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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCAAGTGCAAAGTCATATCCCTTGGAGGCACTAATGGATGACTGCAAGAATTACTTCCTCGAAACTGGACGAAGGGTATCCTTCGAGTACACTCTGCTAGgtatgctcactatgcctggatccatgtgcttaagaggaataatgctaaagctgctttaccaaactaacgcgcctgaactgaattccctccag

Basic information

species Oryza sativa
transcript LOC_Os01g74190.1
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g74190.1 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM2G095663_T01 (Zea mays), 5'ss of exon 3
CCAAGTGCAAAGTCATATCCCTTGGAGGCACTAATGGATGACTGCAAGAATTACTTCCTCGAAACTGGACGAAGGGTATCCTTCGAGTACACTCTGCTAGgtatgctcactatgcctggatccatgtgcttaagaggaataatgctaaagctgctttaccaaactaacgcgcctgaactgaattccct--ccag
|| ||  | ||||| || |||||||  |||||||||||||| ||||||| ||||||||| ||||||||  | ||||||||||||||||||||||||||||||||            ||  || || || || ||  ||| |||  ||   ||     ||   ||||||  | ||  | || ||| | |  ||||
CCTAGCACCAAGTCTTACCCCTTGGGAGCACTAATGGATGATTGCAAGAGTTACTTCCTTGAAACTGGGTGCAGGGTATCCTTCGAGTACACTCTGCTAGgtat--------cagatgattctatctgtttcaggagaa-aatatta---ctcagcgacattactaacatggctagagtggatttcgtggccag

upper sequence: LOC_Os01g74190.1 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM2G168412_T02 (Zea mays), 5'ss of exon 8
CCAAGTGCAAAGTCATATCCCTTGGAGGCACTAATGGATGACTGCAAGAATTACTTCCTCGAAACTGGACGAAGGGTATCCTTCGAGTACACTCTGCTAGgtatgctcactatgcctggatccatgtgcttaagaggaataatgctaaagctgctttaccaaactaacgcgcctgaactgaattccct--ccag
|| || || ||||| || |||||||  |||||||||||||||||||||| ||||||||| |||||||| || ||||||||||||||||||||||||||||||||            ||  || || |  || ||  ||| |||  ||   ||  |  ||   ||||||  | ||  | || ||| | |  ||||
CCTAGCGCCAAGTCTTACCCCTTGGGAGCACTAATGGATGACTGCAAGAGTTACTTCCTTGAAACTGGGCGCAGGGTATCCTTCGAGTACACTCTGCTAGgtat--------cagatgattctatctttttcaggagaa-aatatta---ctcatcgacagtactaacatggctagagtggatttcgtggccag
















