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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGCGCCTTCCTGCTCGCCGCGTTCGCCATGGCCGCCGCCTTCGTCCCCGTGGCCGAGTCCAGGACCACCCCCGTGGAGAAGACGACCACCACCCAAGCAGgtacgcacgttcatggcgtagagagcttgcattcttccatggttggtttgagtggtaatgtgtgttgttcgattacag

Basic information

species Oryza sativa
transcript LOC_Os01g10490.1
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|58602278|gb|CK012806.1|CK012806
EST:     GGCCGAGT-CAGGACCACCCCCGTGGAGAAGACGACCACCACCCAAGCAG                         AGGATGGTGTCAAGAAGCCGGACTGCGTGCCGGCGTTCGACCCGCGCTCGT
genomic: GGCCGAGTCCAGGACCACCCCCGTGGAGAAGACGACCACCACCCAAGCAGgtacgcacgt ... tcgattacagAGGATGGTGTCAAGAAGCCGGACTGCGTGCCGGCGTTCGACCCGCGCTCGT
EST: gi|13164983|gb|AU173780.1|AU173780
EST:     GGCCGAGTCCAGGACCACCCCCGTGGAGAAGACGACCACCACCCAAGCAG                         AGGATGGTGTCAAGAAGCCGGACTGCGTGCCGGCGTTCGACCCGCGCTCGT
genomic: GGCCGAGTCCAGGACCACCCCCGTGGAGAAGACGACCACCACCCAAGCAGgtacgcacgt ... tcgattacagAGGATGGTGTCAAGAAGCCGGACTGCGTGCCGGCGTTCGACCCGCGCTCGT
EST: gi|66921881|gb|CX108729.1|CX108729
EST:     GGCCGAGT-CAGGACCACCCCCGTGGAGAAGACGACCACCACCCAAGCAG                         AGGATGGTGTCAAGAAGCCGGACTGCGTGCCGGCGTTCGACCCGCGCTCGT
genomic: GGCCGAGTCCAGGACCACCCCCGTGGAGAAGACGACCACCACCCAAGCAGgtacgcacgt ... tcgattacagAGGATGGTGTCAAGAAGCCGGACTGCGTGCCGGCGTTCGACCCGCGCTCGT
EST: gi|13807022|gb|AU181780.1|AU181780
EST:     GGCCGAGTCCAGGACCACCCCCGTGGAGAAGACGACCACCACCCAAGCAG                         AGGATGGTGTCAAGAAGCCGGACTGCGTGCCGGCGTTCGACCCGCGCTCGT
genomic: GGCCGAGTCCAGGACCACCCCCGTGGAGAAGACGACCACCACCCAAGCAGgtacgcacgt ... tcgattacagAGGATGGTGTCAAGAAGCCGGACTGCGTGCCGGCGTTCGACCCGCGCTCGT
EST: gi|88451697|gb|CI694460.1|CI694460
EST:     GGCCGAGTCCAGGACCACCCCCGTGGAGAAGACGACCACCACCCAAGCAG                         AGGATGGTGTCAAGAAGCCGGACTGCGTGCCGGCGTTCGACCCGCGCTCGT
genomic: GGCCGAGTCCAGGACCACCCCCGTGGAGAAGACGACCACCACCCAAGCAGgtacgcacgt ... tcgattacagAGGATGGTGTCAAGAAGCCGGACTGCGTGCCGGCGTTCGACCCGCGCTCGT
EST: gi|87009579|gb|CI309100.1|CI309100
EST:     GGCCGAGTCCAGGACCACCCCCGTGGAGAAGACGACCACCACCCAAGCAG                         AGGATGGTGTCAAGAAGCCGGACTGCGTGCCGGCGTTCGACCCGCGCTCGT
genomic: GGCCGAGTCCAGGACCACCCCCGTGGAGAAGACGACCACCACCCAAGCAGgtacgcacgt ... tcgattacagAGGATGGTGTCAAGAAGCCGGACTGCGTGCCGGCGTTCGACCCGCGCTCGT
EST: gi|58601454|gb|CK011982.1|CK011982
EST:     CCCCGTGGAGAAGACGACCACCACCCAAGCAG                         AGGATGGTGTCAAGAAGCCGGACTGCGTGCCGGCGTTCGACCCGCGCTCGT
genomic: CCCCGTGGAGAAGACGACCACCACCCAAGCAGgtacgcacgt ... tcgattacagAGGATGGTGTCAAGAAGCCGGACTGCGTGCCGGCGTTCGACCCGCGCTCGT
EST: gi|88307847|gb|CI646282.1|CI646282
EST:     GGCCGAGTCCAGGACCACCCCCGTGGAGAAGACGACCACCACCCAAGCAG                         AGGATGGTGTCAAGAAGCCGGACTGCGTGCCGGCGTTCGACCCGCGCTCGT
genomic: GGCCGAGTCCAGGACCACCCCCGTGGAGAAGACGACCACCACCCAAGCAGgtacgcacgt ... tcgattacagAGGATGGTGTCAAGAAGCCGGACTGCGTGCCGGCGTTCGACCCGCGCTCGT
EST: gi|88394636|gb|CI609345.1|CI609345
EST:     GGCCGAGTCCAGGACCACCCCCGTGGAGAAGACGACCACCACCCAAGCAG                         AGGATGGTGTCAAGAAGCCGGATTGCGTGCCGGCGTTCGACCCGCGCTCGT
genomic: GGCCGAGTCCAGGACCACCCCCGTGGAGAAGACGACCACCACCCAAGCAGgtacgcacgt ... tcgattacagAGGATGGTGTCAAGAAGCCGGACTGCGTGCCGGCGTTCGACCCGCGCTCGT

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: 63 (upstream exon), 46 (downstream exon)
Score: 2

TGCGCCTTCCTGCTCGCCGCGTTCGCCATGGCCGCCGCCTTCGTCCCCGTGGCCGAGTCCAGGACCACCCCCGTGGAGAAGACGACCACCACCCAAGCAGgtacgcacgt ... tcgattacagAGGATGGTGTCAAGAAGCCGGACTGCGTGCCGGCGTTCGACCCGCGCTCGTTCCCCGGCCACGGCGGCACCACGACTCCGACGCCGATCCCGGGCCACCA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGCGCCTTCCTGCTCGCCGCGTTCGCCATGGCCGCCGCCTTCGTCCCCGTGGCCGAGTCCAGGACCACCCCCGTGGAGAAGACGACCACCACCCAAGCAGgtacgcacgttcatggcgtagagagcttgcattcttccatggttggtttgagtggtaatgtgtgttgttcgattacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA