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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGGCGGCCACCACCTCCACCTCCTCCTCGCCGCCGCCGTCGTCCTCCTCCTCACCGTCGCGGGGCTGCCCCTCGCTTCCGCCTCCGAGTCCGACCACAAGgtgcgttgtcgcccgctcccccaccccctctctctctctctctctctctctctctctctctctcttccttccttcctttcttccttcccttaaccctaga...

Basic information

species Oryza sativa
transcript LOC_Os11g07910.1
intron # 1
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|88851745|gb|CI674947.1|CI674947
EST:     TCACCGTCGCGGGGCTGCCCCTCGCTTCCGCCTCCGAGTCCGACCACAAG                         TACAAAGCTGAAGAAACGGTTAAACTCTGGGTAAACAAGGTTGGCCCGTAC
genomic: TCACCGTCGCGGGGCTGCCCCTCGCTTCCGCCTCCGAGTCCGACCACAAGgtgcgttgtc ... ttttatgcagTACAAAGCTGAAGAAACGGTTAAACTCTGGGTAAACAAGGTTGGCCCGTAC
EST: gi|29630127|gb|CB635136.1|CB635136
EST:     TCACCGTCGCGGGGCTGCCCCTCGCTTCCGCCTCCGAGTCCGACCACGAG                         TACAAAGCTGAAGAAACAGTTAAACTCTGGGTAGACAAGGTTGGCCCGGAC
genomic: TCACCGTCGCGGGGCTGCCCCTCGCTTCCGCCTCCGAGTCCGACCACAAGgtgcgttgtc ... ttttatgcagTACAAAGCTGAAGAAACGGTTAAACTCTGGGTAAACAAGGTTGGCCCGTAC
EST: gi|88422337|gb|CI689147.1|CI689147
EST:     CACCGTCGCGGGGCTNGCCC-TCGNTTCCGCCTCCGAGTCCGANCACAAG                         TACAAAGCTGAAGAAANGGTTAAACTCTGGGTAAACAAGGTTGGCCCGTAC
genomic: CACCGTCGCGGGGCT-GCCCCTCGCTTCCGCCTCCGAGTCCGACCACAAGgtgcgttgtc ... ttttatgcagTACAAAGCTGAAGAAACGGTTAAACTCTGGGTAAACAAGGTTGGCCCGTAC
EST: gi|88733806|gb|CI756983.1|CI756983
EST:     TCACCGTCGCGGGGCTGCCCCTCGCTTCCGCCTCCGAGTCCGACCACAAG                         TACAAAGCTGAAGAAACGGTTAAACTCTGGGTAAACAAGGTTGGCCCGTAC
genomic: TCACCGTCGCGGGGCTGCCCCTCGCTTCCGCCTCCGAGTCCGACCACAAGgtgcgttgtc ... ttttatgcagTACAAAGCTGAAGAAACGGTTAAACTCTGGGTAAACAAGGTTGGCCCGTAC
EST: gi|88591655|gb|CI709704.1|CI709704
EST:     TCACCGTCGCGGGGCTGCCCCTCGCTTCCGCCTCCGAGTCCGACCACAAG                         TACAAAGCTGAAGAAACGGTTAAACTCTGGGTAAACAAGGTTGGCCCGTAC
genomic: TCACCGTCGCGGGGCTGCCCCTCGCTTCCGCCTCCGAGTCCGACCACAAGgtgcgttgtc ... ttttatgcagTACAAAGCTGAAGAAACGGTTAAACTCTGGGTAAACAAGGTTGGCCCGTAC
EST: gi|88729589|gb|CI751392.1|CI751392
EST:     TCACCGTCGCGGGGCTGCCCCTCGCTTCCGCCTCCGAGTCCGACCACAAG                         TACAAAGCTGAAGAAACGGTTAAACTCTGGGTAAACAAGGTTGGCCCGTAC
genomic: TCACCGTCGCGGGGCTGCCCCTCGCTTCCGCCTCCGAGTCCGACCACAAGgtgcgttgtc ... ttttatgcagTACAAAGCTGAAGAAACGGTTAAACTCTGGGTAAACAAGGTTGGCCCGTAC
EST: gi|86892079|gb|CI305187.1|CI305187
EST:     TCACCGTCGCGGGGCTGCCCCTCGCTTCCGCCTCCGAGTCCGACCACAAG                         TACAAAGCTGAAGAAACGGTTAAACTCTGGGTAAACAAGGTTGGCCCGTAC
genomic: TCACCGTCGCGGGGCTGCCCCTCGCTTCCGCCTCCGAGTCCGACCACAAGgtgcgttgtc ... ttttatgcagTACAAAGCTGAAGAAACGGTTAAACTCTGGGTAAACAAGGTTGGCCCGTAC
EST: gi|88393200|gb|CI616684.1|CI616684
EST:     TCACCGTCGCGGGGCTGGCCCTCGCTTCCGGCTCCGAGTCCGACCACAAG                         TACAAAGCTGAAGAAACGGTTAAACCTCTGGGTAAACAAGGTTGGCCCGTA
genomic: TCACCGTCGCGGGGCTGCCCCTCGCTTCCGCCTCCGAGTCCGACCACAAGgtgcgttgtc ... ttttatgcagTACAAAGCTGAAGAAACGGTTAAAC-TCTGGGTAAACAAGGTTGGCCCGTA
EST: gi|88585282|gb|CI702903.1|CI702903
EST:     TCACCGTCGCGGGGCTGCCCCTCGCTTCCGCCTCCGAGTCCGACCACAAG                         TACAAAGCTGAAGAAACGGTTAAACTCTGGGTAAACAAGGTTGGCCCGTAC
genomic: TCACCGTCGCGGGGCTGCCCCTCGCTTCCGCCTCCGAGTCCGACCACAAGgtgcgttgtc ... ttttatgcagTACAAAGCTGAAGAAACGGTTAAACTCTGGGTAAACAAGGTTGGCCCGTAC
EST: gi|88432740|gb|CI690584.1|CI690584
EST:     TCACCGTCGCGGGGCTGCCCCTCGCTTCCGCCTCCGAGTCCGACCACAAG                         TACAAAGCTGAAGAAACGGTTAAACTCTGGGTAAACAAGGTTGGCCCGTAC
genomic: TCACCGTCGCGGGGCTGCCCCTCGCTTCCGCCTCCGAGTCCGACCACAAGgtgcgttgtc ... ttttatgcagTACAAAGCTGAAGAAACGGTTAAACTCTGGGTAAACAAGGTTGGCCCGTAC
EST: gi|88762940|gb|CI772496.1|CI772496
EST:     TCACCGTCGCGGGGCTGCCCCTCGCTTCCGCCTCCGAGTCCGACCACAAG                         TACAAAGCTGAAGAAACGGTTAAACTCTGGGTAAACAAGGTTGGCCCGTAC
genomic: TCACCGTCGCGGGGCTGCCCCTCGCTTCCGCCTCCGAGTCCGACCACAAGgtgcgttgtc ... ttttatgcagTACAAAGCTGAAGAAACGGTTAAACTCTGGGTAAACAAGGTTGGCCCGTAC
EST: gi|88587417|gb|CI705162.1|CI705162
EST:     TCACCGTCGCGGGGCTGCCCCTCGCTTCCGCCTCCGAGTCCGACCACAAG                         TACAAAGCTGAAGAAACGGTTAAACTCTGGGTAAACAAGGTTGGCCCGTAC
genomic: TCACCGTCGCGGGGCTGCCCCTCGCTTCCGCCTCCGAGTCCGACCACAAGgtgcgttgtc ... ttttatgcagTACAAAGCTGAAGAAACGGTTAAACTCTGGGTAAACAAGGTTGGCCCGTAC
