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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagacattgcttgttttttattttttgttccctacgagagtgttctattgtctgatgcggattcaagcttatcggcataacaattgacacaactcatgcagGCTTTTGTGAGCATTTAAATAGACAAAGTCCTGGCGGCGGCGGCGGCATCATCTCCATTTTTGAGAAACTTAAATTTTACATTTGGAAATTCAGATGCCC

Basic information

species Oryza sativa
transcript LOC_Os02g17320.2
intron # 15
splice site 3'
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|88273348|gb|CI388804.1|CI388804
EST:     GATTATCAGTCATCAACACCATTCTTTTGTGATGAGAAAAATCGTGTCAG                         GCTTTTGTGAGCATTTAAATAGACAAAGTCCTGGCGGCGGCGGC---ATCA
genomic: GATTATCAGTCATCAACACCATTCTTTTGTGATGAGAAAAATCGTGTCAGgtgagacatt ... actcatgcagGCTTTTGTGAGCATTTAAATAGACAAAGTCCTGGCGGCGGCGGCGGCATCA
EST: gi|29633369|gb|CB638378.1|CB638378
EST:     GATTATCAGTCATCAACACCATTCTTTTGTGATGAGAAAAATCGTGTCAG                         GCTTTTGTGAGCATTTAAATAGACAAAGTCCTGGCGGCGGCGGCGGCATCA
genomic: GATTATCAGTCATCAACACCATTCTTTTGTGATGAGAAAAATCGTGTCAGgtgagacatt ... actcatgcagGCTTTTGTGAGCATTTAAATAGACAAAGTCCTGGCGGCGGCGGCGGCATCA
EST: gi|88254969|gb|CI353793.1|CI353793
EST:     GATTATCAGTCATCAACACCATTCTTTTGTGATGAGAAAAATCGTGTCAG                         GCTTTTGTGAGCATTTAAATAGACAAAGTCCTGGCGGCGGCGGCGGCATCA
genomic: GATTATCAGTCATCAACACCATTCTTTTGTGATGAGAAAAATCGTGTCAGgtgagacatt ... actcatgcagGCTTTTGTGAGCATTTAAATAGACAAAGTCCTGGCGGCGGCGGCGGCATCA
EST: gi|86886699|gb|CI334613.1|CI334613
EST:     GATTATCAGTCATCAACACCATTCTTTTGTGATGAGAAAAATCGTGTCAG                         GCTTTTGTGAGCATTTAAATAGACAAAGTCCTGGCGGCGGCGGCGGCATCA
genomic: GATTATCAGTCATCAACACCATTCTTTTGTGATGAGAAAAATCGTGTCAGgtgagacatt ... actcatgcagGCTTTTGTGAGCATTTAAATAGACAAAGTCCTGGCGGCGGCGGCGGCATCA
EST: gi|87037876|gb|CI192498.1|CI192498
EST:     GATTATCAGTCATCAACACCATTCTTTTGTGATGAGAAAAATCGTGTCAG                         GCTTTTGTGAGCATTTAAATAGACAAAGTCCTGGCGGCGGCGGCGGCATCA
genomic: GATTATCAGTCATCAACACCATTCTTTTGTGATGAGAAAAATCGTGTCAGgtgagacatt ... actcatgcagGCTTTTGTGAGCATTTAAATAGACAAAGTCCTGGCGGCGGCGGCGGCATCA
EST: gi|3760815|gb|C98069.1|C98069
EST:     GATTATCAGTCATCAACACCATTCTTTTGTGATGAGAAAAATCGTGTCAG                         GCTTTTGTGAGCATTTAAATAGACAAAGTCCTGGCGGCGGCGGCGGCATCA
genomic: GATTATCAGTCATCAACACCATTCTTTTGTGATGAGAAAAATCGTGTCAGgtgagacatt ... actcatgcagGCTTTTGTGAGCATTTAAATAGACAAAGTCCTGGCGGCGGCGGCGGCATCA
EST: gi|16578897|gb|BI812992.1|BI812992
EST:     TGATGAGAAAAATCGTGTCAG                         GCTTTTGTGAGCATTTAAATAGACAAAGTCCTGGCGGCGGCGGCAGGCATC
genomic: TGATGAGAAAAATCGTGTCAGgtgagacatt ... actcatgcagGCTTTTGTGAGCATTTAAATAGACAAAGTCCTGGCGGCGGCGGC-GGCATC
EST: gi|33683400|gb|CF311639.1|CF311639
EST:     GATTATCAGTCATCAACACCATTCTTTTGTGATGAGAAAAATCGTGTCAG                         GCTTTTGTGAGCATTTAAATAGACAAAGTCCTGGCGGCGGCGGCGGCATCA
genomic: GATTATCAGTCATCAACACCATTCTTTTGTGATGAGAAAAATCGTGTCAGgtgagacatt ... actcatgcagGCTTTTGTGAGCATTTAAATAGACAAAGTCCTGGCGGCGGCGGCGGCATCA
EST: gi|86598197|gb|CI354814.1|CI354814
EST:     GATTATCAGTCATCAACACCATTCTTTTTTGATGAGAAAAATCGTGTCAG                         GCTTTTGTGAGCATTTAAATAGACAAAGTCCTGGCGGCGGCGCCGGCATCA
genomic: GATTATCAGTCATCAACACCATTCTTTTGTGATGAGAAAAATCGTGTCAGgtgagacatt ... actcatgcagGCTTTTGTGAGCATTTAAATAGACAAAGTCCTGGCGGCGGCGGCGGCATCA
EST: gi|87029276|gb|CI276544.1|CI276544
EST:     GATTATCAGTCATCAACACCATTCTTTTGTGATGAGAAAAATCGTGTCAG                         GCTTTTGTGAGCATTTAAATAGACAAAGTCCTGGCGGCGGCGGCGGCATCA
genomic: GATTATCAGTCATCAACACCATTCTTTTGTGATGAGAAAAATCGTGTCAGgtgagacatt ... actcatgcagGCTTTTGTGAGCATTTAAATAGACAAAGTCCTGGCGGCGGCGGCGGCATCA
EST: gi|88233330|gb|CI233179.1|CI233179
EST:     GATTATCAGTCATCAACACCATTCTTTTGTGATGAGAAAAATCGTGTCAG                         GCTTTTGTGAGCATTTAAATAGACAAAGTCCTGGCGGGGGCGGCGGCATCA
genomic: GATTATCAGTCATCAACACCATTCTTTTGTGATGAGAAAAATCGTGTCAGgtgagacatt ... actcatgcagGCTTTTGTGAGCATTTAAATAGACAAAGTCCTGGCGGCGGCGGCGGCATCA
EST: gi|88262887|gb|CI364465.1|CI364465
EST:     GATTATCAGTCATCAACACCATTCTTTTGTGATGAGAAAAATCGTGTCAG                         GCTTTTGTGAGCATTTAAATAGACAAAGTCCTGGCGGCGGCGGCGGCATCA
genomic: GATTATCAGTCATCAACACCATTCTTTTGTGATGAGAAAAATCGTGTCAGgtgagacatt ... actcatgcagGCTTTTGTGAGCATTTAAATAGACAAAGTCCTGGCGGCGGCGGCGGCATCA
EST: gi|86843464|gb|CI339536.1|CI339536
EST:     GATTATCAGTCATCAACACCATTCTTTTGTGATGAGAAAAATCGTGTCAG                         GCTTTTGTGAGCATTTAAATAGACAAAGTCCTGGCGGCGGCGGCGGCATCA
genomic: GATTATCAGTCATCAACACCATTCTTTTGTGATGAGAAAAATCGTGTCAGgtgagacatt ... actcatgcagGCTTTTGTGAGCATTTAAATAGACAAAGTCCTGGCGGCGGCGGCGGCATCA
EST: gi|86498530|gb|CI141163.1|CI141163
EST:     GATTATCAGTCATCAACACCATTCTTTTGTGATGAGAAAAATCGTGTCAG                         GCTTTTGTGAGCATTTAAATAGACAAAGTCCTGCCGGCGGCGGCGGCATCA
genomic: GATTATCAGTCATCAACACCATTCTTTTGTGATGAGAAAAATCGTGTCAGgtgagacatt ... actcatgcagGCTTTTGTGAGCATTTAAATAGACAAAGTCCTGGCGGCGGCGGCGGCATCA
EST: gi|86505781|gb|CI148414.1|CI148414
EST:     GATTATCAGTCATCAACACCATTCTTTTGTGATGAGAAAAATCGTGTCAG                         GCTTTTGTGAGCATTTAAATAGACAAAGTCCTGCCGCCGCCGGCGGCATCA
genomic: GATTATCAGTCATCAACACCATTCTTTTGTGATGAGAAAAATCGTGTCAGgtgagacatt ... actcatgcagGCTTTTGTGAGCATTTAAATAGACAAAGTCCTGGCGGCGGCGGCGGCATCA
EST: gi|29675373|gb|CB671648.1|CB671648
EST:     GATTATCAGTCATCAACACCATTCTTTTGTGATGAGAAAAATCGTGTCAG                         GCTTTTGTGAGCATTTAAATAGACAAAGTCCTGGCGGCGGCGGCGGCATCA
genomic: GATTATCAGTCATCAACACCATTCTTTTGTGATGAGAAAAATCGTGTCAGgtgagacatt ... actcatgcagGCTTTTGTGAGCATTTAAATAGACAAAGTCCTGGCGGCGGCGGCGGCATCA
EST: gi|29627016|gb|CB632027.1|CB632027
EST:     GATTATCAGTCATCAACACCATTCTTTTGTGATGAGAAAAATCGTGTCAG                         GCTTTTGTGAGCATTTAAATAGACAAAGTCCTGGCGGCGGCGGCGGCATCA
genomic: GATTATCAGTCATCAACACCATTCTTTTGTGATGAGAAAAATCGTGTCAGgtgagacatt ... actcatgcagGCTTTTGTGAGCATTTAAATAGACAAAGTCCTGGCGGCGGCGGCGGCATCA
EST: gi|157650102|gb|EX449736.1|EX449736
EST:     GATTATCAGTCATCAACACCATTCTTTTGTGATGAGAAAAATCGTGTCAG                         GCTTTTGTAAGCATTTAAATAGACAAAGTCCTGGCGGCGGCGGCGGCATCA
genomic: GATTATCAGTCATCAACACCATTCTTTTGTGATGAGAAAAATCGTGTCAGgtgagacatt ... actcatgcagGCTTTTGTGAGCATTTAAATAGACAAAGTCCTGGCGGCGGCGGCGGCATCA
EST: gi|86537180|gb|CI177386.1|CI177386
EST:     GATTATCAGTCATCAACACCATTCTTTTGTGATGAGAAAAATCGTGTCAG                         GCTTTTGTGAGCATTTAAATAGACAAAGTCCTGGCGGCGGCGGCGGCATCA
genomic: GATTATCAGTCATCAACACCATTCTTTTGTGATGAGAAAAATCGTGTCAGgtgagacatt ... actcatgcagGCTTTTGTGAGCATTTAAATAGACAAAGTCCTGGCGGCGGCGGCGGCATCA
EST: gi|29669519|gb|CB665794.1|CB665794
EST:     GATTATCAGTCATCAACACCATTCTTTTGTGATGAGAAAAATCGTGTCAG                         GCTTTTGTGAGCATTTAAATAGACAAAGTCCTGGCGGCGGCGGCGGCATCA
genomic: GATTATCAGTCATCAACACCATTCTTTTGTGATGAGAAAAATCGTGTCAGgtgagacatt ... actcatgcagGCTTTTGTGAGCATTTAAATAGACAAAGTCCTGGCGGCGGCGGCGGCATCA
EST: gi|29643326|gb|CB648333.1|CB648333
EST:     GATTATCAGTCATCAACACCATTCTTTTGTGATGAGAAAAATCGTGTCAG                         GCTTTTGTGAGCATTTAAATAGACAAAGTCCTGGCGGCGGCGGCGGCATCA
genomic: GATTATCAGTCATCAACACCATTCTTTTGTGATGAGAAAAATCGTGTCAGgtgagacatt ... actcatgcagGCTTTTGTGAGCATTTAAATAGACAAAGTCCTGGCGGCGGCGGCGGCATCA
EST: gi|86536638|gb|CI176844.1|CI176844
EST:     GATTATCAGTCATCAACACCATTCTTTTGTGATGAGAAAAATCGTGTCAG                         GCTTTTGTGAGCATTTAAATAGACAAAGTCCTGGCGGCGGCGGCGGCATCA
genomic: GATTATCAGTCATCAACACCATTCTTTTGTGATGAGAAAAATCGTGTCAGgtgagacatt ... actcatgcagGCTTTTGTGAGCATTTAAATAGACAAAGTCCTGGCGGCGGCGGCGGCATCA
EST: gi|86486730|gb|CI129363.1|CI129363
EST:     GATTATCAGTCATCAACACCTTTCTTTTGTGATGAGAAAAATCGTGTCAG                         GCTTTTGTGAGCATTTAAATAGACAAAGTCCTGGCGGCGGCGGCGGCATCA
genomic: GATTATCAGTCATCAACACCATTCTTTTGTGATGAGAAAAATCGTGTCAGgtgagacatt ... actcatgcagGCTTTTGTGAGCATTTAAATAGACAAAGTCCTGGCGGCGGCGGCGGCATCA

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: 49 (upstream exon), 31 (downstream exon)
Score: 4

GCGTCATCCCTGGGATGGGTGAGTTTGGGGATAGGTACTTTGGGACAGATGATTATCAGTCATCAACACCATTCTTTTGTGATGAGAAAAATCGTGTCAGgtgagacatt ... actcatgcagGCTTTTGTGAGCATTTAAATAGACAAAGTCCTGGCGGCGGCGGCGGCATCATCTCCATTTTTGAGAAACTTAAATTTTACATTTGGAAATTCAGATGCCC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attgtctgatgcggattcaagcttatcggcataacaattgacacaactcatgcagGCTTTTGTGAGCATTTAAATAGACAAAGTCCTGGCGGCGGCGGCGGCATCATCTCCATTTTTGAGAAACTTAAATTTTACATTTGGAAATTCAGATGCCC
                                   aattgac  putative branch site (score: 4)
                              ataacaatt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagacattgcttgttttttattttttgttccctacgagagtgttctattgtctgatgcggattcaagcttatcggcataacaattgacacaactcatgcagGCTTTTGTGAGCATTTAAATAGACAAAGTCCTGGCGGCGGCGGCGGCATCATCTCCATTTTTGAGAAACTTAAATTTTACATTTGGAAATTCAGATGCCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG