Skip to another splice site:
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 5'  3'   		2  
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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GACGACATGCCTAAGATAAAGACAAGCCGTGTCAAGTATCCTGAAGGATGGGAGCTTATAGAACCAACTCTGCGTGATTTGGAAGCCAAGATGAGGGAAGgtatgcacatatctgtaatatgtaacagttcgtcgatttcttttcccagtatatatattgttatttattatttcctaccacagggtggtaatgatgtgattttctgattgctaaaaggtaatgtgattttcggatgcag

Basic information

species Oryza sativa
transcript LOC_Os05g37390.1
intron # 2
splice site 5'
intron type U2

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|88582892|gb|CI700335.1|CI700335
EST:     GGAGCTTATAGAACCAACTCTGCGTGATTTGGAAGCCAAGATGAGGGAAG                         CCGAGAATGATCCACATGATGGGAAGAGGAAGTGCGAAGCTCTCTGGCCAA
genomic: GGAGCTTATAGAACCAACTCTGCGTGATTTGGAAGCCAAGATGAGGGAAGgtatgcacat ... tcggatgcagCCGAGAATGATCCACATGATGGGAAGAGGAAGTGCGAAGCTCTCTGGCCAA
EST: gi|88586964|gb|CI704687.1|CI704687
EST:     GGAGCTTATAGAACCAACTCTGCGTGATTTGGAAGCCAAGATGAGGGAAG                         CCGAGAATGATCCACATGATGGGAAGAGGAAGTGCGAAGCTCTCTGGCCAA
genomic: GGAGCTTATAGAACCAACTCTGCGTGATTTGGAAGCCAAGATGAGGGAAGgtatgcacat ... tcggatgcagCCGAGAATGATCCACATGATGGGAAGAGGAAGTGCGAAGCTCTCTGGCCAA
EST: gi|88431086|gb|CI574257.1|CI574257
EST:     GGAGCTTATAGAACCAACTCTGCGTGATTTGGAAGCCAAGATGAGGGAAG                         CCGAGAATGATCCACATGATGGGAAGAGGAAGTGCGAAGCTCTCTGGCCAA
genomic: GGAGCTTATAGAACCAACTCTGCGTGATTTGGAAGCCAAGATGAGGGAAGgtatgcacat ... tcggatgcagCCGAGAATGATCCACATGATGGGAAGAGGAAGTGCGAAGCTCTCTGGCCAA
EST: gi|88337950|gb|CI676929.1|CI676929
EST:     GGAGCTTATAGAACCAACTCTGCGTGATTTGGAAGCCAAGATGAGGGAAG                         CCGAGAATGATCCACATGATGGGAAGAGGAAGTGCGAAGCTCTCTGGCCAA
genomic: GGAGCTTATAGAACCAACTCTGCGTGATTTGGAAGCCAAGATGAGGGAAGgtatgcacat ... tcggatgcagCCGAGAATGATCCACATGATGGGAAGAGGAAGTGCGAAGCTCTCTGGCCAA
EST: gi|33659505|gb|CF282118.1|CF282118
EST:     GGAGCTTATAGAACCAACTCTGCGTGATTTGGAAGCCAAGATGAGGGAAG                         CCGAGAATGATCCACATGATGGGAAGAGGAAGTGCGAAGCTCTCTGGCCAA
genomic: GGAGCTTATAGAACCAACTCTGCGTGATTTGGAAGCCAAGATGAGGGAAGgtatgcacat ... tcggatgcagCCGAGAATGATCCACATGATGGGAAGAGGAAGTGCGAAGCTCTCTGGCCAA
EST: gi|88588594|gb|CI706423.1|CI706423
EST:     GGAGCTTATAGAACCAACTCTGCGTGATTTGGAAGCCAAGATGAGGGAAG                         CCGAGAATGATCCACATGATGGGAAGAGGAAGTGCGAAGCTCTCTGGCCAA
genomic: GGAGCTTATAGAACCAACTCTGCGTGATTTGGAAGCCAAGATGAGGGAAGgtatgcacat ... tcggatgcagCCGAGAATGATCCACATGATGGGAAGAGGAAGTGCGAAGCTCTCTGGCCAA
EST: gi|88825373|gb|CI775938.1|CI775938
EST:     GGAGCTTATAGAACCAACTCTGCGTGATTTGGAAGCCAAGATGAGGGAAG                         CCGAGAATGATCCACATGATGGGAAGAGGAAGTGCGAAGCTCTCTGGCCAA
