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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaattttctctcttttgtggaaagaaatcgcctattttgggggagggttgattcatgggagcttagttcttgcgatttgtggggtgtggttgttgttgttgttgttgcagAAGAAGGAGAACTTGGGCAACGCGCGGCGGGGGATGGGGGTCAAGCCTGGCCCGCGCCGCAATGTCCTCTCGGCAATCAACAATGGCGGTGGCACGAACA

Basic information

species Oryza sativa
transcript LOC_Os04g53760.2
intron # 1
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|88386555|gb|CI575333.1|CI575333
EST:     ATGGCCTCCTCCCTCACGCCCCGTAGCCCTTACCCG                         AAGAAGGAGAACTTGGGCAACGCGCGGCGGGGGATGGGGGTCAAGCCTGGC
genomic: ATGGCCTCCTCCCTCACGCCCCGTAGCCCTTACCCGgtaattttct ... gttgttgcagAAGAAGGAGAACTTGGGCAACGCGCGGCGGGGGATGGGGGTCAAGCCTGGC
EST: gi|88371328|gb|CI600176.1|CI600176
EST:     ACTAATCCCAGTTCATGGCCTCCTCCCTCACGCCCCGTAGCCCTTACCCG                         AAGAAGGAGAACTTGGGCAACGCGCGGCGGGGGATGGGGGTCAAGCCTGGC
genomic: ACTAATCCCAGTTCATGGCCTCCTCCCTCACGCCCCGTAGCCCTTACCCGgtaattttct ... gttgttgcagAAGAAGGAGAACTTGGGCAACGCGCGGCGGGGGATGGGGGTCAAGCCTGGC
EST: gi|88449325|gb|CI582197.1|CI582197
EST:     ATGGCCTCCTCCCTCACGCCCCGTAGCCCTTACCCG                         AAGAAGGAGAACTTGGGCAACGCGCGGCGGGGGATGGGGGTCAAGCCTGGC
genomic: ATGGCCTCCTCCCTCACGCCCCGTAGCCCTTACCCGgtaattttct ... gttgttgcagAAGAAGGAGAACTTGGGCAACGCGCGGCGGGGGATGGGGGTCAAGCCTGGC
EST: gi|88389664|gb|CI603163.1|CI603163
EST:     ATGGCCTCCTCCCTCACGCCCCGTAGCCCTTACCCG                         AAGAAGGAGAACTTGGGCAACGCGCGGCGGGGGATGGGGGTCAAGCCTGGC
genomic: ATGGCCTCCTCCCTCACGCCCCGTAGCCCTTACCCGgtaattttct ... gttgttgcagAAGAAGGAGAACTTGGGCAACGCGCGGCGGGGGATGGGGGTCAAGCCTGGC
EST: gi|29635281|gb|CB640290.1|CB640290
EST:     AGCCCTTACCCG                         AAGAAGGAGAACTTGGGCAACGCGCGGCGGGGGATGGGGGTCAAGCCTGGC
genomic: AGCCCTTACCCGgtaattttct ... gttgttgcagAAGAAGGAGAACTTGGGCAACGCGCGGCGGGGGATGGGGGTCAAGCCTGGC
EST: gi|88300304|gb|CI584723.1|CI584723
EST:     ATGGCCTCCTCCCTCACGCCCCGTAGCCCTTACCCG                         AAGAAGGAGAACTTGGGCAACGCGCGGCGGGGGATGGGGGTCAAGCCTGGC
genomic: ATGGCCTCCTCCCTCACGCCCCGTAGCCCTTACCCGgtaattttct ... gttgttgcagAAGAAGGAGAACTTGGGCAACGCGCGGCGGGGGATGGGGGTCAAGCCTGGC
EST: gi|88422750|gb|CI573912.1|CI573912
EST:     ATGGCCTCCTCCCTCACGCCCCGTAGCCCTTACCCG                         AAGAAGGAGAACTTGGGCAACGCGCGGCGGGGGATGGGGGTCAAGCCTGGC
genomic: ATGGCCTCCTCCCTCACGCCCCGTAGCCCTTACCCGgtaattttct ... gttgttgcagAAGAAGGAGAACTTGGGCAACGCGCGGCGGGGGATGGGGGTCAAGCCTGGC
EST: gi|88386498|gb|CI575276.1|CI575276
EST:     ATGGCCTCCTCCCTCACGCCCCGTAGCCCTTACCCG                         AAGAAGGAGAACTTGGGCAACGCGCGGCGGGGGATGGGGGTCAAGCCTGGC
