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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGAAAGTAGGAGACTTCGATGTATCCAATCAGTCCCCGGACATGGCGGCTCGCCTCCACTCCACTCGTGTTCTTGGCACCTTCGGTTATCATGCTCCTGAgtatgcacccaaacatttcatgttcttgatctgttactcatcaagtaggcaatttttaggatgaaatgtgctcttatacgactgtacttactgttctattttggaatctgccag

Basic information

species Oryza sativa
transcript LOC_Os01g21970.1
intron # 5
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|86854619|gb|CI258912.1|CI258912
EST:     TCTTGGCACCTTCGGTTATCATGCTCCTGA                         GTACGCGATGACAGGGCAGCTTAGCACGAAGAGCGATGTCTATAGCTTCGG
genomic: TCTTGGCACCTTCGGTTATCATGCTCCTGAgtatgcaccc ... aatctgccagGTACGCGATGACAGGGCAGCTTAGCACGAAGAGCGATGTCTATAGCTTCGG
EST: gi|10611406|gb|AU108279.1|AU108279
EST:     TCATGCTCCTGA                         GTACGCGATGACAGGGGCAGCTTTACCNCGAAGAGCGATNTCTATAGCTTC
genomic: TCATGCTCCTGAgtatgcaccc ... aatctgccagGTACGCGATGACA-GGGCAGC-TTAGCACGAAGAGCGATGTCTATAGCTTC
EST: gi|86596982|gb|CI270778.1|CI270778
EST:     GGTTATCATGCTCCTGA                         GTACGCGATGACAGGGCAGCTTAGCACGAAGAGCGATGTCTATAGCTTCGG
genomic: GGTTATCATGCTCCTGAgtatgcaccc ... aatctgccagGTACGCGATGACAGGGCAGCTTAGCACGAAGAGCGATGTCTATAGCTTCGG
EST: gi|86595077|gb|CI260316.1|CI260316
EST:     CGCCTCCACTCCACTCGTGTTCTTGGCACCTTCGGTTATCATGCTCCTGA                         GTACGCGATGACAGGGCAGCTTAGCACGAAGAGCGATGTCTATAGCTTCGG
genomic: CGCCTCCACTCCACTCGTGTTCTTGGCACCTTCGGTTATCATGCTCCTGAgtatgcaccc ... aatctgccagGTACGCGATGACAGGGCAGCTTAGCACGAAGAGCGATGTCTATAGCTTCGG
EST: gi|88998535|gb|CI259868.1|CI259868
EST:     CTTGGCACCTTCGGTTATCATGCTCCTGA                         GTACGCGATGACAGGGCAGCTTAGCACGAAGAGCGATGTCTATAGCTTCGG
genomic: CTTGGCACCTTCGGTTATCATGCTCCTGAgtatgcaccc ... aatctgccagGTACGCGATGACAGGGCAGCTTAGCACGAAGAGCGATGTCTATAGCTTCGG
EST: gi|86593903|gb|CI260132.1|CI260132
EST:     GTTATCATGCTCCTGA                         GTACGCGATGACAGGGCAGCTTAGCACGAAGAGCGATGTCTATAGCTTCGG
genomic: GTTATCATGCTCCTGAgtatgcaccc ... aatctgccagGTACGCGATGACAGGGCAGCTTAGCACGAAGAGCGATGTCTATAGCTTCGG
EST: gi|10611410|gb|AU108281.1|AU108281
EST:     GCTTCCANTCCACTCGTGTTCTTGGGCA-CTTCGGTTATCATGCTCCTGA                         GTACGCGATGACAGGGCAGNTTAGCACGAAGAGCGATGTCTATAGCTTCGG
genomic: GCCTCCACTCCACTCGTGTTCTT-GGCACCTTCGGTTATCATGCTCCTGAgtatgcaccc ... aatctgccagGTACGCGATGACAGGGCAGCTTAGCACGAAGAGCGATGTCTATAGCTTCGG
EST: gi|87029526|gb|CI257321.1|CI257321
EST:     CGCCTCCACTCCACTCGTGTTC-TGGCACCTTCGGTTATCATGCTCCTGA                         GTACGCGATGACAGGGCAGCTTAGCACGAAGAGCGATGTCTATAGCTTCGG
genomic: CGCCTCCACTCCACTCGTGTTCTTGGCACCTTCGGTTATCATGCTCCTGAgtatgcaccc ... aatctgccagGTACGCGATGACAGGGCAGCTTAGCACGAAGAGCGATGTCTATAGCTTCGG
EST: gi|10611412|gb|AU108282.1|AU108282
EST:     ACTCGTGTTCTTGGGCA-CTTCGGTTATCATGCTCCTGA                         GTACGCGATGACAGGGCAGCTTAGCACGAAGAGCGATGTCTATAGCTTCGG
genomic: ACTCGTGTTCTT-GGCACCTTCGGTTATCATGCTCCTGAgtatgcaccc ... aatctgccagGTACGCGATGACAGGGCAGCTTAGCACGAAGAGCGATGTCTATAGCTTCGG
EST: gi|86493686|gb|CI136319.1|CI136319
EST:     CGGTTATCATGCTCCTGA                         GTACGCGATGACAGGGCAGCTTAGCACGAAGAGCGATGTCTATAGCTTCGG
genomic: CGGTTATCATGCTCCTGAgtatgcaccc ... aatctgccagGTACGCGATGACAGGGCAGCTTAGCACGAAGAGCGATGTCTATAGCTTCGG
EST: gi|86854455|gb|CI256577.1|CI256577
EST:     TTATCATGCTCCTGA                         GTACGCGATGACAGGTCAGCTTAGCACGAAGAGCGATGTCTATAGCTTCGG
genomic: TTATCATGCTCCTGAgtatgcaccc ... aatctgccagGTACGCGATGACAGGGCAGCTTAGCACGAAGAGCGATGTCTATAGCTTCGG
EST: gi|58678481|gb|CK067168.1|CK067168
EST:     CGCCTCCACTCCACTCGTGTTCTTGGCACCTTCGGTTATCATGCTCCTGA                         GTACGCGATGACAGGGCAGCTTAGCACGAAGAGCGATGTCTATAGCTTCGG
genomic: CGCCTCCACTCCACTCGTGTTCTTGGCACCTTCGGTTATCATGCTCCTGAgtatgcaccc ... aatctgccagGTACGCGATGACAGGGCAGCTTAGCACGAAGAGCGATGTCTATAGCTTCGG
EST: gi|10611408|gb|AU108280.1|AU108280
EST:     GCCTCCANTCCAATCGTGTTCTTGGGCA-CTTCGGTTATCATGCTCCTGA                         GTACGCGATGACAGGGCAGCTTAGCACGAAGAGCGATGTCTATAGCTTCGG
genomic: GCCTCCACTCCACTCGTGTTCTT-GGCACCTTCGGTTATCATGCTCCTGAgtatgcaccc ... aatctgccagGTACGCGATGACAGGGCAGCTTAGCACGAAGAGCGATGTCTATAGCTTCGG
EST: gi|87024282|gb|CI257023.1|CI257023
EST:     CGCCTCCACTCCACTCGTGTTCTTGGCACCTTCGGTTATCATGCTCCTGA                         GTACGCGATGACAGGGCAGCTTAGCACGAAGAGCGATGTCTATAGCTTCGG
genomic: CGCCTCCACTCCACTCGTGTTCTTGGCACCTTCGGTTATCATGCTCCTGAgtatgcaccc ... aatctgccagGTACGCGATGACAGGGCAGCTTAGCACGAAGAGCGATGTCTATAGCTTCGG

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: 119

CGAAAGTAGGAGACTTCGATGTATCCAATCAGTCCCCGGACATGGCGGCTCGCCTCCACTCCACTCGTGTTCTTGGCACCTTCGGTTATCATGCTCCTGAgtatgcaccc ... aatctgccagGTACGCGATGACAGGGCAGCTTAGCACGAAGAGCGATGTCTATAGCTTCGGAGTCGTGTTGCTGGAGCTTTTAACTGGTCGCAAACCGGTCGATCATACG




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