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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtgttgatagagcaattaacagctccactccgttaagtcagctacgttggaatgctgagttttgtacctgtcatctatttagcataaatgactaaaacactgtacaatcaccttttaaggtataagctaatacccccatcatcatccgtatgctgattatgcagGTCCGGACACACTTTGCAAGACCAAATTGGAAAAAAGTCCTATCTAAAATTGCCTCGAAGCATCCATTTGCTAAGATAG

Basic information

species Zea mays
transcript GRMZM2G138152_T03
intron # 11
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|6031473|gb|AW076375.1|AW076375
EST:     AAGCTTTGAACCATGCAAAGAATGGCGTTGACATTGTCTCTGGAACTAAA                         GTCCGGACACACTTTGCAAGACCAAATTGGAAAAAAGTCCTATCTAAAATT
genomic: AAGCTTTGAACCATGCAAAGAATGGCGTTGACATTGTCTCTGGAACTAAAgtaagtgttg ... gattatgcagGTCCGGACACACTTTGCAAGACCAAATTGGAAAAAAGTCCTATCTAAAATT
EST: gi|60339853|gb|DN206826.1|DN206826
EST:     AAGCTTTGAACCATGCAAAGAATGGCGTTGACATTGTCTCTGGAACTAAA                         GTCCGGACACACTTTGCAAGACCAAATTGGAAAAAAGTCCTATCTAAAATT
genomic: AAGCTTTGAACCATGCAAAGAATGGCGTTGACATTGTCTCTGGAACTAAAgtaagtgttg ... gattatgcagGTCCGGACACACTTTGCAAGACCAAATTGGAAAAAAGTCCTATCTAAAATT

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 4 RNA-Seq libraries.


Block sizes: 41 (upstream exon), 42 (downstream exon)
Score: 29

GAGTGTTTATGAGGAAGGAGATGCTCGGTCAGCGCTCATCACCATGCTTCAAGCTTTGAACCATGCAAAGAATGGCGTTGACATTGTCTCTGGAACTAAAgtaagtgttg ... gattatgcagGTCCGGACACACTTTGCAAGACCAAATTGGAAAAAAGTCCTATCTAAAATTGCCTCGAAGCATCCATTTGCTAAGATAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 36

GAGTGTTTATGAGGAAGGAGATGCTCGGTCAGCGCTCATCACCATGCTTCAAGCTTTGAACCATGCAAAGAATGGCGTTGACATTGTCTCTGGAACTAAAgtaagtgttg ... gattatgcagGTCCGGACACACTTTGCAAGACCAAATTGGAAAAAAGTCCTATCTAAAATTGCCTCGAAGCATCCATTTGCTAAGATAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 64

GAGTGTTTATGAGGAAGGAGATGCTCGGTCAGCGCTCATCACCATGCTTCAAGCTTTGAACCATGCAAAGAATGGCGTTGACATTGTCTCTGGAACTAAAgtaagtgttg ... gattatgcagGTCCGGACACACTTTGCAAGACCAAATTGGAAAAAAGTCCTATCTAAAATTGCCTCGAAGCATCCATTTGCTAAGATAG


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 158

GAGTGTTTATGAGGAAGGAGATGCTCGGTCAGCGCTCATCACCATGCTTCAAGCTTTGAACCATGCAAAGAATGGCGTTGACATTGTCTCTGGAACTAAAgtaagtgttg ... gattatgcagGTCCGGACACACTTTGCAAGACCAAATTGGAAAAAAGTCCTATCTAAAATTGCCTCGAAGCATCCATTTGCTAAGATAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

accttttaaggtataagctaatacccccatcatcatccgtatgctgattatgcagGTCCGGACACACTTTGCAAGACCAAATTGGAAAAAAGTCCTATCTAAAATTGCCTCGAAGCATCCATTTGCTAAGATAG
                                         tgctgat  putative branch site (score: 158)
                                            tgattat  TA-rich tract