genomic: ATGGCCTCCTCCCTCACGCCCCGTAGCCCTTACCCGgtaattttct ... gttgttgcagAAGAAGGAGAACTTGGGCAACGCGCGGCGGGGGATGGGGGTCAAGCCTGGC
EST: gi|88403245|gb|CI570986.1|CI570986
EST:     ATGGCCTCCTCCCTCACGCCCCGTAGCCCTTACCCG                         AAGAAGGAGAACTTGGGCAACGCGCGGCGGGGGATGGGGGTCAAGCCTGGC
genomic: ATGGCCTCCTCCCTCACGCCCCGTAGCCCTTACCCGgtaattttct ... gttgttgcagAAGAAGGAGAACTTGGGCAACGCGCGGCGGGGGATGGGGGTCAAGCCTGGC
EST: gi|88385811|gb|CI568479.1|CI568479
EST:     ATGGCCTCCTCCCTCACGCCCCGTAGCCCTTACCCG                         AAGACGGAGAACTTGGGCAACGCGCGGCGGGGGATGGGGGTCAAGCCTGGC
genomic: ATGGCCTCCTCCCTCACGCCCCGTAGCCCTTACCCGgtaattttct ... gttgttgcagAAGAAGGAGAACTTGGGCAACGCGCGGCGGGGGATGGGGGTCAAGCCTGGC
EST: gi|88430893|gb|CI571883.1|CI571883
EST:     TGGCCTCCTCCCTCACGCCCCGTAGCCCTTACCCG                         AAGAAGGAGAACTTGGGCAACGCGCGGCGGGGGATGGGGGTCAAGCCTGGC
genomic: TGGCCTCCTCCCTCACGCCCCGTAGCCCTTACCCGgtaattttct ... gttgttgcagAAGAAGGAGAACTTGGGCAACGCGCGGCGGGGGATGGGGGTCAAGCCTGGC
EST: gi|88427363|gb|CI569401.1|CI569401
EST:     AGTTCATGGCCTCCTCCCTCACGCCCCGTAGCCCTTACCCG                         AAGAAGGAGAACTTGGGCAACGCGCGGCGGGGGATGGGGGTCAAGCCTGGC
genomic: AGTTCATGGCCTCCTCCCTCACGCCCCGTAGCCCTTACCCGgtaattttct ... gttgttgcagAAGAAGGAGAACTTGGGCAACGCGCGGCGGGGGATGGGGGTCAAGCCTGGC
EST: gi|88362880|gb|CI614236.1|CI614236
EST:     ACTAATCCCAGTTCATGGCCTCCTCCCTCACGCCCCGTAGCCCTTACCCG                         AAGAAGGAGAAATTGGGCAACGCGCGGCGGGGGATGGGGGTCAAGCCTGGC
genomic: ACTAATCCCAGTTCATGGCCTCCTCCCTCACGCCCCGTAGCCCTTACCCGgtaattttct ... gttgttgcagAAGAAGGAGAACTTGGGCAACGCGCGGCGGGGGATGGGGGTCAAGCCTGGC
EST: gi|88399908|gb|CI585827.1|CI585827
EST:     ACTAATCCCAGTTCATGGCCTCCTCCCTCACGCCCCGTAGCCCTTACCCG                         AAGAAGGAGAACTTGGGCAACGCGCGGCGGGGGATGGGGGTCAAGCCTGGC
genomic: ACTAATCCCAGTTCATGGCCTCCTCCCTCACGCCCCGTAGCCCTTACCCGgtaattttct ... gttgttgcagAAGAAGGAGAACTTGGGCAACGCGCGGCGGGGGATGGGGGTCAAGCCTGGC
EST: gi|88454426|gb|CI569998.1|CI569998
EST:     ATGGCCTCCTCCCTCACGCCCCGTAGCCCTTACCCG                         AAGAAGGAGAACTTGGGCAACGCGCGGCGGGGGATGGGGGTCAAGCCTGGC
genomic: ATGGCCTCCTCCCTCACGCCCCGTAGCCCTTACCCGgtaattttct ... gttgttgcagAAGAAGGAGAACTTGGGCAACGCGCGGCGGGGGATGGGGGTCAAGCCTGGC

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: 67 (upstream exon), 67 (downstream exon)
Score: 17

CCGCCACCACTGAGGAGGAGAGAACCCTAACTATAACCCCTAATCCTGCCACTAATCCCAGTTCATGGCCTCCTCCCTCACGCCCCGTAGCCCTTACCCGgtaattttct ... gttgttgcagAAGAAGGAGAACTTGGGCAACGCGCGGCGGGGGATGGGGGTCAAGCCTGGCCCGCGCCGCAATGTCCTCTCGGCAATCAACAATGGCGGTGGCACGAACA




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