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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattatccttttgctaccttcttgtgacaagtagggggtaaacaattgttgccaacattatacttttctgaaaaaaaaaagataagtacaaacggcacaataccatggtcgtcagGCTTCGCCAAGGAGTGGAACATTGTACTTGGAGCTGGACGGCGAGAACAGGAGAGTCCGGATCCAGGGAGAAGCTGTCACTGTGATGGCCGGGACTCTCT

Basic information

species Oryza sativa
transcript LOC_Os01g16146.1
intron # 5
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|33808571|gb|CF330171.1|CF330171
EST:     CACCTTACTGGGGTGGAAAGCTGGGGAAACAAAAACTTACGGCGTTTCAG                         GCTTCGCCAAGGAGTGGAACATTGTACTTGGAGCTGGACGGCGAGAACAGG
genomic: CACCTTACTGGGGTGGAAAGCTGGGGAAACAAAAACTTACGGCGTTTCAGgtattatcct ... tggtcgtcagGCTTCGCCAAGGAGTGGAACATTGTACTTGGAGCTGGACGGCGAGAACAGG
EST: gi|88275856|gb|CI396460.1|CI396460
EST:     CACCTTACTGGGGTGGAAAGCTGGGGAAACAAAAACTTACGGCGTTTCAG                         GCTTCGCCAAGGAGTGGAACATTGTACTTGGAGCTGGACGGCGAGAACAGG
genomic: CACCTTACTGGGGTGGAAAGCTGGGGAAACAAAAACTTACGGCGTTTCAGgtattatcct ... tggtcgtcagGCTTCGCCAAGGAGTGGAACATTGTACTTGGAGCTGGACGGCGAGAACAGG
EST: gi|88511717|gb|CI439223.1|CI439223
EST:     CACCTTACTGGGGTGGAAAGCTGGGGAAACAAAAACTTACGGCGTTTCAG                         GCTTCNCCAAGGAGTGGAACATTNTACTTGGAGCTGGACGGCGAGAACAGG
genomic: CACCTTACTGGGGTGGAAAGCTGGGGAAACAAAAACTTACGGCGTTTCAGgtattatcct ... tggtcgtcagGCTTCGCCAAGGAGTGGAACATTGTACTTGGAGCTGGACGGCGAGAACAGG
EST: gi|88223894|gb|CI223743.1|CI223743
EST:     CACCTTACTGGGGTGGAAAGCTGGGGAAACAAAAACTTACGGCGTTTCAG                         GCTTCGCCAAGGAGTGGAACATTGTACTTGGAGCTGGACGGCGAGAACAGG
genomic: CACCTTACTGGGGTGGAAAGCTGGGGAAACAAAAACTTACGGCGTTTCAGgtattatcct ... tggtcgtcagGCTTCGCCAAGGAGTGGAACATTGTACTTGGAGCTGGACGGCGAGAACAGG
EST: gi|86522833|gb|CI163039.1|CI163039
EST:     CACCTTACTGGGGTGGAAAGCTGGGGAAACAAAAACTTACGGCGTTTCAG                         GCTTCGCCAAGGAGTGGAACATTGTACTTGGAGCTGGACGGCGAGAACAGG
genomic: CACCTTACTGGGGTGGAAAGCTGGGGAAACAAAAACTTACGGCGTTTCAGgtattatcct ... tggtcgtcagGCTTCGCCAAGGAGTGGAACATTGTACTTGGAGCTGGACGGCGAGAACAGG
EST: gi|88264915|gb|CI367566.1|CI367566
EST:     CACCTTACTGGGGTGGAAAGCTGGGGAAACAAAAACTTACGGCGTTTCAG                         GCTTCGCCAAGGAGTGGAACATTGTACTTGGAGCTGGACGGCGAGAACAGG
genomic: CACCTTACTGGGGTGGAAAGCTGGGGAAACAAAAACTTACGGCGTTTCAGgtattatcct ... tggtcgtcagGCTTCGCCAAGGAGTGGAACATTGTACTTGGAGCTGGACGGCGAGAACAGG
EST: gi|88218690|gb|CI218539.1|CI218539
EST:     CACCTTACTGGGGTGGAAAGCTGGGGAAACAAAAACTTACGGCGTTTCAG                         GCTTCGCCAAGGAGTGGAACATTGTACTTGGAGCTGGACGGCGAGAACAGG
genomic: CACCTTACTGGGGTGGAAAGCTGGGGAAACAAAAACTTACGGCGTTTCAGgtattatcct ... tggtcgtcagGCTTCGCCAAGGAGTGGAACATTGTACTTGGAGCTGGACGGCGAGAACAGG
EST: gi|88979995|gb|CI026285.1|CI026285
EST:     CACCTTACTGGGGTGGAAAGCTGGGGAAACAAAAACTTACGGCGTTTCAG                         GCTTCGCCAAGGAGTGGAACATTGTACTTGGAGCTGGACGGCGAGAACAGG
genomic: CACCTTACTGGGGTGGAAAGCTGGGGAAACAAAAACTTACGGCGTTTCAGgtattatcct ... tggtcgtcagGCTTCGCCAAGGAGTGGAACATTGTACTTGGAGCTGGACGGCGAGAACAGG
EST: gi|33808573|gb|CF330172.1|CF330172
EST:     CACCTTACTGGGGTGGAAAGCTGGGGAAACAAAAACTTACGGCGTTTCAG                         GCTTCGCCAAGGAGTGGAACATTGTACTTGGAGCTGGACGGCGAGAACAGG
genomic: CACCTTACTGGGGTGGAAAGCTGGGGAAACAAAAACTTACGGCGTTTCAGgtattatcct ... tggtcgtcagGCTTCGCCAAGGAGTGGAACATTGTACTTGGAGCTGGACGGCGAGAACAGG
EST: gi|86483314|gb|CI125947.1|CI125947
EST:     CACCTTACTGGGGTGGAAAGCTGGGGAAACAAAAACTTACGGCGTTTCAG                         GCTTCGCCAAGGAGTGGAACATTGTACTCGGAGCTGGACGGCGAGAACAGG
genomic: CACCTTACTGGGGTGGAAAGCTGGGGAAACAAAAACTTACGGCGTTTCAGgtattatcct ... tggtcgtcagGCTTCGCCAAGGAGTGGAACATTGTACTTGGAGCTGGACGGCGAGAACAGG
EST: gi|88258968|gb|CI363261.1|CI363261
EST:     CACCTTACTGGGGTGGAAAGCTGGGGAAACAAAAACTTACGGCGTTTCAG                         GCTTCGCCAAAGAGTGGAACATTGTACTTGGAGCT-GACGGCGAGAACAGG
genomic: CACCTTACTGGGGTGGAAAGCTGGGGAAACAAAAACTTACGGCGTTTCAGgtattatcct ... tggtcgtcagGCTTCGCCAAGGAGTGGAACATTGTACTTGGAGCTGGACGGCGAGAACAGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tacttttctgaaaaaaaaaagataagtacaaacggcacaataccatggtcgtcagGCTTCGCCAAGGAGTGGAACATTGTACTTGGAGCTGGACGGCGAGAACAGGAGAGTCCGGATCCAGGGAGAAGCTGTCACTGTGATGGCCGGGACTCTCT
          aaaaaaaaaagataag  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtattatccttttgctaccttcttgtgacaagtagggggtaaacaattgttgccaacattatacttttctgaaaaaaaaaagataagtacaaacggcacaataccatggtcgtcagGCTTCGCCAAGGAGTGGAACATTGTACTTGGAGCTGGACGGCGAGAACAGGAGAGTCCGGATCCAGGGAGAAGCTGTCACTGTGATGGCCGGGACTCTCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG