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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtgctagtctagtttgcagatattacatatatggtatttcatctgtggttatttttatttttgttcattaccgttcagcattaggttggtataatcagttatactgcatcccatatttttttctcagGGTGTGCCCTCACTATTTTCCGATTTAAGCCCACTGTATGAACATCCTGGCAAG

Basic information

species Zea mays
transcript GRMZM2G047093_T01
intron # 10
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|22490182|gb|BU050105.1|BU050105
EST:     AGAAGTTCCAGGAGGCAGCAGACAACTATGTCAGACCTCTATTAACAAAG                         GGTGTGCCCTCACTATTTTCCGATTTAAGCCCACTGTATGAACATCCTGGC
genomic: AGAAGTTCCAGGAGGCAGCAGACAACTATGTCAGACCTCTATTAACAAAGgtaagtgcta ... tttttctcagGGTGTGCCCTCACTATTTTCCGATTTAAGCCCACTGTATGAACATCCTGGC
EST: gi|19057925|gb|BM736592.1|BM736592
EST:     AGAAGTTCCAGGAGGCAGCAGACAACTATGTCAGACCTCTATTAACAAAG                         GGTGTGCCCTCACTATTTTCCGATTTAAGCCCACTGTATGAACATCCTGGC
genomic: AGAAGTTCCAGGAGGCAGCAGACAACTATGTCAGACCTCTATTAACAAAGgtaagtgcta ... tttttctcagGGTGTGCCCTCACTATTTTCCGATTTAAGCCCACTGTATGAACATCCTGGC
EST: gi|18963332|gb|BM660375.1|BM660375
EST:     AGAAGTTCCAGGAGGCAGCAGACAACTATGTCAGACCTCTATTAACAAAG                         GGTGTGCCCTCACTATTTTCCGATTTAAGCCCACTGTATGAACATCCTGGC
genomic: AGAAGTTCCAGGAGGCAGCAGACAACTATGTCAGACCTCTATTAACAAAGgtaagtgcta ... tttttctcagGGTGTGCCCTCACTATTTTCCGATTTAAGCCCACTGTATGAACATCCTGGC
EST: gi|31349081|gb|CD433438.1|CD433438
EST:     AGAAGTTCCAGGAGGCAGCAGACAACTATGTCAGACCTCTATTAACAAAG                         GGTGTGCCCTCACTATTTTCCGATTTAAGCCCACTGTATGAACATCCTGGC
genomic: AGAAGTTCCAGGAGGCAGCAGACAACTATGTCAGACCTCTATTAACAAAGgtaagtgcta ... tttttctcagGGTGTGCCCTCACTATTTTCCGATTTAAGCCCACTGTATGAACATCCTGGC

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: 46 (upstream exon), 48 (downstream exon)
Score: 182

CGTATCCCTCTTGATTTTCTGGAAGGTGAGAAGTTCCAGGAGGCAGCAGACAACTATGTCAGACCTCTATTAACAAAGgtaagtgcta ... tttttctcagGGTGTGCCCTCACTATTTTCCGATTTAAGCCCACTGTATGAACATCCTGGCAAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 203

CGTATCCCTCTTGATTTTCTGGAAGGTGAGAAGTTCCAGGAGGCAGCAGACAACTATGTCAGACCTCTATTAACAAAGgtaagtgcta ... tttttctcagGGTGTGCCCTCACTATTTTCCGATTTAAGCCCACTGTATGAACATCCTGGCAAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 143

CGTATCCCTCTTGATTTTCTGGAAGGTGAGAAGTTCCAGGAGGCAGCAGACAACTATGTCAGACCTCTATTAACAAAGgtaagtgcta ... tttttctcagGGTGTGCCCTCACTATTTTCCGATTTAAGCCCACTGTATGAACATCCTGGCAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 105

CGTATCCCTCTTGATTTTCTGGAAGGTGAGAAGTTCCAGGAGGCAGCAGACAACTATGTCAGACCTCTATTAACAAAGgtaagtgcta ... tttttctcagGGTGTGCCCTCACTATTTTCCGATTTAAGCCCACTGTATGAACATCCTGGCAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttcagcattaggttggtataatcagttatactgcatcccatatttttttctcagGGTGTGCCCTCACTATTTTCCGATTTAAGCCCACTGTATGAACATCCTGGCAAG
                                    tcccatatttttttct  CT-rich tract
                 tataatcagttata  TA-rich tract