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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTACGCGGCGAACAGgtacgctacatcctacagtgtcctgcaggctgcaggcggcggcagcggtgccaatccggcgaggaaggttcgggattttgtattgacttgactgattgatccggttccgtttggtttttggtggactgcag

Basic information

species Zea mays
transcript GRMZM2G112072_T02
intron # 2
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|22133591|gb|BQ833790.1|BQ833790
EST:     AGTTCTTCGGCTACGCGGCGAACAG                         CATCCTCTACAACCGCGCCGTGTACCCGGGGGAGAGCTTCGCCAAGGTGAA
genomic: AGTTCTTCGGCTACGCGGCGAACAGgtacgctaca ... tggactgcagCATCCTCTACAACCGCGCCGTGTACCCGGGGGAGAGCTTCGCCAAGGTGAA
EST: gi|76285399|gb|DV024967.1|DV024967
EST:     AGTTCTTCGGCTACGCGGCGAACAG                         CATCCTCTACAACCGCGCCGTGTACCCGGGGGAGAGCTTCGCCAAGGTGAA
genomic: AGTTCTTCGGCTACGCGGCGAACAGgtacgctaca ... tggactgcagCATCCTCTACAACCGCGCCGTGTACCCGGGGGAGAGCTTCGCCAAGGTGAA
EST: gi|26558570|gb|CA830805.1|CA830805
EST:     AGTTCTTCGGCTACGCGGCGAACAG                         CATCCTCTACAACCGCGCCGTGTACCCGGGGGAGAGCTTCGCCAAGGTGAA
genomic: AGTTCTTCGGCTACGCGGCGAACAGgtacgctaca ... tggactgcagCATCCTCTACAACCGCGCCGTGTACCCGGGGGAGAGCTTCGCCAAGGTGAA
EST: gi|94479774|gb|EB708732.1|EB708732
EST:     AGTTCTTCGGCTACGCGGCGAACAG                         CATCCTCTACAACCGCGCCGTGTACCCGGGGGAGAGCTTCGCCAAGGTGAA
genomic: AGTTCTTCGGCTACGCGGCGAACAGgtacgctaca ... tggactgcagCATCCTCTACAACCGCGCCGTGTACCCGGGGGAGAGCTTCGCCAAGGTGAA
EST: gi|28909485|gb|CB331838.1|CB331838
EST:     AGTTCTTCGGCTACGCGGCGAACAG                         CATCCTCTACAACCGCGCCGTGTACCCGGGGGAGAGCTTCGCCAAGGTGAA
genomic: AGTTCTTCGGCTACGCGGCGAACAGgtacgctaca ... tggactgcagCATCCTCTACAACCGCGCCGTGTACCCGGGGGAGAGCTTCGCCAAGGTGAA
EST: gi|32790909|gb|CD943145.1|CD943145
EST:     AGTTCTTCGGCTACGCGGCGAACAG                         CATCGTCTACAACCGCGCCGTGTACCCGGGGGAGAGCTTCGCCAAGGTGAA
genomic: AGTTCTTCGGCTACGCGGCGAACAGgtacgctaca ... tggactgcagCATCCTCTACAACCGCGCCGTGTACCCGGGGGAGAGCTTCGCCAAGGTGAA
EST: gi|87155656|gb|DY400445.1|DY400445
EST:     AGTTCTTCGGCTACGCGGCGAACAG                         CATCCTCTACAACCGCGCCGTGTACCCGGGGGAGAGCTTCGCCAAGGTGAA
genomic: AGTTCTTCGGCTACGCGGCGAACAGgtacgctaca ... tggactgcagCATCCTCTACAACCGCGCCGTGTACCCGGGGGAGAGCTTCGCCAAGGTGAA
EST: gi|211074049|gb|FL055815.1|FL055815
EST:     AGTTCTTCGGCTACGCGGCGAACAG                         CATCCTCTACAACCGCGCCGTGTACCCGGGGGAGAGCTTCGCCAAGGTGAA
genomic: AGTTCTTCGGCTACGCGGCGAACAGgtacgctaca ... tggactgcagCATCCTCTACAACCGCGCCGTGTACCCGGGGGAGAGCTTCGCCAAGGTGAA
EST: gi|76937083|gb|DV175029.1|DV175029
EST:     AGTTCTTCGGCTACGCGGCGAACAG                         CATCCTCTACAACCGCGCCGTGTACCCGGGGGAGAGCTTCGCCAAGGTGAA
genomic: AGTTCTTCGGCTACGCGGCGAACAGgtacgctaca ... tggactgcagCATCCTCTACAACCGCGCCGTGTACCCGGGGGAGAGCTTCGCCAAGGTGAA
EST: gi|32800575|gb|CD952811.1|CD952811
EST:     AGTTCTTCGGCTACGCGGCGAACAG                         CATCGTCTACAACCGCGCCGTGTACCCGGGGGAGAGCTTCGCCAAGGTGAA
genomic: AGTTCTTCGGCTACGCGGCGAACAGgtacgctaca ... tggactgcagCATCCTCTACAACCGCGCCGTGTACCCGGGGGAGAGCTTCGCCAAGGTGAA
EST: gi|211074048|gb|FL055814.1|FL055814
EST:     AGTTCTTCGGCTACGCGGCGAACAG                         CATCCTCTACAACCGCGCCGTGTACCCGGGGGAGAGCTTCGCCAAGGTGAA
genomic: AGTTCTTCGGCTACGCGGCGAACAGgtacgctaca ... tggactgcagCATCCTCTACAACCGCGCCGTGTACCCGGGGGAGAGCTTCGCCAAGGTGAA

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: 16 (upstream exon), 48 (downstream exon)
Score: 53

GCTACGCGGCGAACAGgtacgctaca ... tggactgcagCATCCTCTACAACCGCGCCGTGTACCCGGGGGAGAGCTTCGCCAAGGTGAAGAAGTACGGGCTCACCATGCCGCTCACGCAGGACGAGTGGGTTAACTTC


Block sizes: 16 (upstream exon), 30 (downstream exon)
Score: 3

GCTACGCGGCGAACAGgtacgctaca ... tggactgcagCATCCTCTACAACCGCGCCGTGTACCCGGGGGAGAGCTTCGCCAAGGTGAAGAAGTACGGGCTCACCATGCCGCTCACGCAGGACGAGTGGGTTAACTTC


Block sizes: 16 (upstream exon), 43 (downstream exon)
Score: 11

GCTACGCGGCGAACAGgtacgctaca ... tggactgcagCATCCTCTACAACCGCGCCGTGTACCCGGGGGAGAGCTTCGCCAAGGTGAAGAAGTACGGGCTCACCATGCCGCTCACGCAGGACGAGTGGGTTAACTTC


Block sizes: 16 (upstream exon), 28 (downstream exon)
Score: 1

GCTACGCGGCGAACAGgtacgctaca ... tggactgcagCATCCTCTACAACCGCGCCGTGTACCCGGGGGAGAGCTTCGCCAAGGTGAAGAAGTACGGGCTCACCATGCCGCTCACGCAGGACGAGTGGGTTAACTTC