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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCGTTCCAACAACCTCTCCGCCTCCTCGTCCCCGTCCTCAACCTCACCGCCTCCCCGCCGCAGTAGCAGAGTCGCCCGCCGCCGCGCATCCGCATGGCAGgtcagtgcatgcctccccttccccttccccttccccttcccctccatgatcggaattgaatccaaagcctcgagctcctcaacctccccgactgcctcat...

Basic information

species Oryza sativa
transcript LOC_Os07g26610.2
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|88431706|gb|CI576897.1|CI576897
EST:     CTCCCCGCCGCAGTAGCAGAGTCGCCCGCCGCCGCGCATCCGCATGGCAG                         CTGCTCAAGGTAGCAGCGTTGTCCCATCCTCTGCGAAAGTTGACTTTTTAA
genomic: CTCCCCGCCGCAGTAGCAGAGTCGCCCGCCGCCGCGCATCCGCATGGCAGgtcagtgcat ... ttcattgcagCTGCTCAAGGTAGCAGCGTTGTCCCATCCTCTGCGAAAGTTGACTTTTTAA
EST: gi|88356963|gb|CI620851.1|CI620851
EST:     CTCCCCGCCGCAGTAGCAGAGTCGCCCGCCGCCGCGCATCCGCATGGCAG                         CTGCTCAAGGTAGCAGCGTTGTCCCATCCTCTGCGAAAGTTGACTTTTTAA
genomic: CTCCCCGCCGCAGTAGCAGAGTCGCCCGCCGCCGCGCATCCGCATGGCAGgtcagtgcat ... ttcattgcagCTGCTCAAGGTAGCAGCGTTGTCCCATCCTCTGCGAAAGTTGACTTTTTAA
EST: gi|86900888|gb|CI304093.1|CI304093
EST:     CTCCCCGCCGCAGTAGCAGAGTCGCCCGCCGCCGCGCATCCGCATGGCAG                         CTGCTCAAGGTAGCAGCGTTGTCCCATCCTCTGCGAAAGTTGACTTTTTAA
genomic: CTCCCCGCCGCAGTAGCAGAGTCGCCCGCCGCCGCGCATCCGCATGGCAGgtcagtgcat ... ttcattgcagCTGCTCAAGGTAGCAGCGTTGTCCCATCCTCTGCGAAAGTTGACTTTTTAA
EST: gi|88740306|gb|CI763814.1|CI763814
EST:     CTCCCCGCCGCAGTAGCAGAGTCGCCCGCCGCCGCGCATCCGCATGGCAG                         CTGCTCAAGGTAGCAGCGTTGTCCCATCCTCTGCGAAAGTTGACTTTTTAA
genomic: CTCCCCGCCGCAGTAGCAGAGTCGCCCGCCGCCGCGCATCCGCATGGCAGgtcagtgcat ... ttcattgcagCTGCTCAAGGTAGCAGCGTTGTCCCATCCTCTGCGAAAGTTGACTTTTTAA
EST: gi|88718727|gb|CI742237.1|CI742237
EST:     CTCCCCGCCGCAGTAGCAGAGTCGCCCGCCGCCGCGCATCCGCATGGCAG                         CTGCTCAAGGTAGCAGCGTTGTCCCATCCTCTGCGAAAGTTGACTTTTTAA
genomic: CTCCCCGCCGCAGTAGCAGAGTCGCCCGCCGCCGCGCATCCGCATGGCAGgtcagtgcat ... ttcattgcagCTGCTCAAGGTAGCAGCGTTGTCCCATCCTCTGCGAAAGTTGACTTTTTAA
EST: gi|88365076|gb|CI616495.1|CI616495
EST:     CTCCCCGCCGCAGTAGCAGAGTCGCCCGCCGCCGCGCATCCGCATGGCAG                         C
genomic: CTCCCCGCCGCAGTAGCAGAGTCGCCCGCCGCCGCGCATCCGCATGGCAGgtcagtgcat ... ttcattgcag-
EST: gi|88365076|gb|CI616495.1|CI616495
EST:     CTCCCCGCCGCAGTAGCAGAGTCGCCCGCCGCCGCGCATCCGCATGGCAG                         C
genomic: CTCCCCGCCGCAGTAGCAGAGTCGCCCGCCGCCGCGCATCCGCATGGCAGgtcagtgcat ... ttcattgcag-
EST: gi|88298983|gb|CI567986.1|CI567986
EST:     CTCCCCGCCGCAGTAGAAGAGTCGCCCGCCGCCGCGCATCCGCATGGCAG                         CTGCTCAAGGTAGCAGCGTTGTCCCATCCTCTGCGAAAGTTGACTTTTTAA
genomic: CTCCCCGCCGCAGTAGCAGAGTCGCCCGCCGCCGCGCATCCGCATGGCAGgtcagtgcat ... ttcattgcagCTGCTCAAGGTAGCAGCGTTGTCCCATCCTCTGCGAAAGTTGACTTTTTAA
EST: gi|88765250|gb|CI774344.1|CI774344
EST:     CTCCCCGCCGCAGTAGCAGAGTCGCCCGCCGCCGCGCATCCGCATGGCAG                         CTGCTCAAGGTAGCAGCGTTGTCCCATCCTCTGCGAAAGTTGACTTTTTAA
genomic: CTCCCCGCCGCAGTAGCAGAGTCGCCCGCCGCCGCGCATCCGCATGGCAGgtcagtgcat ... ttcattgcagCTGCTCAAGGTAGCAGCGTTGTCCCATCCTCTGCGAAAGTTGACTTTTTAA
EST: gi|88695537|gb|CI737575.1|CI737575
EST:     CTCCCCGCCGCAGTAGCAGAGTCGCCCGCCGCCGCGCATCCGCATGGCAG                         CTGCTCAAGGTAGCAGCGTTGTCCCATCCTCTGCGAAAGTTGACTTTTTAA
genomic: CTCCCCGCCGCAGTAGCAGAGTCGCCCGCCGCCGCGCATCCGCATGGCAGgtcagtgcat ... ttcattgcagCTGCTCAAGGTAGCAGCGTTGTCCCATCCTCTGCGAAAGTTGACTTTTTAA
EST: gi|88392307|gb|CI612781.1|CI612781
EST:     CTCCCCGCCGCAGTAGCAGAGTCGCCCGCCGCCGCGCATCCGCATGGCAG                         CTGCTCAAGGTAGCAGCGTTGTCCCATCCTCTGCGAAAGTTGACTTTTTAA
genomic: CTCCCCGCCGCAGTAGCAGAGTCGCCCGCCGCCGCGCATCCGCATGGCAGgtcagtgcat ... ttcattgcagCTGCTCAAGGTAGCAGCGTTGTCCCATCCTCTGCGAAAGTTGACTTTTTAA
EST: gi|88364874|gb|CI614492.1|CI614492
EST:     CTCCCCGCCGCAGTAGCAGAGTCGCCCGCCGCCGCGCATCCGCATGGCAG                         CTGCTCAAGGTAGAAGGGTTGTCCCATCCTCTGCGAAAGTTGACTTTTTAA
genomic: CTCCCCGCCGCAGTAGCAGAGTCGCCCGCCGCCGCGCATCCGCATGGCAGgtcagtgcat ... ttcattgcagCTGCTCAAGGTAGCAGCGTTGTCCCATCCTCTGCGAAAGTTGACTTTTTAA
EST: gi|88399621|gb|CI583355.1|CI583355
EST:     CTCCCCGCCGCAGTAGCAGAGTCGCCCGCCGCCGCGCATCCGCATGGCAG                         CTGCTCAAGGTAGCAGCGTTGTCCCATCCTCTGCGAAAGTTGACTTTTTAA
genomic: CTCCCCGCCGCAGTAGCAGAGTCGCCCGCCGCCGCGCATCCGCATGGCAGgtcagtgcat ... ttcattgcagCTGCTCAAGGTAGCAGCGTTGTCCCATCCTCTGCGAAAGTTGACTTTTTAA
EST: gi|88736243|gb|CI759751.1|CI759751
EST:     CTCCCCGCCGCAGTAGCAGAGTCGCCCGCCGCCGCGCATCCGCATGGCAG                         CTGCTCAAGGTAGCAGCGTTGTCCCATCCTCTGCGAAAGTTGACTTTTTAA
genomic: CTCCCCGCCGCAGTAGCAGAGTCGCCCGCCGCCGCGCATCCGCATGGCAGgtcagtgcat ... ttcattgcagCTGCTCAAGGTAGCAGCGTTGTCCCATCCTCTGCGAAAGTTGACTTTTTAA
