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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttggcaatgaaaaatatagagcacctcaactaactgaagttgatttagcttaaattagaacaacttgttgacttatgctggatacatttatgcattgcagGGTCGTGGAGGACCAGGGATGGCATCTAATGTTGGTTGGTTTTTTTTGTTCACCATTTAGTTTATGTATATTCTTTCAATTTCTATGCGTATTTTATGTT

Basic information

species Zea mays
transcript GRMZM2G096480_T03
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|211352084|gb|FL106817.1|FL106817
EST:     TGTTGATTTTGCTGAAAGNTGG-AGGA-CACTGATAGAA-TANAGAAAAG                         GNTCGTGGGAGGACCAGG-ATGGCATCTAATG
genomic: TGTTGATTTTGCTGAAAG-TGGGAGGAACACTGATAGAAATAGAGAAAAGgtcgacaatc ... tgcattgcagGGTCGTGG-AGGACCAGGGATGGCATCTAATG
EST: gi|211354488|gb|FL106828.1|FL106828
EST:     GTGTTGATTTTGCTGAAAGTGGGAGGAACACTGATAGAAATAGAGAAAAG                         GGTCGTGGAGGACCAGGGATGGCATCTAATGGTTGGTTTGGNNNNNNNNGT
genomic: GTGTTGATTTTGCTGAAAGTGGGAGGAACACTGATAGAAATAGAGAAAAGgtcgacaatc ... tgcattgcagGGTCGTGGAGGACCAGGGATGGCATCTAATG-TTGGTT-GGTTTTTTTTGT
EST: gi|211354485|gb|FL106825.1|FL106825
EST:     GTGTTGATTTTGCTGAAAGTGGGAGGAACACTGATAGAAATAGAGAAAAG                         GGTCGTGGAGGACCAGGGATGGCATCTAATGTTG
genomic: GTGTTGATTTTGCTGAAAGTGGGAGGAACACTGATAGAAATAGAGAAAAGgtcgacaatc ... tgcattgcagGGTCGTGGAGGACCAGGGATGGCATCTAATGTTG

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: 38 (upstream exon), 45 (downstream exon)
Score: 24

AAGTGCACGCCGGAACCTTCAGGGTTACGAGATTAATGGTCGTCAGTTACGTGTTGATTTTGCTGAAAGTGGGAGGAACACTGATAGAAATAGAGAAAAGgtcgacaatc ... tgcattgcagGGTCGTGGAGGACCAGGGATGGCATCTAATGTTGGTTGGTTTTTTTTGTTCACCATTTAGTTTATGTATATTCTTTCAATTTCTATGCGTATTTTATGTT


Block sizes: 49 (upstream exon), 34 (downstream exon)
Score: 27

AAGTGCACGCCGGAACCTTCAGGGTTACGAGATTAATGGTCGTCAGTTACGTGTTGATTTTGCTGAAAGTGGGAGGAACACTGATAGAAATAGAGAAAAGgtcgacaatc ... tgcattgcagGGTCGTGGAGGACCAGGGATGGCATCTAATGTTGGTTGGTTTTTTTTGTTCACCATTTAGTTTATGTATATTCTTTCAATTTCTATGCGTATTTTATGTT


Block sizes: 49 (upstream exon), 35 (downstream exon)
Score: 22

AAGTGCACGCCGGAACCTTCAGGGTTACGAGATTAATGGTCGTCAGTTACGTGTTGATTTTGCTGAAAGTGGGAGGAACACTGATAGAAATAGAGAAAAGgtcgacaatc ... tgcattgcagGGTCGTGGAGGACCAGGGATGGCATCTAATGTTGGTTGGTTTTTTTTGTTCACCATTTAGTTTATGTATATTCTTTCAATTTCTATGCGTATTTTATGTT


Block sizes: 49 (upstream exon), 34 (downstream exon)
Score: 33

AAGTGCACGCCGGAACCTTCAGGGTTACGAGATTAATGGTCGTCAGTTACGTGTTGATTTTGCTGAAAGTGGGAGGAACACTGATAGAAATAGAGAAAAGgtcgacaatc ... tgcattgcagGGTCGTGGAGGACCAGGGATGGCATCTAATGTTGGTTGGTTTTTTTTGTTCACCATTTAGTTTATGTATATTCTTTCAATTTCTATGCGTATTTTATGTT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tagcttaaattagaacaacttgttgacttatgctggatacatttatgcattgcagGGTCGTGGAGGACCAGGGATGGCATCTAATGTTGGTTGGTTTTTTTTGTTCACCATTTAGTTTATGTATATTCTTTCAATTTCTATGCGTATTTTATGTT
                    tgttgac  putative branch site (score: 33)
     taaattagaa  TA-rich tract