EST: gi|58667768|gb|CK056454.1|CK056454
EST:     TCACCGTCGCGGGGCTGCCCCTCGCTTCCGCCTCCGAGTCCGACCACAAG                         TACAAAGCTGAAGAAACAGTTAAACTCTGGGTAAACAAGGTTGGCCCGTAC
genomic: TCACCGTCGCGGGGCTGCCCCTCGCTTCCGCCTCCGAGTCCGACCACAAGgtgcgttgtc ... ttttatgcagTACAAAGCTGAAGAAACGGTTAAACTCTGGGTAAACAAGGTTGGCCCGTAC
EST: gi|87014296|gb|CI305074.1|CI305074
EST:     TCACCGTCGCGGGGCTGCCCCTCGCTTCCGCCTCCGAGTCCGACCACAAG                         TACAAAGCTGAAGAAACGGTTAAACTCTGGGTAAACAAGGTTGGCCCGTAC
genomic: TCACCGTCGCGGGGCTGCCCCTCGCTTCCGCCTCCGAGTCCGACCACAAGgtgcgttgtc ... ttttatgcagTACAAAGCTGAAGAAACGGTTAAACTCTGGGTAAACAAGGTTGGCCCGTAC
EST: gi|88336758|gb|CI644007.1|CI644007
EST:     TCACCGTCGCGGGGCTGCCCCTCGCTTCCGCCTCCGAGTCCGACCANAAG                         TACAAAGCTGAAGAAACGGTTAAACTCTGGGTAAACAAGGTTGGCCCGTAC
genomic: TCACCGTCGCGGGGCTGCCCCTCGCTTCCGCCTCCGAGTCCGACCACAAGgtgcgttgtc ... ttttatgcagTACAAAGCTGAAGAAACGGTTAAACTCTGGGTAAACAAGGTTGGCCCGTAC
EST: gi|86900951|gb|CI304156.1|CI304156
EST:     TCACCGTCGCGGGGCTGCCCCTCGCTTCCGCCTCCGAGTCCGACCACAAG                         TACAAAGCTGAAGAAACGGTTAAACTCTGGGTAAACAAGGTTGGCCCGTAC
genomic: TCACCGTCGCGGGGCTGCCCCTCGCTTCCGCCTCCGAGTCCGACCACAAGgtgcgttgtc ... ttttatgcagTACAAAGCTGAAGAAACGGTTAAACTCTGGGTAAACAAGGTTGGCCCGTAC
EST: gi|29623264|gb|CB628275.1|CB628275
EST:     TCACCGTCGCGGGGCTGCCCCTCGCTTCCGCCTCCGAGTCCGACCACAAG                         TACAAAGCTGAAGAAACAGTTAAACTCTGGGTAAACAAGGTTGGCCCGTAC
genomic: TCACCGTCGCGGGGCTGCCCCTCGCTTCCGCCTCCGAGTCCGACCACAAGgtgcgttgtc ... ttttatgcagTACAAAGCTGAAGAAACGGTTAAACTCTGGGTAAACAAGGTTGGCCCGTAC
EST: gi|86909162|gb|CI302765.1|CI302765
EST:     TCACCGTCGCGGGGCTGCCCCTCGCTTCCGCCTCCGAGTCCGACCACAAG                         TACAAAGCTGAAGACACGGTTAAACTCTGGGTCAACAAGGTTGGCCCGTAC
genomic: TCACCGTCGCGGGGCTGCCCCTCGCTTCCGCCTCCGAGTCCGACCACAAGgtgcgttgtc ... ttttatgcagTACAAAGCTGAAGAAACGGTTAAACTCTGGGTAAACAAGGTTGGCCCGTAC
EST: gi|88695117|gb|CI739155.1|CI739155
EST:     TCACCGTCGCGGGGCTGCCCCTCGCTTCCGCCTCCGAGTCCGACCACAAG                         TACAAAGCTGAAGAAACGGTTAAANTCTGGGTAAACAAGGTTGGCCCGTAC
