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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCGCGGCCGCCGCTGGCCATGCCGCTCGCCGTGCTTCTTCTCTTCGCCTGTTCTTCCGGCGTCGCAGCCGCGGCCGCTCAGGGCATCGAGCGGATCAAAGgtatgtgcgtctgttgctccggtaatccaattaattacgcgccgtcggttgttgcatagatctgaggaatcacacgcgtgctatgcccctcgtcgcgttt...

Basic information

species Oryza sativa
transcript LOC_Os10g10080.1
intron # 1
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|8859262|gb|AU096580.1|AU096580
EST:     TCAGGGCATCGAGCGGATCAAAG                         ACGATCCTGTTGGAAAGCTGAAGGTGTATGTCTACGAGCTGCCCCCCAAGT
genomic: TCAGGGCATCGAGCGGATCAAAGgtatgtgcgt ... gctagagaagACGATCCTGTTGGAAAGCTGAAGGTGTATGTCTACGAGCTGCCCCCCAAGT
EST: gi|88737284|gb|CI760792.1|CI760792
EST:     TTCTTCCGGCGTCGCAGCCGCGGCCGCTCAGGGCATCGAGCGGATCAAAG                         ACGATCCTGTTGGAAAGCTGAAGGTGTATGTCTACGAGCTGCCCCCCAAGT
genomic: TTCTTCCGGCGTCGCAGCCGCGGCCGCTCAGGGCATCGAGCGGATCAAAGgtatgtgcgt ... gctagagaagACGATCCTGTTGGAAAGCTGAAGGTGTATGTCTACGAGCTGCCCCCCAAGT
EST: gi|8857145|gb|AU094463.1|AU094463
EST:     TCAGGGCATCGAGCGGATCAAAG                         ACGATCCTGTTGGAAAGCTGAAGGTGTATGTCTACGAGCTGCCCCCCAAGT
genomic: TCAGGGCATCGAGCGGATCAAAGgtatgtgcgt ... gctagagaagACGATCCTGTTGGAAAGCTGAAGGTGTATGTCTACGAGCTGCCCCCCAAGT
EST: gi|87012095|gb|CI291550.1|CI291550
EST:     TTCTTCCGGCGTCGCAGCCGCGGCCGCTCAGGGCATCGAGCGGATCAAAG                         ACGATCCTGTTGGAAAGCTGAAGGTGTATGTCTACGAGCTGCCCCCCAAGT
genomic: TTCTTCCGGCGTCGCAGCCGCGGCCGCTCAGGGCATCGAGCGGATCAAAGgtatgtgcgt ... gctagagaagACGATCCTGTTGGAAAGCTGAAGGTGTATGTCTACGAGCTGCCCCCCAAGT
EST: gi|29678567|gb|CB674842.1|CB674842
EST:     TTCTTCCGGCGTCGCAGCCGCGGCCGCTCAGGGCATCGAGCGGATCAAAGAGAAG                     
genomic: TTCTTCCGGCGTCGCAGCCGCGGCCGCTCAGGGCATCGAGCGGATC----A-AAGgtatgtgcgt ... gctaga
EST: gi|58613328|gb|CK041040.1|CK041040
EST:     TTCTTCCGGCGTCGCAGCCGCGGACGCTCAGGGCATCGAGCGGATCAAAG                         ACGATCCTGTTGGAAAGCTGAAGGTGTATGTCTACGAGCTGCCCCCCAAGT
genomic: TTCTTCCGGCGTCGCAGCCGCGGCCGCTCAGGGCATCGAGCGGATCAAAGgtatgtgcgt ... gctagagaagACGATCCTGTTGGAAAGCTGAAGGTGTATGTCTACGAGCTGCCCCCCAAGT
EST: gi|29659811|gb|CB656086.1|CB656086
EST:     TTCTTCCGGCGTCGCAGCCGCGGCCGCTCAGGGCATCGAGCGGATCAAAGAGAAG                     
genomic: TTCTTCCGGCGTCGCAGCCGCGGCCGCTCAGGGCATCGAGCGGATC----A-AAGgtatgtgcgt ... gctaga
EST: gi|10109106|gb|AU055744.2|AU055744
EST:     GGCCGCTCAGGGCATCGAGCGGATCAAAG                         ACGATCCTGTTGGAAAGCTGAAGGTGTATGTCTACGAGCTGCCCCCCAAGT
genomic: GGCCGCTCAGGGCATCGAGCGGATCAAAGgtatgtgcgt ... gctagagaagACGATCCTGTTGGAAAGCTGAAGGTGTATGTCTACGAGCTGCCCCCCAAGT

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: 73 (upstream exon), 73 (downstream exon)
Score: 19

GCGCGGCCGCCGCTGGCCATGCCGCTCGCCGTGCTTCTTCTCTTCGCCTGTTCTTCCGGCGTCGCAGCCGCGGCCGCTCAGGGCATCGAGCGGATCAAAGgtatgtgcgt ... gctagagaagACGATCCTGTTGGAAAGCTGAAGGTGTATGTCTACGAGCTGCCCCCCAAGTACAACAAGAACATTGTGGCGAAAGATTCCAGATGCCTCAGCCACATGTT




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCGCGGCCGCCGCTGGCCATGCCGCTCGCCGTGCTTCTTCTCTTCGCCTGTTCTTCCGGCGTCGCAGCCGCGGCCGCTCAGGGCATCGAGCGGATCAAAGgtatgtgcgtctgttgctccggtaatccaattaattacgcgccgtcggttgttgcatagatctgaggaatcacacgcgtgctatgcccctcgtcgcgttt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gccgtcg
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