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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtttagtttccatgcattccatctaatttcatgaaaaatatattttttacaaaaggtactcgatccattctcttctctagagcagATAAGAGACTTGCATGTTGCTCGGACAGAGGAAGATATTGGATTCTATGCTGGATTTCTTG

Basic information

species Oryza sativa
transcript LOC_Os12g03860.7
intron # 2
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|87008889|gb|CI304832.1|CI304832
EST:     CTCTGCCAATCTCTTCCTTGTTCCCCTTCCTGTACTTCATG                         ATAAGAGACTTGCATGTTGCTCGGACAGAGGAAGATATTGGATTCTATGCT
genomic: CTCTGCCAATCTCTTCCTTGTTCCCCTTCCTGTACTTCATGgtaagtttag ... tctagagcagATAAGAGACTTGCATGTTGCTCGGACAGAGGAAGATATTGGATTCTATGCT
EST: gi|33795182|gb|CF323464.1|CF323464
EST:     CTCTGCCAATCTCTTCCTTGTTCCCCTTCCTGTACTTCATG                         AGCAGATAAGAGACTTGCATGTTGCTCGGACAGAGGAAGATATTGGATTCT
genomic: CTCTGCCAATCTCTTCCTTGTTCCCCTTCCTGTACTTCATGgtaagtttag ... tctagagcagA-----TAAGAGACTTGCATGTTGCTCGGACAGAGGAAGATATTGGATTCT
EST: gi|88571513|gb|CI662886.1|CI662886
EST:     CTCTGCCAATCTCTTCCTTGTTCCCCTTCCTGTACTTCATG                         ATAAGAGACTTGCATGTTGCTCGGACAGAGGAAGATATTGGATTCTATGCT
genomic: CTCTGCCAATCTCTTCCTTGTTCCCCTTCCTGTACTTCATGgtaagtttag ... tctagagcagATAAGAGACTTGCATGTTGCTCGGACAGAGGAAGATATTGGATTCTATGCT
EST: gi|88372054|gb|CI641689.1|CI641689
EST:     CTCTGCCAATCTCTTCCTTGTTCCCCTTCCTGTACTTCATG                         ATAAGAGACTTGCATGTTGCTCGGACAGAGGAAGATATTGGATTCTATGCT
genomic: CTCTGCCAATCTCTTCCTTGTTCCCCTTCCTGTACTTCATGgtaagtttag ... tctagagcagATAAGAGACTTGCATGTTGCTCGGACAGAGGAAGATATTGGATTCTATGCT
EST: gi|88694564|gb|CI738602.1|CI738602
EST:     CTCTGCCAATCTCTTCCTTGTTCCCCTTCCTGTACTTCATG                         ATAAGAGACTTGCATGTCGCTCGGACAGAGGAAGATATCGGAT
genomic: CTCTGCCAATCTCTTCCTTGTTCCCCTTCCTGTACTTCATGgtaagtttag ... tctagagcagATAAGAGACTTGCATGTTGCTCGGACAGAGGAAGATATTGGAT
EST: gi|33677540|gb|CF305779.1|CF305779
EST:     CTCTGCCAATCTCTTCCTTGTTCCCCTTCCTGTACTTCATG                         ATAAGAGACTTGCATGTTGCTCGGACAGAGGAAGATATTGGATTCTATGCT
genomic: CTCTGCCAATCTCTTCCTTGTTCCCCTTCCTGTACTTCATGgtaagtttag ... tctagagcagATAAGAGACTTGCATGTTGCTCGGACAGAGGAAGATATTGGATTCTATGCT
EST: gi|88342532|gb|CI637108.1|CI637108
EST:     CTCTGCCAATCTCTTCCTTGTTCCCCTTCCTGTACTTCATG                         ATAAGAGACTTGCATGTTGCTCGGACAGAGGAAGATATTGGATTCTATGCT
genomic: CTCTGCCAATCTCTTCCTTGTTCCCCTTCCTGTACTTCATGgtaagtttag ... tctagagcagATAAGAGACTTGCATGTTGCTCGGACAGAGGAAGATATTGGATTCTATGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgaaaaatatattttttacaaaaggtactcgatccattctcttctctagagcagATAAGAGACTTGCATGTTGCTCGGACAGAGGAAGATATTGGATTCTATGCTGGATTTCTTG
                                 tccattctcttctct  CT-rich tract
     aaatatattttttaca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtttagtttccatgcattccatctaatttcatgaaaaatatattttttacaaaaggtactcgatccattctcttctctagagcagATAAGAGACTTGCATGTTGCTCGGACAGAGGAAGATATTGGATTCTATGCTGGATTTCTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA