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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgtgctttgtgtaattgacgctgtgtgacttgcaatcggctcgcttgtgactgaatgaatacctgacgccgtgttggttttcagGCTGCGTGGGAGATCTTCACTCCGCTGCTGCACGACATCGACGACGGCAAGGTGAAGGCCCTGCCGTACAAGCCGGGAACCCGGGGACCCCCAGAGGCCG

Basic information

species Oryza sativa
transcript LOC_Os02g38840.2
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g38840.2 (Oryza sativa), 3'ss of exon 15
lower sequence: GRMZM2G031107_T02 (Zea mays), 3'ss of exon 15
gtttgtgctttgtgtaattgacgctgtgtgac--ttgcaatcggctcgcttgtgactgaatgaatacctgacgccgtgttggtt---ttcagGCTGCGTGGGAGATCTTCACTCCGCTGCTGCACGACATCGACGACGGCAAGGTGAAGGCCCTGCCGTACAAGCCGGGAACCCGGGGACCCCCAGAGGCCG
          | ||| | || |  ||  |  |  ||||| | ||||  ||||||| |      ||  |||||   ||||  |||    |||||| || ||||| |||||||||||  |||| ||||||||||| |  |||||| | | | || | |||||||||||||||||||| ||||| |  || ||||
---------gtttgtgactggccatgcatttcctttgcagt-ggcttccttgtgaatttgcttat-tctgacaatgtgtctgttggtctcagGCCGCATGGGAAATCTTCACTCCTTTGCTTCACGACATCGATGGTGGCAAGCTCAGGTCCGTTCCGTACAAGCCGGGAACCCGAGGACCGCAGGAAGCCG
















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|88219092|gb|CI220365.1|CI220365
EST:     GATAAGAGGGGATCAGCAGCACTTTGTTCGCCGAGACGAACTGAAG                         GCTGCGTGGGAGATCTTCACTCCGCTGCTGCACGACATCGACGACGGCAAG
genomic: GATAAGAGGGGATCAGCAGCACTTTGTTCGCCGAGACGAACTGAAGgtttgtgctt ... tggttttcagGCTGCGTGGGAGATCTTCACTCCGCTGCTGCACGACATCGACGACGGCAAG
EST: gi|86862356|gb|CI345349.1|CI345349
EST:     GATAAGAGGGGATCAGCAGCACTTTGTTCGCCGAGACGAACTGAAG                         GCTGCGTGGGAGATCTTCACTCCGCTGCTGCACGACATCGACGACGGCAAG
genomic: GATAAGAGGGGATCAGCAGCACTTTGTTCGCCGAGACGAACTGAAGgtttgtgctt ... tggttttcagGCTGCGTGGGAGATCTTCACTCCGCTGCTGCACGACATCGACGACGGCAAG
EST: gi|88273363|gb|CI388819.1|CI388819
EST:     GATAAGAGGGGATCAGCAGCACTTTGTTCGCCGAGACGAACTGAAG                         GCTGCGTGGGAGATCTTCACTCCGCTGCTGCACGACATCGACGACGGCAAG
genomic: GATAAGAGGGGATCAGCAGCACTTTGTTCGCCGAGACGAACTGAAGgtttgtgctt ... tggttttcagGCTGCGTGGGAGATCTTCACTCCGCTGCTGCACGACATCGACGACGGCAAG
EST: gi|88275573|gb|CI396177.1|CI396177
EST:     GATAAGAGGGGATCAGCAGCACTTTGTTCGCCGAGACGAACTGAAG                         GCTGCGTGGGAGATCTTCACTCCGCTGCTGCACGACATCGACGACGGCAAG
genomic: GATAAGAGGGGATCAGCAGCACTTTGTTCGCCGAGACGAACTGAAGgtttgtgctt ... tggttttcagGCTGCGTGGGAGATCTTCACTCCGCTGCTGCACGACATCGACGACGGCAAG
EST: gi|88245497|gb|CI245346.1|CI245346
EST:     GATAAGAGGGGATCAGCAGCACTTTGTTCGCCGAGACGAACTGAAG                         GCTGCGTGGGAGATCTTCACTCCGCTGCTGCACGACATCGACGACGGCAAG
genomic: GATAAGAGGGGATCAGCAGCACTTTGTTCGCCGAGACGAACTGAAGgtttgtgctt ... tggttttcagGCTGCGTGGGAGATCTTCACTCCGCTGCTGCACGACATCGACGACGGCAAG
EST: gi|88996866|gb|CI389532.1|CI389532
EST:     GATAAGAGGGGATCAGCAGCACTTTGTTCGCCGAGACGAACTGAAG                         GCTGCGTGGGAGATCTTCACTCCGCTGCTGCACGACATCGACGACGGCAAG
genomic: GATAAGAGGGGATCAGCAGCACTTTGTTCGCCGAGACGAACTGAAGgtttgtgctt ... tggttttcagGCTGCGTGGGAGATCTTCACTCCGCTGCTGCACGACATCGACGACGGCAAG
EST: gi|88518045|gb|CI445598.1|CI445598
EST:     GATAAGAGGGGATCAGCAGCACTTTGTTCGCCGAGACGAACTGAAG                         GCTGCGTGGGAGATCTTCACTCCGCTGCTGCACGACATCGACGACGGCAAG
genomic: GATAAGAGGGGATCAGCAGCACTTTGTTCGCCGAGACGAACTGAAGgtttgtgctt ... tggttttcagGCTGCGTGGGAGATCTTCACTCCGCTGCTGCACGACATCGACGACGGCAAG
EST: gi|86432491|gb|CI086102.1|CI086102
EST:     GATAAGAGGGGATCAGCAGCACTTTGTTCGCCGAGACGAACTGAAG                         GCTGCGTGGGAGATCTTCACTCCGCTGCTGCACGACATCGACGACGGCAAG
genomic: GATAAGAGGGGATCAGCAGCACTTTGTTCGCCGAGACGAACTGAAGgtttgtgctt ... tggttttcagGCTGCGTGGGAGATCTTCACTCCGCTGCTGCACGACATCGACGACGGCAAG
EST: gi|88472832|gb|CI410103.1|CI410103
EST:     GATAAGAGGGGATCAGCAGCACTTTGTTCGCCGAGACGAACTGAAG                         GCTGCGTGGGAGATCTTCACTCCGCTGCTGCACGACATCGACGACGGCAAG
genomic: GATAAGAGGGGATCAGCAGCACTTTGTTCGCCGAGACGAACTGAAGgtttgtgctt ... tggttttcagGCTGCGTGGGAGATCTTCACTCCGCTGCTGCACGACATCGACGACGGCAAG
EST: gi|89176067|gb|CI043088.1|CI043088
EST:     GATAAGAGGGGATCAGCAGCACTTTGTTCGCCGAGACGAACTGAAG                         GCTGCGTGGGAGATCTTCACTCCGCTGCTGCACGACATCGACGACGGCAAG
genomic: GATAAGAGGGGATCAGCAGCACTTTGTTCGCCGAGACGAACTGAAGgtttgtgctt ... tggttttcagGCTGCGTGGGAGATCTTCACTCCGCTGCTGCACGACATCGACGACGGCAAG
EST: gi|86843192|gb|CI341351.1|CI341351
EST:     GATAAGAGGGGATCAGCAGCACTTTGTTCGCCGAGACGAACTGAAG                         GCTGCGTGGGAGATCTTCACTCCGCTGCTGCACGACATCGACGACGGCAAG
