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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGGCTCGGTCGCTTCGCCACCTCCGTCCTCCCCCCGCGCTCGGTCGCTCGCCACCTGCTCTCCCCTCCCTCCACGTTGCTCGCGCCCGCGCTTATATAAGgtacgccgcctcgactctccaaacccctccgcgtggacctaaggtccggcgcgccgagatggagctgatggatctagggtttcggttgcggcggcggtcctgtag

Basic information

species Zea mays
transcript GRMZM2G064426_T02
intron # 1
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|31664551|gb|CD573484.1|CD573484
EST:     CCACCTGCTCTCCCCTCCCTCCACGTTGCTCGCGCCCGCGCTTATATAAG                         TGCAGGAGGAGCTCATGGCGGACGCTCCGGCGAGCCCTGGGGGCGGAGGCG
genomic: CCACCTGCTCTCCCCTCCCTCCACGTTGCTCGCGCCCGCGCTTATATAAGgtacgccgcc ... ggtcctgtagTGCAGGAGGAGCTCATGGCGGACGCTCCGGCGAGCCCTGGGGGCGGAGGCG
EST: gi|211326581|gb|FL327335.1|FL327335
EST:     CCACCTGCTCTCCCCTCCCTCCACGTTGCTCGCGCCCGCGCTTATATAAG                         TGCAGGAGGAGCTCATGGCGGACGCTCCGGCGAGCCCTGGGGGCGGAGGCG
genomic: CCACCTGCTCTCCCCTCCCTCCACGTTGCTCGCGCCCGCGCTTATATAAGgtacgccgcc ... ggtcctgtagTGCAGGAGGAGCTCATGGCGGACGCTCCGGCGAGCCCTGGGGGCGGAGGCG
EST: gi|211038566|gb|FL344527.1|FL344527
EST:     CCACCTGCTCTCCCCTCCCTCCACGTTGCTCGCGCCCGCGCTTATATAAG                         TGCAGGAGGAGCTCATGGCGGATGCTCCGGCGAGCCCTGGGGGCGGCGGCG
genomic: CCACCTGCTCTCCCCTCCCTCCACGTTGCTCGCGCCCGCGCTTATATAAGgtacgccgcc ... ggtcctgtagTGCAGGAGGAGCTCATGGCGGACGCTCCGGCGAGCCCTGGGGGCGGAGGCG
EST: gi|211259760|gb|FL311703.1|FL311703
EST:     CCACCTGCTCTCCCCTCCCTCCACGTTGCTCGCGCCCGCGCTTATATAAG                         TGCAGGAGGAGCTCATGGCGGATGCTCCGGCGAGCCCTGGGGGCGGCGGCG
genomic: CCACCTGCTCTCCCCTCCCTCCACGTTGCTCGCGCCCGCGCTTATATAAGgtacgccgcc ... ggtcctgtagTGCAGGAGGAGCTCATGGCGGACGCTCCGGCGAGCCCTGGGGGCGGAGGCG
EST: gi|211260502|gb|FL345526.1|FL345526
EST:     CCACCTGCTCTCCCCTCCCTCCACGTTGCTCGCGCCCGCGCTTATATAAG                         TGCAGGAGGAGCTCATGGCGGATGCTCCGGCGAGCCCTGGGGGCGGCGGCG
genomic: CCACCTGCTCTCCCCTCCCTCCACGTTGCTCGCGCCCGCGCTTATATAAGgtacgccgcc ... ggtcctgtagTGCAGGAGGAGCTCATGGCGGACGCTCCGGCGAGCCCTGGGGGCGGAGGCG
EST: gi|29543654|gb|CB604034.1|CB604034
EST:     CCACCTGCTCTCCCCTCCCTCCACGTTGCTCGCGCCCGCGCTTATATAAG                         TGCAGGAGGAGCTCATGGCGGACGCTCCGGCGAGCCCTGGGGGCGGAGGCG
genomic: CCACCTGCTCTCCCCTCCCTCCACGTTGCTCGCGCCCGCGCTTATATAAGgtacgccgcc ... ggtcctgtagTGCAGGAGGAGCTCATGGCGGACGCTCCGGCGAGCCCTGGGGGCGGAGGCG
EST: gi|71446912|gb|DR827962.1|DR827962
EST:     CCACCTGCTCTCCCCTCCCTCCACGTTGCTCGCGCCCGCGCTTATATAAG                         TGCAGGAGGAGCTCATGGCGGACGCTCCGGCGAGCCCTGGGGGCGGAGGCG
genomic: CCACCTGCTCTCCCCTCCCTCCACGTTGCTCGCGCCCGCGCTTATATAAGgtacgccgcc ... ggtcctgtagTGCAGGAGGAGCTCATGGCGGACGCTCCGGCGAGCCCTGGGGGCGGAGGCG
EST: gi|211272416|gb|FL334356.1|FL334356
EST:     CCACCTGCTCTCCCCTCCCTCCACGTTGCTCGCGCCCGCGCTTATATAAG                         TGCAGGAGGAGCTCATGGCGNACGCTCCGGCGAGCCCTGGGGGCGNAGGCG
genomic: CCACCTGCTCTCCCCTCCCTCCACGTTGCTCGCGCCCGCGCTTATATAAGgtacgccgcc ... ggtcctgtagTGCAGGAGGAGCTCATGGCGGACGCTCCGGCGAGCCCTGGGGGCGGAGGCG
