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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAAAGATGACTAAAGAAGAGGAAGATGAAGAATACCTCGAAGAGGAAGAAGATGCCCTTGCTGGTGCAGGGGGGAACACATTTAGTTTCACAACCTTCATgtgagccctttgctgactatttgttactaccttgatatatgttatttccttgctttaataactacctcaagtcgagggaagaattacttgttaaatagat...

Basic information

species Zea mays
transcript GRMZM5G897073_T04
intron # 4
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|88752874|gb|DY537015.1|DY537015
EST:     ATGCCCTTGCTGGTGCAGGGGGGAACACATTTTAGTTTCACAACCTTCAT                         GCCTCTTAACCCCTCTGATCCTGGGGGGTGGCAGATTAGACTCCGAAGGGG
genomic: ATGCCCTTGCTGGTGCAGGGGGGAACACATTT-AGTTTCACAACCTTCATgtgagccctt ... tctgttgcagGC-TCTTAACCCCTCTGATCCTGGTGCGTGGCAGATTAGACTCCGATGGGG
EST: gi|32837950|gb|CD977628.1|CD977628
EST:     ATGCCCTTGCTGGTGCAGGGGGGAACCACATTTAGTTTCACAACCTTCAT                         GCTCTTAACCCCTCTGATCCTGGTGCGTGGCAGATTAGACTCCGATGGGGA
genomic: ATGCCCTTGCTGGTGCAGGGGGGAA-CACATTTAGTTTCACAACCTTCATgtgagccctt ... tctgttgcagGCTCTTAACCCCTCTGATCCTGGTGCGTGGCAGATTAGACTCCGATGGGGA
EST: gi|60345564|gb|DN212537.1|DN212537
EST:     GATGCCCTTGCTGGTGCAGGGGGGAACACATTTAGTTTCACAACCTTCAT                         GCTCTTAACCCCTCTGATCCTGGTGCGTGGCAGATTAGACTCCGATGGGGA
genomic: GATGCCCTTGCTGGTGCAGGGGGGAACACATTTAGTTTCACAACCTTCATgtgagccctt ... tctgttgcagGCTCTTAACCCCTCTGATCCTGGTGCGTGGCAGATTAGACTCCGATGGGGA
EST: gi|91050400|gb|EB160818.1|EB160818
EST:     GATGCCCTTGCTGGTGCAGGGGGGAACACATTTAGTTTCACAACCTTCAT                         GCTCTTAACCCCTCTGATCCTGGTGCGTGGCAGATTAGACTCCGATGGGGA
genomic: GATGCCCTTGCTGGTGCAGGGGGGAACACATTTAGTTTCACAACCTTCATgtgagccctt ... tctgttgcagGCTCTTAACCCCTCTGATCCTGGTGCGTGGCAGATTAGACTCCGATGGGGA
EST: gi|32838909|gb|CD978590.1|CD978590
EST:     ATGCCCTTGCTGGTGCAGGGGGGAACCACATTTAGTTTCACAACCTTCAT                         GCTCTTAACCCCTCTGATCCTGGTGCGTGGCAGATTAGACTCCGATGGGGA
genomic: ATGCCCTTGCTGGTGCAGGGGGGAA-CACATTTAGTTTCACAACCTTCATgtgagccctt ... tctgttgcagGCTCTTAACCCCTCTGATCCTGGTGCGTGGCAGATTAGACTCCGATGGGGA

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), 49 (downstream exon)
Score: 102

CAAAGATGACTAAAGAAGAGGAAGATGAAGAATACCTCGAAGAGGAAGAAGATGCCCTTGCTGGTGCAGGGGGGAACACATTTAGTTTCACAACCTTCATgtgagccctt ... tctgttgcagGCTCTTAACCCCTCTGATCCTGGTGCGTGGCAGATTAGACTCCGATGGGGAAGTCACTAGCGAGGTGGATCAAGTTCGTGCTCTTCAGGAAGAAGTCGTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 17

CAAAGATGACTAAAGAAGAGGAAGATGAAGAATACCTCGAAGAGGAAGAAGATGCCCTTGCTGGTGCAGGGGGGAACACATTTAGTTTCACAACCTTCATgtgagccctt ... tctgttgcagGCTCTTAACCCCTCTGATCCTGGTGCGTGGCAGATTAGACTCCGATGGGGAAGTCACTAGCGAGGTGGATCAAGTTCGTGCTCTTCAGGAAGAAGTCGTC


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 9

CAAAGATGACTAAAGAAGAGGAAGATGAAGAATACCTCGAAGAGGAAGAAGATGCCCTTGCTGGTGCAGGGGGGAACACATTTAGTTTCACAACCTTCATgtgagccctt ... tctgttgcagGCTCTTAACCCCTCTGATCCTGGTGCGTGGCAGATTAGACTCCGATGGGGAAGTCACTAGCGAGGTGGATCAAGTTCGTGCTCTTCAGGAAGAAGTCGTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 32

CAAAGATGACTAAAGAAGAGGAAGATGAAGAATACCTCGAAGAGGAAGAAGATGCCCTTGCTGGTGCAGGGGGGAACACATTTAGTTTCACAACCTTCATgtgagccctt ... tctgttgcagGCTCTTAACCCCTCTGATCCTGGTGCGTGGCAGATTAGACTCCGATGGGGAAGTCACTAGCGAGGTGGATCAAGTTCGTGCTCTTCAGGAAGAAGTCGTC