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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cgtggaattaaaacaaaaaagaaaatttatttctttggctgtaactttttacgctgtcagttaaaaattggatcttagattgttgcgtttctatttgtagATGGATGATTTGTTGTTATCGGAGCCTGATGTGACGATAGCTGCTACGAGATACCTCCTATTCAATTTAAAGTACTTTCCGTCGGCGTCTTCTGAGCGAC

Basic information

species Oryza sativa
transcript LOC_Os01g55020.3
intron # 3
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|87019350|gb|CI279860.1|CI279860
EST:     ACTCTAGGTGGAATGTAGCAGATTATAGTCCCGTCAACTCAAATCTACAG                         ATGGATGATTTGTTGTTATCGGAGCCTGATGTGACGATAGCTGCTACGAGA
genomic: ACTCTAGGTGGAATGTAGCAGATTATAGTCCCGTCAACTCAAATCTACAGgtctggcaag ... ctatttgtagATGGATGATTTGTTGTTATCGGAGCCTGATGTGACGATAGCTGCTACGAGA
EST: gi|86599649|gb|CI253634.1|CI253634
EST:     ACTCTAGGTGGAATGTAGCAGATTATAGTCCCGTCAACTCAAATCTACAG                         ATGGATGATTTGTTGTTATCGGAGCCTGATGTGACGATAGCTGCTACGAGA
genomic: ACTCTAGGTGGAATGTAGCAGATTATAGTCCCGTCAACTCAAATCTACAGgtctggcaag ... ctatttgtagATGGATGATTTGTTGTTATCGGAGCCTGATGTGACGATAGCTGCTACGAGA
EST: gi|88445161|gb|CI552214.1|CI552214
EST:     ACTCTAGGTGGAATGTAGCAGATTATAGTCCCGTCAACTCAAATCTACAG                         ATGGATGATTTGTTGTTATCGGAGCCTGATGTGACGATAGCTGCTACGAGA
genomic: ACTCTAGGTGGAATGTAGCAGATTATAGTCCCGTCAACTCAAATCTACAGgtctggcaag ... ctatttgtagATGGATGATTTGTTGTTATCGGAGCCTGATGTGACGATAGCTGCTACGAGA
EST: gi|87022331|gb|CI282283.1|CI282283
EST:     ACTCTAGGTGGAATGTAGCAGATTATAGTCCCGTCAACTCAAATCTACAG                         ATGGATGATTTGTTGTTATCGGAGCCTGATGTGACGATAGCTGCTACGAGA
genomic: ACTCTAGGTGGAATGTAGCAGATTATAGTCCCGTCAACTCAAATCTACAGgtctggcaag ... ctatttgtagATGGATGATTTGTTGTTATCGGAGCCTGATGTGACGATAGCTGCTACGAGA
EST: gi|88408344|gb|CI551473.1|CI551473
EST:     ACTCTAGGTGGAATGTAGCAGATTATAGTCCCGTCAACTCAAATCTACAG                         ATGGATGATTTGTTGTTATCGGAGCCTGATGTGACGATAGCTGCTACGAGA
genomic: ACTCTAGGTGGAATGTAGCAGATTATAGTCCCGTCAACTCAAATCTACAGgtctggcaag ... ctatttgtagATGGATGATTTGTTGTTATCGGAGCCTGATGTGACGATAGCTGCTACGAGA

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: 52 (upstream exon), 72 (downstream exon)
Score: 13

CTGGCAATGATGACGTGTGACAAACTCTAGGTGGAATGTAGCAGATTATAGTCCCGTCAACTCAAATCTACAGgtctggcaag ... ctatttgtagATGGATGATTTGTTGTTATCGGAGCCTGATGTGACGATAGCTGCTACGAGATACCTCCTATTCAATTTAAAGTACTTTCCGTCGGCGTCTTCTGAGCGAC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttttacgctgtcagttaaaaattggatcttagattgttgcgtttctatttgtagATGGATGATTTGTTGTTATCGGAGCCTGATGTGACGATAGCTGCTACGAGATACCTCCTATTCAATTTAAAGTACTTTCCGTCGGCGTCTTCTGAGCGAC
                                          tttctattt  CT-rich tract
             agttaaaaatt  TA-rich tract