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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgattctgtctccccaaataatatcttatgttcaagtgagctatgcatgtcagatttaatttatggagtgaagaatttactttgtaatcaagaacttccatctaacattaactgttgatatttttttatgttcaagtgtaaccttgcttaccactttcatgtgttctataaatccagGTTACAAGGCCGTCAAATTTCCAGGATTTCTACATATATGCATTTCGTTATTGCCTCACAG

Basic information

species Zea mays
transcript GRMZM2G067067_T01
intron # 6
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|211009144|gb|FL186797.1|FL186797
EST:     TAAACTGAAGAAAGCATTTCCTGAACTGGTTCAAGAG                         GTTACAAGGCCGTCAAATTTCCAGGATTTCTACATATATGCATTTCGTTAT
genomic: TAAACTGAAGAAAGCATTTCCTGAACTGGTTCAAGAGgtgattctgt ... ataaatccagGTTACAAGGCCGTCAAATTTCCAGGATTTCTACATATATGCATTTCGTTAT
EST: gi|32864042|gb|CF003724.1|CF003724
EST:     CAGACAGCATCAGTAAACTGAAGAAAGCATTTCCTGAACTGGTTCAAGAG                         GTTACAAGGCCGTCAAATTTCCAGGATTTCTACATATATGCATTTCGTTAT
genomic: CAGACAGCATCAGTAAACTGAAGAAAGCATTTCCTGAACTGGTTCAAGAGgtgattctgt ... ataaatccagGTTACAAGGCCGTCAAATTTCCAGGATTTCTACATATATGCATTTCGTTAT
EST: gi|74233001|gb|DT640915.1|DT640915
EST:     CAGACAGCATCAGTAAACTGAAGAAAGCATTTCCTGAACTGGTTCAAGAG                         GTTACAAGGCCGTCAAATTTCCAGGATTTCTACATATATGCATTTCGTTAT
genomic: CAGACAGCATCAGTAAACTGAAGAAAGCATTTCCTGAACTGGTTCAAGAGgtgattctgt ... ataaatccagGTTACAAGGCCGTCAAATTTCCAGGATTTCTACATATATGCATTTCGTTAT

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: 115

GATGAATGGAGAGCTGGTTTGAAAGCTCTTCGAGCAGACAGCATCAGTAAACTGAAGAAAGCATTTCCTGAACTGGTTCAAGAGgtgattctgt ... ataaatccagGTTACAAGGCCGTCAAATTTCCAGGATTTCTACATATATGCATTTCGTTATTGCCTCACAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 179

GATGAATGGAGAGCTGGTTTGAAAGCTCTTCGAGCAGACAGCATCAGTAAACTGAAGAAAGCATTTCCTGAACTGGTTCAAGAGgtgattctgt ... ataaatccagGTTACAAGGCCGTCAAATTTCCAGGATTTCTACATATATGCATTTCGTTATTGCCTCACAG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 155

GATGAATGGAGAGCTGGTTTGAAAGCTCTTCGAGCAGACAGCATCAGTAAACTGAAGAAAGCATTTCCTGAACTGGTTCAAGAGgtgattctgt ... ataaatccagGTTACAAGGCCGTCAAATTTCCAGGATTTCTACATATATGCATTTCGTTATTGCCTCACAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 164

GATGAATGGAGAGCTGGTTTGAAAGCTCTTCGAGCAGACAGCATCAGTAAACTGAAGAAAGCATTTCCTGAACTGGTTCAAGAGgtgattctgt ... ataaatccagGTTACAAGGCCGTCAAATTTCCAGGATTTCTACATATATGCATTTCGTTATTGCCTCACAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttttatgttcaagtgtaaccttgcttaccactttcatgtgttctataaatccagGTTACAAGGCCGTCAAATTTCCAGGATTTCTACATATATGCATTTCGTTATTGCCTCACAG
                      tgcttac  putative branch site (score: 164)
                                         ttctataaat  TA-rich tract