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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgttcacagtcacagaagcttaatgttaccagttaggttgagaatttaatgttccccacctccttattacgagatttggttgtatgtttactgcttcagGTTAGAGCTGTGGCGTGAGCAGCATGTTGAGTATTTGACGAGAGGGCTGAAACATCTTGGACCAAGCTTCCATGTGCTCGATGCCAA

Basic information

species Oryza sativa
transcript LOC_Os01g53600.1
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|58674014|gb|CK062700.1|CK062700
EST:     GAAATCTACCGCGTCCTCTTCGGCAACGCGCCAAACGCCAATTCCCTCAT                         GTTAGAGCTGTGGCGTGAGCAGCATGTTGAGTATTTGACGAGAGGCCTGAA
genomic: GAAATCTACCGCGTCCTCTTCGGCAACGCGCCCAACGCCAATTCCCTCATgtaagcgaac ... actgcttcagGTTAGAGCTGTGGCGTGAGCAGCATGTTGAGTATTTGACGAGAGGGCTGAA
EST: gi|29673186|gb|CB669461.1|CB669461
EST:     GAAATCTACCGCGTCCTCTTCGGCAACGCGCCCAACGCCAATTCCCTCAT                         GTTAGAGCTGTGGCGTGAGCAGCATGTTGAGTATTTGACGAGAGGGCTGAA
genomic: GAAATCTACCGCGTCCTCTTCGGCAACGCGCCCAACGCCAATTCCCTCATgtaagcgaac ... actgcttcagGTTAGAGCTGTGGCGTGAGCAGCATGTTGAGTATTTGACGAGAGGGCTGAA
EST: gi|29674619|gb|CB670894.1|CB670894
EST:     CAATTCCCTCAT                         GTTACATCTGTGGCGTGAGCAGCATGTTGAGTATTTGACGAGAGGGCTGAA
genomic: CAATTCCCTCATgtaagcgaac ... actgcttcagGTTAGAGCTGTGGCGTGAGCAGCATGTTGAGTATTTGACGAGAGGGCTGAA
EST: gi|29674660|gb|CB670935.1|CB670935
EST:     CAATTCCCTCAT                         GTTAGAGCTGTGGCGTGAGCAGCATGTTGAGTATTTGACGAGAGGGCTGAA
genomic: CAATTCCCTCATgtaagcgaac ... actgcttcagGTTAGAGCTGTGGCGTGAGCAGCATGTTGAGTATTTGACGAGAGGGCTGAA

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: 60 (upstream exon), 65 (downstream exon)
Score: 14

GGCTGACTGTGACGCAGGTGGAGCAGATGAAGGTGGAGGCGAAGGTGGGCGAAATCTACCGCGTCCTCTTCGGCAACGCGCCCAACGCCAATTCCCTCATgtaagcgaac ... actgcttcagGTTAGAGCTGTGGCGTGAGCAGCATGTTGAGTATTTGACGAGAGGGCTGAAACATCTTGGACCAAGCTTCCATGTGCTCGATGCCAA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttaatgttccccacctccttattacgagatttggttgtatgtttactgcttcagGTTAGAGCTGTGGCGTGAGCAGCATGTTGAGTATTTGACGAGAGGGCTGAAACATCTTGGACCAAGCTTCCATGTGCTCGATGCCAA
 atttaat  putative branch site (score: 14)
                                              ctgcttc  putative PPT
                                      tatgttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttgttcacagtcacagaagcttaatgttaccagttaggttgagaatttaatgttccccacctccttattacgagatttggttgtatgtttactgcttcagGTTAGAGCTGTGGCGTGAGCAGCATGTTGAGTATTTGACGAGAGGGCTGAAACATCTTGGACCAAGCTTCCATGTGCTCGATGCCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT