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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcgaaattaacttctttcagtttgcctctattgggatgcctatttatgcaccaaaggtcacttataaagctttatttatatgttcaacagATGAAGTGGGGAACACAGCAGCATTCTTAGCATCGCCGTTGGCATCTGCAATCACTGGATCAACTATCTATGTTGACAATGGGCTCAATACAATGGGACT

Basic information

species Oryza sativa
transcript LOC_Os09g10600.1
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g10600.1 (Oryza sativa), 3'ss of exon 12
lower sequence: GLYMA11G10770.1 (Glycine max), 3'ss of exon 12
gtcgaaattaacttctttcagtttgcctctattggg-atgcctatttatgcaccaaaggtcacttataaagctttatttatat---gttcaacagATGAAGTGGGGAACACAGCAGCATTCTTAGCATCGCCGTTGGCATCTGCAATCACTGGATCAACTATCTATGTTGACAATGGGCTCAATACAATGGGACT
    | |||  | ||       || | | || ||   | |     || |  | |   | | | ||  | | ||   || | ||   ||    |||| || ||||| |||||||| || ||||||||||| || ||||||||||| ||||||||  |   | | || ||||||||||| || ||| | |||||  |
-gtaacattttcatcagaattattacttgtaatgtacacgttccattttcaatctgtgattatttgcacaactgagttgaaattttgtcgtgcagAGGAGGTGGGCAACACAGCTGCCTTCTTAGCATCACCTTTGGCATCTGCTATCACTGGTACTGTTCTATACGTTGACAATGGTCTGAATGCTATGGGTGT

upper sequence: LOC_Os09g10600.1 (Oryza sativa), 3'ss of exon 12
lower sequence: GLYMA12G03060.1 (Glycine max), 3'ss of exon 13
gtcgaaattaacttctttcagtttgcctctattggg-atgcctatttatgcaccaaaggtcacttataaagctttatttatat---gttcaacagATGAAGTGGGGAACACAGCAGCATTCTTAGCATCGCCGTTGGCATCTGCAATCACTGGATCAACTATCTATGTTGACAATGGGCTCAATACAATGGGACT
    | |||  | ||       || | | || ||   | |     || |  | |   | | | ||  |   ||   || ||||   ||    |||| || |||||  ||||||| || ||||||||||| || ||||||||||| ||||||||  |   | | |||||||||||||| || ||| | |||||  |
-gtaacattttcatcagaattattccttgtaatgtacaggttccattttcaatctgtgattatttgcaccactgagttgatattttgtcttgcagAGGAGGTGGGCTACACAGCTGCCTTCTTAGCATCACCTTTGGCATCTGCTATCACTGGTACTGTTCTATATGTTGACAATGGTCTGAATGCTATGGGTGT

upper sequence: LOC_Os09g10600.1 (Oryza sativa), 3'ss of exon 12
lower sequence: Vv06s0004g01310.t01 (Vitis vinifera), 3'ss of exon 12
-------gtcgaaattaacttctttcagtttgcctctattgggatgcc--tatttatg--caccaaaggtcacttataaagctttatttat-atgttcaacagATGAAGTGGGGAACACAGCAGCATTCTTAGCATCGCCGTTGGCATCTGCAATCACTGGATCAACTATCTATGTTGACAATGGGCTCAATACAATGGGACT
          ||||     ||| | |  || |  | |||    ||  |  |||||||   |  | |   ||| |  | || ||  ||  || |  |  ||||||||| ||||||||||| || || ||||| ||||| ||  |||||||||| ||||||||  |    || || || || || || || ||| |||||||  |
gtgggttactgaaaaccctttcatgcctttggtttatatgctcatttcattatttattgtcctctaccatca-tcgttaatctgaataaatcaaatggaacagATGAGGTGGGGAACACTGCTGCCTTCTTGGCATCACCTCTGGCATCTGCCATCACTGGTGCTGTCATATACGTCGATAACGGTCTGAATGCAATGGGTGT