genomic: TCACCGTCGCGGGGCTGCCCCTCGCTTCCGCCTCCGAGTCCGACCACAAGgtgcgttgtc ... ttttatgcagTACAAAGCTGAAGAAACGGTTAAACTCTGGGTAAACAAGGTTGGCCCGTAC
EST: gi|88588858|gb|CI706700.1|CI706700
EST:     TCACCGTCGCGGGGCTGCCCCTCGCTTCCGCCTCCGAGTCCGACCACAAG                         TACAAAGCTGAAGAAACGGTTAAACTCTGGGTAAACAAGGTTGGCCCGTAC
genomic: TCACCGTCGCGGGGCTGCCCCTCGCTTCCGCCTCCGAGTCCGACCACAAGgtgcgttgtc ... ttttatgcagTACAAAGCTGAAGAAACGGTTAAACTCTGGGTAAACAAGGTTGGCCCGTAC
EST: gi|88694217|gb|CI738255.1|CI738255
EST:     TCACCGTCGCGGGGCTGCCCCTCGCTTCCGCCTCCGAGTCCGACCACAAG                         TACAAAGCTGAAGAAACGGTTAAACTCTGGGTAAACAAGGTTGGCCCGTAC
genomic: TCACCGTCGCGGGGCTGCCCCTCGCTTCCGCCTCCGAGTCCGACCACAAGgtgcgttgtc ... ttttatgcagTACAAAGCTGAAGAAACGGTTAAACTCTGGGTAAACAAGGTTGGCCCGTAC
EST: gi|88579966|gb|CI691963.1|CI691963
EST:     TCACCGTCGCGGGGCTGCCCCTCGCTTCCGCCTCCGAGTCCGACCACAAG                         TACAAAGCTGAAGAAACGGTTAAACTCTGGGTAAACAAGGTTGGCCCGTAC
genomic: TCACCGTCGCGGGGCTGCCCCTCGCTTCCGCCTCCGAGTCCGACCACAAGgtgcgttgtc ... ttttatgcagTACAAAGCTGAAGAAACGGTTAAACTCTGGGTAAACAAGGTTGGCCCGTAC
EST: gi|88339854|gb|CI649111.1|CI649111
EST:     TCANCGTCGCGGGGCTGCCCCTCGCTTCCGCCTCCGAGTCCGACCACAAG                         TACAAAGCTGAAGAAACGGTTAAACTCTGGGTAAACAAGGTTGGCCCGTAC
genomic: TCACCGTCGCGGGGCTGCCCCTCGCTTCCGCCTCCGAGTCCGACCACAAGgtgcgttgtc ... ttttatgcagTACAAAGCTGAAGAAACGGTTAAACTCTGGGTAAACAAGGTTGGCCCGTAC
EST: gi|88733489|gb|CI756666.1|CI756666
EST:     TCACCGTCGCGGGGCTGCCCCTCGCTTCCGCCTCCGAGTCCGACCACAAG                         TACAAAGCTGAAGAAACGGTTAAACTCTGGGTAAACAAGGTTGGCCCGTAC
genomic: TCACCGTCGCGGGGCTGCCCCTCGCTTCCGCCTCCGAGTCCGACCACAAGgtgcgttgtc ... ttttatgcagTACAAAGCTGAAGAAACGGTTAAACTCTGGGTAAACAAGGTTGGCCCGTAC
EST: gi|88354303|gb|CI637869.1|CI637869
EST:     TCACCGTCGCGGGGCTGCCCCTCGCTTCCGCCTCCGAGTCCGACCACAAG                         TACAAAGCTGAAGAAACGGTTAAACTCTGGGTAAACAAGGTTGGCCCGTAC
genomic: TCACCGTCGCGGGGCTGCCCCTCGCTTCCGCCTCCGAGTCCGACCACAAGgtgcgttgtc ... ttttatgcagTACAAAGCTGAAGAAACGGTTAAACTCTGGGTAAACAAGGTTGGCCCGTAC
EST: gi|88337177|gb|CI628263.1|CI628263
