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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgattcaggcttttttttttctagcttacatagtgtccagttcaatcctttcaccatgcttgtcatgctaaccagagcttccatggcatagGTGGGGAAACATTCAGTTCCCTCTGCCTTTCGGAAGAGTCCTCAGCCCCTCTGAAAGCTTTATCCATGAACTGGATGAGAAG

Basic information

species Oryza sativa
transcript LOC_Os12g37870.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g37870.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G034083_T01 (Zea mays), 3'ss of exon 5
-----------------------------------gtatgattcaggcttttttttttctagcttacatagtgtccagttcaatcctttcacca------tgcttgtcatgctaaccagagcttccatggcatagGTGGGGAAACATTCAGTTCCCTCTGCCTTTCGGAAGAGTCCTCAGCCCCTCTGAAAGCTTTATCCATGAACTGGATGAGAAG
                                      |          ||  || | | |||     |  |||  |    |  | |||  | |      ||    ||||   | |||    || ||||  | |||||||| || |||  ||| || || || || |||||||| ||||| ||||| ||||| ||||||||||||||||||||||||
gtatgattcatgctttcgatgtacctcacagatctcagttgcctccatattaattgtaccagccatttttatgtgaaagggagacgtttttctactatattgtcaatcataacagccattattttcatg-tacagGTGGGGCAATATTGTGTTTCCCCTACCATTTGGAAGAGTTCTCAGTCCCTCCGAAAGTTTTATCCATGAACTGGATGAGAAG
















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|27577556|gb|CB000251.1|CB000251
EST:     GACATGAGAGGAGAATTGGACGACACAGCTGCCTTTAAGAACTTTAAGAA                         GTGGGGAAACATTCAGTTCCCTCTGCCTTTCGGAAGAGTCCTCAGCCCCTC
genomic: GACATGAGAGGAGAATTGGACGACACAGCTGCCTTTAAGAACTTTAAGAAgtatgattca ... catggcatagGTGGGGAAACATTCAGTTCCCTCTGCCTTTCGGAAGAGTCCTCAGCCCCTC
EST: gi|33807858|gb|CF329821.1|CF329821
EST:     GACATGAGAGGAGAATTGGACGACACAGCTGCCTTTAAGAACTTTAAGAA                         GTGGGGAAACATTCAGTTCCCTCTGCCTTTCGGAAGAGTCCTCAGCCCCTC
genomic: GACATGAGAGGAGAATTGGACGACACAGCTGCCTTTAAGAACTTTAAGAAgtatgattca ... catggcatagGTGGGGAAACATTCAGTTCCCTCTGCCTTTCGGAAGAGTCCTCAGCCCCTC
EST: gi|29669993|gb|CB666268.1|CB666268
EST:     GACATGAGAGGAGAATTGGACGACACAGCTGCCTTTAAGAACTTTAAGAA                         GTGGGGAAACATTCAGTTCCCTCTGCCTTTCGGAAGAGTCCTCAGCCCCTC
genomic: GACATGAGAGGAGAATTGGACGACACAGCTGCCTTTAAGAACTTTAAGAAgtatgattca ... catggcatagGTGGGGAAACATTCAGTTCCCTCTGCCTTTCGGAAGAGTCCTCAGCCCCTC
EST: gi|58600487|gb|CK011015.1|CK011015
EST:     GACATGAGAGGAGAATTGGACGACACAGCTGCCTTTAAGAACTTTAAGAA                         GTGGGGAAACATTCAGTTCCCTCTGCCTTTCGGAAGAGTCCTCAGCCCCTC
genomic: GACATGAGAGGAGAATTGGACGACACAGCTGCCTTTAAGAACTTTAAGAAgtatgattca ... catggcatagGTGGGGAAACATTCAGTTCCCTCTGCCTTTCGGAAGAGTCCTCAGCCCCTC
EST: gi|29638061|gb|CB643070.1|CB643070
EST:     ACATGAGAGGAGAATTGGACGACACAGCTGCCTTTAAGAACTTTAAGAA                         GTGGGGAAACATTCAGTTCCCTCTGCCTTTCGGAAGAGTCCTCAGCCCCTC
genomic: ACATGAGAGGAGAATTGGACGACACAGCTGCCTTTAAGAACTTTAAGAAgtatgattca ... catggcatagGTGGGGAAACATTCAGTTCCCTCTGCCTTTCGGAAGAGTCCTCAGCCCCTC
EST: gi|33800763|gb|CF326252.1|CF326252
EST:     GACATGAGAGGAGAATTGGACGACACAGCTGCCTTTAAGAACTTTAAGAA                         GTGGGGAAACATTCAGTTCCCTCTGCCTTTCGGAAGAGTCCTCAGCCCCTC
genomic: GACATGAGAGGAGAATTGGACGACACAGCTGCCTTTAAGAACTTTAAGAAgtatgattca ... catggcatagGTGGGGAAACATTCAGTTCCCTCTGCCTTTCGGAAGAGTCCTCAGCCCCTC
EST: gi|58589196|gb|CF987504.1|CF987504
EST:     GACATGAGAGGAGAATTGGACGACACAGCTGCCTTTAAGAACTTTAAGAA                         GTGGGGAAACATTCAGTTCCCTCTGCCTTTCGGAAGAGTCCTCAGCCCCTC
genomic: GACATGAGAGGAGAATTGGACGACACAGCTGCCTTTAAGAACTTTAAGAAgtatgattca ... catggcatagGTGGGGAAACATTCAGTTCCCTCTGCCTTTCGGAAGAGTCCTCAGCCCCTC

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: 71 (upstream exon), 73 (downstream exon)
Score: 74

TCCTTGAGATGAATCCGTTCACCATGGTGAATGGGGAACCATATCCTCTAGACATGAGAGGAGAATTGGACGACACAGCTGCCTTTAAGAACTTTAAGAAgtatgattca ... catggcatagGTGGGGAAACATTCAGTTCCCTCTGCCTTTCGGAAGAGTCCTCAGCCCCTCTGAAAGCTTTATCCATGAACTGGATGAGAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccagttcaatcctttcaccatgcttgtcatgctaaccagagcttccatggcatagGTGGGGAAACATTCAGTTCCCTCTGCCTTTCGGAAGAGTCCTCAGCCCCTCTGAAAGCTTTATCCATGAACTGGATGAGAAG
                             tgctaac  putative branch site (score: 74)
                                         cttccat  putative PPT