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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtgtgcttgcttgattcccctcctccgcccgcattgcgatctgagtctcgcgacgcgcctgctgttctttccgacgtttgagcggtttgctgaactgtttcgttgttggtgcagGCAAGCCGGGAGCAGCGCTCGCCAG

Basic information

species Oryza sativa
transcript LOC_Os10g32550.1
intron # 1
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|8528178|gb|AU092993.1|AU092993
EST:     CAGCCTCGCCTCCAAGGCTCG                         GCAAGCCGGGAGCAGCGCTCGCCAG
genomic: CAGCCTCGCCTCCAAGGCTCGgtgagtgtgc ... gttggtgcagGCAAGCCGGGAGCAGCGCTCGCCAG
EST: gi|88730338|gb|CI753951.1|CI753951
EST:     CTCGGCTCCGCCATGTACCGCGCGGCCGCCAGCCTCGCCTCCAAGGCTCG                         GCAAGCCGGGAGCAGCGCTCGCCAG
genomic: CTCGGCTCCGCCATGTACCGCGCGGCCGCCAGCCTCGCCTCCAAGGCTCGgtgagtgtgc ... gttggtgcagGCAAGCCGGGAGCAGCGCTCGCCAG
EST: gi|58673475|gb|CK062161.1|CK062161
EST:     CTCGGCTCCGCCATGTACCGCGCGGCCGCCAGCCTCGCCTCCAAGGCTCG                         GCAAGCCGGGAGCAGCGCTCGCCAG
genomic: CTCGGCTCCGCCATGTACCGCGCGGCCGCCAGCCTCGCCTCCAAGGCTCGgtgagtgtgc ... gttggtgcagGCAAGCCGGGAGCAGCGCTCGCCAG
EST: gi|58689551|gb|CK078238.1|CK078238
EST:     CAGCCTCGCCTCCAAGGCTCG                         GCAAGCCGGGAGCAGCGCTCGCCAG
genomic: CAGCCTCGCCTCCAAGGCTCGgtgagtgtgc ... gttggtgcagGCAAGCCGGGAGCAGCGCTCGCCAG
EST: gi|58685403|gb|CK074090.1|CK074090
EST:     TCGGCTCCGCCATGTACCGCGCGGCCGCCAGCCTCGCCTCCAAGGGCTCG                         GCAAGCCGGGAGCAGCGCTCGCCAG
genomic: TCGGCTCCGCCATGTACCGCGCGGCCGCCAGCCTCGCCTCCAA-GGCTCGgtgagtgtgc ... gttggtgcagGCAAGCCGGGAGCAGCGCTCGCCAG
EST: gi|58597481|gb|CK008009.1|CK008009
EST:     CTCGGCTCCGCCATGTACCGCGCGGCCGCC-GCCTCGCCTCCAA-GCTCG                         GCAAGCCGGGAGCAGCGCTCGCCAG
genomic: CTCGGCTCCGCCATGTACCGCGCGGCCGCCAGCCTCGCCTCCAAGGCTCGgtgagtgtgc ... gttggtgcagGCAAGCCGGGAGCAGCGCTCGCCAG
EST: gi|29632103|gb|CB637112.1|CB637112
EST:     CTCGGCTCCGCCATGTACCGCGCGGCCGCCAGCCTCGCCTCCAAGGCTCG                         GCAAGCCGGGAGCAGCGCTCGCCAG
genomic: CTCGGCTCCGCCATGTACCGCGCGGCCGCCAGCCTCGCCTCCAAGGCTCGgtgagtgtgc ... gttggtgcagGCAAGCCGGGAGCAGCGCTCGCCAG
EST: gi|58652508|gb|CK041188.1|CK041188
EST:     CTCGGCTCCGGCATGTACCGCGCGGCCGCCAGCCTCGCCTCCAAGGCTCG                         GCAAGCCGGGAGCAGCGCTCGCCAG
genomic: CTCGGCTCCGCCATGTACCGCGCGGCCGCCAGCCTCGCCTCCAAGGCTCGgtgagtgtgc ... gttggtgcagGCAAGCCGGGAGCAGCGCTCGCCAG
EST: gi|29627179|gb|CB632190.1|CB632190
EST:     CTCGGCTCCGCCATGTACCGCGCGGCCGCCAGCCTCGCCTCCAAGGCTCG                         GCAAGCCGGGAGCAGCGCTCGCCAG
genomic: CTCGGCTCCGCCATGTACCGCGCGGCCGCCAGCCTCGCCTCCAAGGCTCGgtgagtgtgc ... gttggtgcagGCAAGCCGGGAGCAGCGCTCGCCAG

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), 25 (downstream exon)
Score: 2

TCACCTCCCCTCCCCTCCCATCCCTCCTCCTCCCTAGCCCCAGGTCGCTGCTCGGCTCCGCCATGTACCGCGCGGCCGCCAGCCTCGCCTCCAAGGCTCGgtgagtgtgc ... gttggtgcagGCAAGCCGGGAGCAGCGCTCGCCAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtgtgcttgcttgattcccctcctccgcccgcattgcgatctgagtctcgcgacgcgcctgctgttctttccgacgtttgagcggtttgctgaactgtttcgttgttggtgcagGCAAGCCGGGAGCAGCGCTCGCCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG