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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCATCCCGGCGGCTCTCCGCCACCCGCATGCCCACGCCGCCGGCCTCCGCCTCCTCCGCTCCTCGGGAGACCCCTGCCCGCCCTGCACCCTTCCGTTTAGgtaaaagaaaaatcatggcctgaatctcttcttcttctttttttttgtttcttagatgttttgtctaagttgttttggagcatctctcccgttaccttgg...

Basic information

species Oryza sativa
transcript LOC_Os03g46740.1
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|88339807|gb|CI649064.1|CI649064
EST:     CTCCTCCGCTCCTCGGGAGACCCCTGCCCGCCCTGCACCCTTCCGTTTAG                         GTTATGTGGAGTGCCATTAAAAAAGGGCCATGTGTACGCTGGTGCTGTATC
genomic: CTCCTCCGCTCCTCGGGAGACCCCTGCCCGCCCTGCACCCTTCCGTTTAGgtaaaagaaa ... gcttaggcagGTTATGTGGAGTGCCATTAAAAAAGGGCCATGTGTACGCTGGTGCTGTATC
EST: gi|58677591|gb|CK066278.1|CK066278
EST:     CTCCTCCGCTCCTCGGGAGACCCCTGCCCGCCCTGCACCCTTCCGTTTAG                         GTTATGTGGAGTGCCATTAAAAAAGGGCCATGTGTACGCTGGTGCTGTATC
genomic: CTCCTCCGCTCCTCGGGAGACCCCTGCCCGCCCTGCACCCTTCCGTTTAGgtaaaagaaa ... gcttaggcagGTTATGTGGAGTGCCATTAAAAAAGGGCCATGTGTACGCTGGTGCTGTATC
EST: gi|88326323|gb|CI660146.1|CI660146
EST:     CTCCTCCGCTCCTCGGGAGACCCCTGCCCGCCCTGCACCCTTCCGTTTAG                         GTTATGTGGAGTGCCATTAAAAAAGGGCCATGTGTACGCTGGTGCTGTATC
genomic: CTCCTCCGCTCCTCGGGAGACCCCTGCCCGCCCTGCACCCTTCCGTTTAGgtaaaagaaa ... gcttaggcagGTTATGTGGAGTGCCATTAAAAAAGGGCCATGTGTACGCTGGTGCTGTATC
EST: gi|88413348|gb|CI581363.1|CI581363
EST:     GCTCCTCGGGAGACCCCTGCCCGCCCTGCACCCTTCCGTTTAG                         GTTATGTGGAGTGCCATTAAAAAAGGGCCATGTGTACGCTGGTGCTGTATC
genomic: GCTCCTCGGGAGACCCCTGCCCGCCCTGCACCCTTCCGTTTAGgtaaaagaaa ... gcttaggcagGTTATGTGGAGTGCCATTAAAAAAGGGCCATGTGTACGCTGGTGCTGTATC
EST: gi|88406435|gb|CI598928.1|CI598928
EST:     CTCCTCCGCTCCTCGGGAGACCCCTGCCCGCCCTGCACCCTTCCGTTTAG                         GTTATGTGGAGTGCCATTAAAAAAGGGCCATGTGTACGCTGGTGCTGTATC
genomic: CTCCTCCGCTCCTCGGGAGACCCCTGCCCGCCCTGCACCCTTCCGTTTAGgtaaaagaaa ... gcttaggcagGTTATGTGGAGTGCCATTAAAAAAGGGCCATGTGTACGCTGGTGCTGTATC
EST: gi|88740828|gb|CI763343.1|CI763343
EST:     CTCCTCCGCTCCTCGGGAGACCCCTGCCCGCCCTGCACCCTTCCGTTTAG                         GTTATGTGGAGTGCCATTAAAAAAGGGCCATGTGTACGCTGGTGCTGTATC
genomic: CTCCTCCGCTCCTCGGGAGACCCCTGCCCGCCCTGCACCCTTCCGTTTAGgtaaaagaaa ... gcttaggcagGTTATGTGGAGTGCCATTAAAAAAGGGCCATGTGTACGCTGGTGCTGTATC
EST: gi|88720833|gb|CI744132.1|CI744132
EST:     CTCCTCCGCTCCTCGGGAGACCCCTGCCCGCCCTGCACCCTTCCGTTTAGGCAGG                     
genomic: CTCCTCCGCTCCTCGGGAGACCCCTGCCCGCCCTGCACCCTTCCGTTT----A-Ggtaaaagaaa ... gcttag
EST: gi|88729886|gb|CI753107.1|CI753107
EST:     CTCCTCCGCTCCTCGGGAGAACCCTGCCCGCCCTGCACCCTTCCGTTTAG                         GTTATGTGGAGTGCCATTAAAAAAGGGCCATGTGTACGCTGGTGCTGTATC
