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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTCTCCGCGAGGCGCAACGAAGGCACAAAACCCTTACCTCCATCAAACCCTAGCGCTCGTGTCCCCGTTTAGCTCCCGTCGCCGCTACCATGGGCTCAGgtaatccgatccctccgactcgtgggctaaattctctattatttgtggcttgttctcttgcggagaattttttttcttgatcatggatgttatggtgattag

Basic information

species Zea mays
transcript GRMZM2G132804_T01
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|31664621|gb|CD573554.1|CD573554
EST:     CTAGCGCTCGTGTCCCCGTTTAGCTCCCGTCGCCGCTACCATGGGCTCAG                         ATGCGGATATGGAGGACTACGGGTTCGAGTACTCAGACGAGGAGCCGGAGG
genomic: CTAGCGCTCGTGTCCCCGTTTAGCTCCCGTCGCCGCTACCATGGGCTCAGgtaatccgat ... tggtgattagATGCGGATATGGAGGACTACGGGTTCGAGTACTCAGACGAGGAGCCGGAGG
EST: gi|29946668|gb|CB816265.1|CB816265
EST:     CTAGCGCTCGTGTCCCCGTTTAGCTCCCGTCGCCGCTACCATGGGCTCAG                         ATGCGGATATGGAGGACTACGGGTTCGAGTACTCAGACGAGGAGCCGGAGG
genomic: CTAGCGCTCGTGTCCCCGTTTAGCTCCCGTCGCCGCTACCATGGGCTCAGgtaatccgat ... tggtgattagATGCGGATATGGAGGACTACGGGTTCGAGTACTCAGACGAGGAGCCGGAGG
EST: gi|211131141|gb|FL290028.1|FL290028
EST:     CTAGCGCTCGTGTCCCCGTTTTGCTCCCGTCGCCGCTACCATGGGCTCAG                         ATGCGGATATGGAGGACTACGGGTTCGAGTACTCAGACGAGGAGCCGGAGG
genomic: CTAGCGCTCGTGTCCCCGTTTAGCTCCCGTCGCCGCTACCATGGGCTCAGgtaatccgat ... tggtgattagATGCGGATATGGAGGACTACGGGTTCGAGTACTCAGACGAGGAGCCGGAGG
EST: gi|29946544|gb|CB816202.1|CB816202
EST:     CTAGCGCTCG-GTCCCCGTTTAGCT-CCGTCGCCGCTACCATGGGCTCAG                         ATGCGGATATGGAGGACTACGGGTTCGAGTACTCAGACGAGGAGCCGGAGG
genomic: CTAGCGCTCGTGTCCCCGTTTAGCTCCCGTCGCCGCTACCATGGGCTCAGgtaatccgat ... tggtgattagATGCGGATATGGAGGACTACGGGTTCGAGTACTCAGACGAGGAGCCGGAGG
EST: gi|211131142|gb|FL290029.1|FL290029
EST:     CTAGCGCTCGTGTCCCCGTTTTGCTCCCGTCGCCGCTACCATGGGCTCAG                         ATGCGGATATGGAGGACTACGGGTTCGAGTACTCAGACGAGGAGCCGGAGG
genomic: CTAGCGCTCGTGTCCCCGTTTAGCTCCCGTCGCCGCTACCATGGGCTCAGgtaatccgat ... tggtgattagATGCGGATATGGAGGACTACGGGTTCGAGTACTCAGACGAGGAGCCGGAGG

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), 49 (downstream exon)
Score: 156

GTTCTCCGCGAGGCGCAACGAAGGCACAAAACCCTTACCTCCATCAAACCCTAGCGCTCGTGTCCCCGTTTAGCTCCCGTCGCCGCTACCATGGGCTCAGgtaatccgat ... tggtgattagATGCGGATATGGAGGACTACGGGTTCGAGTACTCAGACGAGGAGCCGGAGGAGCAGGATGTCGATATCGAGAACCAGTATTACAACTCTAAAG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 82

GTTCTCCGCGAGGCGCAACGAAGGCACAAAACCCTTACCTCCATCAAACCCTAGCGCTCGTGTCCCCGTTTAGCTCCCGTCGCCGCTACCATGGGCTCAGgtaatccgat ... tggtgattagATGCGGATATGGAGGACTACGGGTTCGAGTACTCAGACGAGGAGCCGGAGGAGCAGGATGTCGATATCGAGAACCAGTATTACAACTCTAAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 55

GTTCTCCGCGAGGCGCAACGAAGGCACAAAACCCTTACCTCCATCAAACCCTAGCGCTCGTGTCCCCGTTTAGCTCCCGTCGCCGCTACCATGGGCTCAGgtaatccgat ... tggtgattagATGCGGATATGGAGGACTACGGGTTCGAGTACTCAGACGAGGAGCCGGAGGAGCAGGATGTCGATATCGAGAACCAGTATTACAACTCTAAAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 68

GTTCTCCGCGAGGCGCAACGAAGGCACAAAACCCTTACCTCCATCAAACCCTAGCGCTCGTGTCCCCGTTTAGCTCCCGTCGCCGCTACCATGGGCTCAGgtaatccgat ... tggtgattagATGCGGATATGGAGGACTACGGGTTCGAGTACTCAGACGAGGAGCCGGAGGAGCAGGATGTCGATATCGAGAACCAGTATTACAACTCTAAAG