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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctcaagatatacttcacaaggctgtagtagatctcagtttgtacatcttcataaaagatatacttggcgttttatgctaactttgcttttcattgttcagGTTCTAAAGCAGTCTGCTGTCGCTTACTTGAACGGATCTGATTATGCATCTCAG

Basic information

species Zea mays
transcript GRMZM2G011575_T02
intron # 3
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|91048056|gb|EB158474.1|EB158474
EST:     AAGCATTTCTCCAACTTCTGTTAAGTTCGACTAATGGGGACAACATTGAG                         GTTCTAAAGCAGTCTGCTGTCGCTTACTTGAACGGATCTGATTATGCATCT
genomic: AAGCATTTCTCCAACTTCTGTTAAGTTCGACTAATGGGGACAACATTGAGgttatgtagt ... cattgttcagGTTCTAAAGCAGTCTGCTGTCGCTTACTTGAACGGATCTGATTATGCATCT
EST: gi|71307834|gb|DR790138.1|DR790138
EST:     AAGCATTTCTCCAACTTCTGTTAAGTTCGACTAATGGGGACAACATTGAG                         GTTCTAAAGCAGTCTGCTGTCGCTTACTTGAACGGATCTGATTATGCATCT
genomic: AAGCATTTCTCCAACTTCTGTTAAGTTCGACTAATGGGGACAACATTGAGgttatgtagt ... cattgttcagGTTCTAAAGCAGTCTGCTGTCGCTTACTTGAACGGATCTGATTATGCATCT
EST: gi|29167999|gb|CB411259.1|CB411259
EST:     AAGCATTTCTCCAACTTCTGTTAAGTTCGACTAATGGGGACAACATTGAG                         GTTCTAAAGCAGTCTGCTGTCGCTTACTTGAACGGATCCGATTATGCATCT
genomic: AAGCATTTCTCCAACTTCTGTTAAGTTCGACTAATGGGGACAACATTGAGgttatgtagt ... cattgttcagGTTCTAAAGCAGTCTGCTGTCGCTTACTTGAACGGATCTGATTATGCATCT
EST: gi|31358140|gb|CD442497.1|CD442497
EST:     AAGCATTTCTCCAACTTCTGTTAAGTTCGACTAATGGGGACAACATTGAG                         GTTCTAAAGCAGTCTGCTGTCGCTTACTTGAACGGATCTGATTATGCATCT
genomic: AAGCATTTCTCCAACTTCTGTTAAGTTCGACTAATGGGGACAACATTGAGgttatgtagt ... cattgttcagGTTCTAAAGCAGTCTGCTGTCGCTTACTTGAACGGATCTGATTATGCATCT
EST: gi|211502392|gb|FK960892.1|FK960892
EST:     AAGCATTTCTCCAACTTCTGTTAAGTTCGACTAATGGGGACAACATTGAG                         GTTCTAAAGCAGTCTGCTGTCGCTTACTTGAACGGATC
genomic: AAGCATTTCTCCAACTTCTGTTAAGTTCGACTAATGGGGACAACATTGAGgttatgtagt ... cattgttcagGTTCTAAAGCAGTCTGCTGTCGCTTACTTGAACGGATC
EST: gi|148933022|gb|EE285909.2|EE285909
EST:     AAGCATTTCTCCAACTTCTGTTAAGTTCGACTAATGGGGACAACATTGAG                         GTTCTAAAGCAGTCTGCTGTCGCTTACTTGAACGGATCTGATTATGCATCT
genomic: AAGCATTTCTCCAACTTCTGTTAAGTTCGACTAATGGGGACAACATTGAGgttatgtagt ... cattgttcagGTTCTAAAGCAGTCTGCTGTCGCTTACTTGAACGGATCTGATTATGCATCT

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), 46 (downstream exon)
Score: 89

GCTGCATGTGATGAAACTTCTGAGGAAGCAGAACAAGCATTTCTCCAACTTCTGTTAAGTTCGACTAATGGGGACAACATTGAGgttatgtagt ... cattgttcagGTTCTAAAGCAGTCTGCTGTCGCTTACTTGAACGGATCTGATTATGCATCTCAG


Block sizes: 49 (upstream exon), 40 (downstream exon)
Score: 29

GCTGCATGTGATGAAACTTCTGAGGAAGCAGAACAAGCATTTCTCCAACTTCTGTTAAGTTCGACTAATGGGGACAACATTGAGgttatgtagt ... cattgttcagGTTCTAAAGCAGTCTGCTGTCGCTTACTTGAACGGATCTGATTATGCATCTCAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 50

GCTGCATGTGATGAAACTTCTGAGGAAGCAGAACAAGCATTTCTCCAACTTCTGTTAAGTTCGACTAATGGGGACAACATTGAGgttatgtagt ... cattgttcagGTTCTAAAGCAGTCTGCTGTCGCTTACTTGAACGGATCTGATTATGCATCTCAG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 43

GCTGCATGTGATGAAACTTCTGAGGAAGCAGAACAAGCATTTCTCCAACTTCTGTTAAGTTCGACTAATGGGGACAACATTGAGgttatgtagt ... cattgttcagGTTCTAAAGCAGTCTGCTGTCGCTTACTTGAACGGATCTGATTATGCATCTCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcttcataaaagatatacttggcgttttatgctaactttgcttttcattgttcagGTTCTAAAGCAGTCTGCTGTCGCTTACTTGAACGGATCTGATTATGCATCTCAG
                             tgctaac  putative branch site (score: 43)
                                   ctttgcttttcatt  CT-rich tract
     ataaaagatatactt  TA-rich tract