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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GACCTTGTTTTAACTGAAGTTGAACTTCCCTTGATGTCTGGGTTCCTGCTGCTCTCCACGATCATGGAACATGACGCATGCAAGAATATCCCCGTCATAAgtatgtatccaacttgactctatgccatgcctttctcatatctttctaatcccattactccatctgatgcttcatttttctattggtctcag

Basic information

species Oryza sativa
transcript LOC_Os09g36220.2
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g36220.2 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G367834_T01 (Zea mays), 5'ss of exon 2
GACCTTGTTTTAACTGAAGTTGAACTTCCCTTGATGTCTGGGTTCCTGCTGCTCTCCACGATCATGGAACATGACGCATGCAAGAATATCCCCGTCATAAgtatgt-atccaacttgactctatgccatgcctttctcatatctttctaatcccattactccatctgatgcttcatttttctattggtctcag
|||||||||||||||||||||||||| || |||||||||||||||||  || | |||||||||||||| ||||| |||| |||||| ||||| || |||||||||| |  |  || |  | |   | ||  ||| || |      |||||| |||  |||    || ||| ||  | ||   ||         
GACCTTGTTTTAACTGAAGTTGAACTGCCTTTGATGTCTGGGTTCCTCTTGTTATCCACGATCATGGAGCATGATGCATCCAAGAACATCCCTGTTATAAgtatgtcactcttctcgtgttttcactat--cttgctaa------tctaatgccaccactaagcctaatggtttttcttgtcatccag-----

upper sequence: LOC_Os09g36220.2 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G179024_T01 (Zea mays), 5'ss of exon 2
GACCTTGTTTTAACTGAAGTTGAACTTCCCTTGATGTCTGGGTTCCTGCTGCTCTCCACGATCATGGAACATGACGCATGCAAGAATATCCCCGTCATAAgtatgtatccaacttgactctatgccatgcctttctcatatctttctaatcccattactccatctgatgcttcatttttctattggtctcag
|||||||||||||||||||||||||| || |||||||||||||||||  || | ||||| |||||||| ||||| || | |||||| ||||| || ||||||||||   ||   |     | |    |  |  |||| | |   |||||| ||| ||||   ||| ||| ||  ||| ||     |      
GACCTTGTTTTAACTGAAGTTGAACTGCCTTTGATGTCTGGGTTCCTCTTGTTATCCACAATCATGGAGCATGATGCGTCCAAGAACATCCCTGTTATAAgtatgt---cactcttgtcgtgt----tttcgctctctttttaatctaatgccactactaagtctaatgttt--tttatcatccag------
















