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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGTTACACGGACATAAAGAAAAGATCATTGTTATCTTCCTTGGAGGATTACAGTACACTACATCTTCAAACTGGCAGACCGATGTGGTCACCTGGgtaagtgactggtaatttgtgcttctggttcatgagtgttctgattaaatggaaatccttctctgcctgtag

Basic information

species Zea mays
transcript GRMZM2G149520_T02
intron # 12
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|18655143|gb|BM499948.1|BM499948
EST:     GATTACAGTACACTACATCTTCAAACTGGCAGACCGATGTGGTCACCTGG                         GTTTGCTTTTACTATATTGAAAAGGTTCATGCCAGAAGATAAACTTGCAGA
genomic: GATTACAGTACACTACATCTTCAAACTGGCAGACCGATGTGGTCACCTGGgtaagtgact ... ctgcctgtagGTTTGCTTTTACTATATTGAAAAGGTTCATGCCAGAAGATAAACTTGCAGA
EST: gi|31353684|gb|CD438041.1|CD438041
EST:     GATTACAGTACACTACATCTTCAAACTGGCAGACCGATGTGGTCACCTGG                         GTTTGCTTTTACTATATTGAAAAGGTTCATGCCAGAAGATAAACTTGCAGA
genomic: GATTACAGTACACTACATCTTCAAACTGGCAGACCGATGTGGTCACCTGGgtaagtgact ... ctgcctgtagGTTTGCTTTTACTATATTGAAAAGGTTCATGCCAGAAGATAAACTTGCAGA
EST: gi|101394193|gb|EB819031.1|EB819031
EST:     GATTACAGTACACTACATCTTCAAACTGGCAGACCGATGTGGTCACCTGG                         GTTTGCTTTTACTATA-TGAAAAAGGTTCATGCCAGAAGATAAACTTGCAG
genomic: GATTACAGTACACTACATCTTCAAACTGGCAGACCGATGTGGTCACCTGGgtaagtgact ... ctgcctgtagGTTTGCTTTTACTATATTG-AAAAGGTTCATGCCAGAAGATAAACTTGCAG
EST: gi|78026164|gb|DV494551.1|DV494551
EST:     GATTACAGTACACTACATCTTCAAACTGGCAGACCGATGTGGTCACCTGG                         GTTTGCTTTTACTATATTGAAAAGGTTCATGCCAGAAGATAAACTTGCAGA
genomic: GATTACAGTACACTACATCTTCAAACTGGCAGACCGATGTGGTCACCTGGgtaagtgact ... ctgcctgtagGTTTGCTTTTACTATATTGAAAAGGTTCATGCCAGAAGATAAACTTGCAGA
EST: gi|32835099|gb|CD974777.1|CD974777
EST:     ACACTACATCTTCAAACTGGCAGACCGATGTGGTCACCTGG                         GTTTGCTTTTACTATATTGAAAAGGTTCATGCCAGAAGATAAACTTGCAGA
genomic: ACACTACATCTTCAAACTGGCAGACCGATGTGGTCACCTGGgtaagtgact ... ctgcctgtagGTTTGCTTTTACTATATTGAAAAGGTTCATGCCAGAAGATAAACTTGCAGA
EST: gi|24766670|gb|CA401817.1|CA401817
EST:     GATTACAGTACACTACATCTTCAAACTGGCAGACCGATGTGGTCACCTGG                         GTTTGCTTTTACTATATTGAAAAGGTTCATGCCAGAAGATAAACTTGCAGA
genomic: GATTACAGTACACTACATCTTCAAACTGGCAGACCGATGTGGTCACCTGGgtaagtgact ... ctgcctgtagGTTTGCTTTTACTATATTGAAAAGGTTCATGCCAGAAGATAAACTTGCAGA

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: 265

GGTTACACGGACATAAAGAAAAGATCATTGTTATCTTCCTTGGAGGATTACAGTACACTACATCTTCAAACTGGCAGACCGATGTGGTCACCTGGgtaagtgact ... ctgcctgtagGTTTGCTTTTACTATATTGAAAAGGTTCATGCCAGAAGATAAACTTGCAGATGTAAAGGGTGCCACCCTCACCGCTGATGGAACAGGAGTTGTATTTGAT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 185

GGTTACACGGACATAAAGAAAAGATCATTGTTATCTTCCTTGGAGGATTACAGTACACTACATCTTCAAACTGGCAGACCGATGTGGTCACCTGGgtaagtgact ... ctgcctgtagGTTTGCTTTTACTATATTGAAAAGGTTCATGCCAGAAGATAAACTTGCAGATGTAAAGGGTGCCACCCTCACCGCTGATGGAACAGGAGTTGTATTTGAT


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 174

GGTTACACGGACATAAAGAAAAGATCATTGTTATCTTCCTTGGAGGATTACAGTACACTACATCTTCAAACTGGCAGACCGATGTGGTCACCTGGgtaagtgact ... ctgcctgtagGTTTGCTTTTACTATATTGAAAAGGTTCATGCCAGAAGATAAACTTGCAGATGTAAAGGGTGCCACCCTCACCGCTGATGGAACAGGAGTTGTATTTGAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 141

GGTTACACGGACATAAAGAAAAGATCATTGTTATCTTCCTTGGAGGATTACAGTACACTACATCTTCAAACTGGCAGACCGATGTGGTCACCTGGgtaagtgact ... ctgcctgtagGTTTGCTTTTACTATATTGAAAAGGTTCATGCCAGAAGATAAACTTGCAGATGTAAAGGGTGCCACCCTCACCGCTGATGGAACAGGAGTTGTATTTGAT