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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTGACACAGCAAGATTTGGTCCGGGGGGAAGGGGAGCAGCCGCCATGTTTGGGTCCCGAGTCCAGGATGAGGTGGAGATGCAGAGGAGGACTACCAACAGgtgcgtgctgccagcttgtgattctttaatcctgtagcttccttttcgtctcttgatgcagaagaggaattcttttcggttctttcaagcatatgtaagg...

Basic information

species Oryza sativa
transcript LOC_Os09g38580.3
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|88579252|gb|CI688232.1|CI688232
EST:     GGGTCCCGACTCCAGGATGAGGTGGAGATGCAGAGGAGGACTACCAACAG                         GATCTTTCCTGATGAGAGACAGGACCAGTTTAAGCTACCGTTTCAAGCTGC
genomic: GGGTCCCGAGTCCAGGATGAGGTGGAGATGCAGAGGAGGACTACCAACAGgtgcgtgctg ... ctatgtgtagGATCTTTCCTGATGAGAGACAGGACCAGTTTAAGCTACCGTTTCAAGCTGC
EST: gi|88591166|gb|CI708084.1|CI708084
EST:     GGGTCCCGAGTCCAGGATGAGGTGGAGATGCAGAGGAGGACTACCAACAG                         GATCTTTCCTGATGAGAGACAGGACCAGTTTAAGCTACCGTTTCAAGCTGC
genomic: GGGTCCCGAGTCCAGGATGAGGTGGAGATGCAGAGGAGGACTACCAACAGgtgcgtgctg ... ctatgtgtagGATCTTTCCTGATGAGAGACAGGACCAGTTTAAGCTACCGTTTCAAGCTGC
EST: gi|13165448|gb|AU174245.1|AU174245
EST:     GGGTCCCGAGTCCAGGATGAGGTGGAGATGCAGAGGAGGACTACCAACAG                         GATCTTTCCTGATGAGAGACAGGACCAGTTTAAGCTACCGTTTCAAGCTGC
genomic: GGGTCCCGAGTCCAGGATGAGGTGGAGATGCAGAGGAGGACTACCAACAGgtgcgtgctg ... ctatgtgtagGATCTTTCCTGATGAGAGACAGGACCAGTTTAAGCTACCGTTTCAAGCTGC
EST: gi|88458398|gb|CI695789.1|CI695789
EST:     GGGTCCCGAGTCCAGGATGAGGTGGAGATGCCGAGGAGGACTACCAACAG                         GATCTTTCCTGATGAGAGACAGGACCAGTTTAAGCTACCGTTTCAAGCTGC
genomic: GGGTCCCGAGTCCAGGATGAGGTGGAGATGCAGAGGAGGACTACCAACAGgtgcgtgctg ... ctatgtgtagGATCTTTCCTGATGAGAGACAGGACCAGTTTAAGCTACCGTTTCAAGCTGC
EST: gi|88371698|gb|CI680801.1|CI680801
EST:     GGGTCCCGAGTCCAGGATGAGGTGGAGATGCAGAGGAGGACTACCAACAG                         GATCTTTCCTGATGAGAGACAGGACCAGTTTAAGCTACCGTTTCAAGCTGC
genomic: GGGTCCCGAGTCCAGGATGAGGTGGAGATGCAGAGGAGGACTACCAACAGgtgcgtgctg ... ctatgtgtagGATCTTTCCTGATGAGAGACAGGACCAGTTTAAGCTACCGTTTCAAGCTGC
EST: gi|88412630|gb|CI690376.1|CI690376
EST:     GGGTCCCGAGTCCAGGATGAGGTGGAGATGCAGAGGAGGACTACCAACAG                         GATCTTTCCTGATGAGAGACAGGACCAGTTTAAGCTACCGTTTCAAGCTGC
genomic: GGGTCCCGAGTCCAGGATGAGGTGGAGATGCAGAGGAGGACTACCAACAGgtgcgtgctg ... ctatgtgtagGATCTTTCCTGATGAGAGACAGGACCAGTTTAAGCTACCGTTTCAAGCTGC
EST: gi|88381594|gb|CI682258.1|CI682258
EST:     GGGTCCCGAGTCCAGGATGAGGTGGAGATGCAGAGGAGGACTACCAACAG                         GATCTTTCCTGATGAGAGACAGGACCAGTTTAAGCTACCGTTTCAAGCTGC
genomic: GGGTCCCGAGTCCAGGATGAGGTGGAGATGCAGAGGAGGACTACCAACAGgtgcgtgctg ... ctatgtgtagGATCTTTCCTGATGAGAGACAGGACCAGTTTAAGCTACCGTTTCAAGCTGC
EST: gi|88579283|gb|CI688264.1|CI688264
EST:     GGGTCCCGAGTCCAGGATGAGGTGGAGATGCAGAGGAGGACTACCAACAG                         GATCTTTCCTGATGAGAGACAGGACCAGTTTAAGCTACCGTTTCAAGCTGC
genomic: GGGTCCCGAGTCCAGGATGAGGTGGAGATGCAGAGGAGGACTACCAACAGgtgcgtgctg ... ctatgtgtagGATCTTTCCTGATGAGAGACAGGACCAGTTTAAGCTACCGTTTCAAGCTGC
EST: gi|88587681|gb|CI704392.1|CI704392
EST:     GGGTCCCGAGTCCAGGATGAGGTGGAGATGCAGAGGAGGACTACCAACAG                         GATCTTTCCTGATGAGAGACAGGACCAGTTTAAGCTACCGTTTCAAGCTGC
genomic: GGGTCCCGAGTCCAGGATGAGGTGGAGATGCAGAGGAGGACTACCAACAGgtgcgtgctg ... ctatgtgtagGATCTTTCCTGATGAGAGACAGGACCAGTTTAAGCTACCGTTTCAAGCTGC
EST: gi|88586750|gb|CI704318.1|CI704318
EST:     GGGTCCCGAGTCCAGGATGAGGTGGAGATGCAGAGGAGGACTACCAACAG                         GATCTTTCCTGATGAGAGACAGGACCAGTTTAAGCTACCGTTTCAAGCTGC
genomic: GGGTCCCGAGTCCAGGATGAGGTGGAGATGCAGAGGAGGACTACCAACAGgtgcgtgctg ... ctatgtgtagGATCTTTCCTGATGAGAGACAGGACCAGTTTAAGCTACCGTTTCAAGCTGC
EST: gi|88315788|gb|CI617261.1|CI617261
EST:     GGGTCCCGAGTCCAGGATGAGGTGGAGATGCAGAGGAGGACTACCAACAG                         GATCTTTCCTGATGAGAGACAGGACCAGTTTAAGCTACCGTTTCAAGCTGC
genomic: GGGTCCCGAGTCCAGGATGAGGTGGAGATGCAGAGGAGGACTACCAACAGgtgcgtgctg ... ctatgtgtagGATCTTTCCTGATGAGAGACAGGACCAGTTTAAGCTACCGTTTCAAGCTGC
EST: gi|88402143|gb|CI614986.1|CI614986
EST:     GGGTCCCGAGTCCAGGATGAGGTGGAGATGCAGAGGAGGACTACCAACAG                         GATCTTTCCTGATGAGAGACAGGACCAGTTTAAGCTACCGTTTCAAGCTGC
genomic: GGGTCCCGAGTCCAGGATGAGGTGGAGATGCAGAGGAGGACTACCAACAGgtgcgtgctg ... ctatgtgtagGATCTTTCCTGATGAGAGACAGGACCAGTTTAAGCTACCGTTTCAAGCTGC
EST: gi|66917156|gb|CX104004.1|CX104004
EST:     GGGTCCCGAGTCCAGGATGAGGTGGAGATGCAGAGGAGGACTACCAACAG                         GATCTTTCCTGATGAGAGACAGGACCAGTTTAAGCTACCGTTTCAAGCTGC
genomic: GGGTCCCGAGTCCAGGATGAGGTGGAGATGCAGAGGAGGACTACCAACAGgtgcgtgctg ... ctatgtgtagGATCTTTCCTGATGAGAGACAGGACCAGTTTAAGCTACCGTTTCAAGCTGC

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: 63 (upstream exon), 70 (downstream exon)
Score: 51

TTGACACAGCAAGATTTGGTCCGGGGGGAAGGGGAGCAGCCGCCATGTTTGGGTCCCGAGTCCAGGATGAGGTGGAGATGCAGAGGAGGACTACCAACAGgtgcgtgctg ... ctatgtgtagGATCTTTCCTGATGAGAGACAGGACCAGTTTAAGCTACCGTTTCAAGCTGCACGGGCTGACAGATTTGGGGTAAACAGGATAGATGCAAAGACTACTGAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTGACACAGCAAGATTTGGTCCGGGGGGAAGGGGAGCAGCCGCCATGTTTGGGTCCCGAGTCCAGGATGAGGTGGAGATGCAGAGGAGGACTACCAACAGgtgcgtgctgccagcttgtgattctttaatcctgtagcttccttttcgtctcttgatgcagaagaggaattcttttcggttctttcaagcatatgtaagg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA