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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaccatttcaggagaagttttgtaagttttatgtgttatacctatgaggcacattttaaaatgcattttatttttttactgcagAATCTTCTAACCAGTAATCCAGGATTGGCTGCTGTTTTTGCTTCCAAGGAACGGTTGACACCTCTTTTTGAATGTCTTGCGCTACCTGTTCCTCCTGAAA

Basic information

species Oryza sativa
transcript LOC_Os10g42439.1
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os10g42439.1 (Oryza sativa), 3'ss of exon 15
lower sequence: GRMZM2G001895_T01 (Zea mays), 3'ss of exon 9
gtaccatttcaggagaagttttgtaagttttatgtgttatacctatgaggcacattt--taaaatgcattttattttttt-------actgcagAATCTTCTAACCAGTAATCCAGGATTGGCTGCTGTTTTTGCTTCCAAGGAACGGTTGACACCTCTTTTTGAATGTCTTGCGCTACCTGTTCCTCCTGAAA
|| |  ||   | | ||||  | |    ||| |   || |   | ||||||||||||  | || ||||| | ||  |||        | ||||||||||||| || ||||||||||| || ||||||||||||||| ||||||                                                   
gtgcttttattgaaaaagtacttt---ctttctaccttttctgTGTGAGGCACATTTACTGAATTGCATGTCATCATTTCGTTTGAAATTGCAGAATCTTCTTACAAGTAATCCAGGCTTAGCTGCTGTTTTTGCTACCAAGG---------------------------------------------------

upper sequence: LOC_Os10g42439.1 (Oryza sativa), 3'ss of exon 15
lower sequence: GRMZM2G049288_T01 (Zea mays), 3'ss of exon 15
gtaccatttcaggagaagt----tttgtaag-ttttatgtgttatacctatgaggcacattttaaaatgcattttatttttttactgcagAATCTTCTAACCAGTAATCCAGGATTGGCTGCTGTTTTTGCTTCCAAGGAACGGTTGACACCTCTTTTTGAATGTCTTGCGCTACCTGTTCCTCCTGAAA
|| |  ||   | | ||||    | |||||  |||| ||||| |     ||       |||        |||||| |||||  | ||||||||||||| || ||||||||||| || ||||||||||||||||||||||| ||  |||  |||||||||||||| ||||| || | ||||||| ||||||
gtgcttttattgaaaaagtactttctgtaaccttttctgtgtgaggaacatttactgaattaatgccgtcattttgttttta-attgcagAATCTTCTTACAAGTAATCCAGGCTTAGCTGCTGTTTTTGCTTCCAAGGAGCGTCTGATTCCTCTTTTTGAATGCCTTGCACTGCATGTTCCTTCTGAAA
















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|29622287|gb|CB627298.1|CB627298
EST:     GAGATTCTGAAGTGATTATGAACCTCCGAAGTGGGCTAACATCACTACAG                         AATCTTCTAACCAGTAATCCAGGATTGGCTGCTGTTTTTGCTTCCAAGGAA
genomic: GAGATTCTGAAGTGATTATGAACCTCCGAAGTGGGCTAACATCACTACAGgtaccatttc ... tttactgcagAATCTTCTAACCAGTAATCCAGGATTGGCTGCTGTTTTTGCTTCCAAGGAA
EST: gi|29630472|gb|CB635481.1|CB635481
EST:     GAGATTCTGAAGTGATTATGAACCTCCGAAGTGGGCTAACATCACTACAG                         AATCTTCTAACCAGTAATCCAGGATTGGCTGCTGTTTTTGCTTCCAAGGAA
genomic: GAGATTCTGAAGTGATTATGAACCTCCGAAGTGGGCTAACATCACTACAGgtaccatttc ... tttactgcagAATCTTCTAACCAGTAATCCAGGATTGGCTGCTGTTTTTGCTTCCAAGGAA
EST: gi|86885712|gb|CI309839.1|CI309839
EST:     GAGATTCTGAAGTGATTATGAACCTCCGAAGTGGGCTAACATCACTACAG                         AATCTTCTAACCAGTAATCCAGGATTGGCTGCTGTTTTTGCTTCCAAGGAA
genomic: GAGATTCTGAAGTGATTATGAACCTCCGAAGTGGGCTAACATCACTACAGgtaccatttc ... tttactgcagAATCTTCTAACCAGTAATCCAGGATTGGCTGCTGTTTTTGCTTCCAAGGAA
EST: gi|88407243|gb|CI583701.1|CI583701
EST:     AGATTCTGAAGTGATTATGAAC-TGCCGAAGTGGGCTAACATCACTACAG                         AATCTTCTAACCAGTAATCCAGGATTGGCTGCTGTTTTTGCTTCCAAGGAA
genomic: AGATTCTGAAGTGATTATGAACCT-CCGAAGTGGGCTAACATCACTACAGgtaccatttc ... tttactgcagAATCTTCTAACCAGTAATCCAGGATTGGCTGCTGTTTTTGCTTCCAAGGAA
EST: gi|29630907|gb|CB635916.1|CB635916
EST:     GAGATTCTGAAGTGATTATGAACCTCCGAAGTGGGCTAACATCACTACAG                         AATCTTCTAACCAGTAATCCAGGATTGGCTGCTGTTTTTGCTTCCAAGGAA
genomic: GAGATTCTGAAGTGATTATGAACCTCCGAAGTGGGCTAACATCACTACAGgtaccatttc ... tttactgcagAATCTTCTAACCAGTAATCCAGGATTGGCTGCTGTTTTTGCTTCCAAGGAA

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: 62 (upstream exon), 71 (downstream exon)
Score: 16

AGGAAAAGAAGAAGATTCATTGGAAAAACACAATAGAGGAGTAACAGATGGAGATTCTGAAGTGATTATGAACCTCCGAAGTGGGCTAACATCACTACAGgtaccatttc ... tttactgcagAATCTTCTAACCAGTAATCCAGGATTGGCTGCTGTTTTTGCTTCCAAGGAACGGTTGACACCTCTTTTTGAATGTCTTGCGCTACCTGTTCCTCCTGAAA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatgtgttatacctatgaggcacattttaaaatgcattttatttttttactgcagAATCTTCTAACCAGTAATCCAGGATTGGCTGCTGTTTTTGCTTCCAAGGAACGGTTGACACCTCTTTTTGAATGTCTTGCGCTACCTGTTCCTCCTGAAA
                                    ttttatttttttact  CT-rich tract
                     acattttaaaatgcat  TA-rich tract