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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CATTGTAAATGGCTGCTGGGAGGGGCATCAGTCAGCTTTTGAAGAAAGCATTTCGTCCATCTgtaagtactgtgagaacttcggttcccccctattcttgtacatggttcttttgctaaaaattataaatttattccacgtcctttctactactgcctctgt...

Basic information

species Oryza sativa
transcript LOC_Os01g70960.1
intron # 2
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|29669775|gb|CB666050.1|CB666050
EST:     CTGCTGGGAGGGGCATCAGTCAGCTTTTGAAGAAAGCATTTCGTCCATCT                         AGCTCATCTCCGCTCTCTTCATCCTGGATAAATCATGAAGAGTCCTCTGGC
genomic: CTGCTGGGAGGGGCATCAGTCAGCTTTTGAAGAAAGCATTTCGTCCATCTgtaagtactg ... aactttgcagAGCTCATCTCCGCTCTCTTCATCCTGGATAAATCATGAAGAGTCCTCTGGC
EST: gi|29669904|gb|CB666179.1|CB666179
EST:     CTGCTGGGAGGGGCATCAGTCAGCTTTTGAAGAAAGCATTTCGTCCATCT                         AGCTCATCTCCGCTCTCTTCATCCTGGATAAATCATGAAGAGTCCTCTGGC
genomic: CTGCTGGGAGGGGCATCAGTCAGCTTTTGAAGAAAGCATTTCGTCCATCTgtaagtactg ... aactttgcagAGCTCATCTCCGCTCTCTTCATCCTGGATAAATCATGAAGAGTCCTCTGGC
EST: gi|88300536|gb|CI587340.1|CI587340
EST:     CTGCTGGGAGGGGCATCAGTCAGCTTTTGAAGAAAGCATTTCGTCCATCT                         AGCTCATCTCCGCTCTCTTCATCCTGGATAAATCATGAAGAGTCCTCTGGC
genomic: CTGCTGGGAGGGGCATCAGTCAGCTTTTGAAGAAAGCATTTCGTCCATCTgtaagtactg ... aactttgcagAGCTCATCTCCGCTCTCTTCATCCTGGATAAATCATGAAGAGTCCTCTGGC
EST: gi|8956916|gb|BE230719.1|BE230719
EST:     CTGCTGGGAGGGGCATCAGTCAGCTTTTGAAGAAAGCATTTCGTCCATCT                         AGCTCATCTCCSTTCTCTTCATCCTGGATAAATCATGAAGAGTCCTCTGGC
genomic: CTGCTGGGAGGGGCATCAGTCAGCTTTTGAAGAAAGCATTTCGTCCATCTgtaagtactg ... aactttgcagAGCTCATCTCCGCTCTCTTCATCCTGGATAAATCATGAAGAGTCCTCTGGC
EST: gi|88424277|gb|CI581832.1|CI581832
EST:     CTGCTGGGAGGGGCATCAGTCAGCTTTTGAAGAAAGCATTTCGTCCATCT                         AGCTCATCTCCGCTCTCTTCATCCTGGATAAATCATGAAGAGTCCTCTGGC
genomic: CTGCTGGGAGGGGCATCAGTCAGCTTTTGAAGAAAGCATTTCGTCCATCTgtaagtactg ... aactttgcagAGCTCATCTCCGCTCTCTTCATCCTGGATAAATCATGAAGAGTCCTCTGGC
EST: gi|55434402|gb|CV730323.1|CV730323
EST:     TGCTGGGATGGGTCATCAGTCAGCTTTTGAAGAAAGCATTTCGTCCATCT                         AGCTCATCTCCGCTCTCTTCATCCTGGATAAATCATGAACAGTCCTCTGGC
genomic: TGCTGGGA-GGGGCATCAGTCAGCTTTTGAAGAAAGCATTTCGTCCATCTgtaagtactg ... aactttgcagAGCTCATCTCCGCTCTCTTCATCCTGGATAAATCATGAAGAGTCCTCTGGC
EST: gi|8857821|gb|AU095139.1|AU095139
EST:     CTGCTGGGAGGGGCATCAGTCAGCTTTTGAAGAAAGCATTTCGTCCATCT                         AGCTCATCTCCGCTCTCTTCATCCTGGATAAATCATGAAGAGTCCTCTGGC
genomic: CTGCTGGGAGGGGCATCAGTCAGCTTTTGAAGAAAGCATTTCGTCCATCTgtaagtactg ... aactttgcagAGCTCATCTCCGCTCTCTTCATCCTGGATAAATCATGAAGAGTCCTCTGGC
EST: gi|117235872|gb|CT847828.1|CT847828
EST:     CTGCTGGGAGGGGCATCAGTCAGCTTTTGAAGAAAGCATTTCGTCCATCT                         AGCTCATCTCCGCTCTCTTCATCCTGGATAAATCATGAAGAGTCCTCTGGC
genomic: CTGCTGGGAGGGGCATCAGTCAGCTTTTGAAGAAAGCATTTCGTCCATCTgtaagtactg ... aactttgcagAGCTCATCTCCGCTCTCTTCATCCTGGATAAATCATGAAGAGTCCTCTGGC

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: 62 (upstream exon), 72 (downstream exon)
Score: 40

CATTGTAAATGGCTGCTGGGAGGGGCATCAGTCAGCTTTTGAAGAAAGCATTTCGTCCATCTgtaagtactg ... aactttgcagAGCTCATCTCCGCTCTCTTCATCCTGGATAAATCATGAAGAGTCCTCTGGCTTCACTGGATTGAGAGCATTGGCTATTCTGGGAGTTGGTGCTTCTGGCC




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CATTGTAAATGGCTGCTGGGAGGGGCATCAGTCAGCTTTTGAAGAAAGCATTTCGTCCATCTgtaagtactgtgagaacttcggttcccccctattcttgtacatggttcttttgctaaaaattataaatttattccacgtcctttctactactgcctctgt

- - - - - - - - - - - - - - -  TCAGCT
- - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - -  AAGAAA