EST:     TCACCGTCGCGGGGCTGCCCCTCGCTTCCGCCTCCGAGTCCGACCACAAG                         TAAAAAGCTGAAGAAACGGTTAAACTCTGGGTAAACAAGGTTGGCCCGTAC
genomic: TCACCGTCGCGGGGCTGCCCCTCGCTTCCGCCTCCGAGTCCGACCACAAGgtgcgttgtc ... ttttatgcagTACAAAGCTGAAGAAACGGTTAAACTCTGGGTAAACAAGGTTGGCCCGTAC
EST: gi|88443541|gb|CI597008.1|CI597008
EST:     TCACCGTCGCGGGGCTGCCCCTCGCTTCCGCCTCCGAGTCCGACCACAAG                         TACAAAGCTGAAGAAACGGTTAAACTCTGGGTAAACAAGGTTGGCCCGTAC
genomic: TCACCGTCGCGGGGCTGCCCCTCGCTTCCGCCTCCGAGTCCGACCACAAGgtgcgttgtc ... ttttatgcagTACAAAGCTGAAGAAACGGTTAAACTCTGGGTAAACAAGGTTGGCCCGTAC
EST: gi|86831804|gb|CI303244.1|CI303244
EST:     TCACCGTCGCGGGGCTGCCCCTCGCTTCCGCCTCCGAGTCCGACCACAAG                         TACAAAGCTGAAGAAACGGTTAAACTCTGGGTAAACAAGGTTGGCCCGTAC
genomic: TCACCGTCGCGGGGCTGCCCCTCGCTTCCGCCTCCGAGTCCGACCACAAGgtgcgttgtc ... ttttatgcagTACAAAGCTGAAGAAACGGTTAAACTCTGGGTAAACAAGGTTGGCCCGTAC
EST: gi|88368107|gb|CI574989.1|CI574989
EST:     TCACCGTCGCGGGGCTGCCCCTCGCTT-CGCCTCCGAGTCCGACCACAAG                         TACAAAGCTGAAGAAAGGGTTAAACTCTGGGTAAACAAGGTTGGCCCGTAC
genomic: TCACCGTCGCGGGGCTGCCCCTCGCTTCCGCCTCCGAGTCCGACCACAAGgtgcgttgtc ... ttttatgcagTACAAAGCTGAAGAAACGGTTAAACTCTGGGTAAACAAGGTTGGCCCGTAC
EST: gi|88306502|gb|CI671253.1|CI671253
EST:     TCACCGTCGCGGGGCTGCCCCTCGCTTCCGCCTCCGAGTCCGACCACAAG                         TACAAAGCTGAAGAAACGGTTAAACTCTGGGTAAACAAGGTTGGCCCGTAC
genomic: TCACCGTCGCGGGGCTGCCCCTCGCTTCCGCCTCCGAGTCCGACCACAAGgtgcgttgtc ... ttttatgcagTACAAAGCTGAAGAAACGGTTAAACTCTGGGTAAACAAGGTTGGCCCGTAC
EST: gi|88296490|gb|CI669266.1|CI669266
EST:     TCACCGTCGCGGGGCTGCCCCTCGCTTCCGCCTCCGAGTCCGACCACAAG                         TACAAAGCTGAAGAAACGGTTAAACTCTGGGTAAACAAGGTTGGCCCGTAC
genomic: TCACCGTCGCGGGGCTGCCCCTCGCTTCCGCCTCCGAGTCCGACCACAAGgtgcgttgtc ... ttttatgcagTACAAAGCTGAAGAAACGGTTAAACTCTGGGTAAACAAGGTTGGCCCGTAC
EST: gi|29626345|gb|CB631356.1|CB631356
EST:     TCACCGTCGCGGGGCTGCCCCTCGCTTCCGCCTCCGAGTCCGACCACAAG                         TACAAAGCTGAAGAAACAGTTAAACTCTGGGTAAACAAGGTTGGCCCGTAC
genomic: TCACCGTCGCGGGGCTGCCCCTCGCTTCCGCCTCCGAGTCCGACCACAAGgtgcgttgtc ... ttttatgcagTACAAAGCTGAAGAAACGGTTAAACTCTGGGTAAACAAGGTTGGCCCGTAC
