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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgaccaattgcgtccaataaaatcatgctccagcagctgctgcctggctgatacagtagctcttaaattgcggcctggctgatacagtagttctttactcccacgctgcttgttctcctttgcagGTGACATGGACACTGACGAGGATATACGTTTGAGATCGATCCTCCTTGTCAATTTGAGGCCAACCACAAGCCTGCAT

Basic information

species Oryza sativa
transcript LOC_Os01g56360.1
intron # 3
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|29672385|gb|CB668660.1|CB668660
EST:     GGTTGGGATCACGTACTCTGCACTGTCGCGCTATTACTACCGGAAGTCAG                         GTGACATGGACACTGACGAGGATATACGTTTGAGATCGATCCTCCTTGTCA
genomic: GGTTGGGATCACGTACTCTGCACTGTCGCGCTATTACTACCGGAAGTCAGgtgaccaatt ... tcctttgcagGTGACATGGACACTGACGAGGATATACGTTTGAGATCGATCCTCCTTGTCA
EST: gi|30226790|gb|CB964682.1|CB964682
EST:     GGTTGGGATCACGTACTCTGCACTGTCGCGCTATTACTACCGGAAGTCAG                         GTGACAAGGACACTGACGAGGATATACGTTTGAGATCGATCCTCCTTGTCA
genomic: GGTTGGGATCACGTACTCTGCACTGTCGCGCTATTACTACCGGAAGTCAGgtgaccaatt ... tcctttgcagGTGACATGGACACTGACGAGGATATACGTTTGAGATCGATCCTCCTTGTCA
EST: gi|30228254|gb|CB966145.1|CB966145
EST:     GGTTGGGATCACGTACTCTGCACTGTCGCGCTATTACTACCGGAAGTCAG                         GTGACAAGGACACTGACGAGGATATACGTTTGAGATCGATCCTCCTTGTCA
genomic: GGTTGGGATCACGTACTCTGCACTGTCGCGCTATTACTACCGGAAGTCAGgtgaccaatt ... tcctttgcagGTGACATGGACACTGACGAGGATATACGTTTGAGATCGATCCTCCTTGTCA
EST: gi|163927643|gb|EG712439.1|EG712439
EST:     GGTTGGGATCACGTACTCTGCACTGTCGCGCTATTACTACCGGAAGTCAG                         GTGACATGGACACTGACGAGGATATACGTTTGAGATCGATCCTCCTTGTCA
genomic: GGTTGGGATCACGTACTCTGCACTGTCGCGCTATTACTACCGGAAGTCAGgtgaccaatt ... tcctttgcagGTGACATGGACACTGACGAGGATATACGTTTGAGATCGATCCTCCTTGTCA
EST: gi|58608842|gb|CK036875.1|CK036875
EST:     GGTTGGGATCACGTACTCTGCACTGTCGCGCTATTACTACCGGAAGTCAG                         GTGACGA-GGACACTGACGAGGATATACGTTTGAGATCGATCCTCCTTGTC
genomic: GGTTGGGATCACGTACTCTGCACTGTCGCGCTATTACTACCGGAAGTCAGgtgaccaatt ... tcctttgcagGTGAC-ATGGACACTGACGAGGATATACGTTTGAGATCGATCCTCCTTGTC
EST: gi|29678634|gb|CB674909.1|CB674909
EST:     ACCGGAAGTCAG                         GTGACATGGACACTGACGAGGATATACGTTTGAGATCGATCCTCCTTGTCA
genomic: ACCGGAAGTCAGgtgaccaatt ... tcctttgcagGTGACATGGACACTGACGAGGATATACGTTTGAGATCGATCCTCCTTGTCA
EST: gi|30228465|gb|CB966355.1|CB966355
EST:     GGTTGGGATCACGTACTCTGCACTGTCGCGCTATTACTACCGGAAGTCAG                         GTGACAAGGACACTGACGAGGATATACGTTTGAGATCGATCCTCCTTGTCG
genomic: GGTTGGGATCACGTACTCTGCACTGTCGCGCTATTACTACCGGAAGTCAGgtgaccaatt ... tcctttgcagGTGACATGGACACTGACGAGGATATACGTTTGAGATCGATCCTCCTTGTCA
EST: gi|38468635|gb|CF952766.1|CF952766
EST:     ACGTACTCTGCACTGTCGCGCTATTACTACCGGAAGTCAG                         GTGACAAGGACACTGACGAGGATATACGTTTGAGATCGATCCTCCTTGTCA
genomic: ACGTACTCTGCACTGTCGCGCTATTACTACCGGAAGTCAGgtgaccaatt ... tcctttgcagGTGACATGGACACTGACGAGGATATACGTTTGAGATCGATCCTCCTTGTCA

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: 69 (upstream exon), 61 (downstream exon)
Score: 10

ACGGTCAATGATGTGCTGGTTGGGATCACGTACTCTGCACTGTCGCGCTATTACTACCGGAAGTCAGgtgaccaatt ... tcctttgcagGTGACATGGACACTGACGAGGATATACGTTTGAGATCGATCCTCCTTGTCAATTTGAGGCCAACCACAAGCCTGCAT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cggcctggctgatacagtagttctttactcccacgctgcttgttctcctttgcagGTGACATGGACACTGACGAGGATATACGTTTGAGATCGATCCTCCTTGTCAATTTGAGGCCAACCACAAGCCTGCAT
      ggctgat  putative branch site (score: 10)
                                   ctgcttgttctccttt  putative PPT
                    ttcttta  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgaccaattgcgtccaataaaatcatgctccagcagctgctgcctggctgatacagtagctcttaaattgcggcctggctgatacagtagttctttactcccacgctgcttgttctcctttgcagGTGACATGGACACTGACGAGGATATACGTTTGAGATCGATCCTCCTTGTCAATTTGAGGCCAACCACAAGCCTGCAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC