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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCTCCAAGGCCATGGGCCGGGACTTGCGTGTGCACTTCAAGgtgagcttcccgagttccaagaatgcatttcgagagatctcgccactgtttttaattggttgattcattgtaatgcatttctgtttttaattgcttgttt...

Basic information

species Oryza sativa
transcript LOC_Os09g08430.1
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|27576713|gb|CA999407.1|CA999407
EST:     CCAAGTCCTCCAAGGCCATGGGCCGGGACTTGCGTGTGCACTTCAAG                         AACACCCGTGAGACAGCTTTTGCTATCAGGAAGTTGCCTCTGGGCAAGGCC
genomic: CCAAGTCCTCCAAGGCCATGGGCCGGGACTTGCGTGTGCACTTCAAGgtgagcttcc ... acaattgcagAACACCCGTGAGACAGCTTTTGCTATCAGGAAGTTGCCTCTGGGCAAGGCC
EST: gi|218489030|gb|FG957547.1|FG957547
EST:     CCTCCAAGGCCATGGGCCGGGACTTGCGTGTGCACTTCAAAG                         AACACCCGTGAGACAGCTTTTGCTATCAGGAAGTTGCCTCTGGGCAAGGC
genomic: CCTCCAAGGCCATGGGCCGGGACTTGCGTGTGCACTTC-AAGgtgagcttcc ... acaattgcagAACACCCGTGAGACAGCTTTTGCTATCAGGAAGTTGCCTCTGGGCAAGGC
EST: gi|11610340|gb|AU166016.1|AU166016
EST:     CCATGGNCCGGGACTTGGCGTGTGCACTTCCAAG                         AACACCCGTGAGCCAGCTTTTGCTATCAGNAAGTTGCNTCTGGGCAAGGC
genomic: CCATGGGCCGGGACTT-GCGTGTGCACTT-CAAGgtgagcttcc ... acaattgcagAACACCCGTGAGACAGCTTTTGCTATCAGGAAGTTGCCTCTGGGCAAGGC
EST: gi|117233205|gb|CT848038.1|CT848038
EST:     CCTCCAAGGCCATGGGCCGGGACTTGCGTGTGCACTTCAAG                         AACACCCGTGAGACAGCTTTTGCTATCAGGAAGTTGCCTCTGGGCAAGGCC
genomic: CCTCCAAGGCCATGGGCCGGGACTTGCGTGTGCACTTCAAGgtgagcttcc ... acaattgcagAACACCCGTGAGACAGCTTTTGCTATCAGGAAGTTGCCTCTGGGCAAGGCC
EST: gi|5607427|gb|AU076125.1|AU076125
EST:     CCTCCAAGGCCATGGGCCGGGACTTGCGTGTGCACTTCAAG                         AACACCCGTGAGACAGCTTTTGCTATCAGGAAGTTGCCTCTGGGCAAGGCC
genomic: CCTCCAAGGCCATGGGCCGGGACTTGCGTGTGCACTTCAAGgtgagcttcc ... acaattgcagAACACCCGTGAGACAGCTTTTGCTATCAGGAAGTTGCCTCTGGGCAAGGCC
EST: gi|33660730|gb|CF291697.1|CF291697
EST:     CCTCCAAGGCCATGGGCCGGGACTTGCGTGTGCACTTCAAG                         AACACCCGTGAGACAGCTTTTGCTATCAGGAAGTTGCCTCTGGGCAAGGCC
genomic: CCTCCAAGGCCATGGGCCGGGACTTGCGTGTGCACTTCAAGgtgagcttcc ... acaattgcagAACACCCGTGAGACAGCTTTTGCTATCAGGAAGTTGCCTCTGGGCAAGGCC
EST: gi|163920102|gb|EG712032.1|EG712032
