtaaatcttctttgtaatagtcatttgagctttgccttggat
|||||| ||||||||||| |||||||||||||||||||||||||| |||||| | || |||||| |||| ||||| |||||||||||||||||||| ||||||  | |       | |    |   ||  ||  |||||| |      ||||| |  |      | ||  |     |   |||  |               
GGATGGTTTGACAAAGACAAACGACTTGGTATTTGTACTTGCAGCTACAAATCTTCCCTGGGAATTGGATGCAGCCATGCTCCGCCGGCTTGAGAAGCGGgtatgtct----agtagttgatttacattatcatataagttgacaaatggattgatctcacctctgtttgtgtctctgtccatcag---------------

upper sequence: LOC_Os01g55260.2 (Oryza sativa), 5'ss of exon 8
lower sequence: AT2G34560.2 (Arabidopsis thaliana), 5'ss of exon 9
GGATGGCTTGACAAAGACGAACGACTTGGTATTTGTACTTGCAGCAACAAATTTACCTTGGGAACTGGACGCAGCTATGCTCCGCCGGCTTGAGAAACGGgtacattttttttacattccggtactatagtccaataagtaggggcgggattaaatttgtaaatcttctttgtaatagtcatttgagctttgccttggat
|||||| ||    || ||||| ||  | ||||||||  | |||||||||||| | || |||||||| || |||||||||||||| || || |||||||| |||   ||||  |  | ||   ||  | |         |||         |    | | ||   ||    |     |  |||| |               
GGATGGGTTACAGAAAACGAATGAGCTCGTATTTGTTTTAGCAGCAACAAATCTCCCCTGGGAACTAGATGCAGCTATGCTCCGGCGTCTAGAGAAACGAgtatccttttact-tactctcatagaacaaaaatgcttgtatcatgattttcttttgtttaggcctcaactagtgaaaccattag---------------
















