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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTTTTCTCCCCGCCTCGCTGCTTCGCCTCTCGTTCCCCAAGGCCCCGAAGCCGCCGGCGCCGCCGCCCTCCTCCGGTTCGAGCTCTCCGCCACCATGgtgagtagcgacctccgaaaccgagccacattcgtttgctccgctatgctctacccgttccgttgtctgacgcgatgccgcgctttgttttttttttgtgtcgcag

Basic information

species Oryza sativa
transcript LOC_Os01g73160.1
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|88388732|gb|CI683519.1|CI683519
EST:     AAGCCGCCGGCGCCGCCGCCCTCCTCCGGTTCGAGCTCTCCGCCACCATG                         ATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACCTCTTCCATG
genomic: AAGCCGCCGGCGCCGCCGCCCTCCTCCGGTTCGAGCTCTCCGCCACCATGgtgagtagcg ... tgtgtcgcagATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACCTCTTCCATG
EST: gi|88392465|gb|CI612939.1|CI612939
EST:     AAGCCGCCGGCGCCGCCGCCCTCCTCCGGTTCGAGCTCTCCGCCACCATG                         ATCATCTGCAAGAAGAACCGCCGCGAGATCTGCAAGTACCTCTTCCATG
genomic: AAGCCGCCGGCGCCGCCGCCCTCCTCCGGTTCGAGCTCTCCGCCACCATGgtgagtagcg ... tgtgtcgcagATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACCTCTTCCATG
EST: gi|88311142|gb|CI658055.1|CI658055
EST:     AAGCCGCCGGCGCCGCCGCCCTCCTCCGGTTCGAGCTCTCCGCCACCATG                         ATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACCTCTTCCATG
genomic: AAGCCGCCGGCGCCGCCGCCCTCCTCCGGTTCGAGCTCTCCGCCACCATGgtgagtagcg ... tgtgtcgcagATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACCTCTTCCATG
EST: gi|25800605|gb|CA756566.1|CA756566
EST:     CCGGTTCGAGCTCTCCGCCACCATG                         ATCATCTCCNAGAAGAACCGCCGCGAGATCTGCAAGTACCTCTTCCATG
genomic: CCGGTTCGAGCTCTCCGCCACCATGgtgagtagcg ... tgtgtcgcagATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACCTCTTCCATG
EST: gi|33673989|gb|CF302228.1|CF302228
EST:     AAGCCGCCGGCGCCGCCGCCCTCCTCCGGTTCGAGCTCTCCGCCACCATG                         ATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACCTCTTCCATG
genomic: AAGCCGCCGGCGCCGCCGCCCTCCTCCGGTTCGAGCTCTCCGCCACCATGgtgagtagcg ... tgtgtcgcagATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACCTCTTCCATG
EST: gi|88724659|gb|CI747918.1|CI747918
EST:     AAGCCGCCGGCGCCGCCGCCCTCCTCCGGTTCGAGCTCTCCGCCACCATG                         ATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACCTCTTCCATG
genomic: AAGCCGCCGGCGCCGCCGCCCTCCTCCGGTTCGAGCTCTCCGCCACCATGgtgagtagcg ... tgtgtcgcagATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACCTCTTCCATG
EST: gi|33660783|gb|CF291750.1|CF291750
EST:     AAGCCGCCGGCGCCGCCGCCCTCCTCCGGTTCGAGCTCTCCGCCACCATG                         ATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACCTCTTCCATG
genomic: AAGCCGCCGGCGCCGCCGCCCTCCTCCGGTTCGAGCTCTCCGCCACCATGgtgagtagcg ... tgtgtcgcagATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACCTCTTCCATG
EST: gi|88301884|gb|CI667730.1|CI667730
EST:     AAGCCGCCGGCGCCGCCGCCCTCCTCCGGTTCGAGCTCTCCGCCACCATG                         ATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACCTCTTCCATG
genomic: AAGCCGCCGGCGCCGCCGCCCTCCTCCGGTTCGAGCTCTCCGCCACCATGgtgagtagcg ... tgtgtcgcagATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACCTCTTCCATG
EST: gi|88739378|gb|CI762886.1|CI762886
EST:     AAGCCGCCGGCGCCGCCGCCCTCCTCCGGTTCGAGCTCTCCGCCACCATG                         ATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACCTCTTCCATG
genomic: AAGCCGCCGGCGCCGCCGCCCTCCTCCGGTTCGAGCTCTCCGCCACCATGgtgagtagcg ... tgtgtcgcagATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACCTCTTCCATG
EST: gi|55435427|gb|CV730845.1|CV730845
EST:     AAGCCGCCGGCGCCGCCGCCCTCCTCCGGTTCGAGCTCTCCGCCACCATG                         ATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACCTCTTCCATG
genomic: AAGCCGCCGGCGCCGCCGCCCTCCTCCGGTTCGAGCTCTCCGCCACCATGgtgagtagcg ... tgtgtcgcagATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACCTCTTCCATG
EST: gi|88378851|gb|CI681669.1|CI681669
EST:     AAGCCGCCGGCGCCGCCGCCCTCCTCCGGTTCGAGCTCTCCGCCACCATG                         ATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACCTCTTCCATG
genomic: AAGCCGCCGGCGCCGCCGCCCTCCTCCGGTTCGAGCTCTCCGCCACCATGgtgagtagcg ... tgtgtcgcagATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACCTCTTCCATG
EST: gi|88353557|gb|CI632948.1|CI632948
EST:     AAGCCGCCGGCGCCGCCGCCCTCCTCCGGTTCGAGCTCTCCGCCACCATG                         ATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACCTCTTCCATG
genomic: AAGCCGCCGGCGCCGCCGCCCTCCTCCGGTTCGAGCTCTCCGCCACCATGgtgagtagcg ... tgtgtcgcagATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACCTCTTCCATG
EST: gi|2428870|gb|C73333.1|C73333
EST:     AAGCCGCCGGCGCCG-CGCCCTCCTCCGGTTCGAGCTCTCCGCCACCATG                         ATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACCTCTTCCATG
genomic: AAGCCGCCGGCGCCGCCGCCCTCCTCCGGTTCGAGCTCTCCGCCACCATGgtgagtagcg ... tgtgtcgcagATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACCTCTTCCATG
EST: gi|33670983|gb|CF299222.1|CF299222
EST:     AAGCCGCCGGCGCCGCCGCCCTCCTCCGGTTCGAGCTCTCCGCCACCATG                         ATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACCTCTTCCATG
genomic: AAGCCGCCGGCGCCGCCGCCCTCCTCCGGTTCGAGCTCTCCGCCACCATGgtgagtagcg ... tgtgtcgcagATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACCTCTTCCATG
EST: gi|66918131|gb|CX104979.1|CX104979
EST:     AAGCCGCCGGCGCCGCCGCCCTCCTCCGGTTCGAGCTCTCCGCCACCATG                         ATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACCTCTTCCATG
genomic: AAGCCGCCGGCGCCGCCGCCCTCCTCCGGTTCGAGCTCTCCGCCACCATGgtgagtagcg ... tgtgtcgcagATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACCTCTTCCATG
EST: gi|88364474|gb|CI644552.1|CI644552
EST:     AAGCCGCCGGCGCCGCCGCCCTCCTCCGGTTCGAGCTCTCCGCCACCATG                         ATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACCTCTTCCATG
genomic: AAGCCGCCGGCGCCGCCGCCCTCCTCCGGTTCGAGCTCTCCGCCACCATGgtgagtagcg ... tgtgtcgcagATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACCTCTTCCATG
EST: gi|88360769|gb|CI647779.1|CI647779
EST:     AAGCCGCCGGCGCCGCCGCCCTCCTCCGGTTCGAGCTCTCCGCCACCATG                         ATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACCTCTTCCATG
genomic: AAGCCGCCGGCGCCGCCGCCCTCCTCCGGTTCGAGCTCTCCGCCACCATGgtgagtagcg ... tgtgtcgcagATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACCTCTTCCATG
EST: gi|88325019|gb|CI645035.1|CI645035
EST:     AAGCCGCCGGCGCCGCCGCCCTCCTCCGGTTCGAGCTCTCCGCCACCATG                         ATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACCTCTTCCATG
genomic: AAGCCGCCGGCGCCGCCGCCCTCCTCCGGTTCGAGCTCTCCGCCACCATGgtgagtagcg ... tgtgtcgcagATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACCTCTTCCATG
EST: gi|88334750|gb|CI676543.1|CI676543
EST:     AAGCCGCCGGCGCCGCCGCCCTCCTCCGGTTCGAGCTCTCCGCCANCATG                         ATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACCTCTTCCATG
genomic: AAGCCGCCGGCGCCGCCGCCCTCCTCCGGTTCGAGCTCTCCGCCACCATGgtgagtagcg ... tgtgtcgcagATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACCTCTTCCATG
EST: gi|88341101|gb|CI638657.1|CI638657
EST:     AAGCCGCCGGCGCCGCCGCCCTCCTCCGGTTCGAGCTCTCCGCCACCATG                         ATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACCTCTTCCATG
genomic: AAGCCGCCGGCGCCGCCGCCCTCCTCCGGTTCGAGCTCTCCGCCACCATGgtgagtagcg ... tgtgtcgcagATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACCTCTTCCATG
EST: gi|88290586|gb|CI666959.1|CI666959
EST:     AAGCCGCCGGCGCCGCCGCCCTCCTCCGGTTCGAGCTCTCCGCCACCATG                         ATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACCTCTTCCATG
genomic: AAGCCGCCGGCGCCGCCGCCCTCCTCCGGTTCGAGCTCTCCGCCACCATGgtgagtagcg ... tgtgtcgcagATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACCTCTTCCATG
EST: gi|86831237|gb|CI297506.1|CI297506
EST:     AAGCCGCCGGCGCCGCCGCCCTCCTCCGGTTCGAGCTCTCCGCCACCATG                         ATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACCTCTTCCATG
genomic: AAGCCGCCGGCGCCGCCGCCCTCCTCCGGTTCGAGCTCTCCGCCACCATGgtgagtagcg ... tgtgtcgcagATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACCTCTTCCATG
EST: gi|88343622|gb|CI677601.1|CI677601
EST:     AAGCCGNCGGCGCCGCCGCCCTCCTCCGGTTCGAGCTCTCCGCCACCATG                         ATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACCTCTTCCATG
genomic: AAGCCGCCGGCGCCGCCGCCCTCCTCCGGTTCGAGCTCTCCGCCACCATGgtgagtagcg ... tgtgtcgcagATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACCTCTTCCATG
EST: gi|33659995|gb|CF290962.1|CF290962
EST:     AAGCCGCCGGCGCCGCCGCCCTCCTCCGGTTCGAGCTCTCCGCCACCATG                         ATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACCTCTTCCATG
genomic: AAGCCGCCGGCGCCGCCGCCCTCCTCCGGTTCGAGCTCTCCGCCACCATGgtgagtagcg ... tgtgtcgcagATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACCTCTTCCATG
EST: gi|88313669|gb|CI671802.1|CI671802
EST:     AAGCCGCCGGCGCCGCCGCCCTCCTCCGGTTCGAGCTCTCCGCCACCATG                         ATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACCTCTTCCATG
genomic: AAGCCGCCGGCGCCGCCGCCCTCCTCCGGTTCGAGCTCTCCGCCACCATGgtgagtagcg ... tgtgtcgcagATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACCTCTTCCATG
EST: gi|88727672|gb|CI749474.1|CI749474
EST:     AAGCCGCCGGCGCCGCCGCCCTCCTCCGGTTCGAGCTCTCCGCCACCATG                         ATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACCTCTTCCATG
genomic: AAGCCGCCGGCGCCGCCGCCCTCCTCCGGTTCGAGCTCTCCGCCACCATGgtgagtagcg ... tgtgtcgcagATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACCTCTTCCATG
EST: gi|88338425|gb|CI645679.1|CI645679
EST:     AAGCCGCCGGCGCCGCCGCCCTCCTCCGGTTCGAGCTCTCCGCCACCATG                         ATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACCTCTTCCATG
genomic: AAGCCGCCGGCGCCGCCGCCCTCCTCCGGTTCGAGCTCTCCGCCACCATGgtgagtagcg ... tgtgtcgcagATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACCTCTTCCATG
EST: gi|33815878|gb|CF333786.1|CF333786
EST:     AAGCCGCCGGCGCCGCCGCCCTCCTCCGGTTCGAGCTCTCCGCCACCATG                         ATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACCTCTTCCATG
genomic: AAGCCGCCGGCGCCGCCGCCCTCCTCCGGTTCGAGCTCTCCGCCACCATGgtgagtagcg ... tgtgtcgcagATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACCTCTTCCATG
EST: gi|88329374|gb|CI653291.1|CI653291
EST:     AAGCCGCCGGCGCCGCCGCCCTCCTCCGGTTCGAGCTCTCCGCCACCATG                         ATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACCTCTTCCATG
genomic: AAGCCGCCGGCGCCGCCGCCCTCCTCCGGTTCGAGCTCTCCGCCACCATGgtgagtagcg ... tgtgtcgcagATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACCTCTTCCATG
EST: gi|88734384|gb|CI757892.1|CI757892
EST:     AAGCCGCCGGCGCCGCCGCCCTCCTCCGGTTCGAGCTCTCCGCCACCATG                         ATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACCTCTTCCATG
genomic: AAGCCGCCGGCGCCGCCGCCCTCCTCCGGTTCGAGCTCTCCGCCACCATGgtgagtagcg ... tgtgtcgcagATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACCTCTTCCATG
EST: gi|88342338|gb|CI645860.1|CI645860
EST:     AAGCCGCCGGCGCCGCCGCCCTCCTCCGGTTCGAGCTCTCCGCCACCATG                         ATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACCTCTTCCATG
genomic: AAGCCGCCGGCGCCGCCGCCCTCCTCCGGTTCGAGCTCTCCGCCACCATGgtgagtagcg ... tgtgtcgcagATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACCTCTTCCATG
EST: gi|55435537|gb|CV730899.1|CV730899
EST:     AAGCCGCCGGCGCCGCCGCCCTCCTCCGGTTCGAGCTCTCCGCCACCATG                         ATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACCTCTTCCATG
genomic: AAGCCGCCGGCGCCGCCGCCCTCCTCCGGTTCGAGCTCTCCGCCACCATGgtgagtagcg ... tgtgtcgcagATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACCTCTTCCATG

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: 60 (upstream exon), 67 (downstream exon)
Score: 23

TTTTTCTCCCCGCCTCGCTGCTTCGCCTCTCGTTCCCCAAGGCCCCGAAGCCGCCGGCGCCGCCGCCCTCCTCCGGTTCGAGCTCTCCGCCACCATGgtgagtagcg ... tgtgtcgcagATCATCTCCAAGAAGAACCGCCGCGAGATCTGCAAGTACCTCTTCCATG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTTTTCTCCCCGCCTCGCTGCTTCGCCTCTCGTTCCCCAAGGCCCCGAAGCCGCCGGCGCCGCCGCCCTCCTCCGGTTCGAGCTCTCCGCCACCATGgtgagtagcgacctccgaaaccgagccacattcgtttgctccgctatgctctacccgttccgttgtctgacgcgatgccgcgctttgttttttttttgtgtcgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTCCTC