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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAAGTGGGTCACCGGCGCCTTCGCCGGCCACACCGCGGTTGTCCTCAAAGATGGTGACGCCAACCTCTGGGTCGCAGAATCAGGCTACGAAAATAACAAGgcagttcttgctggttcagttttttcatagctagagctaggaagctagctttgattcagccttatagctagctaatttatggcaataattgtggcctgcag

Basic information

species Zea mays
transcript GRMZM2G445478_T01
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|148929994|gb|EE285845.2|EE285845
EST:     ATGGTGACGCCAACCTCTGGGTCGCAGAATCAGGCTACGAAAATAACAAG                         GGTGACGAGATCATTAGCATGACTCCGTGGGACGAGTGGTGGGGGATGGCG
genomic: ATGGTGACGCCAACCTCTGGGTCGCAGAATCAGGCTACGAAAATAACAAGgcagttcttg ... tggcctgcagGGTGACGAGATCATTAGCATGACTCCGTGGGACGAGTGGTGGGGGATGGCG
EST: gi|148965941|gb|EE016855.2|EE016855
EST:     ATGGTGACGCCAACCTCTGGGTCGCAGAATCAGGCTACGAAAATAACAAG                         GGTGACGAGATCATTAGCATGACTCCGTGGGACGAGTGGTGGGGGATGGCG
genomic: ATGGTGACGCCAACCTCTGGGTCGCAGAATCAGGCTACGAAAATAACAAGgcagttcttg ... tggcctgcagGGTGACGAGATCATTAGCATGACTCCGTGGGACGAGTGGTGGGGGATGGCG
EST: gi|78118584|gb|DV536968.1|DV536968
EST:     ATGGTGACGCCAACCTCTGGGTCGCAGAATCAGGCTACGAAAATAACAAG                         GGTGACGAGATCATTAGCATGACTCCGTGGGACGAGTGGTGGGGGATGGCG
genomic: ATGGTGACGCCAACCTCTGGGTCGCAGAATCAGGCTACGAAAATAACAAGgcagttcttg ... tggcctgcagGGTGACGAGATCATTAGCATGACTCCGTGGGACGAGTGGTGGGGGATGGCG
EST: gi|149090684|gb|EE180010.2|EE180010
EST:     ATGGTGACGCCAACCTCTGGGTCGCAGAATCAGGCTACGAAAATAACAAG                         GGTGACGAGATCATTAGCATGACTCCGTGGGACGAGTGGTGGGGGATGGCG
genomic: ATGGTGACGCCAACCTCTGGGTCGCAGAATCAGGCTACGAAAATAACAAGgcagttcttg ... tggcctgcagGGTGACGAGATCATTAGCATGACTCCGTGGGACGAGTGGTGGGGGATGGCG
EST: gi|149100003|gb|EE186056.2|EE186056
EST:     ATGGTGACGCCAACCTCTGGGTCGCAGAATCAGGCTACGAAAATAACAAG                         GGTGACGAGATCATTAGCATGACTCCGTGGGACGAGTGGTGGGGGATGGCG
genomic: ATGGTGACGCCAACCTCTGGGTCGCAGAATCAGGCTACGAAAATAACAAGgcagttcttg ... tggcctgcagGGTGACGAGATCATTAGCATGACTCCGTGGGACGAGTGGTGGGGGATGGCG
EST: gi|149069903|gb|EE158301.2|EE158301
EST:     ATGGTGACGCCAACCTCTGGGTCGCAGAATCAGGCTACGAAAATAACAAG                         GGTGACGAGATCATTAGCATGACTCCGTGGGACGAGTGGTGGGGGATGGCG
genomic: ATGGTGACGCCAACCTCTGGGTCGCAGAATCAGGCTACGAAAATAACAAGgcagttcttg ... tggcctgcagGGTGACGAGATCATTAGCATGACTCCGTGGGACGAGTGGTGGGGGATGGCG
EST: gi|148972705|gb|EE023666.2|EE023666
EST:     ATGGTGACGCCAACCTCTGGGTCGCAGAATCAGGCTACGAAAATAACAAG                         GGTGACGAGATCATTAGCATGACTCCGTGGGACGAGTGGTGGGGGATGGCG
genomic: ATGGTGACGCCAACCTCTGGGTCGCAGAATCAGGCTACGAAAATAACAAGgcagttcttg ... tggcctgcagGGTGACGAGATCATTAGCATGACTCCGTGGGACGAGTGGTGGGGGATGGCG
EST: gi|148967220|gb|EE018415.2|EE018415
EST:     ATGGTGACGCCAACCTCTGGGTCGCAGAATCAGGCTACGAAAATAACAAG                         GGTGACGAGATCATTAGCATGACTCCGTGGGACGAGTGGTGGGGGATGGCG
genomic: ATGGTGACGCCAACCTCTGGGTCGCAGAATCAGGCTACGAAAATAACAAGgcagttcttg ... tggcctgcagGGTGACGAGATCATTAGCATGACTCCGTGGGACGAGTGGTGGGGGATGGCG

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: 46 (upstream exon), 48 (downstream exon)
Score: 34

GAAGTGGGTCACCGGCGCCTTCGCCGGCCACACCGCGGTTGTCCTCAAAGATGGTGACGCCAACCTCTGGGTCGCAGAATCAGGCTACGAAAATAACAAGgcagttcttg ... tggcctgcagGGTGACGAGATCATTAGCATGACTCCGTGGGACGAGTGGTGGGGGATGGCGCTCAAGGACGAGTCCAACCCTCAGATAGCGCTTCTGCCGCTGCACCCCG


Block sizes: 41 (upstream exon), 46 (downstream exon)
Score: 28

GAAGTGGGTCACCGGCGCCTTCGCCGGCCACACCGCGGTTGTCCTCAAAGATGGTGACGCCAACCTCTGGGTCGCAGAATCAGGCTACGAAAATAACAAGgcagttcttg ... tggcctgcagGGTGACGAGATCATTAGCATGACTCCGTGGGACGAGTGGTGGGGGATGGCGCTCAAGGACGAGTCCAACCCTCAGATAGCGCTTCTGCCGCTGCACCCCG


Block sizes: 41 (upstream exon), 44 (downstream exon)
Score: 6

GAAGTGGGTCACCGGCGCCTTCGCCGGCCACACCGCGGTTGTCCTCAAAGATGGTGACGCCAACCTCTGGGTCGCAGAATCAGGCTACGAAAATAACAAGgcagttcttg ... tggcctgcagGGTGACGAGATCATTAGCATGACTCCGTGGGACGAGTGGTGGGGGATGGCGCTCAAGGACGAGTCCAACCCTCAGATAGCGCTTCTGCCGCTGCACCCCG


Block sizes: 46 (upstream exon), 48 (downstream exon)
Score: 43

GAAGTGGGTCACCGGCGCCTTCGCCGGCCACACCGCGGTTGTCCTCAAAGATGGTGACGCCAACCTCTGGGTCGCAGAATCAGGCTACGAAAATAACAAGgcagttcttg ... tggcctgcagGGTGACGAGATCATTAGCATGACTCCGTGGGACGAGTGGTGGGGGATGGCGCTCAAGGACGAGTCCAACCCTCAGATAGCGCTTCTGCCGCTGCACCCCG