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|86501179|gb|CI143812.1|CI143812
EST:     ATTTACCTTGGGAACTGGACGCAGCTATGCTCCGCCGGCTTGAGAAACGG                         ATTCTCGTACCTCTTCCTGAGGCTGAAGCAAGGCATGCTATGTTTGAGGAA
genomic: ATTTACCTTGGGAACTGGACGCAGCTATGCTCCGCCGGCTTGAGAAACGGgtacattttt ... tggtcgtcagATTCTCGTACCTCTTCCTGAGGCTGAAGCAAGGCATGCTATGTTTGAGGAA
EST: gi|88847654|gb|CI018345.1|CI018345
EST:     ATTTACCTTGGGAACTGGACGCAGCTATGCTCCGCCGGCTTGAGAAACGG                         ATTCTCGTACCTCTTCCTGAGGCTGAAGCAAGGCATGCTATGTTTGAGGAA
genomic: ATTTACCTTGGGAACTGGACGCAGCTATGCTCCGCCGGCTTGAGAAACGGgtacattttt ... tggtcgtcagATTCTCGTACCTCTTCCTGAGGCTGAAGCAAGGCATGCTATGTTTGAGGAA
EST: gi|86432582|gb|CI086193.1|CI086193
EST:     GCCGGCTTGAGAAACGG                         ATTCTCGTACCTCTTCCTGAGGCTGAAGCAAGGCATGCTATGTTTGAGGAA
genomic: GCCGGCTTGAGAAACGGgtacattttt ... tggtcgtcagATTCTCGTACCTCTTCCTGAGGCTGAAGCAAGGCATGCTATGTTTGAGGAA
EST: gi|87016598|gb|CI275600.1|CI275600
EST:     ATTTACCTTGGGAACTGGACGCAGCTATGCTCCGCCGGCTTGAGAAACGG                         ATTCTCGTACCTCTTCCTGAGGCTGAAGCAAGGCATGCTATGTTTGAGGAA
genomic: ATTTACCTTGGGAACTGGACGCAGCTATGCTCCGCCGGCTTGAGAAACGGgtacattttt ... tggtcgtcagATTCTCGTACCTCTTCCTGAGGCTGAAGCAAGGCATGCTATGTTTGAGGAA
EST: gi|3768081|gb|AU032108.1|AU032108
EST:     ATTTACCTTGGGAACTGGACGCAGCTATGCTCCGCCGGCTTGAGAAACGG                         ATTCTCGTACCTCTTCCTGAGGCTGAAGCAAGGCATGCTATGTTTGAGGAA
genomic: ATTTACCTTGGGAACTGGACGCAGCTATGCTCCGCCGGCTTGAGAAACGGgtacattttt ... tggtcgtcagATTCTCGTACCTCTTCCTGAGGCTGAAGCAAGGCATGCTATGTTTGAGGAA
EST: gi|86493620|gb|CI136253.1|CI136253
EST:     ATTTACCTTGGGAACTGGACGCAGCTATGCTCCGCCGGCTTGAGAAACGG                         ATTCTCGTACCTCTTCCTGAGGCTGAAGCAAGGCATGCTATGTTTGAGGAA
genomic: ATTTACCTTGGGAACTGGACGCAGCTATGCTCCGCCGGCTTGAGAAACGGgtacattttt ... tggtcgtcagATTCTCGTACCTCTTCCTGAGGCTGAAGCAAGGCATGCTATGTTTGAGGAA
EST: gi|87036076|gb|CI189523.1|CI189523
EST:     ATTTACCTTGGGAACTGGACGCAGCTATGCTCCGCCGGCTTGAGAAACGG                         ATTCTCGTACCTCTTCCTGAGGCTGAAGCAAGGCATGCTATGTTTGAGGAA
genomic: ATTTACCTTGGGAACTGGACGCAGCTATGCTCCGCCGGCTTGAGAAACGGgtacattttt ... tggtcgtcagATTCTCGTACCTCTTCCTGAGGCTGAAGCAAGGCATGCTATGTTTGAGGAA
EST: gi|86499978|gb|CI142611.1|CI142611
EST:     ATTTACCTTGGGAACTGGACGCAGCTATGCTCCGCCGGCTTGAGAAAC-G                         ATTCTCGTACCTCTTCCTGAGGCTGAAGCAAGGCATGCTATGTTTGAGGAA
genomic: ATTTACCTTGGGAACTGGACGCAGCTATGCTCCGCCGGCTTGAGAAACGGgtacattttt ... tggtcgtcagATTCTCGTACCTCTTCCTGAGGCTGAAGCAAGGCATGCTATGTTTGAGGAA
EST: gi|8858208|gb|AU095526.1|AU095526
EST:     TTNCCCTTGGGAACTGGACGCAGCTATGTC-CCGCCGGCTTGAGAANCGG                         ATTCTCGTACCTCTTCCTGAGGCTGAAGCAAGGCATGCTATGTTTGAGGAA
genomic: TT-ACCTTGGGAACTGGACGCAGCTATG-CTCCGCCGGCTTGAGAAACGGgtacattttt ... tggtcgtcagATTCTCGTACCTCTTCCTGAGGCTGAAGCAAGGCATGCTATGTTTGAGGAA
EST: gi|88984340|gb|CI020238.1|CI020238
EST:     CAGCTATGCTCCGCCGGCTTGAGAAACGG                         ATTCTCGTACCTCTTCCTGAGGCTGAAGCAAGGCATGCTATGTTTGAGGAA
genomic: CAGCTATGCTCCGCCGGCTTGAGAAACGGgtacattttt ... tggtcgtcagATTCTCGTACCTCTTCCTGAGGCTGAAGCAAGGCATGCTATGTTTGAGGAA

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: 49 (upstream exon), 73 (downstream exon)
Score: 9

GGATGGCTTGACAAAGACGAACGACTTGGTATTTGTACTTGCAGCAACAAATTTACCTTGGGAACTGGACGCAGCTATGCTCCGCCGGCTTGAGAAACGGgtacattttt ... tggtcgtcagATTCTCGTACCTCTTCCTGAGGCTGAAGCAAGGCATGCTATGTTTGAGGAACTTTTGCCATCAACTACCTCAAAGCTAGAGGTTCCATATGATACTTTAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGATGGCTTGACAAAGACGAACGACTTGGTATTTGTACTTGCAGCAACAAATTTACCTTGGGAACTGGACGCAGCTATGCTCCGCCGGCTTGAGAAACGGgtacattttttttacattccggtactatagtccaataagtaggggcgggattaaatttgtaaatcttctttgtaatagtcatttgagctttgccttggat

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggggcgg