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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattgttaacactcccaatgcacagcagaaaaaatataaaatttgttgatcttacaaactataagcaatgttgtgttctttttagGGTAATGATAGGCCTAAAAGCTCTGATGGTGGACCCACTCAGCGCGCTTCAGCAATGGCTGCCTTAACATCAGCGTTCAATCCATCAGCAAAACCCAAAA

Basic information

species Oryza sativa
transcript LOC_Os03g24220.2
intron # 21
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|218486625|gb|FG969617.1|FG969617
EST:     CATTGGCTGCTCTTTCATCTGCATTCAACCCATCTTCCCAAAAGAATAAG                         GGTAATGATAGGCCTAAAAGCTCTGATGGTGGACCCACTCAGCGCGCTTCA
genomic: CATTGGCTGCTCTTTCATCTGCATTCAACCCATCTTCCCAAAAGAATAAGgtattgttaa ... ttctttttagGGTAATGATAGGCCTAAAAGCTCTGATGGTGGACCCACTCAGCGCGCTTCA
EST: gi|58677092|gb|CK065779.1|CK065779
EST:     CATTGGCTGCTCTTTCATCTGCATTCAACCCATCTTCCCAAAAGAATAAG                         GGTAATGATAGGCCTAAAAGCTCTGATGGTGGACCCACTCAGCGCGCTTCA
genomic: CATTGGCTGCTCTTTCATCTGCATTCAACCCATCTTCCCAAAAGAATAAGgtattgttaa ... ttctttttagGGTAATGATAGGCCTAAAAGCTCTGATGGTGGACCCACTCAGCGCGCTTCA
EST: gi|38568672|gb|CD670887.1|CD670887
EST:     CATTGGCTGCTCTTTCATCTGCATTCAACCCATCTTCCCAAAAGAATAAG                         GGTAATGATAGGCCTAAAAGCTCTGATGGTGGACCCACTCAGCGCGCTTCA
genomic: CATTGGCTGCTCTTTCATCTGCATTCAACCCATCTTCCCAAAAGAATAAGgtattgttaa ... ttctttttagGGTAATGATAGGCCTAAAAGCTCTGATGGTGGACCCACTCAGCGCGCTTCA
EST: gi|396941448|gb|HO188657.1|HO188657
EST:     CATTGGCTGCTCTTTCATCTGCATTCAACCCATCTTCCCAAAAGAATAAG                         GGTAATGATAGGCCTAAAAGCTCTGATGGTGGACCCACTCAGCGCGCTTCA
genomic: CATTGGCTGCTCTTTCATCTGCATTCAACCCATCTTCCCAAAAGAATAAGgtattgttaa ... ttctttttagGGTAATGATAGGCCTAAAAGCTCTGATGGTGGACCCACTCAGCGCGCTTCA
EST: gi|29669712|gb|CB665987.1|CB665987
EST:     CATTGGCTGCTCTTTCATCTGCATTCAACCCATCTTCCCAAAAGAATAAG                         GGTAATGATAGGCCTAAAAGCTCTGATGGTGGACCCACTCAGCGCGCTTCA
genomic: CATTGGCTGCTCTTTCATCTGCATTCAACCCATCTTCCCAAAAGAATAAGgtattgttaa ... ttctttttagGGTAATGATAGGCCTAAAAGCTCTGATGGTGGACCCACTCAGCGCGCTTCA
EST: gi|58661440|gb|CK050120.1|CK050120
EST:     CATTGGCTGCTCTTTCGTCTGCATTCAACCCATCTTCCCAAAAGAATAAG                         GGTAATGATAGGCCTAAAAGCTCTGATGGTGGACCCACTCAGCGCGCTTCA
genomic: CATTGGCTGCTCTTTCATCTGCATTCAACCCATCTTCCCAAAAGAATAAGgtattgttaa ... ttctttttagGGTAATGATAGGCCTAAAAGCTCTGATGGTGGACCCACTCAGCGCGCTTCA
EST: gi|38477625|gb|CF961758.1|CF961758
EST:     CATTGGCTGCTCTTTCATCTGCATTCAACCCATCTTCCCAAAAGAATAAG                         GGTAATGATGGGCCTAAAAGCTCTGATGGTGGACCCACTCAGCGCGCTTCA
