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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GACAGAGGAGGAAATGAACAAGGGCCATCTACACAACTCCCTCAACGTGCCCTTCATGTTCGTCACGCCGCAAGgcaagtcagccagccgattaattcactttaatctgtccagatttttacaccatttttcatcgtcgtccaaataactagcgtaatcaatatatatactctt...

Basic information

species Oryza sativa
transcript LOC_Os02g01220.1
intron # 3
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|86887184|gb|CI325999.1|CI325999
EST:     CCCTTCATGTTCGTCACGCCGCAAG                         GGAGGGAAAAGAATCCTCTGTTTGTGGAACAGTTCTCGTCGCTAGTGAGCA
genomic: CCCTTCATGTTCGTCACGCCGCAAGgcaagtcagc ... catgttgcagGGAGGGAAAAGAATCCTCTGTTTGTGGAGCAGTTCTCGTCGCTGGTGAGCA
EST: gi|58593836|gb|CF992144.1|CF992144
EST:     CCATCTACACAACTCCCTCAACGTGCCCTTCATGTTCGTCACGCCGCAAG                         GGAGGGAAAAGAATCCTCTGTTTGTGGAGCAGTTCTCGTCGCTGGTGAGCA
genomic: CCATCTACACAACTCCCTCAACGTGCCCTTCATGTTCGTCACGCCGCAAGgcaagtcagc ... catgttgcagGGAGGGAAAAGAATCCTCTGTTTGTGGAGCAGTTCTCGTCGCTGGTGAGCA
EST: gi|33666398|gb|CF297365.1|CF297365
EST:     CTCAACGTGCCCTTCATGTTCGTCACGCCGCAAG                         GGAGGGAAAAGAATCCTCTGTTTGTGGAGCAGTTCTCGTCGCTGGTGAGCA
genomic: CTCAACGTGCCCTTCATGTTCGTCACGCCGCAAGgcaagtcagc ... catgttgcagGGAGGGAAAAGAATCCTCTGTTTGTGGAGCAGTTCTCGTCGCTGGTGAGCA
EST: gi|86525933|gb|CI166139.1|CI166139
EST:     CCATCTACACAACTCCCTCAACGTGCCCTTCATGTTCGTCACGCCGCAAG                         GGAGGGAAAAGAATCCTCTGTTTGTGGAGCAGTTCTCGTCGCTGGTGAGCA
genomic: CCATCTACACAACTCCCTCAACGTGCCCTTCATGTTCGTCACGCCGCAAGgcaagtcagc ... catgttgcagGGAGGGAAAAGAATCCTCTGTTTGTGGAGCAGTTCTCGTCGCTGGTGAGCA
EST: gi|86547077|gb|CI187283.1|CI187283
EST:     CCATCTACACAACTCCCTCAACGTGCCCTTCATGTTCGTCACGCCGCAAG                         GGAGGGAAAAGAATCCTCTGTTTGTGGAGCAGTTCTCGTCGCTGGTGAGCA
genomic: CCATCTACACAACTCCCTCAACGTGCCCTTCATGTTCGTCACGCCGCAAGgcaagtcagc ... catgttgcagGGAGGGAAAAGAATCCTCTGTTTGTGGAGCAGTTCTCGTCGCTGGTGAGCA
EST: gi|86545060|gb|CI185266.1|CI185266
EST:     CCATCTACACAACTCCCTCAACGTGCCCTTCATGTTCGTCACGCCGCAAG                         GGAGGGAAAAGAATCCTCTGTTTGTGGAGCAGTTCTCGTCGCTGGTGAGCA
genomic: CCATCTACACAACTCCCTCAACGTGCCCTTCATGTTCGTCACGCCGCAAGgcaagtcagc ... catgttgcagGGAGGGAAAAGAATCCTCTGTTTGTGGAGCAGTTCTCGTCGCTGGTGAGCA
EST: gi|88202886|gb|CI200738.1|CI200738
EST:     CCATCTACACAACTCCCTCAACGTGCCCTTCATGTTCGTCACGCCGCAAG                         GGAGGGAAAAGAATCCTCTGTTTGTGGAGCAGTTCTCGTCGCTGGTGAGCA
genomic: CCATCTACACAACTCCCTCAACGTGCCCTTCATGTTCGTCACGCCGCAAGgcaagtcagc ... catgttgcagGGAGGGAAAAGAATCCTCTGTTTGTGGAGCAGTTCTCGTCGCTGGTGAGCA
EST: gi|88998270|gb|CI038155.1|CI038155
EST:     TGCCCTTCATGTTCGTCACGCCGCAAG                         GGAGGGAAAAGAATCCTCTGTTTGTGGAGCAGTTCTCGTCGCTGGTGAGCA
genomic: TGCCCTTCATGTTCGTCACGCCGCAAGgcaagtcagc ... catgttgcagGGAGGGAAAAGAATCCTCTGTTTGTGGAGCAGTTCTCGTCGCTGGTGAGCA
EST: gi|88977408|gb|CI025145.1|CI025145
EST:     CCATCTACACAACTCCCTCAACGTGCCCTTCATGTTCGTCACGCCGCAAG                         GGAGGGAAAAGAATCCTCTGTTTGTGGAGCAGTTCTCGTCGCTGGTGAGCA
genomic: CCATCTACACAACTCCCTCAACGTGCCCTTCATGTTCGTCACGCCGCAAGgcaagtcagc ... catgttgcagGGAGGGAAAAGAATCCTCTGTTTGTGGAGCAGTTCTCGTCGCTGGTGAGCA
EST: gi|88239644|gb|CI238806.1|CI238806
EST:     CGATCTACACAACTCCCTCAACGTGCCCTTCATGTTCGTCACGCCGCAAG                         GGAGGGAAAAGAATCCTCTGTTTGTGGAGCAGTTCTCGTCGCTGGTGAGCA
genomic: CCATCTACACAACTCCCTCAACGTGCCCTTCATGTTCGTCACGCCGCAAGgcaagtcagc ... catgttgcagGGAGGGAAAAGAATCCTCTGTTTGTGGAGCAGTTCTCGTCGCTGGTGAGCA
EST: gi|88201999|gb|CI202354.1|CI202354
EST:     CCATCTACACAACTCCCTCAACGTGCCCTTCATGTTCGTCACGCCGCAAG                         GGAGGGAAAAGAATCCTCTGTTTGTGGAGCAGTTCTCGTCGCTGGTGAGCA
genomic: CCATCTACACAACTCCCTCAACGTGCCCTTCATGTTCGTCACGCCGCAAGgcaagtcagc ... catgttgcagGGAGGGAAAAGAATCCTCTGTTTGTGGAGCAGTTCTCGTCGCTGGTGAGCA
EST: gi|88201185|gb|CI201540.1|CI201540
EST:     CCATCTACACAACTCCCTCAACGTGCCCTTCATGTTCGTCACGCCGCAAG                         GGAGGGAAAAGAATCCTCTGTTTGTGGAGCAGTTCTCGTCGCTGGTGAGCA
genomic: CCATCTACACAACTCCCTCAACGTGCCCTTCATGTTCGTCACGCCGCAAGgcaagtcagc ... catgttgcagGGAGGGAAAAGAATCCTCTGTTTGTGGAGCAGTTCTCGTCGCTGGTGAGCA
EST: gi|88200758|gb|CI200608.1|CI200608
EST:     CAACGTGCCCTTCATGTTCGTCACGCCGCAAG                         GGAGGGAAAAGAATCCTCTGTTTGTGGAGCAGTTCTCGTCGCTGGTGAGCA
genomic: CAACGTGCCCTTCATGTTCGTCACGCCGCAAGgcaagtcagc ... catgttgcagGGAGGGAAAAGAATCCTCTGTTTGTGGAGCAGTTCTCGTCGCTGGTGAGCA
EST: gi|87034626|gb|CI189250.1|CI189250
EST:     TTCATGTTCGTCACGCCGCAAG                         GGAGGGAAAAGAATCCTCTGTTTGTGGAGCAGTTCTCGTCGCTGGTGAGCA
genomic: TTCATGTTCGTCACGCCGCAAGgcaagtcagc ... catgttgcagGGAGGGAAAAGAATCCTCTGTTTGTGGAGCAGTTCTCGTCGCTGGTGAGCA

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: 74 (upstream exon), 69 (downstream exon)
Score: 59

GACAGAGGAGGAAATGAACAAGGGCCATCTACACAACTCCCTCAACGTGCCCTTCATGTTCGTCACGCCGCAAGgcaagtcagc ... catgttgcagGGAGGGAAAAGAATCCTCTGTTTGTGGAGCAGTTCTCGTCGCTGGTGAGCAAAGAGGAGCATGTGGTTGTG




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