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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCGGTTACTTCATGTTTAAAGGTCTCAGTAGGGGCTGAGCAAAGTGAGTTGGCCCAAACATGTGCTCCGAGGCTCACCACCAAGTTTTGGCAGAACTGGAgtaagcaatcgtcacagctcttactgatctgcagtacttccagaattcgtattgatgctgtctctcctgcag

Basic information

species Zea mays
transcript GRMZM2G147430_T01
intron # 12
splice site 5'
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|32916804|gb|CF021616.1|CF021616
EST:     GGCCCAAACATGTGCTCCGAGGCTCACCACCAAGTTTTGGCAGAACTGGA                         GCTAAAGGAAGACAGTTCTCGCACCGTTTACATCAGGAAGGTCATATCTAA
genomic: GGCCCAAACATGTGCTCCGAGGCTCACCACCAAGTTTTGGCAGAACTGGAgtaagcaatc ... tctcctgcagGCTAAAGGAAGACAGTTCTTGAACCGTTTACATCAGGAAGATCATATCTAA
EST: gi|32944474|gb|CF049293.1|CF049293
EST:     GGCCCAAACATGTGCTCCGAGGCTCACCACCAAGTTTTGGCAGAACTGGA                         GCTAAAGGAAGACAGTTCTCGCACCGTTTACATCAGGAAGGTCATATCTAA
genomic: GGCCCAAACATGTGCTCCGAGGCTCACCACCAAGTTTTGGCAGAACTGGAgtaagcaatc ... tctcctgcagGCTAAAGGAAGACAGTTCTTGAACCGTTTACATCAGGAAGATCATATCTAA
EST: gi|32867031|gb|CF006713.1|CF006713
EST:     GGCCCAAACATGTGCTCCGAGGCTCACCACCAAGTTTTGGCAGAACTGGA                         GCTAAAGGAAGACAGTTCTCGCACCGTTTACATCAGGAAGGTCATATCTAA
genomic: GGCCCAAACATGTGCTCCGAGGCTCACCACCAAGTTTTGGCAGAACTGGAgtaagcaatc ... tctcctgcagGCTAAAGGAAGACAGTTCTTGAACCGTTTACATCAGGAAGATCATATCTAA
EST: gi|32945047|gb|CF049866.1|CF049866
EST:     GGCCCAAACATGTGCTCCGAGGCTCACCACCAAGTTTTGGCAGAACTGGA                         GCTAAAGGAAGACAGTTCTCGCACCGTTTACATCAGGAAGGTCATATCTAA
genomic: GGCCCAAACATGTGCTCCGAGGCTCACCACCAAGTTTTGGCAGAACTGGAgtaagcaatc ... tctcctgcagGCTAAAGGAAGACAGTTCTTGAACCGTTTACATCAGGAAGATCATATCTAA
EST: gi|71324133|gb|DR798766.1|DR798766
EST:     GGCCCAAACATGTGTTCCGAGGCTCCCCACCAAGTTTTGGCAGAACTGGA                         GCTAAAGGAAGACAGTTCTTGAACCGTTTACTTCAGGAAGATCATATCTAA
genomic: GGCCCAAACATGTGCTCCGAGGCTCACCACCAAGTTTTGGCAGAACTGGAgtaagcaatc ... tctcctgcagGCTAAAGGAAGACAGTTCTTGAACCGTTTACATCAGGAAGATCATATCTAA
EST: gi|32867088|gb|CF006770.1|CF006770
EST:     GGCCCAAACATGTGCTCCGAGGCTCACCACCAAGTTTTGGCAGAACTGGA                         GCTAAAGGAAGACAGTTCTCGCACCGTTTACATCAGGAAGGTCATATCTAA
genomic: GGCCCAAACATGTGCTCCGAGGCTCACCACCAAGTTTTGGCAGAACTGGAgtaagcaatc ... tctcctgcagGCTAAAGGAAGACAGTTCTTGAACCGTTTACATCAGGAAGATCATATCTAA
EST: gi|93281686|gb|EB673950.1|EB673950
EST:     GGCCCAAACATGTGCTCCGAGGCTCACCACCAAGTTTTGGCAGAACTGGA                         GCTAAAGGAAGACAGTTCTTGAACCGTTTACATCAGGAAGATCATATCTAA
genomic: GGCCCAAACATGTGCTCCGAGGCTCACCACCAAGTTTTGGCAGAACTGGAgtaagcaatc ... tctcctgcagGCTAAAGGAAGACAGTTCTTGAACCGTTTACATCAGGAAGATCATATCTAA
EST: gi|6681786|gb|AW287773.1|AW287773
EST:     GGCCCAAACATGTGCTCCGAGGCTCACCACCAAGTTTTGGCAGAACTGGA                         GCTAAAGGAAGACAGTTCTTGAACCGTTTACATCAGGAAGATCATATCTAA
genomic: GGCCCAAACATGTGCTCCGAGGCTCACCACCAAGTTTTGGCAGAACTGGAgtaagcaatc ... tctcctgcagGCTAAAGGAAGACAGTTCTTGAACCGTTTACATCAGGAAGATCATATCTAA
EST: gi|76292208|gb|DV031776.1|DV031776
EST:     GGCCCAAACATGTGCTCCGAGGCTCACCACCAAGTTTTGGCAGAACTGGA                         GCTAAAGGAAGACAGTTCTTGAACCGTTTACATCAGGAAGATCATATCTAA
genomic: GGCCCAAACATGTGCTCCGAGGCTCACCACCAAGTTTTGGCAGAACTGGAgtaagcaatc ... tctcctgcagGCTAAAGGAAGACAGTTCTTGAACCGTTTACATCAGGAAGATCATATCTAA
EST: gi|60358530|gb|DN225503.1|DN225503
EST:     GGCCCAAACATGTGCTCCGAGGCTCACCACCAAGTTTTGGCAGAACTGGA                         GCTAAAGGAAGACAGTTCTTGAACCGTTTACATCAGGAAGATCATATCTAA
genomic: GGCCCAAACATGTGCTCCGAGGCTCACCACCAAGTTTTGGCAGAACTGGAgtaagcaatc ... tctcctgcagGCTAAAGGAAGACAGTTCTTGAACCGTTTACATCAGGAAGATCATATCTAA

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), 40 (downstream exon)
Score: 32

TCGGTTACTTCATGTTTAAAGGTCTCAGTAGGGGCTGAGCAAAGTGAGTTGGCCCAAACATGTGCTCCGAGGCTCACCACCAAGTTTTGGCAGAACTGGAgtaagcaatc ... tctcctgcagGCTAAAGGAAGACAGTTCTTGAACCGTTTACATCAGGAAGATCATATCTAACAGCTTACGGTCTTATTAAGACAGGTAAACCTATATACCAGCACATGGA


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

TCGGTTACTTCATGTTTAAAGGTCTCAGTAGGGGCTGAGCAAAGTGAGTTGGCCCAAACATGTGCTCCGAGGCTCACCACCAAGTTTTGGCAGAACTGGAgtaagcaatc ... tctcctgcagGCTAAAGGAAGACAGTTCTTGAACCGTTTACATCAGGAAGATCATATCTAACAGCTTACGGTCTTATTAAGACAGGTAAACCTATATACCAGCACATGGA


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

TCGGTTACTTCATGTTTAAAGGTCTCAGTAGGGGCTGAGCAAAGTGAGTTGGCCCAAACATGTGCTCCGAGGCTCACCACCAAGTTTTGGCAGAACTGGAgtaagcaatc ... tctcctgcagGCTAAAGGAAGACAGTTCTTGAACCGTTTACATCAGGAAGATCATATCTAACAGCTTACGGTCTTATTAAGACAGGTAAACCTATATACCAGCACATGGA


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 21

TCGGTTACTTCATGTTTAAAGGTCTCAGTAGGGGCTGAGCAAAGTGAGTTGGCCCAAACATGTGCTCCGAGGCTCACCACCAAGTTTTGGCAGAACTGGAgtaagcaatc ... tctcctgcagGCTAAAGGAAGACAGTTCTTGAACCGTTTACATCAGGAAGATCATATCTAACAGCTTACGGTCTTATTAAGACAGGTAAACCTATATACCAGCACATGGA