genomic: CATTGGCTGCTCTTTCATCTGCATTCAACCCATCTTCCCAAAAGAATAAGgtattgttaa ... ttctttttagGGTAATGATAGGCCTAAAAGCTCTGATGGTGGACCCACTCAGCGCGCTTCA
EST: gi|58673715|gb|CK062401.1|CK062401
EST:     CATNGGCTGCTCTTTCATCTGCATTCAACCCATCTTCCCAAAAGAATAAG                         GGTAATGATAGGCCTAAAAGCTCTGATGGTGGACCCACTCAGCGCGCTTCA
genomic: CATTGGCTGCTCTTTCATCTGCATTCAACCCATCTTCCCAAAAGAATAAGgtattgttaa ... ttctttttagGGTAATGATAGGCCTAAAAGCTCTGATGGTGGACCCACTCAGCGCGCTTCA
EST: gi|56157785|gb|C26501.2|C26501
EST:     CATTGGCTGCTCTTTCATCTGCATTCAACCCATCTTCCCAAAAGAATAAG                         GGTAATGATAGGCCTAAAAGCTCTGATGGTGGACCCACTCAAGCGCGCTTT
genomic: CATTGGCTGCTCTTTCATCTGCATTCAACCCATCTTCCCAAAAGAATAAGgtattgttaa ... ttctttttagGGTAATGATAGGCCTAAAAGCTCTGATGGTGGACCCACTCA-GCGCGCTT-
EST: gi|58672631|gb|CK061317.1|CK061317
EST:     CATTGGCTGCTCTTTCATCTGCATTCAACCCATCTTCCCAAAAGAATAAG                         GGTAATGATAGGCCTAAAAGCTCTGATGGTGGACCCACTCAGCGCGCTTCA
genomic: CATTGGCTGCTCTTTCATCTGCATTCAACCCATCTTCCCAAAAGAATAAGgtattgttaa ... ttctttttagGGTAATGATAGGCCTAAAAGCTCTGATGGTGGACCCACTCAGCGCGCTTCA
EST: gi|58612287|gb|CK039999.1|CK039999
EST:     CATTGGCTGCTCTTTCATCTGCATTCAACCCATCTTCCCAAAAGAATAAG                         GGTAATGATAGGCCTAAAAGCTCTGATGGTGGACCCACTCAGCGCGCTTCA
genomic: CATTGGCTGCTCTTTCATCTGCATTCAACCCATCTTCCCAAAAGAATAAGgtattgttaa ... ttctttttagGGTAATGATAGGCCTAAAAGCTCTGATGGTGGACCCACTCAGCGCGCTTCA
EST: gi|58652765|gb|CK041445.1|CK041445
EST:     CATTGGCTGCTCTTTCATCTGAATTCAAACCATCTTCCCAAAAGAATAAG                         GGTAATGATAGGGCTAAAAGCTCTGATGGTGG
genomic: CATTGGCTGCTCTTTCATCTGCATTCAACCCATCTTCCCAAAAGAATAAGgtattgttaa ... ttctttttagGGTAATGATAGGCCTAAAAGCTCTGATGGTGG

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: 71 (upstream exon), 54 (downstream exon)
Score: 64

AGTGGATCTAAGAGTTCAGGTGATGGTGGACCAACTCAGAGGGCATCAGCATTGGCTGCTCTTTCATCTGCATTCAACCCATCTTCCCAAAAGAATAAGgtattgttaa ... ttctttttagGGTAATGATAGGCCTAAAAGCTCTGATGGTGGACCCACTCAGCGCGCTTCAGCAATGGCTGCCTTAACATCAGCGTTCAATCCATCAGCAAAACCCAAAA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaaatataaaatttgttgatcttacaaactataagcaatgttgtgttctttttagGGTAATGATAGGCCTAAAAGCTCTGATGGTGGACCCACTCAGCGCGCTTCAGCAATGGCTGCCTTAACATCAGCGTTCAATCCATCAGCAAAACCCAAAA
                  atcttac  putative branch site (score: 64)
                                           tgttcttttt  putative PPT
     ataaaatttgttgat  TA-rich tract