genomic: GGAGCTTATAGAACCAACTCTGCGTGATTTGGAAGCCAAGATGAGGGAAGgtatgcacat ... tcggatgcagCCGAGAATGATCCACATGATGGGAAGAGGAAGTGCGAAGCTCTCTGGCCAA
EST: gi|33802337|gb|CF327042.1|CF327042
EST:     GGAGCTTATAGAACCAACTCCGCGTGATTTGGAAGCCAAGATGAGGGAAG                         CCGAGAATGATCCACATGATGGGAAGAGGAAGTGCGAAGCTCTCTGGCCAA
genomic: GGAGCTTATAGAACCAACTCTGCGTGATTTGGAAGCCAAGATGAGGGAAGgtatgcacat ... tcggatgcagCCGAGAATGATCCACATGATGGGAAGAGGAAGTGCGAAGCTCTCTGGCCAA
EST: gi|88591771|gb|CI709824.1|CI709824
EST:     GGAGCTTATAGAACCAACTCTGCGTGATTTGGAAGCCAAGATGAGGGAAG                         CCGAGAATGATCCACATGATGGGAAGAGGAAGTGCGAAGCTCTCTGGCCAA
genomic: GGAGCTTATAGAACCAACTCTGCGTGATTTGGAAGCCAAGATGAGGGAAGgtatgcacat ... tcggatgcagCCGAGAATGATCCACATGATGGGAAGAGGAAGTGCGAAGCTCTCTGGCCAA
EST: gi|88410574|gb|CI686911.1|CI686911
EST:     GGAGCTTATAGAACCAACTCTGCGTGATTTGGAAGCCAAGATGAGGGAAG                         CCGAGAATGATCCACATGATGGGAAGAGGAAGTGCGAAGCTCTCTGGCCAA
genomic: GGAGCTTATAGAACCAACTCTGCGTGATTTGGAAGCCAAGATGAGGGAAGgtatgcacat ... tcggatgcagCCGAGAATGATCCACATGATGGGAAGAGGAAGTGCGAAGCTCTCTGGCCAA
EST: gi|88368228|gb|CI575110.1|CI575110
EST:     GGAGCTTATAGAACCAACTCTGCGTGATTTGGAAGCCAAGATGAGGGAAG                         CCGAGAATGATCCACATGATGGGAAGAGGAAGTGCGAAGCTCTCTGGCCAA
genomic: GGAGCTTATAGAACCAACTCTGCGTGATTTGGAAGCCAAGATGAGGGAAGgtatgcacat ... tcggatgcagCCGAGAATGATCCACATGATGGGAAGAGGAAGTGCGAAGCTCTCTGGCCAA
EST: gi|88356689|gb|CI619175.1|CI619175
EST:     GGAGCTTATAGAACCAACTCTGCGTGATTTGGAAGCCAAGATGAGGGAAG                         CCGAGAATGATCCACATGATGGGAAGAGGAAGTGCGAAGCTCTCTGGCCAA
genomic: GGAGCTTATAGAACCAACTCTGCGTGATTTGGAAGCCAAGATGAGGGAAGgtatgcacat ... tcggatgcagCCGAGAATGATCCACATGATGGGAAGAGGAAGTGCGAAGCTCTCTGGCCAA
EST: gi|88825326|gb|CI775891.1|CI775891
EST:     GGAGCTTATAGAACCAACTCTGCGTGATTTGGAAGCCAAGATGAGGGAAG                         CCGAGAATGATCCACATGATGGGAAGAGGAAGTGCGAAGCTCTCTGGCCAA
genomic: GGAGCTTATAGAACCAACTCTGCGTGATTTGGAAGCCAAGATGAGGGAAGgtatgcacat ... tcggatgcagCCGAGAATGATCCACATGATGGGAAGAGGAAGTGCGAAGCTCTCTGGCCAA
EST: gi|88451859|gb|CI694633.1|CI694633
EST:     GGAGCTTATAGAACCAACTCTGCGTGATTTGGAAGCCAAGATGAGGGAAG                         CCGAGAATGATCCACATGATGGGAAGAGGAAGTGCGAAGCTCTCTGGCCAA
genomic: GGAGCTTATAGAACCAACTCTGCGTGATTTGGAAGCCAAGATGAGGGAAGgtatgcacat ... tcggatgcagCCGAGAATGATCCACATGATGGGAAGAGGAAGTGCGAAGCTCTCTGGCCAA
EST: gi|88587015|gb|CI704739.1|CI704739
EST:     GGAGCTTATAGAACCAACTCTGCGTGATTTGGAAGCCAAGATGAGGGAAG                         CCGAGAATGATCCACATGATGGGAAGAGGAAGTGCGAAGCTCT
genomic: GGAGCTTATAGAACCAACTCTGCGTGATTTGGAAGCCAAGATGAGGGAAGgtatgcacat ... tcggatgcagCCGAGAATGATCCACATGATGGGAAGAGGAAGTGCGAAGCTCT
EST: gi|38477238|gb|CF961371.1|CF961371
EST:     GGAGCTTATAGAACCAACTCTGCGTGATTTGGAAGCCAAGATGAGGGAAG                         CCGAGAATGATCCACATGATGGGAAGAGGAAGTGCGAAGCTCTCTGGCCAA
genomic: GGAGCTTATAGAACCAACTCTGCGTGATTTGGAAGCCAAGATGAGGGAAGgtatgcacat ... tcggatgcagCCGAGAATGATCCACATGATGGGAAGAGGAAGTGCGAAGCTCTCTGGCCAA
EST: gi|55412750|gb|CV725126.1|CV725126
EST:     GGAGCTTATAGAACCAACTCTGCGTGATTTGGAAGCCAAGATGAGGGAAG                         CCGAGAATTATCCACATGATGNAAAGAGGAAGTGCAAAGCTCTCTGGCCAA
genomic: GGAGCTTATAGAACCAACTCTGCGTGATTTGGAAGCCAAGATGAGGGAAGgtatgcacat ... tcggatgcagCCGAGAATGATCCACATGATGGGAAGAGGAAGTGCGAAGCTCTCTGGCCAA
EST: gi|88388381|gb|CI683152.1|CI683152
EST:     GGAGCTTATAGAACCAACTCTGCGTGATTTGGAAGCCAAGATGAGGGAAG                         CCGAGAATGATCCACATGATGGGAAGAGGAAGTGCGAAGCTCTCTGGCCAA
genomic: GGAGCTTATAGAACCAACTCTGCGTGATTTGGAAGCCAAGATGAGGGAAGgtatgcacat ... tcggatgcagCCGAGAATGATCCACATGATGGGAAGAGGAAGTGCGAAGCTCTCTGGCCAA
EST: gi|55432535|gb|CV729288.1|CV729288
EST:     GGAGCTTATAGAACCAACTCTGCGTGATTTGGAAGCCAAGATGAGGGAAG                         CCGAGAATGATCCACATGATGGGAAGAGGAAGTGCGAAGCTCTCTGGCCAA
genomic: GGAGCTTATAGAACCAACTCTGCGTGATTTGGAAGCCAAGATGAGGGAAGgtatgcacat ... tcggatgcagCCGAGAATGATCCACATGATGGGAAGAGGAAGTGCGAAGCTCTCTGGCCAA
EST: gi|88739145|gb|CI762653.1|CI762653
EST:     GGAGCTTATAGAACCAACTCTGCGTGATTTGGAAGCCAAGATGAGGGAAG                         CCGAGAATGATCCACATGATGGGAAGAGGAAGTGCGAAGCTCTCTGGCCAA
genomic: GGAGCTTATAGAACCAACTCTGCGTGATTTGGAAGCCAAGATGAGGGAAGgtatgcacat ... tcggatgcagCCGAGAATGATCCACATGATGGGAAGAGGAAGTGCGAAGCTCTCTGGCCAA
EST: gi|88460072|gb|CI695270.1|CI695270
EST:     GGAGCTTATAGAACCAACTCTGCGTGATTTGGAAGCCAAGATGAGGGAAG                         CCGAGAATGATCCACATGATGGGAAGAGGAAGTGCGAAGCTCTCTGGCCAA
genomic: GGAGCTTATAGAACCAACTCTGCGTGATTTGGAAGCCAAGATGAGGGAAGgtatgcacat ... tcggatgcagCCGAGAATGATCCACATGATGGGAAGAGGAAGTGCGAAGCTCTCTGGCCAA

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), 73 (downstream exon)
Score: 17

GACGACATGCCTAAGATAAAGACAAGCCGTGTCAAGTATCCTGAAGGATGGGAGCTTATAGAACCAACTCTGCGTGATTTGGAAGCCAAGATGAGGGAAGgtatgcacat ... tcggatgcagCCGAGAATGATCCACATGATGGGAAGAGGAAGTGCGAAGCTCTCTGGCCAATCTTTCGTATTTCTCATCAAAAAAGCCGTTACATATATGATCTTTACTA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GACGACATGCCTAAGATAAAGACAAGCCGTGTCAAGTATCCTGAAGGATGGGAGCTTATAGAACCAACTCTGCGTGATTTGGAAGCCAAGATGAGGGAAGgtatgcacatatctgtaatatgtaacagttcgtcgatttcttttcccagtatatatattgttatttattatttcctaccacagggtggtaatgatgtgattttctgattgctaaaaggtaatgtgattttcggatgcag

- - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG