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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAATTCCCCGCATCCAGACCTTTCGGTATCAAATACAAGTTTCACTTAGAGgtaagggattactcataatttgtaatcatgttgctttagtgtgtgtttctatagggtgatttatcttagcacttgtttcttagttgctttaattgagtac...

Basic information

species Oryza sativa
transcript LOC_Os08g08200.1
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g08200.2 (Oryza sativa), 5'ss of exon 9
lower sequence: GRMZM2G042398_T02 (Zea mays), 5'ss of exon 8
-------------------------------------------------AAATTCCCCGCATCCAGACCTTTCGGTATCAAATACAAGTTTCACTTAGAGgtaagggattactcataatttgtaatcatgttgctttagtgtgtgtttctatagggtgatttatcttagcacttgtttct--tagttgctttaatt-gagtac-
                                                 |||||||| ||||||||||| || |||||||| ||||||||||||||||||||||| |   |||  |  || || |  || |  |||  || | |   | || ||| |  || |||||  ||||  ||| |  ||||   ||  |||  | ||  
TTTTCTGGTATAGTAACTGTTCCATTTGTTTCTTTTGATAATGGTGTAGAAATTCCCTGCATCCAGACCGTTTGGTATCAAGTACAAGTTTCACTTAGAGgtaagtggg-acttgtttttcgttaatatatgcctt--gtat-ttcgtttaaaggatcgttgatcttgtcactaatttttaatagtcttttggatttaaatatc

upper sequence: LOC_Os08g08200.2 (Oryza sativa), 5'ss of exon 9
lower sequence: GRMZM2G042398_T01 (Zea mays), 5'ss of exon 10
AAATTCCCCGCATCCAGACCTTTCGGTATCAAATACAAGTTTCACTTAGAGgtaagggattactcataatttgtaatcatgttgctttagtgtgtgtttctatagggtgatttatcttagcacttgtttct--tagttgctttaatt-gagtac-
|||||||| ||||||||||| || |||||||| ||||||||||||||||||||||| |   |||  |  || || |  || |  |||  || | |   | || ||| |  || |||||  ||||  ||| |  ||||   ||  |||  | ||  
AAATTCCCTGCATCCAGACCGTTTGGTATCAAGTACAAGTTTCACTTAGAGgtaagtggg-acttgtttttcgttaatatatgcctt--gtat-ttcgtttaaaggatcgttgatcttgtcactaatttttaatagtcttttggatttaaatatc
















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|86477891|gb|CI120524.1|CI120524
EST:     AAGTCCCCGCATCCAGACCTTTCGGTATCAAATACAAGTTTCACTTAGAG                         GATGCTGTTGATTGCCCGGAATGGGTTGTTCCATTCCATCTCTTCAAATTG
genomic: AATTCCCCGCATCCAGACCTTTCGGTATCAAATACAAGTTTCACTTAGAGgtaagggatt ... caatatgcagGATGCTGTTGATTGCCCGGAATGGGTTGTTCCATTCCATCTCTTCAAATTG
EST: gi|58687919|gb|CK076606.1|CK076606
EST:     AATTCCCCGCATCCAGACCTTTCGGTATCAAATACAAGTTTCACTTAGAG                         GATGCTGTTGATTGCCCGGAATGGGTTGTTCCATTCCATCTCTTCAAATTG
genomic: AATTCCCCGCATCCAGACCTTTCGGTATCAAATACAAGTTTCACTTAGAGgtaagggatt ... caatatgcagGATGCTGTTGATTGCCCGGAATGGGTTGTTCCATTCCATCTCTTCAAATTG
EST: gi|89175372|gb|CI042393.1|CI042393
EST:     TCGGTATCAAATACAAGTTTCACTTAGAG                         GATGCTGTTGATTGCCCGGAATGGGTTGTTCCATTCCATCTCTTCAAATTG
genomic: TCGGTATCAAATACAAGTTTCACTTAGAGgtaagggatt ... caatatgcagGATGCTGTTGATTGCCCGGAATGGGTTGTTCCATTCCATCTCTTCAAATTG
EST: gi|87027891|gb|CI276247.1|CI276247
EST:     CGGTATCAAATACAAGTTTCACTTAGAG                         GATGCTGTTGATTGCCCGGAATGGGTTGTTCCATTCCATCTCTTCAAATTG
genomic: CGGTATCAAATACAAGTTTCACTTAGAGgtaagggatt ... caatatgcagGATGCTGTTGATTGCCCGGAATGGGTTGTTCCATTCCATCTCTTCAAATTG
EST: gi|58693212|gb|CK081899.1|CK081899
EST:     AATTCCCCGCATCCAGACCTTTCGGTATCAAATACAAGTTTCACTTAGAG                         GATGCTGTTGATTGCCCGGAATGGGTTGTTCCATTCCATCTCTTCAAATTG
genomic: AATTCCCCGCATCCAGACCTTTCGGTATCAAATACAAGTTTCACTTAGAGgtaagggatt ... caatatgcagGATGCTGTTGATTGCCCGGAATGGGTTGTTCCATTCCATCTCTTCAAATTG
EST: gi|29689085|gb|CB685360.1|CB685360
EST:     AATTCCCCGCATCCAGACCTTTCGGTATCAAATACAAGTTTCACTTAGAG                         GATGCTGTTGATTGCCCGGAATGGGTTGTTCCATTCCATCTCTTCAAATTG
genomic: AATTCCCCGCATCCAGACCTTTCGGTATCAAATACAAGTTTCACTTAGAGgtaagggatt ... caatatgcagGATGCTGTTGATTGCCCGGAATGGGTTGTTCCATTCCATCTCTTCAAATTG
EST: gi|86854764|gb|CI259050.1|CI259050
EST:     AATTCCCCGCATCCAGACCTTTCGGTATCAAATACAAGTTTCACTTAGAG                         GATGCTGTTGATTGCCCGGAATGGGTTGTTCCATTCCATCTCTTCAAATTG
genomic: AATTCCCCGCATCCAGACCTTTCGGTATCAAATACAAGTTTCACTTAGAGgtaagggatt ... caatatgcagGATGCTGTTGATTGCCCGGAATGGGTTGTTCCATTCCATCTCTTCAAATTG
EST: gi|25801957|gb|CA757918.1|CA757918
EST:     AATTCCCTGCATCCAGACCTTTCGGTATCAAATACAAGTTTCACTTAGAG                         GATGCTGTTGATTGCCCGGAATGGGTTGTTCCATTCCATCTCTTCAAATTG
genomic: AATTCCCCGCATCCAGACCTTTCGGTATCAAATACAAGTTTCACTTAGAGgtaagggatt ... caatatgcagGATGCTGTTGATTGCCCGGAATGGGTTGTTCCATTCCATCTCTTCAAATTG

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: 68 (upstream exon), 69 (downstream exon)
Score: 12

AAATTCCCCGCATCCAGACCTTTCGGTATCAAATACAAGTTTCACTTAGAGgtaagggatt ... caatatgcagGATGCTGTTGATTGCCCGGAATGGGTTGTTCCATTCCATCTCTTCAAATTGCTGGCAGAGGAG




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