genomic: GATAAGAGGGGATCAGCAGCACTTTGTTCGCCGAGACGAACTGAAGgtttgtgctt ... tggttttcagGCTGCGTGGGAGATCTTCACTCCGCTGCTGCACGACATCGACGACGGCAAG
EST: gi|88256221|gb|CI358609.1|CI358609
EST:     GATAAGAGGGGATCAGCAGCACTTTGTTCGCCGAGACGAACTGAAG                         GCTGCGTGGGAGATCTTCACTCCGCTGCTGCACGACATCGACGACGGCAAG
genomic: GATAAGAGGGGATCAGCAGCACTTTGTTCGCCGAGACGAACTGAAGgtttgtgctt ... tggttttcagGCTGCGTGGGAGATCTTCACTCCGCTGCTGCACGACATCGACGACGGCAAG
EST: gi|89180521|gb|CI044800.1|CI044800
EST:     GATAAGAGGGGATCAGCAGCACTTTGTTCGCCGAGACGAACTGAAG                         GCTGCGTGGGAGATCTTCACTCCGCTGCTGCACGACATCGACGACGGCAAG
genomic: GATAAGAGGGGATCAGCAGCACTTTGTTCGCCGAGACGAACTGAAGgtttgtgctt ... tggttttcagGCTGCGTGGGAGATCTTCACTCCGCTGCTGCACGACATCGACGACGGCAAG
EST: gi|88517913|gb|CI444802.1|CI444802
EST:     GATAAGAGGGGATCAGCAGCACTTTGTTCGCCGAGACGAACTGAAG                         GCTGCGTGGGAGATCTTCACTCCGCTGCTGCACGACATCGACGACGGCAAG
genomic: GATAAGAGGGGATCAGCAGCACTTTGTTCGCCGAGACGAACTGAAGgtttgtgctt ... tggttttcagGCTGCGTGGGAGATCTTCACTCCGCTGCTGCACGACATCGACGACGGCAAG
EST: gi|88237644|gb|CI237493.1|CI237493
EST:     GATAAGAGGGGATCAGCAGCACTTTGTTCGCCGAGACGAACTGAAG                         GCTGCGTGGGAGATCTTCACTCCGCTGCTGCACGACATCGACGACGGCAAG
genomic: GATAAGAGGGGATCAGCAGCACTTTGTTCGCCGAGACGAACTGAAGgtttgtgctt ... tggttttcagGCTGCGTGGGAGATCTTCACTCCGCTGCTGCACGACATCGACGACGGCAAG
EST: gi|86535002|gb|CI175208.1|CI175208
EST:     GATAAGAGGGGATCAGCAGCACTTTGTTCGCCGAGACGAACTGAAG                         GCTGCGTGGGAGATCTTCACTCCGCTGCTGCACGACATCGACGACGGCAAG
genomic: GATAAGAGGGGATCAGCAGCACTTTGTTCGCCGAGACGAACTGAAGgtttgtgctt ... tggttttcagGCTGCGTGGGAGATCTTCACTCCGCTGCTGCACGACATCGACGACGGCAAG
EST: gi|88376598|gb|CI537902.1|CI537902
EST:     GATAAGAGGGGATCAGCAGCACTTTGTTCGCCGAGACGAACTGAAG                         GCTGCGTGGGAGATCTTCACTCCGCTGCTGCACGACATCGACGACGGCAAG
genomic: GATAAGAGGGGATCAGCAGCACTTTGTTCGCCGAGACGAACTGAAGgtttgtgctt ... tggttttcagGCTGCGTGGGAGATCTTCACTCCGCTGCTGCACGACATCGACGACGGCAAG
EST: gi|88516425|gb|CI444079.1|CI444079
EST:     GATAAGAGGGGATCAGCAGCACTTTNTTCGCCGAGACGAACTGAAG                         GCTGCGTGGGAGATCTTCACTCCGCTGCTGCACGACATCGACGACGGCAAG
genomic: GATAAGAGGGGATCAGCAGCACTTTGTTCGCCGAGACGAACTGAAGgtttgtgctt ... tggttttcagGCTGCGTGGGAGATCTTCACTCCGCTGCTGCACGACATCGACGACGGCAAG
EST: gi|88262014|gb|CI365590.1|CI365590
EST:     GATAAGAGGGGATCACCAGCACTCTGTTCGCCGAGACGAACTGAAG                         GCTGCGTGGGAGATCTTCACTCCGCTGCTGCACGACATCGACGACGGCAAG
genomic: GATAAGAGGGGATCAGCAGCACTTTGTTCGCCGAGACGAACTGAAGgtttgtgctt ... tggttttcagGCTGCGTGGGAGATCTTCACTCCGCTGCTGCACGACATCGACGACGGCAAG
EST: gi|89192387|gb|CI049848.1|CI049848
EST:     GATAAGAGGGGATCAGCAGCACTTTGTTCGCCGAGACGAACTGAAG                         GCTGCGTGGGAGATCTTCACTCCGCTGCTGCACGACATCGACGACGGCAAG
genomic: GATAAGAGGGGATCAGCAGCACTTTGTTCGCCGAGACGAACTGAAGgtttgtgctt ... tggttttcagGCTGCGTGGGAGATCTTCACTCCGCTGCTGCACGACATCGACGACGGCAAG
EST: gi|88420370|gb|CI559616.1|CI559616
EST:     GATAAGAGGGGATCAGCAGCACTTTGTTCGCCGAGACGAACTGAAG                         GCTGCGTGGGAGATCTTCACTCCGCTGCTGCACGACATCGACGACGGCAAG
genomic: GATAAGAGGGGATCAGCAGCACTTTGTTCGCCGAGACGAACTGAAGgtttgtgctt ... tggttttcagGCTGCGTGGGAGATCTTCACTCCGCTGCTGCACGACATCGACGACGGCAAG
EST: gi|29616737|gb|CB621749.1|CB621749
EST:     GATAAGAGGGGATCAGCAGCACTTTGTTCGCCGAGACGAACTGAAG                         GCTGCGTGGGAGATCTTCACTCCGCTGCTGCACGACATCGACGACGGCAAG
genomic: GATAAGAGGGGATCAGCAGCACTTTGTTCGCCGAGACGAACTGAAGgtttgtgctt ... tggttttcagGCTGCGTGGGAGATCTTCACTCCGCTGCTGCACGACATCGACGACGGCAAG
EST: gi|89190198|gb|CI392248.1|CI392248
EST:     GATAAGAGGGGATCAGCAGCACTTTGTTCGCCGAGACGAACTGAAG                         GCTGCGTGGGAGATCTTCACTCCGCTGCTGCACGACATCGACGACGGCAAG
genomic: GATAAGAGGGGATCAGCAGCACTTTGTTCGCCGAGACGAACTGAAGgtttgtgctt ... tggttttcagGCTGCGTGGGAGATCTTCACTCCGCTGCTGCACGACATCGACGACGGCAAG
EST: gi|88845594|gb|CI084519.1|CI084519
EST:     GATAAGAGGGGATCAGCAGCACTTTGTTCGCCGAGACGAACTGAAG                         GCTGCGTGGGAGATCTTCACTCCGCTGCTGCACGACATCGACGACGGCAAG
genomic: GATAAGAGGGGATCAGCAGCACTTTGTTCGCCGAGACGAACTGAAGgtttgtgctt ... tggttttcagGCTGCGTGGGAGATCTTCACTCCGCTGCTGCACGACATCGACGACGGCAAG
EST: gi|88478723|gb|CI415994.1|CI415994
EST:     GATAAGAGGGGATCAGCAGCACTTTGTTCGCCGAGACGAACTGAAG                         GCTGCGTGGGAGATCTTCACTCCGCTGCTGCACGACATCGACGACGGCAAG
genomic: GATAAGAGGGGATCAGCAGCACTTTGTTCGCCGAGACGAACTGAAGgtttgtgctt ... tggttttcagGCTGCGTGGGAGATCTTCACTCCGCTGCTGCACGACATCGACGACGGCAAG
