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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...attaggttctgtattgagaattcattctagttaattcggtactgatttttaaggaaacaaaaatactcaactgttttaactgaattaattgaactgctagCTCTGAAAGAGGGGGGCATATGGCTTCCTTATTTCGACGATCTTCGATCACCCACCACGCCACCTCAGCTGTGGCATCTGCAGCAGGTGCTCACCGTGCC

Basic information

species Oryza sativa
transcript LOC_Os02g06770.3
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|88332112|gb|CI643529.1|CI643529
EST:     GACTGTTCTCTCGCCCATCGCCGCCGCCTCCGCCGCCTCTGCCCCAG                         CTCTGAAAGAGGGGGGCATATGGCTTCCTTATTTCGACGATCTTCGATCAC
genomic: GACTGTTCTCTCGCCCATCGCCGCCGCCTCCGCCGCCTCTGCCCCAGgtaccagcat ... gaactgctagCTCTGAAAGAGGGGGGCATATGGCTTCCTTATTTCGACGATCTTCGATCAC
EST: gi|88347687|gb|CI655040.1|CI655040
EST:     GACTGTTCTCTCGCCCATCGCCGCCGCCTCCGCCGCCTCTGCCCCAG                         CTCTGAAAGAGGGGGGCATATGGCTTCCTTATTTCGACGATCTTCGATCAC
genomic: GACTGTTCTCTCGCCCATCGCCGCCGCCTCCGCCGCCTCTGCCCCAGgtaccagcat ... gaactgctagCTCTGAAAGAGGGGGGCATATGGCTTCCTTATTTCGACGATCTTCGATCAC
EST: gi|66918327|gb|CX105175.1|CX105175
EST:     CGCCCATCGCCGCCGCCTCCGCCGCCTCTGCCCCAG                         CTCTGAAAGAGGGGGGCATATGGCTTCCTTATTTCGACGATCTTCGATCAC
genomic: CGCCCATCGCCGCCGCCTCCGCCGCCTCTGCCCCAGgtaccagcat ... gaactgctagCTCTGAAAGAGGGGGGCATATGGCTTCCTTATTTCGACGATCTTCGATCAC
EST: gi|163926082|gb|EG711810.1|EG711810
EST:     CTCTGCCCCAG                         CTCTGAAAGAGGGGGGCATATGGCTTCCTTATTTCGACGATCTTCGATCAC
genomic: CTCTGCCCCAGgtaccagcat ... gaactgctagCTCTGAAAGAGGGGGGCATATGGCTTCCTTATTTCGACGATCTTCGATCAC
EST: gi|163925821|gb|EG709617.1|EG709617
EST:     CTCTCGCCCATCGCCGCCGCCTCCGCCGCCTCTGCCCCAG                         CTCTGAAAGAGGGGGGCATATGGCTTCCTTATTTCGACGATCTTCGATCAC
genomic: CTCTCGCCCATCGCCGCCGCCTCCGCCGCCTCTGCCCCAGgtaccagcat ... gaactgctagCTCTGAAAGAGGGGGGCATATGGCTTCCTTATTTCGACGATCTTCGATCAC
EST: gi|88307704|gb|CI644744.1|CI644744
EST:     GACTGTTCTCTCGCCCATCGCCGCCGCCTCCGCCGCCTCTGCCCCAG                         CTCTGAAAGAGGGGGGCATATGGCTTCCTTATTTCGACGATCTTCGATCAC
genomic: GACTGTTCTCTCGCCCATCGCCGCCGCCTCCGCCGCCTCTGCCCCAGgtaccagcat ... gaactgctagCTCTGAAAGAGGGGGGCATATGGCTTCCTTATTTCGACGATCTTCGATCAC

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: 25 (upstream exon), 26 (downstream exon)
Score: 1

GACTGTTCTCTCGCCCATCGCCGCCGCCTCCGCCGCCTCTGCCCCAGgtaccagcat ... gaactgctagCTCTGAAAGAGGGGGGCATATGGCTTCCTTATTTCGACGATCTTCGATCACCCACCACGCCACCTCAGCTGTGGCATCTGCAGCAGGTGCTCACCGTGCC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttttaaggaaacaaaaatactcaactgttttaactgaattaattgaactgctagCTCTGAAAGAGGGGGGCATATGGCTTCCTTATTTCGACGATCTTCGATCACCCACCACGCCACCTCAGCTGTGGCATCTGCAGCAGGTGCTCACCGTGCC
                            ttttaactgaattaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
attaggttctgtattgagaattcattctagttaattcggtactgatttttaaggaaacaaaaatactcaactgttttaactgaattaattgaactgctagCTCTGAAAGAGGGGGGCATATGGCTTCCTTATTTCGACGATCTTCGATCACCCACCACGCCACCTCAGCTGTGGCATCTGCAGCAGGTGCTCACCGTGCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG