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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcggtccctcgttactcacaactgcatttgcaaaagcttgaattcaacttatgttttctttttctctctcaatcggtgtagGGAATGGTAGAAGTCACGATCTCAAGAGGGCGAGTTGTGTGGGAGGATGGCATTCTGAACGTTGTTCCCGGTTCAGGAAGATACGTCAGAACACCGCCTT

Basic information

species Oryza sativa
transcript LOC_Os01g59340.2
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g59340.2 (Oryza sativa), 3'ss of exon 15
lower sequence: GRMZM2G020002_T02 (Zea mays), 3'ss of exon 12
gtcggtccctcgttactcaca-------actgcatttgcaa--aagcttgaattcaacttatgttttctttttctct-ctcaatcggtgtagGGAATGGTAGAAGTCACGATCTCAAGAGGGCGAGTTGTGTGGGAGGATGGCATTCTGAACGTTGTTCCCGGTTCAGGAAGATACGTCAGAACACCGCCTT
|| ||| | || || | ||||        | | |||||      | |||| |     |   ||  |  | |     |  ||| |  |||||||||||||| ||| | || |||||||| || ||||| || |||||||||||| |||||||| |||  || ||||||||| |||||||||  |  || ||||
gttggttcttctttgcacacatgaatcagcagtatttgacgtggaacttgcaacttgcgggtgcatcatgtactaatgttcatttcgtgtagGGAATGGTGGAAATAACAATCTCAAGGGGCCGAGTGGTATGGGAGGATGGCGTTCTGAACATTGCACCTGGTTCAGGACGATACGTCATGATGCCACCTT
















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|86873138|gb|CI328518.1|CI328518
EST:     CACACCATTCAAGGTCCAACACAAATGTGTACGAGGGCAGGAAAGGAAAG                         GGAATGGTAGAAGTCACGATCTCAAGAGGGCGAGTTGTGTGGGAGGATGGC
genomic: CACACCATTCAAGGTCCAACACAAATGTGTACGAGGGCAGGAAAGGAAAGgtcggtccct ... atcggtgtagGGAATGGTAGAAGTCACGATCTCAAGAGGGCGAGTTGTGTGGGAGGATGGC
EST: gi|86431074|gb|CI083497.1|CI083497
EST:     CACACCATTCAAGGTCCAACACAAATGTGTACGAGGGCAGGAAAGGAAAG                         GGAATGGTAGAAGTCACGATCTCAAGAGGGCGAGTTGTGTGGGAGGATGGC
genomic: CACACCATTCAAGGTCCAACACAAATGTGTACGAGGGCAGGAAAGGAAAGgtcggtccct ... atcggtgtagGGAATGGTAGAAGTCACGATCTCAAGAGGGCGAGTTGTGTGGGAGGATGGC
EST: gi|88256979|gb|CI359367.1|CI359367
EST:     CACACCATTCAAGGTCCAACACAAATGTGTACGAGGGCAGGAAAGGAAAG                         GGAATGGTAGAAGTCACGATCTCAAGAGGGCGAGTTGTGTGGGAGGATGGC
genomic: CACACCATTCAAGGTCCAACACAAATGTGTACGAGGGCAGGAAAGGAAAGgtcggtccct ... atcggtgtagGGAATGGTAGAAGTCACGATCTCAAGAGGGCGAGTTGTGTGGGAGGATGGC
EST: gi|87005745|gb|CI316164.1|CI316164
EST:     CACACCATTCAAGGTCCAACACAAATGTGTACGAGGGCAGGAAAGGAAAG                         GGAATGGTAGAAGTCACGATCTCAAGAGGGCGAGTTTTGTGGTAGGATGGC
genomic: CACACCATTCAAGGTCCAACACAAATGTGTACGAGGGCAGGAAAGGAAAGgtcggtccct ... atcggtgtagGGAATGGTAGAAGTCACGATCTCAAGAGGGCGAGTTGTGTGGGAGGATGGC
EST: gi|87026885|gb|CI259538.1|CI259538
EST:     CACACCATTCAAGGTCCAACACAAATGTGTACGAGGGCAGGAAAGGAAAG                         GGAATGGTAGAAGTCACGATCTCAAGAGGGCGAGTTGTGTGGGAGGATGGC
genomic: CACACCATTCAAGGTCCAACACAAATGTGTACGAGGGCAGGAAAGGAAAGgtcggtccct ... atcggtgtagGGAATGGTAGAAGTCACGATCTCAAGAGGGCGAGTTGTGTGGGAGGATGGC
EST: gi|86867735|gb|CI342691.1|CI342691
EST:     CACACCATTCAAGGTCCAACACAAATGTGTACGAGGGCAGGAAAGGAAAG                         GGAATGGTAGAAGTCACGATCTCAAGAGGGCGAGTTGTGTGGGAGGATGGC
genomic: CACACCATTCAAGGTCCAACACAAATGTGTACGAGGGCAGGAAAGGAAAGgtcggtccct ... atcggtgtagGGAATGGTAGAAGTCACGATCTCAAGAGGGCGAGTTGTGTGGGAGGATGGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgcaaaagcttgaattcaacttatgttttctttttctctctcaatcggtgtagGGAATGGTAGAAGTCACGATCTCAAGAGGGCGAGTTGTGTGGGAGGATGGCATTCTGAACGTTGTTCCCGGTTCAGGAAGATACGTCAGAACACCGCCTT
                     cttatgttttcttttt  CT-rich tract
                      ttatgttttcttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcggtccctcgttactcacaactgcatttgcaaaagcttgaattcaacttatgttttctttttctctctcaatcggtgtagGGAATGGTAGAAGTCACGATCTCAAGAGGGCGAGTTGTGTGGGAGGATGGCATTCTGAACGTTGTTCCCGGTTCAGGAAGATACGTCAGAACACCGCCTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA