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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACGATCTGCCTCTTTGGGgtatgttcttctcaatatagtattttcttttctcaatgtgtctacctgttttgccttgtatgatagtttccacatgttttgaacag

Basic information

species Zea mays
transcript GRMZM2G420310_T01
intron # 4
splice site 5'
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|60351142|gb|DN218115.1|DN218115
EST:     TTTATAGACGATCTGCCTCTTTGGG                         GTTTTGTTGGGGAGACTGACAAGAACAGTGAAAACAAGCATTATCTTTACA
genomic: TTTATAGACGATCTGCCTCTTTGGGgtatgttctt ... ttttgaacagGTTTTGTTGGGGAGACTGACAAGAACAGTGAAAACAAGCATTATCTTTACA
EST: gi|211318943|gb|FL142494.1|FL142494
EST:     TTTATAGACGATCTGCCTCTTTGGG                         GGTTTTGNTTGGGGAGACTGACAAGAACAGTGAAAACAAGCATTATCTTTA
genomic: TTTATAGACGATCTGCCTCTTTGGGgtatgttctt ... ttttgaacagG-TTTTG-TTGGGGAGACTGACAAGAACAGTGAAAACAAGCATTATCTTTA
EST: gi|160481321|gb|EY254485.1|EY254485
EST:     TTTATAGACGATCTGCCTCTTTGGG                         GTTTTGTTGGGGAGACTGACAAGAACAGTGAAAACAAGCATTATCTTTACA
genomic: TTTATAGACGATCTGCCTCTTTGGGgtatgttctt ... ttttgaacagGTTTTGTTGGGGAGACTGACAAGAACAGTGAAAACAAGCATTATCTTTACA
EST: gi|78079180|gb|DV507592.1|DV507592
EST:     TTTATAGACGATCTGCCTCTTTGGG                         GTTTTGTTGGGGAGACTGACAAGAACAGTGAAAACAAGCATTATCTTTACA
genomic: TTTATAGACGATCTGCCTCTTTGGGgtatgttctt ... ttttgaacagGTTTTGTTGGGGAGACTGACAAGAACAGTGAAAACAAGCATTATCTTTACA
EST: gi|31356502|gb|CD440859.1|CD440859
EST:     TTTATAGACGATCTGCCTCTTTGGG                         GTTTTGTTGGGGAGACTGACAAGAACAGTGAAAACAAGCATTATCTTTACA
genomic: TTTATAGACGATCTGCCTCTTTGGGgtatgttctt ... ttttgaacagGTTTTGTTGGGGAGACTGACAAGAACAGTGAAAACAAGCATTATCTTTACA
EST: gi|71766500|gb|DR964437.1|DR964437
EST:     TTTATAGACGATCTGCCTCTTTGGG                         GTTTTGTTGGGGAGACTGACAAGAACAGTGAAAACAAGCATTATCTTTACA
genomic: TTTATAGACGATCTGCCTCTTTGGGgtatgttctt ... ttttgaacagGTTTTGTTGGGGAGACTGACAAGAACAGTGAAAACAAGCATTATCTTTACA
EST: gi|89249564|gb|DY621350.1|DY621350
EST:     TTTATAGACGATCTGCCTCTTTGGG                         GTTTTGTTGGGGAGACTGACAAGAACAGTGAAAACAAGCATTATCTTTACA
genomic: TTTATAGACGATCTGCCTCTTTGGGgtatgttctt ... ttttgaacagGTTTTGTTGGGGAGACTGACAAGAACAGTGAAAACAAGCATTATCTTTACA
EST: gi|160481319|gb|EY254483.1|EY254483
EST:     TTTATAGACGATCTGCCTCTTTGGG                         GTTTTGTTGGGGAGACTGACAAGAACAGTGAAAACAAGCATTATCTTTACA
genomic: TTTATAGACGATCTGCCTCTTTGGGgtatgttctt ... ttttgaacagGTTTTGTTGGGGAGACTGACAAGAACAGTGAAAACAAGCATTATCTTTACA
EST: gi|29130633|gb|CB381337.1|CB381337
EST:     TTTATAGACGATCTGNCTCTTTGGG                         GTTTTGTTGGGGAGACTGACAAGAACAGTGNAAACAAGCATTATCTTTACA
genomic: TTTATAGACGATCTGCCTCTTTGGGgtatgttctt ... ttttgaacagGTTTTGTTGGGGAGACTGACAAGAACAGTGAAAACAAGCATTATCTTTACA

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), 48 (downstream exon)
Score: 305

ACGATCTGCCTCTTTGGGgtatgttctt ... ttttgaacagGTTTTGTTGGGGAGACTGACAAGAACAGTGAAAACAAGCATTATCTTTACACGCACAAGAACATCCTTGTTAAATACAATGATAACAGG


Block sizes: 18 (upstream exon), 49 (downstream exon)
Score: 294

ACGATCTGCCTCTTTGGGgtatgttctt ... ttttgaacagGTTTTGTTGGGGAGACTGACAAGAACAGTGAAAACAAGCATTATCTTTACACGCACAAGAACATCCTTGTTAAATACAATGATAACAGG


Block sizes: 18 (upstream exon), 49 (downstream exon)
Score: 333

ACGATCTGCCTCTTTGGGgtatgttctt ... ttttgaacagGTTTTGTTGGGGAGACTGACAAGAACAGTGAAAACAAGCATTATCTTTACACGCACAAGAACATCCTTGTTAAATACAATGATAACAGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 581

ACGATCTGCCTCTTTGGGgtatgttctt ... ttttgaacagGTTTTGTTGGGGAGACTGACAAGAACAGTGAAAACAAGCATTATCTTTACACGCACAAGAACATCCTTGTTAAATACAATGATAACAGG