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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGGAACTGGTTTGAGCATTTTAATTTCTAAGAGGAATCCATCATTGGTGACTTCATTTGCCTTCTTGTCTTGTGGCTATCTCCTTAGTTCATACCATGAGgtttgcttttgaactttcttgatgctcttataattaaatcattctgataaaagttattggttaaccaatcaaatattatatgtattctcag

Basic information

species Oryza sativa
transcript LOC_Os05g34650.1
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g34650.1 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM5G833124_T01 (Zea mays), 5'ss of exon 7
GGGAACTGGTTTGAGCATTTTAATTTCTAAGAGGAATCCATCATTGGTGACTTCATTTGCCTTCTTGTCTTGTGGCTATCTCCTTAGTTCATACCATGAGgtttgcttttgaactttct-----tgatgctcttataattaaatcattctgataaaagttattggttaaccaatcaaatattatatgtattctcag
|||||||||  |||||||  |||| || ||||| ||||||||| |||| |||||||||||||||||||| ||||| ||||| || |||||||| ||||||||   ||||  ||     |     || ||||||| | ||   ||  ||     | ||  |    | ||||  | | |||||||| | |||  ||||
GGGAACTGGAATGAGCATACTAATCTCAAAGAGCAATCCATCACTGGTAACTTCATTTGCCTTCTTGTCGTGTGGATATCTTCTCAGTTCATATCATGAGgtacactttcaaatccattaagtgtgttgctcttgtgatctgattttttcctgataaacttccaggtaacagaactaatattat-tttataatcag
















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|38475296|gb|CF959429.1|CF959429
EST:     CTTCATTTGCCTTCTTGTCTTGTGGCTATCTCCTTAGTTCATACCATGAG                         GTGAGATCTGTTGTGCTGAACACTCTAAACACGGCAAGATTTACTGTGGCA
genomic: CTTCATTTGCCTTCTTGTCTTGTGGCTATCTCCTTAGTTCATACCATGAGgtttgctttt ... gtattctcagGTGAGATCTGTTGTGCTGAACACTCTAAACACGGCAAGATTTACTGTGGCA
EST: gi|33381296|gb|CF196639.1|CF196639
EST:     CTTCATTTGCCTTCTTGTCTTGTGGCTATCTCCTTAGTTCATACCATGAG                         GTGAGATCTGTTGTGCTGAACACTCTAAACACGGCAAGATTTACTGTGGCA
genomic: CTTCATTTGCCTTCTTGTCTTGTGGCTATCTCCTTAGTTCATACCATGAGgtttgctttt ... gtattctcagGTGAGATCTGTTGTGCTGAACACTCTAAACACGGCAAGATTTACTGTGGCA
EST: gi|33666778|gb|CF297745.1|CF297745
EST:     CTTCATTTGCCTTCTTGTCTTGTGGCTATCTCCTTAGTTCATACCATGAG                         GTGAGATCTGTTGTGCTGAACACTCTAAACACGGCAAGATTTACTGTGGCA
genomic: CTTCATTTGCCTTCTTGTCTTGTGGCTATCTCCTTAGTTCATACCATGAGgtttgctttt ... gtattctcagGTGAGATCTGTTGTGCTGAACACTCTAAACACGGCAAGATTTACTGTGGCA
EST: gi|117223389|gb|CT846265.1|CT846265
EST:     CTTCATTTGCCTTCTTGTCTTGTGGCTATCTCCTTAGTTCATACCATGAG                         GTGAGATCTGTTGTGCTGAACACTCTAAACACGGCAAGATTTACTGTGGCA
genomic: CTTCATTTGCCTTCTTGTCTTGTGGCTATCTCCTTAGTTCATACCATGAGgtttgctttt ... gtattctcagGTGAGATCTGTTGTGCTGAACACTCTAAACACGGCAAGATTTACTGTGGCA
EST: gi|58666538|gb|CK055224.1|CK055224
EST:     CTTCATTTGCCTTCTTGTCTTGTGGCTATCTCCTTAGTTCATACCATGAG                         GTGAGATCTGTTGTGCTGAACACTCTAAACACGGCAAGATTTACTGTGGCA
genomic: CTTCATTTGCCTTCTTGTCTTGTGGCTATCTCCTTAGTTCATACCATGAGgtttgctttt ... gtattctcagGTGAGATCTGTTGTGCTGAACACTCTAAACACGGCAAGATTTACTGTGGCA
EST: gi|58684548|gb|CK073235.1|CK073235
EST:     CTTCATTTGCCTTCTTGTCTTGTGGCTATCTCCTTAGTTCATACCATGAG                         GTGAGATCTGTTGTGCTGAACACTCTAAACACGGCAAGATTTACTGTGGCA
genomic: CTTCATTTGCCTTCTTGTCTTGTGGCTATCTCCTTAGTTCATACCATGAGgtttgctttt ... gtattctcagGTGAGATCTGTTGTGCTGAACACTCTAAACACGGCAAGATTTACTGTGGCA
EST: gi|29645586|gb|CB650593.1|CB650593
EST:     CTTCATTTGCCTTCTTGTCTTGTGGCTATCTCCTTAGTTCATACCATGAG                         GTGAGATCTGTTGTGCTGAACACTCTAAACACGGCAAGATTTACTGTGGCA
genomic: CTTCATTTGCCTTCTTGTCTTGTGGCTATCTCCTTAGTTCATACCATGAGgtttgctttt ... gtattctcagGTGAGATCTGTTGTGCTGAACACTCTAAACACGGCAAGATTTACTGTGGCA
EST: gi|58675486|gb|CK064173.1|CK064173
EST:     CTTCATTTGCCTTCTTGTCTTGTGGCTATCTCCTTAGTTCATACCATGAG                         GTGAGATCTGTTGTGCTGAACACTCTAAACACGGCAAGATTTACTGTGGCA
genomic: CTTCATTTGCCTTCTTGTCTTGTGGCTATCTCCTTAGTTCATACCATGAGgtttgctttt ... gtattctcagGTGAGATCTGTTGTGCTGAACACTCTAAACACGGCAAGATTTACTGTGGCA
EST: gi|58674742|gb|CK063429.1|CK063429
EST:     CTTCATTTGCCTTCTTGTCTTGTGGCTATCTCCTTAGTTCATACCATGAG                         GTGAGATCTGTTGTGCTGAACACTCTAAACACGGCAAGATTTACTGTGGCA
genomic: CTTCATTTGCCTTCTTGTCTTGTGGCTATCTCCTTAGTTCATACCATGAGgtttgctttt ... gtattctcagGTGAGATCTGTTGTGCTGAACACTCTAAACACGGCAAGATTTACTGTGGCA

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: 70 (upstream exon), 75 (downstream exon)
Score: 50

GGGAACTGGTTTGAGCATTTTAATTTCTAAGAGGAATCCATCATTGGTGACTTCATTTGCCTTCTTGTCTTGTGGCTATCTCCTTAGTTCATACCATGAGgtttgctttt ... gtattctcagGTGAGATCTGTTGTGCTGAACACTCTAAACACGGCAAGATTTACTGTGGCAGTTGATTCCTTCATTAAGAGCG




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