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|86505190|gb|CI147823.1|CI147823
EST:     GATAGAGTATTCGTACGTGAACGCACCACTGCAGAAGGAGCTCTTGGCAG                         ATGAAGTGGGGAACACAGCAGCATTCTTAGCATCGCCGTTGGCATCTGCAA
genomic: GATAGAGTATTCGTACGTGAACGCACCACTGCAGAAGGAGCTCTTGGCAGgtcgaaatta ... tgttcaacagATGAAGTGGGGAACACAGCAGCATTCTTAGCATCGCCGTTGGCATCTGCAA
EST: gi|88840316|gb|CI079770.1|CI079770
EST:     GATAGAGTATTCGTACGTGAACGCACCACTGCAGAAGGAGCTCTTGGCAG                         ATGAAGTGGGGAACACAGCAGCATTCTTAGCATCGCCGTTGGCATCTGCAA
genomic: GATAGAGTATTCGTACGTGAACGCACCACTGCAGAAGGAGCTCTTGGCAGgtcgaaatta ... tgttcaacagATGAAGTGGGGAACACAGCAGCATTCTTAGCATCGCCGTTGGCATCTGCAA
EST: gi|33693872|gb|CF322111.1|CF322111
EST:     GATAGAGTATTCGTACGTGAACGCACCACTGCAGAAGGAGCTCTTGGCAG                         ATGAAGTGGGGAACACAGCAGCATTCTTAGCATCGCCGTTGGCATCTGCAA
genomic: GATAGAGTATTCGTACGTGAACGCACCACTGCAGAAGGAGCTCTTGGCAGgtcgaaatta ... tgttcaacagATGAAGTGGGGAACACAGCAGCATTCTTAGCATCGCCGTTGGCATCTGCAA
EST: gi|86538458|gb|CI178664.1|CI178664
EST:     CGCACCACTGCAGAAGGAGCTCTTGGCAG                         ATGAAGTGGGGAACACAGCAGCATTCTTAGCATCGCCGTTGGCATCTGCAA
genomic: CGCACCACTGCAGAAGGAGCTCTTGGCAGgtcgaaatta ... tgttcaacagATGAAGTGGGGAACACAGCAGCATTCTTAGCATCGCCGTTGGCATCTGCAA
EST: gi|29640102|gb|CB645111.1|CB645111
EST:     GATAGAGTATTCGTACGTGAACGCACCACTGCAGAAGGAGCTCTTGGCAG                         ATGAAGTGGGGAACACAGCAGCATTCTTAGCATCGCCGTTGGCATCTGCAA
genomic: GATAGAGTATTCGTACGTGAACGCACCACTGCAGAAGGAGCTCTTGGCAGgtcgaaatta ... tgttcaacagATGAAGTGGGGAACACAGCAGCATTCTTAGCATCGCCGTTGGCATCTGCAA
EST: gi|87027842|gb|CI276198.1|CI276198
EST:     GATAGAGTATTCGTACGTGAACGCACCACTGCAGAAGGAGCTCTTGGCAG                         ATGAAGTGGGGAACACAGCAGCATTCTTAGCATCGCCGTTGGCATCTGCAA
genomic: GATAGAGTATTCGTACGTGAACGCACCACTGCAGAAGGAGCTCTTGGCAGgtcgaaatta ... tgttcaacagATGAAGTGGGGAACACAGCAGCATTCTTAGCATCGCCGTTGGCATCTGCAA
EST: gi|58669339|gb|CK058025.1|CK058025
EST:     GATAGAGTATTCGTACGTGAACGCACCACTGCAGAAGGAGCTCTTGGCAG                         ATGAAGTGGGGAACACAGCAGCATTCTTAGCATCGCCGTTGGCATCTGCAA
genomic: GATAGAGTATTCGTACGTGAACGCACCACTGCAGAAGGAGCTCTTGGCAGgtcgaaatta ... tgttcaacagATGAAGTGGGGAACACAGCAGCATTCTTAGCATCGCCGTTGGCATCTGCAA
