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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaggtaatcagcgttagtttaactagagctccgattggaaatccacactactcttttagttagcagctgaaagaatgatgatactgcagGTACCGAAGCAGGTCAAGACACTGAAAATATCCAGGCAGCCACTAACAAAGTGCCTTGCCATGTTGTAGTTAATTTATTTTATAGACTTTTTCATTCCTG

Basic information

species Zea mays
transcript GRMZM2G022061_T05
intron # 12
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|6918688|gb|AW400218.1|AW400218
EST:     TACCGATCCCGCTCGCTCTCCAGTTCCCGGTCGCCCTCTCGCTCTCCAAG                         GTACCGAAGCAGGTCAAGACACTGAAAATATCCAGGCAGCCACTAACAAAG
genomic: TACCGATCCCGCTCGCTCTCCAGTTCCCGGTCGCCCTCTCGCTCTCCAAGgtaggtaatc ... gatactgcagGTACCGAAGCAGGTCAAGACACTGAAAATATCCAGGCAGCCACTAACAAAG
EST: gi|93012252|gb|EB637772.1|EB637772
EST:     TACCGATCCCGCTCGCTCTCCAGTTCCCGGTCGCCCTCTCGCTCTCCAAG                         GTACCGAAGCAGGTCAAGACACTGAAAATATCCAGGCAGCCACTAACAAAG
genomic: TACCGATCCCGCTCGCTCTCCAGTTCCCGGTCGCCCTCTCGCTCTCCAAGgtaggtaatc ... gatactgcagGTACCGAAGCAGGTCAAGACACTGAAAATATCCAGGCAGCCACTAACAAAG
EST: gi|161584781|gb|EY954043.1|EY954043
EST:     CGGTCGCCCTCTCGCTCTCCAAG                         GTACCGAAGCAGGTCAAGACACTGAAAATATCCAGGCAGCCACTAACAAAG
genomic: CGGTCGCCCTCTCGCTCTCCAAGgtaggtaatc ... gatactgcagGTACCGAAGCAGGTCAAGACACTGAAAATATCCAGGCAGCCACTAACAAAG
EST: gi|89250973|gb|DY622759.1|DY622759
EST:     TACCGATCCCGCTCGCTCTCCAGTTCCCGGTCGCCCTCTCGCTCTCCAAG                         GTACCGAAGCAGGTCAAGACACTGAAAATATCCAGGCAGCCACTAACAAAG
genomic: TACCGATCCCGCTCGCTCTCCAGTTCCCGGTCGCCCTCTCGCTCTCCAAGgtaggtaatc ... gatactgcagGTACCGAAGCAGGTCAAGACACTGAAAATATCCAGGCAGCCACTAACAAAG
EST: gi|67024598|gb|CO453347.1|CO453347
EST:     TACCGATCCCGCTCGCTCTCCAGTTCCCGGTCGCCCTCTCGCTCTCCA-G                         GTACCGAAGCANGGTCA-GACACTGAAAATATCCANGCAGCCACTAACAA-
genomic: TACCGATCCCGCTCGCTCTCCAGTTCCCGGTCGCCCTCTCGCTCTCCAAGgtaggtaatc ... gatactgcagGTACCGAAGCA-GGTCAAGACACTGAAAATATCCAGGCAGCCACTAACAAA
EST: gi|37385048|gb|CF629639.1|CF629639
EST:     TACCGATCCCGCTCGCTCTCCAGTTCCCGGTCGCCCTCTCGCTCTCCAAG                         GTACCGAAGCAGGTCAAGACACTGAAAATATCCAGGCAGCCACTAACATAG
genomic: TACCGATCCCGCTCGCTCTCCAGTTCCCGGTCGCCCTCTCGCTCTCCAAGgtaggtaatc ... gatactgcagGTACCGAAGCAGGTCAAGACACTGAAAATATCCAGGCAGCCACTAACAAAG
EST: gi|211251413|gb|FL479559.1|FL479559
EST:     TACCGATCCCGCTCGCTCTCCAGTTCCCGGTCGCCCTCTCGCTCTCCAAG                         GTACCGAAGCAGGTCAAGACACTGAAAATATCCAGGCAGCCACTAACAAAG
genomic: TACCGATCCCGCTCGCTCTCCAGTTCCCGGTCGCCCTCTCGCTCTCCAAGgtaggtaatc ... gatactgcagGTACCGAAGCAGGTCAAGACACTGAAAATATCCAGGCAGCCACTAACAAAG
EST: gi|28987293|gb|CB351559.1|CB351559
EST:     AGTTCCCGGTCGCCCTCTCGCTCTCCAAG                         GTACCGAAGCAGGTCAAGACCCTGAAAATATCCAGGCAGCCCCTAACAAAG
genomic: AGTTCCCGGTCGCCCTCTCGCTCTCCAAGgtaggtaatc ... gatactgcagGTACCGAAGCAGGTCAAGACACTGAAAATATCCAGGCAGCCACTAACAAAG
EST: gi|40335728|gb|CK369798.1|CK369798
EST:     TACCGATCCCGCTCGCTCTCCAGTTCCCGGTCGCCCTCTCGCTCTCCAAG                         GTACCGAAGCAGGTCAAGACACTGAAAATATCCAGGCAGCCACTAACATAG
genomic: TACCGATCCCGCTCGCTCTCCAGTTCCCGGTCGCCCTCTCGCTCTCCAAGgtaggtaatc ... gatactgcagGTACCGAAGCAGGTCAAGACACTGAAAATATCCAGGCAGCCACTAACAAAG
EST: gi|37388853|gb|CF631641.1|CF631641
EST:     TACCGATCCCGCTCGCTCTCCAGTTCCCGGTCGCCCTCTCGCTCTCCAAG                         GTACCGAAGCAGGTCAAGACACTGAAAATATCCAGGCAGCCACTAACAAAG
genomic: TACCGATCCCGCTCGCTCTCCAGTTCCCGGTCGCCCTCTCGCTCTCCAAGgtaggtaatc ... gatactgcagGTACCGAAGCAGGTCAAGACACTGAAAATATCCAGGCAGCCACTAACAAAG
EST: gi|94473364|gb|EB702322.1|EB702322
EST:     TACCGATCCCGCTCGCTCTCCAGTTCCCGGTCGCCCTCTCGCTCTCCAAG                         GTACCGAAGCAGGTCAAGACACTGAAAATATCCAGGCAGCCCCTAACAAAG
genomic: TACCGATCCCGCTCGCTCTCCAGTTCCCGGTCGCCCTCTCGCTCTCCAAGgtaggtaatc ... gatactgcagGTACCGAAGCAGGTCAAGACACTGAAAATATCCAGGCAGCCACTAACAAAG
EST: gi|113777294|gb|DW893575.1|DW893575
EST:     CTCGCTCTCCAGTTCCCGGTCGCCCTCTCGCTCTCCAAG                         GTACCGAAGCAGGTCAAGACACTGAAAATATCCAGGCAGCCACTAACAAAG
genomic: CTCGCTCTCCAGTTCCCGGTCGCCCTCTCGCTCTCCAAGgtaggtaatc ... gatactgcagGTACCGAAGCAGGTCAAGACACTGAAAATATCCAGGCAGCCACTAACAAAG

