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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGATCAAAGGCTACTGGTGCCTTCATCTTGACAGCGAGCCATAACCCAGGTGGTCCTACGGAGgtaccaagtttactgctagtgtctttgttgcaaatcaagtgccacacatgctctatgttattgaatacgcctcactgaactttccag

Basic information

species Zea mays
transcript GRMZM2G023289_T03
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G023289_T03 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os03g50480.1 (Oryza sativa), 5'ss of exon 5
GGATCAAAGGCTACTGGTGCCTTCATCTTGACAGCGAGCCATAACCCAGGTGGTCCTACGGAGgtaccaagtttactgctagtgtctttgttgcaaatcaagtgccacacatgctctatgtt-attgaatacgcctcact-gaactttccag
|||||||||||||||||||||||||| || ||||| || || ||||| ||||||||||| |||||| ||   |||      || ||| || ||| ||||||||| |||  ||  ||| |||| ||     ||   ||| | || |||  |||
GGATCAAAGGCTACTGGTGCCTTCATTTTAACAGCTAGTCACAACCCTGGTGGTCCTACTGAGgtatcacagttatgat--gtatctctgctgctaatcaagtggcacg-attttctgtgtttatcagcaacttttcatttgatcttggcag
















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|211503691|gb|FL022246.1|FL022246
EST:     CTGGTGCCTTCATCTTGACAGCGAGCCATAACCCAGGTGGTCCTACGGAG                         GACTTTGGTATCAAATACAATATGGGAAATGGTGGACCTGCCCCTGAATCC
genomic: CTGGTGCCTTCATCTTGACAGCGAGCCATAACCCAGGTGGTCCTACGGAGgtaccaagtt ... aactttccagGACTTTGGTATCAAATACAATATGGGAAATGGTGGACCTGCCCCTGAATCC
EST: gi|31351485|gb|CD435842.1|CD435842
EST:     CTGGTGCCTTCATCTTGACAGCAAGCCATAATCCAGGTGGTCCTACGGAG                         GACTTTGGTATCAAATACAACATGGGAAATGGTGGACCTGCCCCTGAATCC
genomic: CTGGTGCCTTCATCTTGACAGCGAGCCATAACCCAGGTGGTCCTACGGAGgtaccaagtt ... aactttccagGACTTTGGTATCAAATACAATATGGGAAATGGTGGACCTGCCCCTGAATCC
EST: gi|211099119|gb|FL353128.1|FL353128
EST:     CTGGTGCCTTCATCTTGACAGCGAGCCATAACCCAGGTGGTCCTACGGAG                         GACTTTGGTATCAAATACAATATGGGAAATGGTGGACCTGCCCCTGAATCC
genomic: CTGGTGCCTTCATCTTGACAGCGAGCCATAACCCAGGTGGTCCTACGGAGgtaccaagtt ... aactttccagGACTTTGGTATCAAATACAATATGGGAAATGGTGGACCTGCCCCTGAATCC

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: 208

GGATCAAAGGCTACTGGTGCCTTCATCTTGACAGCGAGCCATAACCCAGGTGGTCCTACGGAGgtaccaagtt ... aactttccagGACTTTGGTATCAAATACAATATGGGAAATGGTGGACCTGCCCCTGAATCCGTTACCGACAAGATTTTCTCTAATACAACGACAATCTCTGAATACCTCA


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 182

GGATCAAAGGCTACTGGTGCCTTCATCTTGACAGCGAGCCATAACCCAGGTGGTCCTACGGAGgtaccaagtt ... aactttccagGACTTTGGTATCAAATACAATATGGGAAATGGTGGACCTGCCCCTGAATCCGTTACCGACAAGATTTTCTCTAATACAACGACAATCTCTGAATACCTCA


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 84

GGATCAAAGGCTACTGGTGCCTTCATCTTGACAGCGAGCCATAACCCAGGTGGTCCTACGGAGgtaccaagtt ... aactttccagGACTTTGGTATCAAATACAATATGGGAAATGGTGGACCTGCCCCTGAATCCGTTACCGACAAGATTTTCTCTAATACAACGACAATCTCTGAATACCTCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 328

GGATCAAAGGCTACTGGTGCCTTCATCTTGACAGCGAGCCATAACCCAGGTGGTCCTACGGAGgtaccaagtt ... aactttccagGACTTTGGTATCAAATACAATATGGGAAATGGTGGACCTGCCCCTGAATCCGTTACCGACAAGATTTTCTCTAATACAACGACAATCTCTGAATACCTCA