EST: gi|88409040|gb|CI556748.1|CI556748
EST:     GATAAGAGGGGATCAGCAGCACTTTGTTCGCCGAGACGAACTGAAG                         GCTGCGTGGGAGATCTTCACTCCGCTGCTGCACGACATCGACGACGGCAAG
genomic: GATAAGAGGGGATCAGCAGCACTTTGTTCGCCGAGACGAACTGAAGgtttgtgctt ... tggttttcagGCTGCGTGGGAGATCTTCACTCCGCTGCTGCACGACATCGACGACGGCAAG
EST: gi|89178707|gb|CI391705.1|CI391705
EST:     GATAAGAGGGGATCAGCAGCACTTTGTTCGCCGAGACGAACTGAAG                         GCTGCGTGGGAGATCTTCACTCCGCTGCTGCACGACATCGACGACGGCAAG
genomic: GATAAGAGGGGATCAGCAGCACTTTGTTCGCCGAGACGAACTGAAGgtttgtgctt ... tggttttcagGCTGCGTGGGAGATCTTCACTCCGCTGCTGCACGACATCGACGACGGCAAG
EST: gi|88257654|gb|CI360240.1|CI360240
EST:     GATAAGAGGGGATCAGCAGCACTTTGTTCGCCGAGACGAACTGAAG                         GCTGCGTGGGAGATCTTCACTCCGCTGCTGCACGACATCGACGACGGCAAG
genomic: GATAAGAGGGGATCAGCAGCACTTTGTTCGCCGAGACGAACTGAAGgtttgtgctt ... tggttttcagGCTGCGTGGGAGATCTTCACTCCGCTGCTGCACGACATCGACGACGGCAAG
EST: gi|218492006|gb|FG967745.1|FG967745
EST:     GATAAGAGGGGATCNGCAGCACTTTGTTCGCCGAGACGAACTGAAT                         GCTGCGTGGGAGATCTTCACTCCGATGCTGCACGACATCGAAGACGGCAAG
genomic: GATAAGAGGGGATCAGCAGCACTTTGTTCGCCGAGACGAACTGAAGgtttgtgctt ... tggttttcagGCTGCGTGGGAGATCTTCACTCCGCTGCTGCACGACATCGACGACGGCAAG
EST: gi|89177186|gb|CI043689.1|CI043689
EST:     GATAAGAGGGGATCAGCAGCACTTTGTTCGCCGAGACGAACTGAAG                         GCTGCGTGGGAGATCTTCACTCCGCTGCTGCACGACATCGACGACGGCAAG
genomic: GATAAGAGGGGATCAGCAGCACTTTGTTCGCCGAGACGAACTGAAGgtttgtgctt ... tggttttcagGCTGCGTGGGAGATCTTCACTCCGCTGCTGCACGACATCGACGACGGCAAG
EST: gi|88242908|gb|CI240759.1|CI240759
EST:     GATAAGAGGGGATCAGCAGCACTTTGTTCGCCGAGACGAACTGAAG                         GCTGCGTGGGAGATCTTCACTCCGCTGCTGCACGACATCGACGACGGCAAG
genomic: GATAAGAGGGGATCAGCAGCACTTTGTTCGCCGAGACGAACTGAAGgtttgtgctt ... tggttttcagGCTGCGTGGGAGATCTTCACTCCGCTGCTGCACGACATCGACGACGGCAAG
EST: gi|88447385|gb|CI544259.1|CI544259
EST:     GATAAGAGGGGATCAGCAGCACTTTGTTCGCCGAGACGAACTGAAG                         GCTGCGTGGGAGATCTTCACTCCGCTGCTGCACGACATCGACGACGGCAAG
genomic: GATAAGAGGGGATCAGCAGCACTTTGTTCGCCGAGACGAACTGAAGgtttgtgctt ... tggttttcagGCTGCGTGGGAGATCTTCACTCCGCTGCTGCACGACATCGACGACGGCAAG
EST: gi|88540877|gb|CI468953.1|CI468953
EST:     GATAAGAGGGGATCAGCAGCACTTTGTTCGCCGAGACGAACTGAAG                         GCTGCGTGGGAGATCTTCACTCCGCTGCTGCACGACATCGACGACGGCAAG
genomic: GATAAGAGGGGATCAGCAGCACTTTGTTCGCCGAGACGAACTGAAGgtttgtgctt ... tggttttcagGCTGCGTGGGAGATCTTCACTCCGCTGCTGCACGACATCGACGACGGCAAG
EST: gi|88537565|gb|CI466523.1|CI466523
EST:     GATAAGAGGGGATCAGCAGCACTTTGTTCGCCGAGACGAACTGAAG                         GCTGCGTGGGAGATCTTCACTCCGCTGCTGCACGACATCGACGACGGCAAG
genomic: GATAAGAGGGGATCAGCAGCACTTTGTTCGCCGAGACGAACTGAAGgtttgtgctt ... tggttttcagGCTGCGTGGGAGATCTTCACTCCGCTGCTGCACGACATCGACGACGGCAAG
EST: gi|88460847|gb|CI552983.1|CI552983
EST:     GATAAGAGGGGATCAGCAGCACTTTGTTCGCCGAGACGAACTGAAG                         GCTGCGTGGGAGATCTTCACTCCGCTGCTGCACGACATCGACGACGGCAAG
genomic: GATAAGAGGGGATCAGCAGCACTTTGTTCGCCGAGACGAACTGAAGgtttgtgctt ... tggttttcagGCTGCGTGGGAGATCTTCACTCCGCTGCTGCACGACATCGACGACGGCAAG
EST: gi|88487048|gb|CI424319.1|CI424319
EST:     GATAAGAGGGGATCAGCAGCACTTTGTTCGCCGAGACGAACTGAAG                         GCTGCGTGGGAGATCTTCACTCCGCTGCTGCACGACATCGACGACGGCAAG
genomic: GATAAGAGGGGATCAGCAGCACTTTGTTCGCCGAGACGAACTGAAGgtttgtgctt ... tggttttcagGCTGCGTGGGAGATCTTCACTCCGCTGCTGCACGACATCGACGACGGCAAG
EST: gi|88531486|gb|CI459965.1|CI459965
EST:     GATAAGAGGGGATCAGCAGCACTTTGTTCGCCGAGACGAACTGAAG                         GCTGCGTGGGAGATCTTCACTCCGCTGCTGCACGACATCGACGACGGCAAG
genomic: GATAAGAGGGGATCAGCAGCACTTTGTTCGCCGAGACGAACTGAAGgtttgtgctt ... tggttttcagGCTGCGTGGGAGATCTTCACTCCGCTGCTGCACGACATCGACGACGGCAAG

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: 46 (upstream exon), 57 (downstream exon)
Score: 11

GATAAGAGGGGATCAGCAGCACTTTGTTCGCCGAGACGAACTGAAGgtttgtgctt ... tggttttcagGCTGCGTGGGAGATCTTCACTCCGCTGCTGCACGACATCGACGACGGCAAGGTGAAGGCCCTGCCGTACAAGCCGGGAACCCGGGGACCCCCAGAGGCCG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgcaatcggctcgcttgtgactgaatgaatacctgacgccgtgttggttttcagGCTGCGTGGGAGATCTTCACTCCGCTGCTGCACGACATCGACGACGGCAAGGTGAAGGCCCTGCCGTACAAGCCGGGAACCCGGGGACCCCCAGAGGCCG
                               acctgac  putative branch site (score: 11)
                                                ttttc  putative PPT
                        aatgaata  TA-rich tract