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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtagtattatccattaattatttagcatgtgcatggtcaattaactaacttgataattatcctcatctgattgttaattatatatcttgttaattttaattctttatatatttttggtgcctcagTTCTGCATCATCATCGGCGTTCTTCTGTCGGTGTTCGCACCAATCGGAGGTCTCCGCTCGATCATCGTGAATGCCCAGAGTTACAAGTTCTTCTCTTGAG

Basic information

species Oryza sativa
transcript LOC_Os12g14100.1
intron # 4
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|87011477|gb|CI279386.1|CI279386
EST:     TGTCGATCATGAAGCCAAAGAGGTTTGGCTTGTCCTGGTGCATCAACTGG                         TTCTGCATCATCATCGGCGTTCTTCTGTCGGTGTTCGCACCAATCGGAGGT
genomic: TGTCGATCATGAAGCCAAAGAGGTTTGGCTTGTCCTGGTGCATCAACTGGgtaagtagta ... ggtgcctcagTTCTGCATCATCATCGGCGTTCTTCTGTCGGTGTTCGCACCAATCGGAGGT
EST: gi|88295265|gb|CI525418.1|CI525418
EST:     GAGGTTTGGCTTGTCCTGGTGCATCAACTGG                         TTCTGCATCATCATCGGCGTTCTTCTGTCGGTGTTCGCACCAATCGGAGGT
genomic: GAGGTTTGGCTTGTCCTGGTGCATCAACTGGgtaagtagta ... ggtgcctcagTTCTGCATCATCATCGGCGTTCTTCTGTCGGTGTTCGCACCAATCGGAGGT
EST: gi|88459833|gb|CI524292.1|CI524292
EST:     TGTCGATCATGAAGCCAAAGAGGTTTGGCTTGTCCTGGTGCATCAACTGG                         TTCTGCATCATCATCGGCGTTCTTCTGTCGGTGTTCGCACCAATCGGAGGT
genomic: TGTCGATCATGAAGCCAAAGAGGTTTGGCTTGTCCTGGTGCATCAACTGGgtaagtagta ... ggtgcctcagTTCTGCATCATCATCGGCGTTCTTCTGTCGGTGTTCGCACCAATCGGAGGT
EST: gi|88259822|gb|CI364313.1|CI364313
EST:     TGTCGATCATGAAGCCAAAGAGGTTTGGCTTGTCCTGGTGCATCAACTGG                         TTCTGCATCATCATCGGCGTTCTTCTGTCGGTGTTCGCACCAATCGGAGGT
genomic: TGTCGATCATGAAGCCAAAGAGGTTTGGCTTGTCCTGGTGCATCAACTGGgtaagtagta ... ggtgcctcagTTCTGCATCATCATCGGCGTTCTTCTGTCGGTGTTCGCACCAATCGGAGGT
EST: gi|88255841|gb|CI353712.1|CI353712
EST:     TGTCGATCATGAAGCCAAAGAGGTTTGGCTTGTCCTGGTGCATCAACTGG                         TTCTGCATCATCATCGGCGTTCTTCTGTCGGTGTTCGCACCAATCGGAGGT
genomic: TGTCGATCATGAAGCCAAAGAGGTTTGGCTTGTCCTGGTGCATCAACTGGgtaagtagta ... ggtgcctcagTTCTGCATCATCATCGGCGTTCTTCTGTCGGTGTTCGCACCAATCGGAGGT
EST: gi|88437345|gb|CI528704.1|CI528704
EST:     TGTCGATCATGAAGCCAAAGAGGTTTGGCTTGTCCTGGTGCATCAACTGG                         TTCTGCATCATCATCGGCGTTCTTCTGTCGGTGTTCGCACCAATCGGAGGT
genomic: TGTCGATCATGAAGCCAAAGAGGTTTGGCTTGTCCTGGTGCATCAACTGGgtaagtagta ... ggtgcctcagTTCTGCATCATCATCGGCGTTCTTCTGTCGGTGTTCGCACCAATCGGAGGT
EST: gi|86864894|gb|CI343939.1|CI343939
EST:     TGTCGATCATGAAGCCAAAGAGGTTTGGCTTGTCCTGGTGCATCAACTGG                         TTCTGCATCATCATCGGCGTTCTTCTGTCGGTGTTCGCACCAATCGGAGGT
genomic: TGTCGATCATGAAGCCAAAGAGGTTTGGCTTGTCCTGGTGCATCAACTGGgtaagtagta ... ggtgcctcagTTCTGCATCATCATCGGCGTTCTTCTGTCGGTGTTCGCACCAATCGGAGGT
EST: gi|88322273|gb|CI537856.1|CI537856
EST:     ATGAAGCCAAAGAGGTTTGGCTTGTCCTGGTGCATCAACTGG                         TTCTGCATCATCATCGGCGTTCTTCTGTCGGTGTTCGCACCAATCGGAGGT
genomic: ATGAAGCCAAAGAGGTTTGGCTTGTCCTGGTGCATCAACTGGgtaagtagta ... ggtgcctcagTTCTGCATCATCATCGGCGTTCTTCTGTCGGTGTTCGCACCAATCGGAGGT

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: 52 (upstream exon), 73 (downstream exon)
Score: 3

TTGCCATGCATTATGTGGCTGTCGATCATGAAGCCAAAGAGGTTTGGCTTGTCCTGGTGCATCAACTGGgtaagtagta ... ggtgcctcagTTCTGCATCATCATCGGCGTTCTTCTGTCGGTGTTCGCACCAATCGGAGGTCTCCGCTCGATCATCGTGAATGCCCAGAGTTACAAGTTCTTCTCTTGAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgttaattatatatcttgttaattttaattctttatatatttttggtgcctcagTTCTGCATCATCATCGGCGTTCTTCTGTCGGTGTTCGCACCAATCGGAGGTCTCCGCTCGATCATCGTGAATGCCCAGAGTTACAAGTTCTTCTCTTGAG
                       ttttaat  putative branch site (score: 3)
     aattatatatcttgtt  TA-rich tract