genomic: CTCCTCCGCTCCTCGGGAGACCCCTGCCCGCCCTGCACCCTTCCGTTTAGgtaaaagaaa ... gcttaggcagGTTATGTGGAGTGCCATTAAAAAAGGGCCATGTGTACGCTGGTGCTGTATC
EST: gi|58693286|gb|CK081973.1|CK081973
EST:     CTCCTCCGCTCCTCGGGAGACCCCTGCCCGCCCTGCACCCTTCCGTTTAG                         GTTATGTGGAGTGCCATTAAAAAAGGGCCATGTGTACGCTGGTGCTGTATC
genomic: CTCCTCCGCTCCTCGGGAGACCCCTGCCCGCCCTGCACCCTTCCGTTTAGgtaaaagaaa ... gcttaggcagGTTATGTGGAGTGCCATTAAAAAAGGGCCATGTGTACGCTGGTGCTGTATC
EST: gi|29620621|gb|CB625632.1|CB625632
EST:     CTCCTCCGCTCCTCGGGAGACCCCTGCCCGCCCTGCACCCTTCCGTTTAG                         GTTATGTGGAGTGCCATTAAAAAAGGGCCATGTGTACGCTGGTGCTGTATC
genomic: CTCCTCCGCTCCTCGGGAGACCCCTGCCCGCCCTGCACCCTTCCGTTTAGgtaaaagaaa ... gcttaggcagGTTATGTGGAGTGCCATTAAAAAAGGGCCATGTGTACGCTGGTGCTGTATC
EST: gi|88307368|gb|CI642011.1|CI642011
EST:     CTCCTCCGCTCCTCGGGAGACCCCTGCCCGCCCTGCACCCTTCCGTTTAG                         GTTATGTGGAGTGCCATTAAAAAAGGGCCATGTGTACGCTGGTGCTGTATC
genomic: CTCCTCCGCTCCTCGGGAGACCCCTGCCCGCCCTGCACCCTTCCGTTTAGgtaaaagaaa ... gcttaggcagGTTATGTGGAGTGCCATTAAAAAAGGGCCATGTGTACGCTGGTGCTGTATC
EST: gi|58693740|gb|CK082427.1|CK082427
EST:     CTCCTCCGCTCCTCGGGAGACCCCTGCCCGCCCTGCACCCTTCCGTTTAG                         GTTATGTGGAGTGCCATTAAAAAAGGGCCATGTGTACGCTGGTGCTGTATC
genomic: CTCCTCCGCTCCTCGGGAGACCCCTGCCCGCCCTGCACCCTTCCGTTTAGgtaaaagaaa ... gcttaggcagGTTATGTGGAGTGCCATTAAAAAAGGGCCATGTGTACGCTGGTGCTGTATC
EST: gi|58672683|gb|CK061369.1|CK061369
EST:     GGGAGA-CCCTGCCCGCCCTGCACCCTTCCGTTTAG                         GTTATGTGGAGTGCCATTAAAAAAGGGCCATGTGTACGCTGGTGCTGTATC
genomic: GGGAGACCCCTGCCCGCCCTGCACCCTTCCGTTTAGgtaaaagaaa ... gcttaggcagGTTATGTGGAGTGCCATTAAAAAAGGGCCATGTGTACGCTGGTGCTGTATC
EST: gi|218505243|gb|FG948331.1|FG948331
EST:     CTCCTCCGCTCCTCGGGAGACCCCTGCCCGCCCTGCACCCTTCCGTTTAGGCAG                      
genomic: CTCCTCCGCTCCTCGGGAGACCCCTGCCCGCCCTGCACCCTTCCGTTT----AGgtaaaagaaa ... gcttagg
EST: gi|58592609|gb|CF990917.1|CF990917
EST:     CTCCTCCGCTCCTCGGGAGACCCCTGCCCGCCCTGCACCCTTCCGTTTAGGCAG                      
genomic: CTCCTCCGCTCCTCGGGAGACCCCTGCCCGCCCTGCACCCTTCCGTTT----AGgtaaaagaaa ... gcttagg

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: 73 (upstream exon), 70 (downstream exon)
Score: 27

CCATCCCGGCGGCTCTCCGCCACCCGCATGCCCACGCCGCCGGCCTCCGCCTCCTCCGCTCCTCGGGAGACCCCTGCCCGCCCTGCACCCTTCCGTTTAGgtaaaagaaa ... gcttaggcagGTTATGTGGAGTGCCATTAAAAAAGGGCCATGTGTACGCTGGTGCTGTATCTGCTACCAGGAGTCCTGGCTTGGGCAATGCAGAGAATCTGCGTGAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCATCCCGGCGGCTCTCCGCCACCCGCATGCCCACGCCGCCGGCCTCCGCCTCCTCCGCTCCTCGGGAGACCCCTGCCCGCCCTGCACCCTTCCGTTTAGgtaaaagaaaaatcatggcctgaatctcttcttcttctttttttttgtttcttagatgttttgtctaagttgttttggagcatctctcccgttaccttgg

- - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -agaaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctctccc