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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTCGATAGAGTTGCCGCATCTGCGCTCAAAGATGTCATTGCTGATTTCTCCCTTGCGCTCTATGAATCTTACAAGACCAGGCAGGAACATGCATCCAGAGgtggttgttcttttcgcttatacttatttcttcatttatccatatcttagtttttaaccacaacaaggaaatctcaacttaactatcatctccgtgcccaattttgttttccttcctttgcag

Basic information

species Zea mays
transcript GRMZM5G824597_T02
intron # 3
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|93012148|gb|EB637668.1|EB637668
EST:     CCTTGCGCTCTATGAATCTTACAAGACCAGGCAGGAACATGCATCCAGAG                         AACAAGAACGAGTGTCACAGCTCATGGAAAATCTAGACTCTGAAAGA
genomic: CCTTGCGCTCTATGAATCTTACAAGACCAGGCAGGAACATGCATCCAGAGgtggttgttc ... tcctttgcagAACAAGAACGAGTGTCACAGCTCATGGAAAATCTAGACTCTGAAAGA
EST: gi|78180984|gb|DV551357.1|DV551357
EST:     CCTTGCGCTCTATGAATCTTACAAGACCAGGCAGGAACATGCATCCAGAG                         AACAAGAACGAGTGTCACAGCTCATGGAAAATCTAGACTCTGAAAGA
genomic: CCTTGCGCTCTATGAATCTTACAAGACCAGGCAGGAACATGCATCCAGAGgtggttgttc ... tcctttgcagAACAAGAACGAGTGTCACAGCTCATGGAAAATCTAGACTCTGAAAGA
EST: gi|94476028|gb|EB704986.1|EB704986
EST:     CCTTGCGCTCTATGAATCTTACAAGACCAGGCAGGAACATGCATCCAGAG                         AACAAGAACGAGTGTCACAGCTCATGGAAAATCTAGACTCTGAAAGA
genomic: CCTTGCGCTCTATGAATCTTACAAGACCAGGCAGGAACATGCATCCAGAGgtggttgttc ... tcctttgcagAACAAGAACGAGTGTCACAGCTCATGGAAAATCTAGACTCTGAAAGA
EST: gi|7844188|gb|AW787410.1|AW787410
EST:     CCTTGCGCTCTATGAATCTTACAAGACCAGGCAGGAACATGCATCCAGAG                         AACAAGAACGAGTGTCACAGCTCATGGAAAATCTAGACTCTGAAAGA
genomic: CCTTGCGCTCTATGAATCTTACAAGACCAGGCAGGAACATGCATCCAGAGgtggttgttc ... tcctttgcagAACAAGAACGAGTGTCACAGCTCATGGAAAATCTAGACTCTGAAAGA
EST: gi|7844190|gb|AW787412.1|AW787412
EST:     CCTTGCGCTCTATGAATCTTACAAGACCAGGCAGGAACATGCATCCAGAG                         AACAAGAACGAGTGTCACAGCTCATGGTAAAATCTAGACTCTGAAAGA
genomic: CCTTGCGCTCTATGAATCTTACAAGACCAGGCAGGAACATGCATCCAGAGgtggttgttc ... tcctttgcagAACAAGAACGAGTGTCACAGCTCATGG-AAAATCTAGACTCTGAAAGA
EST: gi|211498135|gb|FL115228.1|FL115228
EST:     CCTTGCGCTCTATGAATCTTACAAGACCAGGCAGGAACATGCATCCAGAG                         AACAAGAACGAGTGTCACA
genomic: CCTTGCGCTCTATGAATCTTACAAGACCAGGCAGGAACATGCATCCAGAGgtggttgttc ... tcctttgcagAACAAGAACGAGTGTCACA
EST: gi|94476019|gb|EB704977.1|EB704977
EST:     CCTTGCGCTCTATGAATCTTACAAGACCAGGCAGGAACATGCATCCAGAG                         AACAAGAACGAGTGTCACAGCTCATGGAAAATCTAGATTCTGAAAGA
genomic: CCTTGCGCTCTATGAATCTTACAAGACCAGGCAGGAACATGCATCCAGAGgtggttgttc ... tcctttgcagAACAAGAACGAGTGTCACAGCTCATGGAAAATCTAGACTCTGAAAGA
EST: gi|12046853|gb|BF729005.1|BF729005
EST:     CCTTGCGCTCTATGAATCTTACAAGACCAGGCAGGAACATGCATCCAGAG                         AACAAGAACGAGTGTCACAGCTCATGGAAAATCTAGACTCTGAAAGA
genomic: CCTTGCGCTCTATGAATCTTACAAGACCAGGCAGGAACATGCATCCAGAGgtggttgttc ... tcctttgcagAACAAGAACGAGTGTCACAGCTCATGGAAAATCTAGACTCTGAAAGA
EST: gi|7844189|gb|AW787411.1|AW787411
EST:     CCTTGCGCTCTATGAATCTTACAAGACCAGGCAGGAACATGCATCCAGAG                         AACAAGAACGAGTGTCACAGCTCATGTTATATCTAGACTCTGAAAGA
genomic: CCTTGCGCTCTATGAATCTTACAAGACCAGGCAGGAACATGCATCCAGAGgtggttgttc ... tcctttgcagAACAAGAACGAGTGTCACAGCTCATGGAAAATCTAGACTCTGAAAGA
EST: gi|94479639|gb|EB708597.1|EB708597
EST:     CCTTGCGCTCTATGAATCTTACAAGACCAGGCAGGAACATGCATCCAGAG                         AACAAGAACGAGTGTCACAGCTCATGGAAAATCTAGATTCTGAAAGA
genomic: CCTTGCGCTCTATGAATCTTACAAGACCAGGCAGGAACATGCATCCAGAGgtggttgttc ... tcctttgcagAACAAGAACGAGTGTCACAGCTCATGGAAAATCTAGACTCTGAAAGA
EST: gi|60350072|gb|DN217045.1|DN217045
EST:     CCTTGCGCTCTATGAATCTTACAAGACCAGGCAGGAACATGCATCCAGAG                         AACAAGAACGAGTGTCACAGCTCATGGAAAATCTAGACTCTGAAAGA
genomic: CCTTGCGCTCTATGAATCTTACAAGACCAGGCAGGAACATGCATCCAGAGgtggttgttc ... tcctttgcagAACAAGAACGAGTGTCACAGCTCATGGAAAATCTAGACTCTGAAAGA
EST: gi|71326414|gb|DR799890.1|DR799890
EST:     CCTTGCGCTCTATGAATCTTACAAGACCAGGCAGGAACATGCATCCAGAG                         AACAAGAACGAGTGTCACAGCTCATGGAAAATCTAGACTCTGAAAGA
genomic: CCTTGCGCTCTATGAATCTTACAAGACCAGGCAGGAACATGCATCCAGAGgtggttgttc ... tcctttgcagAACAAGAACGAGTGTCACAGCTCATGGAAAATCTAGACTCTGAAAGA

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), 47 (downstream exon)
Score: 71

CTCGATAGAGTTGCCGCATCTGCGCTCAAAGATGTCATTGCTGATTTCTCCCTTGCGCTCTATGAATCTTACAAGACCAGGCAGGAACATGCATCCAGAGgtggttgttc ... tcctttgcagAACAAGAACGAGTGTCACAGCTCATGGAAAATCTAGACTCTGAAAGA


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 53

CTCGATAGAGTTGCCGCATCTGCGCTCAAAGATGTCATTGCTGATTTCTCCCTTGCGCTCTATGAATCTTACAAGACCAGGCAGGAACATGCATCCAGAGgtggttgttc ... tcctttgcagAACAAGAACGAGTGTCACAGCTCATGGAAAATCTAGACTCTGAAAGA


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 62

CTCGATAGAGTTGCCGCATCTGCGCTCAAAGATGTCATTGCTGATTTCTCCCTTGCGCTCTATGAATCTTACAAGACCAGGCAGGAACATGCATCCAGAGgtggttgttc ... tcctttgcagAACAAGAACGAGTGTCACAGCTCATGGAAAATCTAGACTCTGAAAGA


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 48

CTCGATAGAGTTGCCGCATCTGCGCTCAAAGATGTCATTGCTGATTTCTCCCTTGCGCTCTATGAATCTTACAAGACCAGGCAGGAACATGCATCCAGAGgtggttgttc ... tcctttgcagAACAAGAACGAGTGTCACAGCTCATGGAAAATCTAGACTCTGAAAGA