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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACTATATACATACTCCACCCGACACTGGGACTGAGAACAGCCGTTATGGCGATGCAACTTTTTGTTGACGGGGAGgtactcaccttgcagctaaaccaaaaacattctttgtgctgctccgtgcttgaaatttctgttttggtttgtttcaattag

Basic information

species Zea mays
transcript GRMZM2G100707_T01
intron # 12
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|32933286|gb|CF038098.1|CF038098
EST:     TGGGACTGAGAACAGCTGTTATGGCGATGCAACTTTTTGTTGACGGGGAG                         GTCTGGAAGAAAGTTGTATATGTCGACAGACTTGTGCAGCTATTCAGATAT
genomic: TGGGACTGAGAACAGCCGTTATGGCGATGCAACTTTTTGTTGACGGGGAGgtactcacct ... tttcaattagGTCTGGAAGAAAGTTGTATATGTCGACAGACTTGTGCAGCTATTCAGATAT
EST: gi|93015870|gb|EB641390.1|EB641390
EST:     TGGGACTGAGAACAGCCGTTATGGCGATGCAACTTTTTGTTGACGGGGAG                         GTCTGGAAGAAAGTTGTATATGTCGACAGACTTGTGCAGCTATTCAGATAT
genomic: TGGGACTGAGAACAGCCGTTATGGCGATGCAACTTTTTGTTGACGGGGAGgtactcacct ... tttcaattagGTCTGGAAGAAAGTTGTATATGTCGACAGACTTGTGCAGCTATTCAGATAT
EST: gi|211442681|gb|FL456308.1|FL456308
EST:     TGGGACTGAGAACAGCCGTTATGGCGATGCAACTTTTTGTTGACGGGGAG                         GTCTGGAAGAAAGTTGTATATGTCGACAGACTTGTGCAGCTATTCAGATAT
genomic: TGGGACTGAGAACAGCCGTTATGGCGATGCAACTTTTTGTTGACGGGGAGgtactcacct ... tttcaattagGTCTGGAAGAAAGTTGTATATGTCGACAGACTTGTGCAGCTATTCAGATAT
EST: gi|37398356|gb|CF636490.1|CF636490
EST:     TGGGACTGAGAACAGCCGTTATGGCGATGCAACTTTTTGTTGACGGGGAG                         GTCTGGAAGAAAGTTGTATATGTCGACAGACTTGTGCAGCTATTCAGATAT
genomic: TGGGACTGAGAACAGCCGTTATGGCGATGCAACTTTTTGTTGACGGGGAGgtactcacct ... tttcaattagGTCTGGAAGAAAGTTGTATATGTCGACAGACTTGTGCAGCTATTCAGATAT
EST: gi|166414999|gb|EG260297.1|EG260297
EST:     AGAACAGCCGTTATGGCGATGCAACTTTTTGTTGACGGGGAG                         GTCTGGAAGAAAGTTGTATATGTCGACAGACTTGTGCAGCTATTCAGATAT
genomic: AGAACAGCCGTTATGGCGATGCAACTTTTTGTTGACGGGGAGgtactcacct ... tttcaattagGTCTGGAAGAAAGTTGTATATGTCGACAGACTTGTGCAGCTATTCAGATAT
EST: gi|5915101|gb|AW052742.1|AW052742
EST:     TGGGACTGAGAACAGCCGTTATGGCGATGCAACTTTTTGTTGACGGGGAG                         GTCTGGAAGAAAGTTGTATATGTCGACAGACTTGTGCAGCTATTCAGATAT
genomic: TGGGACTGAGAACAGCCGTTATGGCGATGCAACTTTTTGTTGACGGGGAGgtactcacct ... tttcaattagGTCTGGAAGAAAGTTGTATATGTCGACAGACTTGTGCAGCTATTCAGATAT
EST: gi|149097072|gb|EE182879.2|EE182879
EST:     TGGGACTGAGAACAGCCGTTATGGCGATGCAACTTTTTGTTGACGGGGAG                         GTCTGGAAGAAAGTTGTATATGTCGACAGACTTGTGCAGCTATTCAGATAT
genomic: TGGGACTGAGAACAGCCGTTATGGCGATGCAACTTTTTGTTGACGGGGAGgtactcacct ... tttcaattagGTCTGGAAGAAAGTTGTATATGTCGACAGACTTGTGCAGCTATTCAGATAT
EST: gi|211221036|gb|FL467849.1|FL467849
EST:     TGGGACTGAGAACASCCGTTATGGCGATGCAACTTTTTGTTGACGGGGAG                         GTCTGGAAGAAAGTTGTATATGTCGACAGACTTGTGCAGCTATTCAGATAT
genomic: TGGGACTGAGAACAGCCGTTATGGCGATGCAACTTTTTGTTGACGGGGAGgtactcacct ... tttcaattagGTCTGGAAGAAAGTTGTATATGTCGACAGACTTGTGCAGCTATTCAGATAT

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), 48 (downstream exon)
Score: 50

ACTATATACATACTCCACCCGACACTGGGACTGAGAACAGCCGTTATGGCGATGCAACTTTTTGTTGACGGGGAGgtactcacct ... tttcaattagGTCTGGAAGAAAGTTGTATATGTCGACAGACTTGTGCAGCTATTCAGATATGTACCACGTGAACAGCTCACCATTCCTGATTTTGTGTTCCA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 83

ACTATATACATACTCCACCCGACACTGGGACTGAGAACAGCCGTTATGGCGATGCAACTTTTTGTTGACGGGGAGgtactcacct ... tttcaattagGTCTGGAAGAAAGTTGTATATGTCGACAGACTTGTGCAGCTATTCAGATATGTACCACGTGAACAGCTCACCATTCCTGATTTTGTGTTCCA


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

ACTATATACATACTCCACCCGACACTGGGACTGAGAACAGCCGTTATGGCGATGCAACTTTTTGTTGACGGGGAGgtactcacct ... tttcaattagGTCTGGAAGAAAGTTGTATATGTCGACAGACTTGTGCAGCTATTCAGATATGTACCACGTGAACAGCTCACCATTCCTGATTTTGTGTTCCA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 85

ACTATATACATACTCCACCCGACACTGGGACTGAGAACAGCCGTTATGGCGATGCAACTTTTTGTTGACGGGGAGgtactcacct ... tttcaattagGTCTGGAAGAAAGTTGTATATGTCGACAGACTTGTGCAGCTATTCAGATATGTACCACGTGAACAGCTCACCATTCCTGATTTTGTGTTCCA