EST: gi|88737211|gb|CI760719.1|CI760719
EST:     CTCCCCGCCGCAGTAGCAGAGTCGCCCGCCGCCGCGCATCCGCATGGCAG                         CTGCTCAAGGTAGCAGCGTTGTCCCATCCTCTGCGAAAGTTGACTTTTTAA
genomic: CTCCCCGCCGCAGTAGCAGAGTCGCCCGCCGCCGCGCATCCGCATGGCAGgtcagtgcat ... ttcattgcagCTGCTCAAGGTAGCAGCGTTGTCCCATCCTCTGCGAAAGTTGACTTTTTAA
EST: gi|88362534|gb|CI623874.1|CI623874
EST:     CTCCCCGCCGCAGTAGCAGAGTCGCCCGCCGCCGCGCATCCGCATGGCAG                         CTGCTCAAGGTAGCAGCGTTGTCCCATCCTCTGCGAAAGTTGACTTTTTAA
genomic: CTCCCCGCCGCAGTAGCAGAGTCGCCCGCCGCCGCGCATCCGCATGGCAGgtcagtgcat ... ttcattgcagCTGCTCAAGGTAGCAGCGTTGTCCCATCCTCTGCGAAAGTTGACTTTTTAA
EST: gi|88298548|gb|CI563543.1|CI563543
EST:     CTCCCCGCCGCAGTAGCAGAGTCGCCCGCCGCCGCGCATCCGCATGGCAG                         CTGCTCAAGGTAGCAGCGTTGTCCCATCCTCTGCGAAAGTTGACTTTTTAA
genomic: CTCCCCGCCGCAGTAGCAGAGTCGCCCGCCGCCGCGCATCCGCATGGCAGgtcagtgcat ... ttcattgcagCTGCTCAAGGTAGCAGCGTTGTCCCATCCTCTGCGAAAGTTGACTTTTTAA
EST: gi|88761427|gb|CI770983.1|CI770983
EST:     CTCCCCGCCGCAGTAGCAGAGTCGCCCGCCGCCGCGCATCCGCATGGCAG                         CTGCTCAAGGTAGCAGCGTTGTCCCATCCTCTGCGAAAGTTGACTTTTTAA
genomic: CTCCCCGCCGCAGTAGCAGAGTCGCCCGCCGCCGCGCATCCGCATGGCAGgtcagtgcat ... ttcattgcagCTGCTCAAGGTAGCAGCGTTGTCCCATCCTCTGCGAAAGTTGACTTTTTAA
EST: gi|29660678|gb|CB656953.1|CB656953
EST:     CTCCCCGCCGCAGTAGCAGAGTCGCCCGCCGCCGCGCATCCGCATGGCAG                         CTGCTCAAGGTAGCAGCGTTGTCCCATCCTCTGCGAAAGTTGACTTTTTAA
genomic: CTCCCCGCCGCAGTAGCAGAGTCGCCCGCCGCCGCGCATCCGCATGGCAGgtcagtgcat ... ttcattgcagCTGCTCAAGGTAGCAGCGTTGTCCCATCCTCTGCGAAAGTTGACTTTTTAA

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: 23 (upstream exon), 63 (downstream exon)
Score: 2

CCGTTCCAACAACCTCTCCGCCTCCTCGTCCCCGTCCTCAACCTCACCGCCTCCCCGCCGCAGTAGCAGAGTCGCCCGCCGCCGCGCATCCGCATGGCAGgtcagtgcat ... ttcattgcagCTGCTCAAGGTAGCAGCGTTGTCCCATCCTCTGCGAAAGTTGACTTTTTAAAGCTCCAGAATGGCAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCGTTCCAACAACCTCTCCGCCTCCTCGTCCCCGTCCTCAACCTCACCGCCTCCCCGCCGCAGTAGCAGAGTCGCCCGCCGCCGCGCATCCGCATGGCAGgtcagtgcatgcctccccttccccttccccttccccttcccctccatgatcggaattgaatccaaagcctcgagctcctcaacctccccgactgcctcat

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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccccttc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cccctcc