EST: gi|88962699|gb|CI023799.1|CI023799
EST:     GATAGAGTATTCGTACGTGAACGCACCACTGCAGAAGGAGCTCTTGGCAG                         ATGAAGTGGGGAACACAGCAGCATTCTTAGCATCGCCGTTGGCATCTGCAA
genomic: GATAGAGTATTCGTACGTGAACGCACCACTGCAGAAGGAGCTCTTGGCAGgtcgaaatta ... tgttcaacagATGAAGTGGGGAACACAGCAGCATTCTTAGCATCGCCGTTGGCATCTGCAA
EST: gi|88260877|gb|CI361465.1|CI361465
EST:     CGCACCACTGCAGAAGGAGCTCTTGGCAG                         ATGAAGTGGGGAACACAGCAAGCATTCTTAGCATCGCCCTTGACATCTGCA
genomic: CGCACCACTGCAGAAGGAGCTCTTGGCAGgtcgaaatta ... tgttcaacagATGAAGTGGGGAACACAGC-AGCATTCTTAGCATCGCCGTTGGCATCTGCA
EST: gi|29670467|gb|CB666742.1|CB666742
EST:     GATAGAGTATTCGTACGTGAACGCACCACTGCAGAAGGAGCTCTTGGCAG                         ATGAAGTGGGGAACACAGCAGCATTCTTAGCATCGCCGTTGGCATCTGCAA
genomic: GATAGAGTATTCGTACGTGAACGCACCACTGCAGAAGGAGCTCTTGGCAGgtcgaaatta ... tgttcaacagATGAAGTGGGGAACACAGCAGCATTCTTAGCATCGCCGTTGGCATCTGCAA
EST: gi|218501539|gb|FG956143.1|FG956143
EST:     GATAGAGTATTCGTACGTGAACGCACCACTGCAGAAGGAGCTCTTGGCAG                         ATGAAGTGGGGAACACAGCAGCATTCTTAGCATCGCCGTTGGCATCTGCAA
genomic: GATAGAGTATTCGTACGTGAACGCACCACTGCAGAAGGAGCTCTTGGCAGgtcgaaatta ... tgttcaacagATGAAGTGGGGAACACAGCAGCATTCTTAGCATCGCCGTTGGCATCTGCAA
EST: gi|88902832|gb|CI088370.1|CI088370
EST:     GATAGAGTATTCGTACGTGAACGCACCACTGCAGAAGGAGCTCTTGGCAG                         ATGAAGTGGGGAACACAGCAGCATTCTTAGCATCGCCGTTGGCATCTGCAA
genomic: GATAGAGTATTCGTACGTGAACGCACCACTGCAGAAGGAGCTCTTGGCAGgtcgaaatta ... tgttcaacagATGAAGTGGGGAACACAGCAGCATTCTTAGCATCGCCGTTGGCATCTGCAA

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: 75 (upstream exon), 69 (downstream exon)
Score: 13

GTCCATTGGGAAGTCGAGCAGCCAAAGCTATTGGTTTCATCGAGAAGATGATAGAGTATTCGTACGTGAACGCACCACTGCAGAAGGAGCTCTTGGCAGgtcgaaatta ... tgttcaacagATGAAGTGGGGAACACAGCAGCATTCTTAGCATCGCCGTTGGCATCTGCAATCACTGGATCAACTATCTATGTTGACAATGGGCTCAATACAATGGGACT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgcctatttatgcaccaaaggtcacttataaagctttatttatatgttcaacagATGAAGTGGGGAACACAGCAGCATTCTTAGCATCGCCGTTGGCATCTGCAATCACTGGATCAACTATCTATGTTGACAATGGGCTCAATACAATGGGACT
                          ttataaagctttattt  TA-rich tract