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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCAAAGTTTGGGTGTCGCCGTCAGAACGATACGCCATAGTCCCTGACGAGAACgtgagttcgatcagttgacgcgcgtgttgtctgaactctgaagcgaatcgcttaaactgcagcactagttagttacacacacacgcgcgcgtacgagaacactgacagacagagaaaaaagaaaatccgtgtgatgaattcttgccgtgttcgtctgcag

Basic information

species Zea mays
transcript GRMZM2G003565_T02
intron # 11
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|211087172|gb|FL255715.1|FL255715
EST:     AAGTTTGGGTGTCGCCGTCAGAACGATACGCCATAGTCCCTGACGAGAAC                         GTCCGTAAAGCAGGCGGAGGCACGGCACGAGGCAACGGCGCGGACGCGAAC
genomic: AAGTTTGGGTGTCGCCGTCAGAACGATACGCCATAGTCCCTGACGAGAACgtgagttcga ... tcgtctgcagGTCCGTAAAGCAGGCGGAGGCACGGCACGAGGCAACGGCGCCGACGCGAAC
EST: gi|194716840|gb|FK933999.1|FK933999
EST:     AAGTTTGGGTGTCGCCGTCAGAACGATACGCCATTGTCCCTGACGAGAAC                         GTCCGTAAAGCAGGCGGAGGCACGGCACGAGGCAACGGCGCCGACGCGAAC
genomic: AAGTTTGGGTGTCGCCGTCAGAACGATACGCCATAGTCCCTGACGAGAACgtgagttcga ... tcgtctgcagGTCCGTAAAGCAGGCGGAGGCACGGCACGAGGCAACGGCGCCGACGCGAAC
EST: gi|60342864|gb|DN209837.1|DN209837
EST:     AAGTTTGGGTGTCGCCGTCAGAACGATACGCCATAGTCCCTGACGAGAAC                         GTCCGTAAAGCAGGCGGAGGCACGGCACGAGGCAACGGCGCCGACGCGAAC
genomic: AAGTTTGGGTGTCGCCGTCAGAACGATACGCCATAGTCCCTGACGAGAACgtgagttcga ... tcgtctgcagGTCCGTAAAGCAGGCGGAGGCACGGCACGAGGCAACGGCGCCGACGCGAAC
EST: gi|211471127|gb|FL255671.1|FL255671
EST:     AAGTTTGGGTGTCGCCGTCAGAACGATACGCCATAGTCCCTGACGAGAAC                         GTCCGTAAAGCAGGCGGAGGCACGGCACGAGGCAACGGCGCCGACGCGAAC
genomic: AAGTTTGGGTGTCGCCGTCAGAACGATACGCCATAGTCCCTGACGAGAACgtgagttcga ... tcgtctgcagGTCCGTAAAGCAGGCGGAGGCACGGCACGAGGCAACGGCGCCGACGCGAAC
EST: gi|211476174|gb|FL255694.1|FL255694
EST:     AAGTTTGGGTGTCGCCGTCAGAACGATACGCCATTGTCCCTGACGAGAAC                         GTCCGTAAAGCAGGCGGAGGCACGGCACGAGGCAACGGCGCCGACGCGAAC
genomic: AAGTTTGGGTGTCGCCGTCAGAACGATACGCCATAGTCCCTGACGAGAACgtgagttcga ... tcgtctgcagGTCCGTAAAGCAGGCGGAGGCACGGCACGAGGCAACGGCGCCGACGCGAAC
EST: gi|60339276|gb|DN206249.1|DN206249
EST:     AAGTTTGGGTGTCGCCGTCAGAACGATACGCCATAGTCCCTGACGAGAAC                         GTCCGTAAAGCAGGCGGAGGCACGGCACGAGGCAACGGCGCCGACGCGAAC
genomic: AAGTTTGGGTGTCGCCGTCAGAACGATACGCCATAGTCCCTGACGAGAACgtgagttcga ... tcgtctgcagGTCCGTAAAGCAGGCGGAGGCACGGCACGAGGCAACGGCGCCGACGCGAAC

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: 168

CCAAAGTTTGGGTGTCGCCGTCAGAACGATACGCCATAGTCCCTGACGAGAACgtgagttcga ... tcgtctgcagGTCCGTAAAGCAGGCGGAGGCACGGCACGAGGCAACGGCGCCGACGCGAACGTGCCGGAGAACGACGTGAAGAGGATGCGCGTGCAGTCGTCGTAGTAGG


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 86

CCAAAGTTTGGGTGTCGCCGTCAGAACGATACGCCATAGTCCCTGACGAGAACgtgagttcga ... tcgtctgcagGTCCGTAAAGCAGGCGGAGGCACGGCACGAGGCAACGGCGCCGACGCGAACGTGCCGGAGAACGACGTGAAGAGGATGCGCGTGCAGTCGTCGTAGTAGG


Block sizes: 49 (upstream exon), 44 (downstream exon)
Score: 28

CCAAAGTTTGGGTGTCGCCGTCAGAACGATACGCCATAGTCCCTGACGAGAACgtgagttcga ... tcgtctgcagGTCCGTAAAGCAGGCGGAGGCACGGCACGAGGCAACGGCGCCGACGCGAACGTGCCGGAGAACGACGTGAAGAGGATGCGCGTGCAGTCGTCGTAGTAGG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 239

CCAAAGTTTGGGTGTCGCCGTCAGAACGATACGCCATAGTCCCTGACGAGAACgtgagttcga ... tcgtctgcagGTCCGTAAAGCAGGCGGAGGCACGGCACGAGGCAACGGCGCCGACGCGAACGTGCCGGAGAACGACGTGAAGAGGATGCGCGTGCAGTCGTCGTAGTAGG