EST: gi|149102150|gb|EE287580.2|EE287580
EST:     CCACCTGCTCTCCCCTCCCTCCACGTTGCTCGCGCCCGCGCTTATATAAG                         TGCAGGAGGAGCTCATGGCGGACGCTCCGGCGAGCCCTGGGGGCGGAGGCG
genomic: CCACCTGCTCTCCCCTCCCTCCACGTTGCTCGCGCCCGCGCTTATATAAGgtacgccgcc ... ggtcctgtagTGCAGGAGGAGCTCATGGCGGACGCTCCGGCGAGCCCTGGGGGCGGAGGCG
EST: gi|211533900|gb|FL308309.1|FL308309
EST:     CCACCTGCTCTCCCCTCCCTCCACGTTGCTCGCGCCCGCGCTTATATAAG                         TGCAGGAGGAGCTCATGGCGGATGCTCCGGCGAGCCCTGAGGGCGGCGGCG
genomic: CCACCTGCTCTCCCCTCCCTCCACGTTGCTCGCGCCCGCGCTTATATAAGgtacgccgcc ... ggtcctgtagTGCAGGAGGAGCTCATGGCGGACGCTCCGGCGAGCCCTGGGGGCGGAGGCG
EST: gi|211009572|gb|FL317976.1|FL317976
EST:     CCACCTGCTCTCCCCTCCCTCCACGTTGCTCGCGCCCGCGCTTATATAAG                         TGCAGGAGGAGCTCATGGCGGATGCTCCGGCGAGCCCTGGGGG-SGCGGCG
genomic: CCACCTGCTCTCCCCTCCCTCCACGTTGCTCGCGCCCGCGCTTATATAAGgtacgccgcc ... ggtcctgtagTGCAGGAGGAGCTCATGGCGGACGCTCCGGCGAGCCCTGGGGGCGGAGGCG
EST: gi|149107729|gb|EE189603.2|EE189603
EST:     CCACCTGCTCTCCCCTCCCTCCACGTTGCTCGCGCCCGCGCTTATATAAG                         TGCAGGAGGAGCTCATGGCGGACGCTCCGGCGAGCCCTGGGGGCGGAGGCG
genomic: CCACCTGCTCTCCCCTCCCTCCACGTTGCTCGCGCCCGCGCTTATATAAGgtacgccgcc ... ggtcctgtagTGCAGGAGGAGCTCATGGCGGACGCTCCGGCGAGCCCTGGGGGCGGAGGCG
EST: gi|37418186|gb|CF646760.1|CF646760
EST:     CCACCTGCTCTCCCCTCCCTCCACGTTGCTCGCGCCCGCGCTTATATAAG                         TGCAGGAGGAGCTCATGGCGGACGCTCCGGCGAGCCCTGGGGGCGGAGGCG
genomic: CCACCTGCTCTCCCCTCCCTCCACGTTGCTCGCGCCCGCGCTTATATAAGgtacgccgcc ... ggtcctgtagTGCAGGAGGAGCTCATGGCGGACGCTCCGGCGAGCCCTGGGGGCGGAGGCG
EST: gi|211255094|gb|FL319900.1|FL319900
EST:     CCACCTGCTCTCCCCTCCCTCCACGTTGCTCGCGCCCGCGCTTATATAAG                         TGCAGGAGGAGCTCATGGCGGACGCTCCGGCGAGCCCTGGGGGCGGAGGCG
genomic: CCACCTGCTCTCCCCTCCCTCCACGTTGCTCGCGCCCGCGCTTATATAAGgtacgccgcc ... ggtcctgtagTGCAGGAGGAGCTCATGGCGGACGCTCCGGCGAGCCCTGGGGGCGGAGGCG
EST: gi|76930838|gb|DV172525.1|DV172525
EST:     CCACCTGCTCTCCCCTCCCTCCACGTTGCTCGCGCCCGCGCTTATATAAG                         TGCAGGAGGAGCTCATGGCGGACGCTCCGGCGAGCCCTGGGGGCGGAGGCG
genomic: CCACCTGCTCTCCCCTCCCTCCACGTTGCTCGCGCCCGCGCTTATATAAGgtacgccgcc ... ggtcctgtagTGCAGGAGGAGCTCATGGCGGACGCTCCGGCGAGCCCTGGGGGCGGAGGCG
EST: gi|211354847|gb|FL354346.1|FL354346
EST:     CCACCTGCTCTCCCCTCCCTCCACGTTGCTCGCGCCCGCGCTTATATAAG                         TGCAGGAGGAGCTCATGGCGGATGCTCCGGCGAGCCCTGGGGGCGGCGGCG
genomic: CCACCTGCTCTCCCCTCCCTCCACGTTGCTCGCGCCCGCGCTTATATAAGgtacgccgcc ... ggtcctgtagTGCAGGAGGAGCTCATGGCGGACGCTCCGGCGAGCCCTGGGGGCGGAGGCG
EST: gi|26557696|gb|CA829931.1|CA829931
EST:     CCACCTGCTCTCCCCTCCCTCCACGTTGCTCGCGCCCGCGCTTATATAAG                         TGCAGGAGGAGCTCATGGCGGACGCTCCGGCGAGCCCTGGGGGCGGAGGCG
genomic: CCACCTGCTCTCCCCTCCCTCCACGTTGCTCGCGCCCGCGCTTATATAAGgtacgccgcc ... ggtcctgtagTGCAGGAGGAGCTCATGGCGGACGCTCCGGCGAGCCCTGGGGGCGGAGGCG

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: 47 (upstream exon), 48 (downstream exon)
Score: 64

CGGCTCGGTCGCTTCGCCACCTCCGTCCTCCCCCCGCGCTCGGTCGCTCGCCACCTGCTCTCCCCTCCCTCCACGTTGCTCGCGCCCGCGCTTATATAAGgtacgccgcc ... ggtcctgtagTGCAGGAGGAGCTCATGGCGGACGCTCCGGCGAGCCCTGGGGGCGGAGGCGGGAGCCACGAGAGCGGGAGCCCCAGGGGCGGCGGAGGTGGAGGCGGTGG


Block sizes: 47 (upstream exon), 41 (downstream exon)
Score: 29

CGGCTCGGTCGCTTCGCCACCTCCGTCCTCCCCCCGCGCTCGGTCGCTCGCCACCTGCTCTCCCCTCCCTCCACGTTGCTCGCGCCCGCGCTTATATAAGgtacgccgcc ... ggtcctgtagTGCAGGAGGAGCTCATGGCGGACGCTCCGGCGAGCCCTGGGGGCGGAGGCGGGAGCCACGAGAGCGGGAGCCCCAGGGGCGGCGGAGGTGGAGGCGGTGG


Block sizes: 49 (upstream exon), 40 (downstream exon)
Score: 25

CGGCTCGGTCGCTTCGCCACCTCCGTCCTCCCCCCGCGCTCGGTCGCTCGCCACCTGCTCTCCCCTCCCTCCACGTTGCTCGCGCCCGCGCTTATATAAGgtacgccgcc ... ggtcctgtagTGCAGGAGGAGCTCATGGCGGACGCTCCGGCGAGCCCTGGGGGCGGAGGCGGGAGCCACGAGAGCGGGAGCCCCAGGGGCGGCGGAGGTGGAGGCGGTGG


Block sizes: 46 (upstream exon), 48 (downstream exon)
Score: 13

CGGCTCGGTCGCTTCGCCACCTCCGTCCTCCCCCCGCGCTCGGTCGCTCGCCACCTGCTCTCCCCTCCCTCCACGTTGCTCGCGCCCGCGCTTATATAAGgtacgccgcc ... ggtcctgtagTGCAGGAGGAGCTCATGGCGGACGCTCCGGCGAGCCCTGGGGGCGGAGGCGGGAGCCACGAGAGCGGGAGCCCCAGGGGCGGCGGAGGTGGAGGCGGTGG