EST: gi|88329904|gb|CI651581.1|CI651581
EST:     TCACCGTCGCGGGGCTGCCCCTCGCTTCCGCCTCCGAGTCCGACCACAAG                         TACAAAGCTGAAGAAACGGTTAAACTCTGGGTAAACAAGGTTGGCCCGTAC
genomic: TCACCGTCGCGGGGCTGCCCCTCGCTTCCGCCTCCGAGTCCGACCACAAGgtgcgttgtc ... ttttatgcagTACAAAGCTGAAGAAACGGTTAAACTCTGGGTAAACAAGGTTGGCCCGTAC
EST: gi|88725055|gb|CI748314.1|CI748314
EST:     TCACCGTCGCGGGGCTGGCCCTCGCTTCCGCCTCCGAGTCCGACCACAAG                         TACAAAGCTGAAGAAACGGTTAAACTCTGGGTAAACAAGGTTGGCCCGTAC
genomic: TCACCGTCGCGGGGCTGCCCCTCGCTTCCGCCTCCGAGTCCGACCACAAGgtgcgttgtc ... ttttatgcagTACAAAGCTGAAGAAACGGTTAAACTCTGGGTAAACAAGGTTGGCCCGTAC
EST: gi|88391960|gb|CI683780.1|CI683780
EST:     TCACCGTCGCGGGGCTGCCCCTCGCTTCCGCCTCCGAGTCCGACCACAAG                         TACAAAGCTGAAGAAACGGTTAAACTCTGGGTAAACAAGGTTGGCCCGTAC
genomic: TCACCGTCGCGGGGCTGCCCCTCGCTTCCGCCTCCGAGTCCGACCACAAGgtgcgttgtc ... ttttatgcagTACAAAGCTGAAGAAACGGTTAAACTCTGGGTAAACAAGGTTGGCCCGTAC
EST: gi|88398094|gb|CI585597.1|CI585597
EST:     TCACCGTCGCGGGGCTGCCCCTCGCTTCCGCCTCCGAGTCCGACCACAAG                         TACAAAGCTGAAGAAACGGTTAAACTCTGGGTAAACAAGGTTGGCCCGTAC
genomic: TCACCGTCGCGGGGCTGCCCCTCGCTTCCGCCTCCGAGTCCGACCACAAGgtgcgttgtc ... ttttatgcagTACAAAGCTGAAGAAACGGTTAAACTCTGGGTAAACAAGGTTGGCCCGTAC

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: 37 (upstream exon), 70 (downstream exon)
Score: 12

CGGCGGCCACCACCTCCACCTCCTCCTCGCCGCCGCCGTCGTCCTCCTCCTCACCGTCGCGGGGCTGCCCCTCGCTTCCGCCTCCGAGTCCGACCACAAGgtgcgttgtc ... ttttatgcagTACAAAGCTGAAGAAACGGTTAAACTCTGGGTAAACAAGGTTGGCCCGTACAATAACCCGCAAGAAACTTACAACTATTACAGCCTCCCATTTTGTCAGC




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CGGCGGCCACCACCTCCACCTCCTCCTCGCCGCCGCCGTCGTCCTCCTCCTCACCGTCGCGGGGCTGCCCCTCGCTTCCGCCTCCGAGTCCGACCACAAGgtgcgttgtcgcccgctcccccaccccctctctctctctctctctctctctctctctctctctcttccttccttcctttcttccttcccttaaccctaga

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctccccc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccccctc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctctctct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccttccc