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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgcgagatttcatcttattgtttagtccgagtactgatgaaatctgatcatcgttgcctttttttgcagGAGCAGCAAAATTTTAGAGCTTTCGTCAGTGGGAAGTCAAGAACGCACCTCAGACTCTCCTGCTTGCCATGTGGTGCTCATAGTTCCCTTTACTTTTTCG

Basic information

species Zea mays
transcript GRMZM2G122897_T01
intron # 8
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|94479829|gb|EB708787.1|EB708787
EST:     CAGCAGTAGCTTCGTTGAATCCAACAGTGTTCTTATCCTTTGCATTGAAG                         GAGCAGCAAAATTTTAGAGCTTTCGTCAGTGGGAAGTCAAGAACGCACCTC
genomic: CAGCAGTAGCTTCGTTGAATCCAACAGTGTTCTTATCCTTTGCATTGAAGgtatgcgaga ... ttttttgcagGAGCAGCAAAATTTTAGAGCTTTCGTCAGTGGGAAGTCAAGAACGCACCTC
EST: gi|101382674|gb|EB813391.1|EB813391
EST:     CAGCAGTAGCTTCGTTGAATCCAACAGTGTTTTTATCCTTTGCATTGAAG                         GAGCAGCAAAATTTTAGAGCTTTCGTCAGTGGGAAGTCAAGAACGCACCTC
genomic: CAGCAGTAGCTTCGTTGAATCCAACAGTGTTCTTATCCTTTGCATTGAAGgtatgcgaga ... ttttttgcagGAGCAGCAAAATTTTAGAGCTTTCGTCAGTGGGAAGTCAAGAACGCACCTC
EST: gi|13149667|gb|BG319989.1|BG319989
EST:     CAGCAGTAGCTTCGTTGAATCCAACAGTGTTCTTATCCTTTGCATTGAAG                         GAGCAGCAAAATTTTAGAGCTTTCGTCAGTGGGAAGTCAAGAACGCACCTC
genomic: CAGCAGTAGCTTCGTTGAATCCAACAGTGTTCTTATCCTTTGCATTGAAGgtatgcgaga ... ttttttgcagGAGCAGCAAAATTTTAGAGCTTTCGTCAGTGGGAAGTCAAGAACGCACCTC
EST: gi|94474977|gb|EB703935.1|EB703935
EST:     CAGCAGTAGCTTCGTTGAATCCAACAGTGTTCTTATCCTTTGCATTGAAG                         GAGCAGCAAAATTTTAGAGCTTTCGTCAGTGGGAAGTCAAGAACGCACCTC
genomic: CAGCAGTAGCTTCGTTGAATCCAACAGTGTTCTTATCCTTTGCATTGAAGgtatgcgaga ... ttttttgcagGAGCAGCAAAATTTTAGAGCTTTCGTCAGTGGGAAGTCAAGAACGCACCTC
EST: gi|76017778|gb|DT944948.1|DT944948
EST:     CAGCAGTAGCTTCGTTGAATCCAACAGTGTTCTTATCCTTTGCATTGAAG                         GAGCAGCAAAATTTTAGAGCTTTCGTCAGTGGGAAGTCAAGAACGCACCTC
genomic: CAGCAGTAGCTTCGTTGAATCCAACAGTGTTCTTATCCTTTGCATTGAAGgtatgcgaga ... ttttttgcagGAGCAGCAAAATTTTAGAGCTTTCGTCAGTGGGAAGTCAAGAACGCACCTC

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 3 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 272

CCGTGGAGCGCATCAAGGCGGCGGTGATCTCCGGCCAGAGCAATCCCCAGCAGCAGTAGCTTCGTTGAATCCAACAGTGTTCTTATCCTTTGCATTGAAGgtatgcgaga ... ttttttgcagGAGCAGCAAAATTTTAGAGCTTTCGTCAGTGGGAAGTCAAGAACGCACCTCAGACTCTCCTGCTTGCCATGTGGTGCTCATAGTTCCCTTTACTTTTTCG


Block sizes: 44 (upstream exon), 42 (downstream exon)
Score: 25

CCGTGGAGCGCATCAAGGCGGCGGTGATCTCCGGCCAGAGCAATCCCCAGCAGCAGTAGCTTCGTTGAATCCAACAGTGTTCTTATCCTTTGCATTGAAGgtatgcgaga ... ttttttgcagGAGCAGCAAAATTTTAGAGCTTTCGTCAGTGGGAAGTCAAGAACGCACCTCAGACTCTCCTGCTTGCCATGTGGTGCTCATAGTTCCCTTTACTTTTTCG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 120

CCGTGGAGCGCATCAAGGCGGCGGTGATCTCCGGCCAGAGCAATCCCCAGCAGCAGTAGCTTCGTTGAATCCAACAGTGTTCTTATCCTTTGCATTGAAGgtatgcgaga ... ttttttgcagGAGCAGCAAAATTTTAGAGCTTTCGTCAGTGGGAAGTCAAGAACGCACCTCAGACTCTCCTGCTTGCCATGTGGTGCTCATAGTTCCCTTTACTTTTTCG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttattgtttagtccgagtactgatgaaatctgatcatcgttgcctttttttgcagGAGCAGCAAAATTTTAGAGCTTTCGTCAGTGGGAAGTCAAGAACGCACCTCAGACTCTCCTGCTTGCCATGTGGTGCTCATAGTTCCCTTTACTTTTTCG
                                    tcgttgccttttttt  CT-rich tract
                                            ttttttt  TA-rich tract