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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgaacataacttgcctgaacctttgctgcttgtcaattcagggagtgagctagttagtagtagtaatggcatgcaactgaaaaggccgtcttcctgttgtggagcagTACGTCCTCAAGGTCGGCGAGGGGTTCGCCGCGCACTGCATCAGCGGGTTCACGGCTCTGGACGTGCCCCCTCCGGTAGGCCCTCTGTG

Basic information

species Zea mays
transcript GRMZM2G130333_T01
intron # 11
splice site 3'
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|211345528|gb|FL476187.1|FL476187
EST:     CCGTTGCGTTCAGCATCGGTGGAAGGGCGTTCGAGCTCCGGCCTGACCAG                         TACGTCCTCAAGGTCGGCGAGGGGTTCGCCGCGCACTGCATCAGCGGGTTC
genomic: CCGTTGCGTTCAGCATCGGTGGAAGGGCGTTCGAGCTCCGGCCTGACCAGgtgaacataa ... tgtggagcagTACGTCCTCAAGGTCGGCGAGGGGTTCGCCGCGCACTGCATCAGCGGGTTC
EST: gi|211475048|gb|FL213523.1|FL213523
EST:     CCGTTGCGTTCAGCATCGGTGGAAGGGCGTTCGAGCTCCGGCCTGACCAG                         TACGTCCTCAAGGTCGGCGAGGGGTTCGCCGCGCACTGCATCAGCGGGTTC
genomic: CCGTTGCGTTCAGCATCGGTGGAAGGGCGTTCGAGCTCCGGCCTGACCAGgtgaacataa ... tgtggagcagTACGTCCTCAAGGTCGGCGAGGGGTTCGCCGCGCACTGCATCAGCGGGTTC
EST: gi|110200388|gb|EC882285.1|EC882285
EST:     CCGTTGCGTTCAGCATCGGTGGAAGGGCGTTCGAGCTCCGGCCTGACCAG                         TACGTCCTCAAGGTCGGCGAGGGGTTCGCCGCGCACTGCATCAGCGGGTTC
genomic: CCGTTGCGTTCAGCATCGGTGGAAGGGCGTTCGAGCTCCGGCCTGACCAGgtgaacataa ... tgtggagcagTACGTCCTCAAGGTCGGCGAGGGGTTCGCCGCGCACTGCATCAGCGGGTTC
EST: gi|5649987|gb|AI920347.1|AI920347
EST:     CCGTTGCGTTCAGCATCGGTGGAAGGGCGTTCGAGCTCCGGCCTGACCAG                         TACGTCCTCAAGGTCGGCGAGGGGTTCGCCGCGCACTGCATCAGCGGGTTC
genomic: CCGTTGCGTTCAGCATCGGTGGAAGGGCGTTCGAGCTCCGGCCTGACCAGgtgaacataa ... tgtggagcagTACGTCCTCAAGGTCGGCGAGGGGTTCGCCGCGCACTGCATCAGCGGGTTC
EST: gi|211089522|gb|FL476385.1|FL476385
EST:     CCGTTGCGTTCAGCATCGGTGGAAGGGCGTTCGAGCTCCGGCCTGACCAG                         TACGTCCTCAAGGTCGGCGAGGGGTTCGCCGCGCACTGCATCAGCGGGTTC
genomic: CCGTTGCGTTCAGCATCGGTGGAAGGGCGTTCGAGCTCCGGCCTGACCAGgtgaacataa ... tgtggagcagTACGTCCTCAAGGTCGGCGAGGGGTTCGCCGCGCACTGCATCAGCGGGTTC
EST: gi|50332328|gb|CO527454.1|CO527454
EST:     CCGTTGCGTTCAGCATCGGTGGAAGGGCGTTCGAGCTCCGGCCTGACCAG                         TACGTCCTCAAGGTCGGCGAGGGGTTCGCCGCGCACTGCATCAGCGGGTTC
genomic: CCGTTGCGTTCAGCATCGGTGGAAGGGCGTTCGAGCTCCGGCCTGACCAGgtgaacataa ... tgtggagcagTACGTCCTCAAGGTCGGCGAGGGGTTCGCCGCGCACTGCATCAGCGGGTTC
EST: gi|211345527|gb|FL476186.1|FL476186
EST:     CCGTTGCGTTCAGCATCGGTGGAAGGGCGTTCGAGCTCCGGCCTGACCAG                         TACGTCCTCAAGGTCGGCGAGGGGTTCGCCGCGCACTGCATCAGCGGGTTC
genomic: CCGTTGCGTTCAGCATCGGTGGAAGGGCGTTCGAGCTCCGGCCTGACCAGgtgaacataa ... tgtggagcagTACGTCCTCAAGGTCGGCGAGGGGTTCGCCGCGCACTGCATCAGCGGGTTC

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: 30 (upstream exon), 20 (downstream exon)
Score: 2

CGATCCGGTGGGGTCGCGCGTGGACTGCGGACGCGTGGGTTCCCTGCAGACCGTTGCGTTCAGCATCGGTGGAAGGGCGTTCGAGCTCCGGCCTGACCAGgtgaacataa ... tgtggagcagTACGTCCTCAAGGTCGGCGAGGGGTTCGCCGCGCACTGCATCAGCGGGTTCACGGCTCTGGACGTGCCCCCTCCGGTAGGCCCTCTGTG


Block sizes: 46 (upstream exon), 43 (downstream exon)
Score: 10

CGATCCGGTGGGGTCGCGCGTGGACTGCGGACGCGTGGGTTCCCTGCAGACCGTTGCGTTCAGCATCGGTGGAAGGGCGTTCGAGCTCCGGCCTGACCAGgtgaacataa ... tgtggagcagTACGTCCTCAAGGTCGGCGAGGGGTTCGCCGCGCACTGCATCAGCGGGTTCACGGCTCTGGACGTGCCCCCTCCGGTAGGCCCTCTGTG


Block sizes: 34 (upstream exon), 30 (downstream exon)
Score: 3

CGATCCGGTGGGGTCGCGCGTGGACTGCGGACGCGTGGGTTCCCTGCAGACCGTTGCGTTCAGCATCGGTGGAAGGGCGTTCGAGCTCCGGCCTGACCAGgtgaacataa ... tgtggagcagTACGTCCTCAAGGTCGGCGAGGGGTTCGCCGCGCACTGCATCAGCGGGTTCACGGCTCTGGACGTGCCCCCTCCGGTAGGCCCTCTGTG


Block sizes: 49 (upstream exon), 42 (downstream exon)
Score: 15

CGATCCGGTGGGGTCGCGCGTGGACTGCGGACGCGTGGGTTCCCTGCAGACCGTTGCGTTCAGCATCGGTGGAAGGGCGTTCGAGCTCCGGCCTGACCAGgtgaacataa ... tgtggagcagTACGTCCTCAAGGTCGGCGAGGGGTTCGCCGCGCACTGCATCAGCGGGTTCACGGCTCTGGACGTGCCCCCTCCGGTAGGCCCTCTGTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttagtagtagtaatggcatgcaactgaaaaggccgtcttcctgttgtggagcagTACGTCCTCAAGGTCGGCGAGGGGTTCGCCGCGCACTGCATCAGCGGGTTCACGGCTCTGGACGTGCCCCCTCCGGTAGGCCCTCTGTG
                                    tcttcctgtt  CT-rich tract
        tagtaat  TA-rich tract