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|8860133|gb|AU097451.1|AU097451
EST:     TTACTTCCTCG-AACTGGACGAAGGGTATCCTTCNAGTACACTCTGCTAG                         CTGGGATTAATGACGCAAAGGAGCATGCTGAAGAACTTGCAGAGCTACTGC
genomic: TTACTTCCTCGAAACTGGACGAAGGGTATCCTTCGAGTACACTCTGCTAGgtatgctcac ... ttccctccagCTGGGATTAATGACGCAAAGGAGCATGCTGAAGAACTTGCAGAGCTACTGC
EST: gi|87015982|gb|CI279734.1|CI279734
EST:     TTACTTCCTCGAAACTGGACGAAGGGTATCCTTCGAGTACACTCTGCTAG                         CTGGGATTAATGACGCAAAGGAGCATGCTGAAGAACTTGCAGAGCTACTGC
genomic: TTACTTCCTCGAAACTGGACGAAGGGTATCCTTCGAGTACACTCTGCTAGgtatgctcac ... ttccctccagCTGGGATTAATGACGCAAAGGAGCATGCTGAAGAACTTGCAGAGCTACTGC
EST: gi|33684141|gb|CF312380.1|CF312380
EST:     TTACTTCCTCGAAACTGGACGAAGGGTATCCTTCGAGTACACTCTGCTAG                         CTGGGATTAATGACGCAAAGGAGCATGCTGAAGAACTTGCAGAGCTACTGN
genomic: TTACTTCCTCGAAACTGGACGAAGGGTATCCTTCGAGTACACTCTGCTAGgtatgctcac ... ttccctccagCTGGGATTAATGACGCAAAGGAGCATGCTGAAGAACTTGCAGAGCTACTG-
EST: gi|88829806|gb|CI004844.1|CI004844
EST:     TTACTTCCTCGAAACTGGACGAAGGGTATCCTTCGAGTACACTCTGCTAG                         CTGGGATTAATGACGCAAAGGAGCATGCTGAAGAACTTGCAGAGCTACTGC
genomic: TTACTTCCTCGAAACTGGACGAAGGGTATCCTTCGAGTACACTCTGCTAGgtatgctcac ... ttccctccagCTGGGATTAATGACGCAAAGGAGCATGCTGAAGAACTTGCAGAGCTACTGC
EST: gi|8859557|gb|AU096875.1|AU096875
EST:     TTACTTCCTCGAAACTGGACGAAGGGTATCCTTCGAGTACACTCTGCTAG                         CTGGGATTAATGACGCAAAGGAGCATGCTGAAGAACTTGCAGAGCTACTGC
genomic: TTACTTCCTCGAAACTGGACGAAGGGTATCCTTCGAGTACACTCTGCTAGgtatgctcac ... ttccctccagCTGGGATTAATGACGCAAAGGAGCATGCTGAAGAACTTGCAGAGCTACTGC
EST: gi|89193096|gb|CI050394.1|CI050394
EST:     ACGAAGGGTATCCTTCGAGTACACTCTGCTAG                         CTGGGATTAATGACGCAAAGGAGCATGCTGAAGAACTTGCAGAGCTACTGC
genomic: ACGAAGGGTATCCTTCGAGTACACTCTGCTAGgtatgctcac ... ttccctccagCTGGGATTAATGACGCAAAGGAGCATGCTGAAGAACTTGCAGAGCTACTGC
EST: gi|33381455|gb|CF196798.1|CF196798
EST:     TTACTTCCTCGAAACTGGACGAAGGGTATCCTTCGAGTACACTCTGCTAG                         CTGGGATTAATGACGCAAAGGAGCATGCTGAAGAACTTGCAGAGCTACTGC
genomic: TTACTTCCTCGAAACTGGACGAAGGGTATCCTTCGAGTACACTCTGCTAGgtatgctcac ... ttccctccagCTGGGATTAATGACGCAAAGGAGCATGCTGAAGAACTTGCAGAGCTACTGC
EST: gi|8858615|gb|AU095933.1|AU095933
EST:     TTACTTCCTCGAAACTGGACGAAGGGTATCCTTCGAGTACACTCTGCTAG                         CTGGGATTAATGACGCAAAGGAGCATGCTGAAGAACTTGCAGAGCTACTGC
genomic: TTACTTCCTCGAAACTGGACGAAGGGTATCCTTCGAGTACACTCTGCTAGgtatgctcac ... ttccctccagCTGGGATTAATGACGCAAAGGAGCATGCTGAAGAACTTGCAGAGCTACTGC
EST: gi|86540664|gb|CI180870.1|CI180870
EST:     TTACTTCCTCGAAACTGGACGAAGGGTATCCTTCGAGTACACTCTGCTAG                         CTGGGATTAATGACGCAAAGGAGCATGCTGCAGAACTTGCAGAGCTACTGC
genomic: TTACTTCCTCGAAACTGGACGAAGGGTATCCTTCGAGTACACTCTGCTAGgtatgctcac ... ttccctccagCTGGGATTAATGACGCAAAGGAGCATGCTGAAGAACTTGCAGAGCTACTGC
EST: gi|86597829|gb|CI276615.1|CI276615
EST:     TTACTTCCTCGAAACTGGACGAAGGGTATCCTTCGAGTACACTCTGCTAG                         CTGGGATTAATGACGCAAAGGAGCATGCTGAAGAACTTGCAGAGCTACTGC
genomic: TTACTTCCTCGAAACTGGACGAAGGGTATCCTTCGAGTACACTCTGCTAGgtatgctcac ... ttccctccagCTGGGATTAATGACGCAAAGGAGCATGCTGAAGAACTTGCAGAGCTACTGC
EST: gi|86498774|gb|CI141407.1|CI141407
EST:     TTACTTCCTCGAAACTGGACGAAGGGTATCCTTCGAGTACACTCTGCTAG                         CTGGGATTAATGACGCAAAGGAGCATGCTGAAGAACTTGCAGAGCTACTGC
genomic: TTACTTCCTCGAAACTGGACGAAGGGTATCCTTCGAGTACACTCTGCTAGgtatgctcac ... ttccctccagCTGGGATTAATGACGCAAAGGAGCATGCTGAAGAACTTGCAGAGCTACTGC
EST: gi|86251798|gb|CI018990.1|CI018990
EST:     CTTCGAGTACACTCTGCTAG                         CTGGGATTAATGACGCAAAGGAGCATGCTGAAGAACTTGCAGAGCTACTGC
genomic: CTTCGAGTACACTCTGCTAGgtatgctcac ... ttccctccagCTGGGATTAATGACGCAAAGGAGCATGCTGAAGAACTTGCAGAGCTACTGC

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: 51 (upstream exon), 64 (downstream exon)
Score: 9

CCAAGTGCAAAGTCATATCCCTTGGAGGCACTAATGGATGACTGCAAGAATTACTTCCTCGAAACTGGACGAAGGGTATCCTTCGAGTACACTCTGCTAGgtatgctcac ... ttccctccagCTGGGATTAATGACGCAAAGGAGCATGCTGAAGAACTTGCAGAGCTACTGCATACATGTGGCGGTGGTTATCATGTGAACCTAATTCCTTATAATCCGAT




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