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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaactgacttaatatttccttttttatgttctcgaatgtgcttcgagtccaactatcgtgtattgatcatgttcttttgttgtgtgtgtttatgttaatgtatagGTTGGTCCTTTCAATCCCGGCAAAGGTGACAAAGCGAAACTGAAAGTGAAAGTCCGCCTTAACATCCATGGGGTGGTCACAGTTGAATCAGCAACA

Basic information

species Oryza sativa
transcript LOC_Os01g08560.1
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|29619080|gb|CB624092.1|CB624092
EST:     ATGTTGATACTGGTGATTTGCAAATATCACCAAAGATCAGCACTTACACG                         GTTGGTCCTTTCAATCCCGGCAAAGGTGACAAAGCGAAACTGAAAGTGAAA
genomic: ATGTTGATACTGGTGATTTGCAAATATCACCAAAGATCAGCACTTACACGgtaactgact ... taatgtatagGTTGGTCCTTTCAATCCCGGCAAAGGTGACAAAGCGAAACTGAAAGTGAAA
EST: gi|58611243|gb|CK038955.1|CK038955
EST:     ATGTTGATACTGGTGAGTTGCAAATATCACCAAAGATCAGCACTTACACG                         GTTGGTCCTTTCAATCCCGGCAAAGGTGACAAAGCGAAACTGAAAGTGAAA
genomic: ATGTTGATACTGGTGATTTGCAAATATCACCAAAGATCAGCACTTACACGgtaactgact ... taatgtatagGTTGGTCCTTTCAATCCCGGCAAAGGTGACAAAGCGAAACTGAAAGTGAAA
EST: gi|58695736|gb|CK084423.1|CK084423
EST:     ATGTTGATACTGGTGATTTGCAAATATCACCAAAGATCAGCACTTACACG                         GTTGGTCCTTTCAATCCCGGCAAAGGTGACAAAGCGAAACTGAAAGTGAAA
genomic: ATGTTGATACTGGTGATTTGCAAATATCACCAAAGATCAGCACTTACACGgtaactgact ... taatgtatagGTTGGTCCTTTCAATCCCGGCAAAGGTGACAAAGCGAAACTGAAAGTGAAA

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: 72 (upstream exon), 75 (downstream exon)
Score: 118

TAAAGCATTGACCTTCTATAGGTCCAATACATTTCAAGTAGATGTCACGTATGTTGATACTGGTGATTTGCAAATATCACCAAAGATCAGCACTTACACGgtaactgact ... taatgtatagGTTGGTCCTTTCAATCCCGGCAAAGGTGACAAAGCGAAACTGAAAGTGAAAGTCCGCCTTAACATCCATGGGGTGGTCACAGTTGAATCAGCAACA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aactatcgtgtattgatcatgttcttttgttgtgtgtgtttatgttaatgtatagGTTGGTCCTTTCAATCCCGGCAAAGGTGACAAAGCGAAACTGAAAGTGAAAGTCCGCCTTAACATCCATGGGGTGGTCACAGTTGAATCAGCAACA
                                          tgttaat  putative branch site (score: 118)
                                      tttatgttaatgtata  TA-rich tract