EST:     CCTCCAAGGCCATGGGCCGGGACTTGCGTGTGCACTTCAAG                         AACACCCGTGAGACAGCTTTTGCTATCAGGAAGTTGCCTCTGGGCAAGGCC
genomic: CCTCCAAGGCCATGGGCCGGGACTTGCGTGTGCACTTCAAGgtgagcttcc ... acaattgcagAACACCCGTGAGACAGCTTTTGCTATCAGGAAGTTGCCTCTGGGCAAGGCC
EST: gi|33669752|gb|CF297991.1|CF297991
EST:     CCTCCAAGGCCATGGGCCGGGACTTGCGTGTGCACTTCAATG                         ATCACCCGTGAGACAGCTTTTGCTATCAGGAAGTTGCCTCTGGGCAAGGC
genomic: CCTCCAAGGCCATGGGCCGGGACTTGCGTGTGCACTTCAA-Ggtgagcttcc ... acaattgcagAACACCCGTGAGACAGCTTTTGCTATCAGGAAGTTGCCTCTGGGCAAGGC
EST: gi|11172622|gb|AU164376.1|AU164376
EST:     AGGCCATGGGCCGGGACTTGCGTGTGCACTTTCAAG                         AACACCCGTGAGACAGCTTTTGCTAATCAGGAAGTTGCCTCTGGGCAAAG
genomic: AGGCCATGGGCCGGGACTTGCGTGTGCAC-TTCAAGgtgagcttcc ... acaattgcagAACACCCGTGAGACAGCTTTTGCT-ATCAGGAAGTTGCCTCTGGGC-AAG
EST: gi|33660061|gb|CF291028.1|CF291028
EST:     CCTCCAAGGCCATGGGCCGGGACTTGCGTGTGCACTTCAAG                         AACACCCGTGAGACAGCTTTTGCTATCAGGAAGTTGCCTCTGGGCAAGGCC
genomic: CCTCCAAGGCCATGGGCCGGGACTTGCGTGTGCACTTCAAGgtgagcttcc ... acaattgcagAACACCCGTGAGACAGCTTTTGCTATCAGGAAGTTGCCTCTGGGCAAGGCC
EST: gi|86601750|gb|CI256255.1|CI256255
EST:     TTGCGTGTGCACTTCAAG                         AACACCCGTGAGACAGCTTTTGCTATCAGGAAGTTGCCTCTGGGCAAGGCC
genomic: TTGCGTGTGCACTTCAAGgtgagcttcc ... acaattgcagAACACCCGTGAGACAGCTTTTGCTATCAGGAAGTTGCCTCTGGGCAAGGCC
EST: gi|38471990|gb|CF956121.1|CF956121
EST:     CCTCCAAGGCCATGGGCCGGGACTTGCGTGTGCACTTCAAG                         AACACCCGTGAGACAGCTTTTGCTATCAGGAAGTTGCCTCTGGGCAAGGCC
genomic: CCTCCAAGGCCATGGGCCGGGACTTGCGTGTGCACTTCAAGgtgagcttcc ... acaattgcagAACACCCGTGAGACAGCTTTTGCTATCAGGAAGTTGCCTCTGGGCAAGGCC
EST: gi|8858037|gb|AU095355.1|AU095355
EST:     CCTCCAAGGCCATGGGCCGGNGACTTGCGTGTGCACTTCAAG                         AACACCCGTGAGACAGCTTTTGCTATCAGGAAGTTGCCTCTGGGCAAGGCC
genomic: CCTCCAAGGCCATGGGCCGG-GACTTGCGTGTGCACTTCAAGgtgagcttcc ... acaattgcagAACACCCGTGAGACAGCTTTTGCTATCAGGAAGTTGCCTCTGGGCAAGGCC
EST: gi|27577501|gb|CB000196.1|CB000196
EST:     CCTCCAAGGCCATGGGCCGGGACTTGCGTGTGCACTTCAAG                         AACACCCGTGAGACAGCTTTTGCTATCAGGAAGTTGCCTCTGGGCAAGGCC
genomic: CCTCCAAGGCCATGGGCCGGGACTTGCGTGTGCACTTCAAGgtgagcttcc ... acaattgcagAACACCCGTGAGACAGCTTTTGCTATCAGGAAGTTGCCTCTGGGCAAGGCC
EST: gi|55411166|gb|CV723542.1|CV723542
EST:     CCTCCAAGGCCATGGGCCGGGACTTGCGTGTGCACTTCAAG                         AACACCCGTGAGACAGCTTTTGCTATCAGGAAGTTGCCTCTGGGCAAGGCC
genomic: CCTCCAAGGCCATGGGCCGGGACTTGCGTGTGCACTTCAAGgtgagcttcc ... acaattgcagAACACCCGTGAGACAGCTTTTGCTATCAGGAAGTTGCCTCTGGGCAAGGCC
EST: gi|218494176|gb|FG955167.1|FG955167
EST:     TCCTCCAAGGCCATGGGCCGGGACTTGCGTGTGCACTTCAAG                         AACACCCGTGAGACAGCTTTTGCTATCAGGAAGTTGCCTCTGGGCAAGGCC
genomic: TCCTCCAAGGCCATGGGCCGGGACTTGCGTGTGCACTTCAAGgtgagcttcc ... acaattgcagAACACCCGTGAGACAGCTTTTGCTATCAGGAAGTTGCCTCTGGGCAAGGCC
EST: gi|286646|gb|D15453.1|D15453
EST:     CCTCCAAGGCCATGGGCCGGGACTTGCGTGTGCACTTCAAG                         AACACCCGTGAGACAGCTTTTGCTATCAGGAAGTTGCCTCTGGGCAAGGCC
genomic: CCTCCAAGGCCATGGGCCGGGACTTGCGTGTGCACTTCAAGgtgagcttcc ... acaattgcagAACACCCGTGAGACAGCTTTTGCTATCAGGAAGTTGCCTCTGGGCAAGGCC
EST: gi|218495984|gb|FG958578.1|FG958578
EST:     AGTCCTCCAAGGCCATGGGCCGGGACTTGCGTGTGCACTTCAAG                         AACACCCGTGAGACAGCTTTTGCTATCAGGAAGTTGCCTCTGGGCAAGGCC
genomic: AGTCCTCCAAGGCCATGGGCCGGGACTTGCGTGTGCACTTCAAGgtgagcttcc ... acaattgcagAACACCCGTGAGACAGCTTTTGCTATCAGGAAGTTGCCTCTGGGCAAGGCC
EST: gi|10931615|gb|AU161889.1|AU161889
EST:     TTGCGTGTGCACTTCAAG                         AACACCCGTGAGACA-CTTTTGCTATCAGGAAGTTGCCTCTGGGCAAGGCC
genomic: TTGCGTGTGCACTTCAAGgtgagcttcc ... acaattgcagAACACCCGTGAGACAGCTTTTGCTATCAGGAAGTTGCCTCTGGGCAAGGCC
EST: gi|11565004|gb|AU165640.1|AU165640
EST:     CCATGGCCCGGGNACTTGGCGTGTGCACTTCAAG                         AACACCCGTAAGNCAGCTTTTGCTATCAGGAAGTTGCNTTTGGGCAAGNCC
genomic: CCATGGGCCGGG-ACTT-GCGTGTGCACTTCAAGgtgagcttcc ... acaattgcagAACACCCGTGAGACAGCTTTTGCTATCAGGAAGTTGCCTCTGGGCAAGGCC

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: 75 (upstream exon), 75 (downstream exon)
Score: 306

CCTCCAAGGCCATGGGCCGGGACTTGCGTGTGCACTTCAAGgtgagcttcc ... acaattgcagAACACCCGTGAGACAGCTTTTGCTATCAGGAAGTTGCCTCTGGGCAAGGCCAAGAGGTACCTTGAGGATGTGATTGCCCACAAGCAAGCTATCCCCTTCC




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