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: 49 (upstream exon), 43 (downstream exon)
Score: 129

AAGGCGGCGATATAGCAGAAGCCGTAGTAGGAGCAGAAGCCCAAGAAGGTACCGATCCCGCTCGCTCTCCAGTTCCCGGTCGCCCTCTCGCTCTCCAAGgtaggtaatc ... gatactgcagGTACCGAAGCAGGTCAAGACACTGAAAATATCCAGGCAGCCACTAACAAAGTGCCTTGCCATGTTGTAGTTAATTTATTTTATAGACTTTTTCATTCCTG


Block sizes: 46 (upstream exon), 44 (downstream exon)
Score: 73

AAGGCGGCGATATAGCAGAAGCCGTAGTAGGAGCAGAAGCCCAAGAAGGTACCGATCCCGCTCGCTCTCCAGTTCCCGGTCGCCCTCTCGCTCTCCAAGgtaggtaatc ... gatactgcagGTACCGAAGCAGGTCAAGACACTGAAAATATCCAGGCAGCCACTAACAAAGTGCCTTGCCATGTTGTAGTTAATTTATTTTATAGACTTTTTCATTCCTG


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 112

AAGGCGGCGATATAGCAGAAGCCGTAGTAGGAGCAGAAGCCCAAGAAGGTACCGATCCCGCTCGCTCTCCAGTTCCCGGTCGCCCTCTCGCTCTCCAAGgtaggtaatc ... gatactgcagGTACCGAAGCAGGTCAAGACACTGAAAATATCCAGGCAGCCACTAACAAAGTGCCTTGCCATGTTGTAGTTAATTTATTTTATAGACTTTTTCATTCCTG


Block sizes: 44 (upstream exon), 39 (downstream exon)
Score: 56

AAGGCGGCGATATAGCAGAAGCCGTAGTAGGAGCAGAAGCCCAAGAAGGTACCGATCCCGCTCGCTCTCCAGTTCCCGGTCGCCCTCTCGCTCTCCAAGgtaggtaatc ... gatactgcagGTACCGAAGCAGGTCAAGACACTGAAAATATCCAGGCAGCCACTAACAAAGTGCCTTGCCATGTTGTAGTTAATTTATTTTATAGACTTTTTCATTCCTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttggaaatccacactactcttttagttagcagctgaaagaatgatgatactgcagGTACCGAAGCAGGTCAAGACACTGAAAATATCCAGGCAGCCACTAACAAAGTGCCTTGCCATGTTGTAGTTAATTTATTTTATAGACTTTTTCATTCCTG
                   ttttagtta  TA-rich tract