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|58609928|gb|CK037961.1|CK037961
EST:     GCTCTCCACGATCATGGAACATGACGCATGCAAGAATATCCCCGTCATAA                         TGATGTCTTCAAATGATTCCGTTAGCATGGTTTTCAAATGCATGCTAAAGG
genomic: GCTCTCCACGATCATGGAACATGACGCATGCAAGAATATCCCCGTCATAAgtatgtatcc ... ttggtctcagTGATGTCTTCAAATGATTCCGTTAGCATGGTTTTCAAATGCATGCTAAAGG
EST: gi|33676452|gb|CF304691.1|CF304691
EST:     GCTCTCCACGATCATGGAACATGACGCATGCAAGAATATCCCCGTCATAA                         TGATGTCTTCAAATGATTCCGTTAGCATGGTTTTCAAATGCATGCTAAAGG
genomic: GCTCTCCACGATCATGGAACATGACGCATGCAAGAATATCCCCGTCATAAgtatgtatcc ... ttggtctcagTGATGTCTTCAAATGATTCCGTTAGCATGGTTTTCAAATGCATGCTAAAGG
EST: gi|29670836|gb|CB667111.1|CB667111
EST:     GCTCTCCACGATCATGGAACATGACGCATGCAAGAATATCCCCGTCATAA                         TGATGTCTTCAAATGATTCCGTTAGCATGGTTTTCAAATGCATGCTAAAGG
genomic: GCTCTCCACGATCATGGAACATGACGCATGCAAGAATATCCCCGTCATAAgtatgtatcc ... ttggtctcagTGATGTCTTCAAATGATTCCGTTAGCATGGTTTTCAAATGCATGCTAAAGG
EST: gi|33676098|gb|CF304337.1|CF304337
EST:     GCTCTCCACGATCATGGAACATGACGCATGCAAGAATATCCCCGTCATAA                         TGATGTCTTCAAATGATTCCGTTAGCATGGTTTTCAAATGCATGCTAAAGG
genomic: GCTCTCCACGATCATGGAACATGACGCATGCAAGAATATCCCCGTCATAAgtatgtatcc ... ttggtctcagTGATGTCTTCAAATGATTCCGTTAGCATGGTTTTCAAATGCATGCTAAAGG
EST: gi|2428269|gb|C72732.1|C72732
EST:     GCTCTCCACGATCATGGAACATGACGCATGCAAGAATATCCCCGTCATAA                         TGATGTCTTCAAATGATTCCGTTAGCATGGTTTTCAAATGCATGCTAAAGG
genomic: GCTCTCCACGATCATGGAACATGACGCATGCAAGAATATCCCCGTCATAAgtatgtatcc ... ttggtctcagTGATGTCTTCAAATGATTCCGTTAGCATGGTTTTCAAATGCATGCTAAAGG
EST: gi|58664572|gb|CK053258.1|CK053258
EST:     GCTCTCCACGATCATGGAACATGACGCATGCAAGAATATCCCCGTCATAA                         TGATGTCTTCAAATGATTCCGTTAGCATGGTTTTCAAATGCATGCTAAAGG
genomic: GCTCTCCACGATCATGGAACATGACGCATGCAAGAATATCCCCGTCATAAgtatgtatcc ... ttggtctcagTGATGTCTTCAAATGATTCCGTTAGCATGGTTTTCAAATGCATGCTAAAGG
EST: gi|33678437|gb|CF306676.1|CF306676
EST:     GCTCTCCACGATCATGGAACATGACGCATGCAAGAATATCCCCGTCATAA                         TGATGTCTTCAAATGATTCCGTTAGCATGGCTTTCAAATGCATGCTAAAGG
genomic: GCTCTCCACGATCATGGAACATGACGCATGCAAGAATATCCCCGTCATAAgtatgtatcc ... ttggtctcagTGATGTCTTCAAATGATTCCGTTAGCATGGTTTTCAAATGCATGCTAAAGG
EST: gi|29638275|gb|CB643284.1|CB643284
EST:     GCTCTCCACGATCATGGAACATGACGCATGCAAGAATATCCCCGTCATAA                         TGATGTCTTCAAATGATTCCGTTAGCATGGTTTTCAAATGCATGCTAAAGG
genomic: GCTCTCCACGATCATGGAACATGACGCATGCAAGAATATCCCCGTCATAAgtatgtatcc ... ttggtctcagTGATGTCTTCAAATGATTCCGTTAGCATGGTTTTCAAATGCATGCTAAAGG
EST: gi|58689405|gb|CK078092.1|CK078092
EST:     GCTCTCCACGATCATGGAACATGACGCATGCAAGAATATCCCCGTCATAA                         TGATGTCTTCAAATGATTCCGTTAGCATGGTTTTCAAATGCATGCTAAAGG
genomic: GCTCTCCACGATCATGGAACATGACGCATGCAAGAATATCCCCGTCATAAgtatgtatcc ... ttggtctcagTGATGTCTTCAAATGATTCCGTTAGCATGGTTTTCAAATGCATGCTAAAGG
EST: gi|29634410|gb|CB639419.1|CB639419
EST:     GCTCTCCACGATCATGGAACATGACGCATGCAAGAATATCCCCGTCATAA                         TGATGTCTTCAAATGATTCCGTTAGCATGGTTTTCAAATGCATGCTAAAGG
genomic: GCTCTCCACGATCATGGAACATGACGCATGCAAGAATATCCCCGTCATAAgtatgtatcc ... ttggtctcagTGATGTCTTCAAATGATTCCGTTAGCATGGTTTTCAAATGCATGCTAAAGG
EST: gi|33675681|gb|CF303920.1|CF303920
EST:     GCTCTCCACGATCATGGAACATGACGCATGCAAGAATATCCCCGTCATAA                         TGATGTCTTCAAATGATTCCGTTAGCATGGTTTTCAAATGCATGCTAAAGG
genomic: GCTCTCCACGATCATGGAACATGACGCATGCAAGAATATCCCCGTCATAAgtatgtatcc ... ttggtctcagTGATGTCTTCAAATGATTCCGTTAGCATGGTTTTCAAATGCATGCTAAAGG
EST: gi|218502279|gb|FG970191.1|FG970191
EST:     GCTCTCCACGATCATGGAACATGACGCATGCAAGAATATCCCCGTCATAA                         TGATGTCTTCAAATGATTCCGTTAGCATGGTTTTCAAATGCATGCTAAAGG
genomic: GCTCTCCACGATCATGGAACATGACGCATGCAAGAATATCCCCGTCATAAgtatgtatcc ... ttggtctcagTGATGTCTTCAAATGATTCCGTTAGCATGGTTTTCAAATGCATGCTAAAGG
EST: gi|29625624|gb|CB630635.1|CB630635
EST:     GCTCTCCACGATCATGGAACATGACGCATGCAAGAATATCCCCGTCATAA                         TGATGTCTTCAAATGATTCCGTTAGCATGGTTTTCAAATGCATGCTAAAGG
genomic: GCTCTCCACGATCATGGAACATGACGCATGCAAGAATATCCCCGTCATAAgtatgtatcc ... ttggtctcagTGATGTCTTCAAATGATTCCGTTAGCATGGTTTTCAAATGCATGCTAAAGG
EST: gi|29635476|gb|CB640485.1|CB640485
EST:     GCTCTCCACGATCATGGAACATGACGCATGCAAGAATATCCCCGTCATAA                         TGATGTCTTCAAATGATTCCGTTAGCATGGTTTTCAAATGCATGCTAAAGG
genomic: GCTCTCCACGATCATGGAACATGACGCATGCAAGAATATCCCCGTCATAAgtatgtatcc ... ttggtctcagTGATGTCTTCAAATGATTCCGTTAGCATGGTTTTCAAATGCATGCTAAAGG
EST: gi|33676865|gb|CF305104.1|CF305104
EST:     GCTCTCCACGATCATGGAACATGACGCATGCAAGAATATCCCCGTCATAA                         TGATGTCTTCAAATGATTCCGTTAGCATGGTTTTCAAATGCATGCTAAAGG
genomic: GCTCTCCACGATCATGGAACATGACGCATGCAAGAATATCCCCGTCATAAgtatgtatcc ... ttggtctcagTGATGTCTTCAAATGATTCCGTTAGCATGGTTTTCAAATGCATGCTAAAGG

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: 70 (upstream exon), 75 (downstream exon)
Score: 55

GACCTTGTTTTAACTGAAGTTGAACTTCCCTTGATGTCTGGGTTCCTGCTGCTCTCCACGATCATGGAACATGACGCATGCAAGAATATCCCCGTCATAAgtatgtatcc ... ttggtctcagTGATGTCTTCAAATGATTCCGTTAGCATGGTTTTCAAATGCATGCTAAAGGGTGCTGCAGATTTCCTTGTTAAGCCAATACGGAAGAATGAATTAAGGAA




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Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GACCTTGTTTTAACTGAAGTTGAACTTCCCTTGATGTCTGGGTTCCTGCTGCTCTCCACGATCATGGAACATGACGCATGCAAGAATATCCCCGTCATAAgtatgtatccaacttgactctatgccatgcctttctcatatctttctaatcccattactccatctgatgcttcatttttctattggtctcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA