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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgttcttcctctggctgctcccaagccttcctttgatgatcgtaggttcattcagtgctgcattctgcgagttttcttctcaagtttcctttgaatgcgttttgcagGGACGCGAGGCAAAGCTGCTTCGAAGTGAAGTGTTGACTGAAAGCAGCGGTGCATGGTTGGTTTGGGAAAGCGAACGGACTAATCAGTTTTAGAATGCTT

Basic information

species Zea mays
transcript GRMZM2G357972_T02
intron # 7
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|78544370|gb|DV621868.1|DV621868
EST:     ATTTGAATGCCTGTGCGGAAGCAGATACTGCCGTGGTAGAAAGCATTCGA                         GGACGCGAGGCAAAGCTGCTTCGAAGTGAAGTGTTGACTGAAAGCAGCGGT
genomic: ATTTGAATGCCTGTGCGGAAGCAGATACTGCCGTGGTAGAAAGCATTCGAgtatgttctt ... cgttttgcagGGACGCGAGGCAAAGCTGCTTCGAAGTGAAGTGTTGACTGAAAGCAGCGGT
EST: gi|78125802|gb|DV544186.1|DV544186
EST:     ATTTGAATGCCTGTGCGGAAGCAGATACTGCCGTGGTAGAAAGCATTCGA                         GGACGCGAGGCAAAGCTGCTTCGAAGTGAAGTGTTGACTGAAAGCAGCGGT
genomic: ATTTGAATGCCTGTGCGGAAGCAGATACTGCCGTGGTAGAAAGCATTCGAgtatgttctt ... cgttttgcagGGACGCGAGGCAAAGCTGCTTCGAAGTGAAGTGTTGACTGAAAGCAGCGGT
EST: gi|37386622|gb|CF630499.1|CF630499
EST:     ATTTGAATGCCTGTGCGGAAGCAGATACTGCCGTGGTAGAAAGCATTCGA                         GGACGCGAGGCAAAGCTGCTTCGAAGTGAAGTGTTGACTGAAAGCAGCGGT
genomic: ATTTGAATGCCTGTGCGGAAGCAGATACTGCCGTGGTAGAAAGCATTCGAgtatgttctt ... cgttttgcagGGACGCGAGGCAAAGCTGCTTCGAAGTGAAGTGTTGACTGAAAGCAGCGGT
EST: gi|76926465|gb|DV170878.1|DV170878
EST:     ATTTGAATGCCTGTGCGGAAGCAGATACTGCCGTGGTAGAAAGCATTCGA                         GGACGCGAGGCAAAGCTGCTTCGAAGTGAAGTGTTGACTGAAAGCAGCGGT
genomic: ATTTGAATGCCTGTGCGGAAGCAGATACTGCCGTGGTAGAAAGCATTCGAgtatgttctt ... cgttttgcagGGACGCGAGGCAAAGCTGCTTCGAAGTGAAGTGTTGACTGAAAGCAGCGGT
EST: gi|24767854|gb|CA402990.1|CA402990
EST:     ATTTGAATGCCTGTGCGGAAGCAGATACTGCCGTGGTAGAAAGCATTCGA                         GGACGCGAGGCAAAGCTGCTTCGAAGTGAAGTGTTGACTGAAAGCAGCGGT
genomic: ATTTGAATGCCTGTGCGGAAGCAGATACTGCCGTGGTAGAAAGCATTCGAgtatgttctt ... cgttttgcagGGACGCGAGGCAAAGCTGCTTCGAAGTGAAGTGTTGACTGAAAGCAGCGGT
EST: gi|5296185|gb|AI782865.1|AI782865
EST:     ATTTGAATGCCTGTGCGGAAGCAGATACTGCCGTGGTAGAAAGCATTCGA                         GGACGCGAGGCAAAGCTGCTTCGAAGTGAAGTGTTGACTGAAAGCAGCGGT
genomic: ATTTGAATGCCTGTGCGGAAGCAGATACTGCCGTGGTAGAAAGCATTCGAgtatgttctt ... cgttttgcagGGACGCGAGGCAAAGCTGCTTCGAAGTGAAGTGTTGACTGAAAGCAGCGGT
EST: gi|32931110|gb|CF035922.1|CF035922
EST:     ATTTGAATGCCTGTGCGGAAGCAGATACTGCCGTGGTAGAAAGCATTCGA                         GGACGCGAGGCAAAGCTGCTTCGAAGTGAAGTGTTGACTGCAAGCAGCGAT
genomic: ATTTGAATGCCTGTGCGGAAGCAGATACTGCCGTGGTAGAAAGCATTCGAgtatgttctt ... cgttttgcagGGACGCGAGGCAAAGCTGCTTCGAAGTGAAGTGTTGACTGAAAGCAGCGGT
EST: gi|32796222|gb|CD948458.1|CD948458
EST:     ATTTGAATGCCTGTGCGGAAGCAGATACTGCCGTGGTAGAAAGCATTCGA                         GGACGCGAGGCAAAGCTGCTTCGAAGTGAAGTGTTGACTGCAAGCAGCGAT
genomic: ATTTGAATGCCTGTGCGGAAGCAGATACTGCCGTGGTAGAAAGCATTCGAgtatgttctt ... cgttttgcagGGACGCGAGGCAAAGCTGCTTCGAAGTGAAGTGTTGACTGAAAGCAGCGGT
EST: gi|22541936|gb|BU092374.1|BU092374
EST:     ATTTGAATGCCTGTGCGGAAGCAGATACTGCCGTGGTAGAAAGCCTTCGA                         GGACGCGAGGCAAAGCTGCTTCGAAGTGAAGTGTTGACTGAAAGCAGCGGT
genomic: ATTTGAATGCCTGTGCGGAAGCAGATACTGCCGTGGTAGAAAGCATTCGAgtatgttctt ... cgttttgcagGGACGCGAGGCAAAGCTGCTTCGAAGTGAAGTGTTGACTGAAAGCAGCGGT
EST: gi|5915516|gb|AW053157.1|AW053157
EST:     ATTTGAATGCCTGTGCGGAAGCAGATACTGCCGTGGTAGAAAGCATTCGA                         GGACGCGAGGCAAAGCTGCTTCGAAGTGAAGTGTTGACTGAAAGCAGCGGT
genomic: ATTTGAATGCCTGTGCGGAAGCAGATACTGCCGTGGTAGAAAGCATTCGAgtatgttctt ... cgttttgcagGGACGCGAGGCAAAGCTGCTTCGAAGTGAAGTGTTGACTGAAAGCAGCGGT
EST: gi|50338839|gb|CO533965.1|CO533965
EST:     ATTTGAATGCCTGTGCGGAAGCAGATACTGCCGTGGTAGAAAGCATTCGA                         GGACGCGAGGCAAAGCTGCTTCGAAGTGAAGTGTTGACTGAAAGCAGCGGT
genomic: ATTTGAATGCCTGTGCGGAAGCAGATACTGCCGTGGTAGAAAGCATTCGAgtatgttctt ... cgttttgcagGGACGCGAGGCAAAGCTGCTTCGAAGTGAAGTGTTGACTGAAAGCAGCGGT
EST: gi|12968346|gb|BG265292.1|BG265292
EST:     ATTTGAATGCCTGTGCGGAAGCAGATACTGCCGTGGTAGAAAGCATTCGA                         GGACGCGAGGCAAAGCTGCTTCGAAGTGAAGTGTTGACTGAAAGCAGCGGT
genomic: ATTTGAATGCCTGTGCGGAAGCAGATACTGCCGTGGTAGAAAGCATTCGAgtatgttctt ... cgttttgcagGGACGCGAGGCAAAGCTGCTTCGAAGTGAAGTGTTGACTGAAAGCAGCGGT
EST: gi|76926464|gb|DV170877.1|DV170877
EST:     ATTTGAATGCCTGTGCGGAAGCAGATACTGCCGTGGTAGAAAGCATTCGA                         GGACGCGAGGCAAAGCTGCTTCGAAGTGAAGTGTTGACTGAAAGCAGCGGT
genomic: ATTTGAATGCCTGTGCGGAAGCAGATACTGCCGTGGTAGAAAGCATTCGAgtatgttctt ... cgttttgcagGGACGCGAGGCAAAGCTGCTTCGAAGTGAAGTGTTGACTGAAAGCAGCGGT
EST: gi|78091874|gb|DV520248.1|DV520248
EST:     ATTTGAATGCCTGTGCGGAAGCAGATACTGCCGTGGTAGAAAGCATTCGA                         GGACGCGAGGCAAAGCTGCTTCGAAGTGAAGTGTTGACTGAAAGCAGCGGT
genomic: ATTTGAATGCCTGTGCGGAAGCAGATACTGCCGTGGTAGAAAGCATTCGAgtatgttctt ... cgttttgcagGGACGCGAGGCAAAGCTGCTTCGAAGTGAAGTGTTGACTGAAAGCAGCGGT
EST: gi|166553572|gb|EG289391.1|EG289391
EST:     ATTTGAATGCCTGTGCGGAAGCAGATACTGCCGTGGTAGAAAGCATTCGA                         GGACGCGAGGCAAAGCTGC
genomic: ATTTGAATGCCTGTGCGGAAGCAGATACTGCCGTGGTAGAAAGCATTCGAgtatgttctt ... cgttttgcagGGACGCGAGGCAAAGCTGC

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), 48 (downstream exon)
Score: 133

GATTATGGTATTGATTTTGATGGTGATAAGCATCCTGTCAAATCATTTGAATGCCTGTGCGGAAGCAGATACTGCCGTGGTAGAAAGCATTCGAgtatgttctt ... cgttttgcagGGACGCGAGGCAAAGCTGCTTCGAAGTGAAGTGTTGACTGAAAGCAGCGGTGCATGGTTGGTTTGGGAAAGCGAACGGACTAATCAGTTTTAGAATGCTT


Block sizes: 49 (upstream exon), 44 (downstream exon)
Score: 59

GATTATGGTATTGATTTTGATGGTGATAAGCATCCTGTCAAATCATTTGAATGCCTGTGCGGAAGCAGATACTGCCGTGGTAGAAAGCATTCGAgtatgttctt ... cgttttgcagGGACGCGAGGCAAAGCTGCTTCGAAGTGAAGTGTTGACTGAAAGCAGCGGTGCATGGTTGGTTTGGGAAAGCGAACGGACTAATCAGTTTTAGAATGCTT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 86

GATTATGGTATTGATTTTGATGGTGATAAGCATCCTGTCAAATCATTTGAATGCCTGTGCGGAAGCAGATACTGCCGTGGTAGAAAGCATTCGAgtatgttctt ... cgttttgcagGGACGCGAGGCAAAGCTGCTTCGAAGTGAAGTGTTGACTGAAAGCAGCGGTGCATGGTTGGTTTGGGAAAGCGAACGGACTAATCAGTTTTAGAATGCTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 84

GATTATGGTATTGATTTTGATGGTGATAAGCATCCTGTCAAATCATTTGAATGCCTGTGCGGAAGCAGATACTGCCGTGGTAGAAAGCATTCGAgtatgttctt ... cgttttgcagGGACGCGAGGCAAAGCTGCTTCGAAGTGAAGTGTTGACTGAAAGCAGCGGTGCATGGTTGGTTTGGGAAAGCGAACGGACTAATCAGTTTTAGAATGCTT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cagtgctgcattctgcgagttttcttctcaagtttcctttgaatgcgttttgcagGGACGCGAGGCAAAGCTGCTTCGAAGTGAAGTGTTGACTGAAAGCAGCGGTGCATGGTTGGTTTGGGAAAGCGAACGGACTAATCAGTTTTAGAATGCTT
                   ttttctt  TA-rich tract