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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acttacttgctatccttcttcagggaattatacctaactttttaagtcatttgaactttgaaaccaatctaaaattgacgcttctccttttcacaggaagCACCATTCGACTTGCTGAGGGACAG

Basic information

species Oryza sativa
transcript LOC_Os01g14140.2
intron # 1
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|88571066|gb|CI662439.1|CI662439
EST:     ATCCCTCCTGCTCTTCTCCCTGGGGCTTGTGCTCCTCTACTTCTCCTCAG                         CACCATTCGACTTGCTGAGGGACAG
genomic: ATCCCTCCTGCTCTTCTCCCTGGGGCTTGTGCTCCTCTACTTCTCCTCAGgtaagcacat ... tcacaggaagCACCATTCGACTTGCTGAGGGACAG
EST: gi|88412635|gb|CI690381.1|CI690381
EST:     ATCCCTCCTGCTCTTCTCCCTGGGGCTTGTGCTCCTCTACTTCTCCTCAGGAAG                      
genomic: ATCCCTCCTGCTCTTCTCCCTGGGGCTTGTGCTCCTCTACTTCTCCTC----AGgtaagcacat ... tcacagg
EST: gi|163927940|gb|EG713516.1|EG713516
EST:     ATCCCTCCTGCTCTTCTCCCTGGGGCTTGTGCTCCTCTACTTCTCCTCAGGAAG                      
genomic: ATCCCTCCTGCTCTTCTCCCTGGGGCTTGTGCTCCTCTACTTCTCCTC----AGgtaagcacat ... tcacagg
EST: gi|86260931|gb|CI066606.1|CI066606
EST:     GGCTTGTGCTCCTCTACTTCTCCTCAGGAAG                      
genomic: GGCTTGTGCTCCTCTACTTCTCCTC----AGgtaagcacat ... tcacagg
EST: gi|66913626|gb|CX100474.1|CX100474
EST:     ATCCCTCCTGCTCTTCTCCCTGGGGCTTGTGCTCCTCTACTTCTCCTCAGGAAG                      
genomic: ATCCCTCCTGCTCTTCTCCCTGGGGCTTGTGCTCCTCTACTTCTCCTC----AGgtaagcacat ... tcacagg
EST: gi|88741066|gb|CI764574.1|CI764574
EST:     ATCCCTCCTGCTCTTCTCCCTGGGGCTTGTGCTCCTCTACTTCTCCTCAGGAAG                      
genomic: ATCCCTCCTGCTCTTCTCCCTGGGGCTTGTGCTCCTCTACTTCTCCTC----AGgtaagcacat ... tcacagg
EST: gi|88851563|gb|CI671003.1|CI671003
EST:     ATCCCTCCTGCTCTTCTCCCTGGGGCTTGTGCTCCTCTACTTCTCCTCAGGAAG                      
genomic: ATCCCTCCTGCTCTTCTCCCTGGGGCTTGTGCTCCTCTACTTCTCCTC----AGgtaagcacat ... tcacagg

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: 66 (upstream exon), 65 (downstream exon)
Score: 8

TGCTGGTGCCTGCTCCAGAGCAAGATGGCAAGAGGGGCTCAGCCATCTGCATCCCTCCTGCTCTTCTCCCTGGGGCTTGTGCTCCTCTACTTCTCCTCAGgtaagcacat ... tcacaggaagCACCATTCGACTTGCTGAGGGACAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtcatttgaactttgaaaccaatctaaaattgacgcttctccttttcacaggaagCACCATTCGACTTGCTGAGGGACAG
                           aattgac  putative branch site (score: 8)
                                 cgcttctccttttcac  CT-rich tract
                    aatctaaaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acttacttgctatccttcttcagggaattatacctaactttttaagtcatttgaactttgaaaccaatctaaaattgacgcttctccttttcacaggaagCACCATTCGACTTGCTGAGGGACAG

- -tacttgc
- - - - - - - - - - - - - - - - - - - - - - - tcatttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaccaa