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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtccgtaaaattttgatagatcttttcaaaagagaatgcagatttttctagatgttctgaacatacataattgatcatatttctcgtcatggccacttggttttgcagGTCTTACAGTTGCTTCGTTTTGCTACCTACAGTTTTTCCCATATCCTTTCGATGGCGATG

Basic information

species Zea mays
transcript GRMZM2G050658_T03
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|32851915|gb|CD991596.1|CD991596
EST:     GGACGACTACTGGCATCATTGGCAAGATGTATTTGCAGGGGGTCTTATAG                         GTCTTACAGTTGCTTCGTTTTGCTACCTACAGTTTTTCCCATATCCTTTCG
genomic: GGACGACTACTGGCATCATTGGCAAGATGTATTTGCAGGGGGTCTTATAGgtccgtaaaa ... ggttttgcagGTCTTACAGTTGCTTCGTTTTGCTACCTACAGTTTTTCCCATATCCTTTCG
EST: gi|38229749|gb|CF920062.1|CF920062
EST:     GGACGACTACTGGCATCATTGGCAAGATGTATTTGCAGGGGGTCTTATAG                         GTCTTACAGTTGCTTCGTTTTGCTACCTACAGTTTTTCCCATATCCTTTCG
genomic: GGACGACTACTGGCATCATTGGCAAGATGTATTTGCAGGGGGTCTTATAGgtccgtaaaa ... ggttttgcagGTCTTACAGTTGCTTCGTTTTGCTACCTACAGTTTTTCCCATATCCTTTCG
EST: gi|78103665|gb|DV522093.1|DV522093
EST:     GGACGACTACTGGCATCATTGGCAAGATGTATTTGCAGGGGGTCTTATAG                         GTCTTACAGTTGCTTCGTTTTGCTACCTACAGTTTTTCCCATATCCTTTCG
genomic: GGACGACTACTGGCATCATTGGCAAGATGTATTTGCAGGGGGTCTTATAGgtccgtaaaa ... ggttttgcagGTCTTACAGTTGCTTCGTTTTGCTACCTACAGTTTTTCCCATATCCTTTCG
EST: gi|211132096|gb|FL293580.1|FL293580
EST:     GGACGACTACTGGCATCATTGGCAAGATGTATTTGCAGGGGGTCTTATAG                         GTCTTACAGTTGCTTCGTTTTGCTACCTACAGTTTTTCCCATATCCTTTCG
genomic: GGACGACTACTGGCATCATTGGCAAGATGTATTTGCAGGGGGTCTTATAGgtccgtaaaa ... ggttttgcagGTCTTACAGTTGCTTCGTTTTGCTACCTACAGTTTTTCCCATATCCTTTCG
EST: gi|149072273|gb|EE160529.2|EE160529
EST:     GGACGACTACTGGCATCATTGGCAAGATGTATTTGCAGGGGGTCTTATAG                         GTCTTACAGTTGCTTCGTTTTGCTACCTACAGTTTTTCCCATATCCTTTCG
genomic: GGACGACTACTGGCATCATTGGCAAGATGTATTTGCAGGGGGTCTTATAGgtccgtaaaa ... ggttttgcagGTCTTACAGTTGCTTCGTTTTGCTACCTACAGTTTTTCCCATATCCTTTCG
EST: gi|89759809|gb|DY688508.1|DY688508
EST:     GGACGACTACTGGCATCATTGGCAAGATGTATTTGCAGGGGGTCTTATAG                         GTCTTACAGTTGCTTCGTTTTGCTACCTACAGTTTTTCCCATATCCTTTCG
genomic: GGACGACTACTGGCATCATTGGCAAGATGTATTTGCAGGGGGTCTTATAGgtccgtaaaa ... ggttttgcagGTCTTACAGTTGCTTCGTTTTGCTACCTACAGTTTTTCCCATATCCTTTCG
EST: gi|13178326|gb|BG349584.1|BG349584
EST:     GGACGACTACTGGCATCATTGGCAAGATGTATTTGCAGGGGGTCTTATAG                         GTCTTACAGTTGCTTCGTTTTGCTACCTACAGTTTTTCCCATATCCTTTCG
genomic: GGACGACTACTGGCATCATTGGCAAGATGTATTTGCAGGGGGTCTTATAGgtccgtaaaa ... ggttttgcagGTCTTACAGTTGCTTCGTTTTGCTACCTACAGTTTTTCCCATATCCTTTCG
EST: gi|13178327|gb|BG349585.1|BG349585
EST:     GGACGACTACTGGCATCATTGGCAAGATGTATTTGCAGGGGGTCTTATAG                         GTCTTACAGTTGCTTCGTTTTGCTACCTACAGTTTTTCCCATATCCTTTCG
genomic: GGACGACTACTGGCATCATTGGCAAGATGTATTTGCAGGGGGTCTTATAGgtccgtaaaa ... ggttttgcagGTCTTACAGTTGCTTCGTTTTGCTACCTACAGTTTTTCCCATATCCTTTCG
EST: gi|211413509|gb|FK952159.1|FK952159
EST:     GGACGACTACTGGCATCATTGGCAAGATGTATTTGCAGGGGGTCTTATAG                         GTCTTACAGTTGCTTCGTTTTGCTACCTACAGTTTTTCCCATATCCTTTCG
genomic: GGACGACTACTGGCATCATTGGCAAGATGTATTTGCAGGGGGTCTTATAGgtccgtaaaa ... ggttttgcagGTCTTACAGTTGCTTCGTTTTGCTACCTACAGTTTTTCCCATATCCTTTCG
EST: gi|86471570|gb|DY237940.1|DY237940
EST:     GGACGACTACTGGCATCATTGGCAAGATGTATTTGCAGGGGGTTTTATAG                         GTTTTACAGTTGCTTCGTTTTGCTACCTACAGTTTTTCCCATATCCTTTCG
genomic: GGACGACTACTGGCATCATTGGCAAGATGTATTTGCAGGGGGTCTTATAGgtccgtaaaa ... ggttttgcagGTCTTACAGTTGCTTCGTTTTGCTACCTACAGTTTTTCCCATATCCTTTCG

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: 48 (upstream exon), 49 (downstream exon)
Score: 92

ATTGTGTTCCTGCCTCTCCTTACTGCCGCACTTGTGGCTGTTTCTCGAGTGGACGACTACTGGCATCATTGGCAAGATGTATTTGCAGGGGGTCTTATAGgtccgtaaaa ... ggttttgcagGTCTTACAGTTGCTTCGTTTTGCTACCTACAGTTTTTCCCATATCCTTTCGATGGCGATG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 119

ATTGTGTTCCTGCCTCTCCTTACTGCCGCACTTGTGGCTGTTTCTCGAGTGGACGACTACTGGCATCATTGGCAAGATGTATTTGCAGGGGGTCTTATAGgtccgtaaaa ... ggttttgcagGTCTTACAGTTGCTTCGTTTTGCTACCTACAGTTTTTCCCATATCCTTTCGATGGCGATG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 168

ATTGTGTTCCTGCCTCTCCTTACTGCCGCACTTGTGGCTGTTTCTCGAGTGGACGACTACTGGCATCATTGGCAAGATGTATTTGCAGGGGGTCTTATAGgtccgtaaaa ... ggttttgcagGTCTTACAGTTGCTTCGTTTTGCTACCTACAGTTTTTCCCATATCCTTTCGATGGCGATG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 172

ATTGTGTTCCTGCCTCTCCTTACTGCCGCACTTGTGGCTGTTTCTCGAGTGGACGACTACTGGCATCATTGGCAAGATGTATTTGCAGGGGGTCTTATAGgtccgtaaaa ... ggttttgcagGTCTTACAGTTGCTTCGTTTTGCTACCTACAGTTTTTCCCATATCCTTTCGATGGCGATG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttctgaacatacataattgatcatatttctcgtcatggccacttggttttgcagGTCTTACAGTTGCTTCGTTTTGCTACCTACAGTTTTTCCCATATCCTTTCGATGGCGATG
               aattgat  putative branch site (score: 172)
             ataattgatcatattt  TA-rich tract