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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATTTTTCTTCTTGGTGCTGTTGCGAAACTTGGTGCAACCGTCGTTACGTATCCCCTTCTAGTTGTTAAGgtgattaattattggattggtgataaccacagttgttcacttgcatatttgagtgcataccataaatcaagccttttcttcgtgcag

Basic information

species Zea mays
transcript GRMZM2G540403_T03
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G540403_T02 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os03g15860.1 (Oryza sativa), 5'ss of exon 9
ATTTTTCTTCTTGGTGCTGTTGCGAAACTTGGTGCAACCGTCGTTACGTATCCCCTTCTAGTTGTTAAGgtgattaattattggattggtgataaccacagttgttcacttgcatatttgagtg--catacca---taaatcaagccttttcttcgtgcag
||||| ||||||||||||||||| ||||| ||||| || || ||||| ||||| ||||||||||| |||||||||| ||     |   || | | |  |||  |||    |||| | |||||    |||  ||   |||| || |  |||| ||  | |||
ATTTTCCTTCTTGGTGCTGTTGCCAAACTGGGTGCGACTGTTGTTACATATCCTCTTCTAGTTGTGAAGgtgattatttga-acaccagttacagcagcagccgtttctgtgcacaattgagcagacatgtcaagttaaaccatgttttttttttctacag
















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|24934302|gb|CA452520.1|CA452520
EST:     TTGCGAAACTTGGTGCAACCGTCGTTACGTATCCCCTTCTAGTTGTTAAG                         GCAAGACTTCAGGCAAAGCACATGATTAACGATGACAAGAGGCATCGCTAC
genomic: TTGCGAAACTTGGTGCAACCGTCGTTACGTATCCCCTTCTAGTTGTTAAGgtgattaatt ... cttcgtgcagGCAAGACTTCAGGCAAAGCACATGATTAACGATGACAAGAGGCATCGCTAC
EST: gi|32935002|gb|CF039814.1|CF039814
EST:     TTGCGAAACTTGGTGCAACCGTCGTTACGTATCCCCTTCTAGTTGTTAAG                         GCAAGACTTCAGGCAAAGCACATGATTAACGATGACAAGAGGCATCGCTAC
genomic: TTGCGAAACTTGGTGCAACCGTCGTTACGTATCCCCTTCTAGTTGTTAAGgtgattaatt ... cttcgtgcagGCAAGACTTCAGGCAAAGCACATGATTAACGATGACAAGAGGCATCGCTAC
EST: gi|211096941|gb|FL476436.1|FL476436
EST:     TTGCGAAACTTGGTGCAACCGTCGTTACGTATCCCCTTCTAGTTGTTAAG                         GCAAGACTTCAGGCAAAGCACATGATTAACGATGACAAGAGGCATCGCTAC
genomic: TTGCGAAACTTGGTGCAACCGTCGTTACGTATCCCCTTCTAGTTGTTAAGgtgattaatt ... cttcgtgcagGCAAGACTTCAGGCAAAGCACATGATTAACGATGACAAGAGGCATCGCTAC
EST: gi|32929640|gb|CF034452.1|CF034452
EST:     TTGCGAAACTTGGTGCAACCGTCGTTACGTATCCCCTTCTAGTTGTTAAG                         GCAAGACTTCAGGCAAAGCACATGATTAACGATGACAAGAGGCATCGCTAC
genomic: TTGCGAAACTTGGTGCAACCGTCGTTACGTATCCCCTTCTAGTTGTTAAGgtgattaatt ... cttcgtgcagGCAAGACTTCAGGCAAAGCACATGATTAACGATGACAAGAGGCATCGCTAC
EST: gi|71422924|gb|DR805897.1|DR805897
EST:     TTGCGAAACTTGGTGCAACCGTCGTTACGTATCCCCTTCTAGTTGTTAAG                         GCAAGACTTCAGGCAAAGCACATGATTAACGATGACAAGAGGCATCGCTAC
genomic: TTGCGAAACTTGGTGCAACCGTCGTTACGTATCCCCTTCTAGTTGTTAAGgtgattaatt ... cttcgtgcagGCAAGACTTCAGGCAAAGCACATGATTAACGATGACAAGAGGCATCGCTAC

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: 142

ATTTTTCTTCTTGGTGCTGTTGCGAAACTTGGTGCAACCGTCGTTACGTATCCCCTTCTAGTTGTTAAGgtgattaatt ... cttcgtgcagGCAAGACTTCAGGCAAAGCACATGATTAACGATGACAAGAGGCATCGCTACAAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 204

ATTTTTCTTCTTGGTGCTGTTGCGAAACTTGGTGCAACCGTCGTTACGTATCCCCTTCTAGTTGTTAAGgtgattaatt ... cttcgtgcagGCAAGACTTCAGGCAAAGCACATGATTAACGATGACAAGAGGCATCGCTACAAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 284

ATTTTTCTTCTTGGTGCTGTTGCGAAACTTGGTGCAACCGTCGTTACGTATCCCCTTCTAGTTGTTAAGgtgattaatt ... cttcgtgcagGCAAGACTTCAGGCAAAGCACATGATTAACGATGACAAGAGGCATCGCTACAAAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 184

ATTTTTCTTCTTGGTGCTGTTGCGAAACTTGGTGCAACCGTCGTTACGTATCCCCTTCTAGTTGTTAAGgtgattaatt ... cttcgtgcagGCAAGACTTCAGGCAAAGCACATGATTAACGATGACAAGAGGCATCGCTACAAAG