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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATGTGAAGGAGCACCCTGTTGTCATCTATATGAAAGGTTATCCTGATGCTCCTAGGTGTGGTTTCAGTGCATTAGCAGTGAAGGTCCTCCAGCAATATGgtaatttgtctataagtgtgcattgtttcaaatgcaattgataatcagcaatcagtttgctcctcaaattttgaaggcaaatcttgtctgctgcag

Basic information

species Zea mays
transcript GRMZM2G080722_T02
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|6587608|gb|AW244926.1|AW244926
EST:     TCCTAGGTGTGGTTTCAGTGCATTAGCAGTGAAGGTCCTCCAGCAATATG                         GGGTGTCCCCATCAGTGCTAGAGATATTCTTTCAGATCTAAAGCTCAAAGA
genomic: TCCTAGGTGTGGTTTCAGTGCATTAGCAGTGAAGGTCCTCCAGCAATATGgtaatttgtc ... tctgctgcagG--TGTCCCCATCAGTGCTAGAGATATTCTTTCAGATCTAAAGCTCAAAGA
EST: gi|211393122|gb|FK956090.1|FK956090
EST:     TCCTAGGTGTGGTTTCAGTGCATTAGCAGTGAAGGTCCTCCAGCAATATG                         GTGTCCCCATCAGTGCTAGAGATATTCTTTCAGATCTAAAGCTCAAAGAGA
genomic: TCCTAGGTGTGGTTTCAGTGCATTAGCAGTGAAGGTCCTCCAGCAATATGgtaatttgtc ... tctgctgcagGTGTCCCCATCAGTGCTAGAGATATTCTTTCAGATCTAAAGCTCAAAGAGA
EST: gi|211395748|gb|FK956105.1|FK956105
EST:     TCCTAGGTGTGGTTTCAGTGCATTAGCAGTGAAGGTCCTCCAGCAATATG                         GTGTCCCCATCAGTG
genomic: TCCTAGGTGTGGTTTCAGTGCATTAGCAGTGAAGGTCCTCCAGCAATATGgtaatttgtc ... tctgctgcagGTGTCCCCATCAGTG
EST: gi|211393118|gb|FK956086.1|FK956086
EST:     TCCTAGGTGTGGTTTCAGTGCATTAGCAGTGAAGGTCCTCCAGCAATATG                         GTGTCCC-ATCAGTGCTAGAGATA
genomic: TCCTAGGTGTGGTTTCAGTGCATTAGCAGTGAAGGTCCTCCAGCAATATGgtaatttgtc ... tctgctgcagGTGTCCCCATCAGTGCTAGAGATA
EST: gi|211393127|gb|FK956095.1|FK956095
EST:     CCTAGGTGTGGTTTCAGTGCATTAGCAGTGAAGGTCCTCCCAGCA-TATG                         GTGTCCCCATCAGTGCTAGAGATATTCTTTCAGATCTAAAGCTCAAAGAG
genomic: CCTAGGTGTGGTTTCAGTGCATTAGCAGTGAAGGTCCTCC-AGCAATATGgtaatttgtc ... tctgctgcagGTGTCCCCATCAGTGCTAGAGATATTCTTTCAGATCTAAAGCTCAAAGAG
EST: gi|116818678|gb|EC861726.1|EC861726
EST:     TCCTAGGTGTGGTTTCAGTGCATTACCAGTGAAGGTCGTCCAGCCATATG                         GTGTCCCCATCAGTGCTAGAGATATTCTTTCAGATCTAAAGCTCAAAGAGA
genomic: TCCTAGGTGTGGTTTCAGTGCATTAGCAGTGAAGGTCCTCCAGCAATATGgtaatttgtc ... tctgctgcagGTGTCCCCATCAGTGCTAGAGATATTCTTTCAGATCTAAAGCTCAAAGAGA
EST: gi|211395747|gb|FK956104.1|FK956104
EST:     TCCTAGGTGTGGTTTCAGTGCATTAGCAGTGAAGGTCCTCCAGCAATATG                         GTGTCCCCATCAGTGCTAGAGATATTCTTTCAGATCTAAAGCTCAAAGAGA
genomic: TCCTAGGTGTGGTTTCAGTGCATTAGCAGTGAAGGTCCTCCAGCAATATGgtaatttgtc ... tctgctgcagGTGTCCCCATCAGTGCTAGAGATATTCTTTCAGATCTAAAGCTCAAAGAGA
EST: gi|211138212|gb|FL122275.1|FL122275
EST:     TCCTAGGTGTGGTTTCAGTGCATTAGCAGTGAAGGTCCTCCAGCAATATG                         GTGTCCCCATCAGTGCTAGAG
genomic: TCCTAGGTGTGGTTTCAGTGCATTAGCAGTGAAGGTCCTCCAGCAATATGgtaatttgtc ... tctgctgcagGTGTCCCCATCAGTGCTAGAG
EST: gi|211215605|gb|FL316840.1|FL316840
EST:     TCCTAGGTGTGGTTTCAGTGCATGAGCAGTGAAGGTCCTCCAGCAATATG                         GTGTCCCCATCAGTGCTAGAGATATTCTTTCAGATCTAAAGCTC
genomic: TCCTAGGTGTGGTTTCAGTGCATTAGCAGTGAAGGTCCTCCAGCAATATGgtaatttgtc ... tctgctgcagGTGTCCCCATCAGTGCTAGAGATATTCTTTCAGATCTAAAGCTC
EST: gi|6020541|gb|AW065469.1|AW065469
EST:     CCTAGGTGTGGTTTCAGTGCATTANGCAGTGAAGGTCCTCCAGCAATATG                         GNGTCCCCATCAGTGCTAGAGATATTCTTTCAGATCTAAAGCTCAAAGAGA
genomic: CCTAGGTGTGGTTTCAGTGCATTA-GCAGTGAAGGTCCTCCAGCAATATGgtaatttgtc ... tctgctgcagGTGTCCCCATCAGTGCTAGAGATATTCTTTCAGATCTAAAGCTCAAAGAGA
EST: gi|211395740|gb|FK956097.1|FK956097
EST:     TCCTAGGTGTGGTTTCAGTGCATCAGCAGTGAAGGTCCTCCAGCAATATG                         GTGTCCCCATCAGTGCTAGAGATATTCTTTCAGATCTAAAGCTCAAAGAGA
genomic: TCCTAGGTGTGGTTTCAGTGCATTAGCAGTGAAGGTCCTCCAGCAATATGgtaatttgtc ... tctgctgcagGTGTCCCCATCAGTGCTAGAGATATTCTTTCAGATCTAAAGCTCAAAGAGA
EST: gi|211395752|gb|FK956109.1|FK956109
EST:     TCCTAGGTGTGGTT-CAGTGCATTAGCAGTGAAGGTCCTCCAGCAATATG                         GTGTCCCCATCA
genomic: TCCTAGGTGTGGTTTCAGTGCATTAGCAGTGAAGGTCCTCCAGCAATATGgtaatttgtc ... tctgctgcagGTGTCCCCATCA
EST: gi|32908664|gb|CF013477.1|CF013477
EST:     TCCTAGGTGTGGTTTCAGTGCATTAGCAGTGAAGGTCCTCCAGCAATATG                         GTGTCCCCATCAGTGCTAGAGATATTCTTTCAGATCTAAAGCTCAAAGAGA
genomic: TCCTAGGTGTGGTTTCAGTGCATTAGCAGTGAAGGTCCTCCAGCAATATGgtaatttgtc ... tctgctgcagGTGTCCCCATCAGTGCTAGAGATATTCTTTCAGATCTAAAGCTCAAAGAGA
EST: gi|149051827|gb|EE155954.2|EE155954
EST:     TCCTAGGTGTGGTTTCAGTGCATTAGCAGTGAAGGTCCTCCAGCAATATG                         GTGTCCCCATCAGTGCTAGAGATATTCTTTCAGATCTAAAGCTCAAAGAGA
genomic: TCCTAGGTGTGGTTTCAGTGCATTAGCAGTGAAGGTCCTCCAGCAATATGgtaatttgtc ... tctgctgcagGTGTCCCCATCAGTGCTAGAGATATTCTTTCAGATCTAAAGCTCAAAGAGA

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: 99

GATGTGAAGGAGCACCCTGTTGTCATCTATATGAAAGGTTATCCTGATGCTCCTAGGTGTGGTTTCAGTGCATTAGCAGTGAAGGTCCTCCAGCAATATGgtaatttgtc ... tctgctgcagGTGTCCCCATCAGTGCTAGAGATATTCTTTCAGATCTAAAGCTCAAAGAGAGTGTTAAAGCATACAG


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

GATGTGAAGGAGCACCCTGTTGTCATCTATATGAAAGGTTATCCTGATGCTCCTAGGTGTGGTTTCAGTGCATTAGCAGTGAAGGTCCTCCAGCAATATGgtaatttgtc ... tctgctgcagGTGTCCCCATCAGTGCTAGAGATATTCTTTCAGATCTAAAGCTCAAAGAGAGTGTTAAAGCATACAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 104

GATGTGAAGGAGCACCCTGTTGTCATCTATATGAAAGGTTATCCTGATGCTCCTAGGTGTGGTTTCAGTGCATTAGCAGTGAAGGTCCTCCAGCAATATGgtaatttgtc ... tctgctgcagGTGTCCCCATCAGTGCTAGAGATATTCTTTCAGATCTAAAGCTCAAAGAGAGTGTTAAAGCATACAG


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 70

GATGTGAAGGAGCACCCTGTTGTCATCTATATGAAAGGTTATCCTGATGCTCCTAGGTGTGGTTTCAGTGCATTAGCAGTGAAGGTCCTCCAGCAATATGgtaatttgtc ... tctgctgcagGTGTCCCCATCAGTGCTAGAGATATTCTTTCAGATCTAAAGCTCAAAGAGAGTGTTAAAGCATACAG