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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttttgaaatgattaatgtgtacatgttgtttatatacatgccatgttttagtaaaaatcaacgctattaaccggcggaaataataaatttggtgtaacagCATCGGAGTCGTCTCAAGTGGGTGTAGGAAGCAAATTGAAGCCATGCACCAAATTTTTCAG

Basic information

species Oryza sativa
transcript LOC_Os06g41384.2
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|58681924|gb|CK070611.1|CK070611
EST:     CAAGCGGGCCGCCCCGGAGGGCACCAACGGCGCCGCCAAGCGCGCGAGAG                         CATCGGAGTCGTCTCAAGTGGGTGTAGGAAGCAAATTGAAGCCATGCACCA
genomic: CAAGCGGGCCGCCCCGGAGGGCACCAACGGCGCCGCCAAGCGCGCGAGAGgtgagcctct ... ggtgtaacagCATCGGAGTCGTCTCAAGTGGGTGTAGGAAGCAAATTGAAGCCATGCACCA
EST: gi|88720128|gb|CI745218.1|CI745218
EST:     CAAGCGGGCCGCCCCGGAGGGCACCAACGGCGCCGCCAAGCGCGCGAGAG                         CATCGGAGTCGTCTCAAGTGGGTGTAGGAAGCAAATTGAAGCCATGCACCA
genomic: CAAGCGGGCCGCCCCGGAGGGCACCAACGGCGCCGCCAAGCGCGCGAGAGgtgagcctct ... ggtgtaacagCATCGGAGTCGTCTCAAGTGGGTGTAGGAAGCAAATTGAAGCCATGCACCA
EST: gi|66923690|gb|CX110538.1|CX110538
EST:     CAAGCGGGCCGCCCCGGAGGGCACCAACGGCGCCGCCAAGCGCGCGAGAG                         CATCGGAGTCGTCTCAAGTGGGTGTAGGAAGCAAATTGAAGCCATGCACCA
genomic: CAAGCGGGCCGCCCCGGAGGGCACCAACGGCGCCGCCAAGCGCGCGAGAGgtgagcctct ... ggtgtaacagCATCGGAGTCGTCTCAAGTGGGTGTAGGAAGCAAATTGAAGCCATGCACCA
EST: gi|2428543|gb|C73006.1|C73006
EST:     CAAGCGGGCCGCCCCGGA-GGCACCAACGGCGCCGCCAAGCGCGCGAGAG                         CATCGGAGTCGTCTCAAGTGGGTGTAGGAAGCAAATTGAAGCCATGCACCA
genomic: CAAGCGGGCCGCCCCGGAGGGCACCAACGGCGCCGCCAAGCGCGCGAGAGgtgagcctct ... ggtgtaacagCATCGGAGTCGTCTCAAGTGGGTGTAGGAAGCAAATTGAAGCCATGCACCA
EST: gi|218481955|gb|FG961963.1|FG961963
EST:     CAAGCGGGCCGCCCCGGAGGGCACCAACGGCGCCGCCAAGCGCGCGAGAG                         CATCGGAGTCGTCTCAAGTGGGTGTAGGAAGCAAATTGAAGCCATGCACCA
genomic: CAAGCGGGCCGCCCCGGAGGGCACCAACGGCGCCGCCAAGCGCGCGAGAGgtgagcctct ... ggtgtaacagCATCGGAGTCGTCTCAAGTGGGTGTAGGAAGCAAATTGAAGCCATGCACCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttagtaaaaatcaacgctattaaccggcggaaataataaatttggtgtaacagCATCGGAGTCGTCTCAAGTGGGTGTAGGAAGCAAATTGAAGCCATGCACCAAATTTTTCAG
                   tattaac  putative branch site (score: 1)
                                aaataataaatttggt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttttgaaatgattaatgtgtacatgttgtttatatacatgccatgttttagtaaaaatcaacgctattaaccggcggaaataataaatttggtgtaacagCATCGGAGTCGTCTCAAGTGGGTGTAGGAAGCAAATTGAAGCCATGCACCAAATTTTTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - -catgttg
- - - - - - - - - - - - - - - - - tacatgc
- - - - - - - - - - - - - - - - - - - - -catgttt
- - - - - - - - - - - - - - - - - - - - - - - - - - - aaatcaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gaaataa