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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCAAGAGGCTGTGTATTGGTTGCGTCTAGTCCTGAAATTCTTACACGAGTCAGTAAGgtatatgaattttggaccttttatgattattcattagattataaaattgtcttctcacaaatgtgcacatttttttaatattctcag

Basic information

species Zea mays
transcript GRMZM2G161337_T02
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G161337_T02 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os03g15780.1 (Oryza sativa), 5'ss of exon 6
GCAAGAGGCTGTGTATTGGTTGCGTCTAGTCCTGAAATTCTTACACGAGTCAGTAAGgtatatgaattttggaccttttatgattattcattagattataaaattgtcttctcacaaatgtgcacatttttttaatattctcag
||||||||||||||  |||| || |||||||| ||||||||||| || || || ||||||| | || |      ||  ||    |  |  || || || |   || |||| |||  ||  | ||   ||||  |   || ||||
GCAAGAGGCTGTGTCCTGGTAGCATCTAGTCCAGAAATTCTTACTCGTGTGAGGAAGgtatgtaaact------ctcctactgatgatagttggaatacattttt-tcttttcattaacattcatccttttaaatctttttcag
















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|33099478|gb|CF059438.1|CF059438
EST:     GCTGTGTATTGGTTGCGTCTAGTCCTGAAATTCTTACACGAGTCAGTAAG                         GGGAAGATTATTAATCGACCACTTGCTGGAACTGTTCGAAGGGGCAAGACA
genomic: GCTGTGTATTGGTTGCGTCTAGTCCTGAAATTCTTACACGAGTCAGTAAGgtatatgaat ... atattctcagGGGAAGATTATTAATCGACCACTTGCTGGAACTGTTCGAAGGGGCAAGACA
EST: gi|31364516|gb|CD448871.1|CD448871
EST:     GCTGTGTATTGGTTGCGTCTAGTCCTGAAATTCTTACACGAGTCAGTAAG                         GGGAAGATTATTAATCGACCACTTGCTGGAACTGTTCGAAGGGGCAAGACA
genomic: GCTGTGTATTGGTTGCGTCTAGTCCTGAAATTCTTACACGAGTCAGTAAGgtatatgaat ... atattctcagGGGAAGATTATTAATCGACCACTTGCTGGAACTGTTCGAAGGGGCAAGACA
EST: gi|5901211|gb|AW042311.1|AW042311
EST:     GCTGTGTATTGGTTGCGTCTAGTCCTGAAATTCTTACACGAGTCAGTAAG                         GGGAAGATTATTAATCGACCACTTGCTGGAACTGTTCGAAGGGGCAAGACA
genomic: GCTGTGTATTGGTTGCGTCTAGTCCTGAAATTCTTACACGAGTCAGTAAGgtatatgaat ... atattctcagGGGAAGATTATTAATCGACCACTTGCTGGAACTGTTCGAAGGGGCAAGACA
EST: gi|116816802|gb|EC859574.1|EC859574
EST:     GCTGTGTATTGGTTGCGTCTAGTCCTGAAATTCTTACACGAGTCAGTAAG                         GGGAAGATTATTAATCGACCACTTGCTGGAACTGTTCGAAGGGGCAAGACA
genomic: GCTGTGTATTGGTTGCGTCTAGTCCTGAAATTCTTACACGAGTCAGTAAGgtatatgaat ... atattctcagGGGAAGATTATTAATCGACCACTTGCTGGAACTGTTCGAAGGGGCAAGACA
EST: gi|33093179|gb|CF053173.1|CF053173
EST:     GCTGTGTATTGGTTGCGTCTAGTCCTGAAATTCTTACACGAGTCAGTAAG                         GGGAAGATTATTAATCGACCACTTGCTGGAACTGTTCGAAGGGGCAAGACA
genomic: GCTGTGTATTGGTTGCGTCTAGTCCTGAAATTCTTACACGAGTCAGTAAGgtatatgaat ... atattctcagGGGAAGATTATTAATCGACCACTTGCTGGAACTGTTCGAAGGGGCAAGACA
EST: gi|71448131|gb|DR829181.1|DR829181
EST:     GCTGTGTATTGGTTGCGTCTAGTCCTGAAATTCTTACACGAGTCAGTAAG                         GGGAAGATTATTAATCGACCACTTGCTGGAACTGTTCGAAGGGGCAAGACA
genomic: GCTGTGTATTGGTTGCGTCTAGTCCTGAAATTCTTACACGAGTCAGTAAGgtatatgaat ... atattctcagGGGAAGATTATTAATCGACCACTTGCTGGAACTGTTCGAAGGGGCAAGACA
EST: gi|7238168|gb|AW573390.1|AW573390
EST:     GCTGNGTATTGGTTGCGTCTAGTCCTGAAATTCTTACACGAGTCAGTAAG                         GGGAAGATTATTAATCGACCACTTGCTGGAACTGTTCGAAGGGGCAAGACA
genomic: GCTGTGTATTGGTTGCGTCTAGTCCTGAAATTCTTACACGAGTCAGTAAGgtatatgaat ... atattctcagGGGAAGATTATTAATCGACCACTTGCTGGAACTGTTCGAAGGGGCAAGACA
EST: gi|211345789|gb|FL266262.1|FL266262
EST:     GCTGTGTATTGGTTGCGTCTAGTCCTGAAATTCTTACACGAGTCAGTAAG                         GGGAAGATTATTAATCGACCACTTGCTGGAACTGTTCGAAGGGGCAAGACA
genomic: GCTGTGTATTGGTTGCGTCTAGTCCTGAAATTCTTACACGAGTCAGTAAGgtatatgaat ... atattctcagGGGAAGATTATTAATCGACCACTTGCTGGAACTGTTCGAAGGGGCAAGACA
EST: gi|32836931|gb|CD976609.1|CD976609
EST:     GCTGTGTATTGGTTGCGTCTAGTCCTGAAATTCTTACACGAGTCAGTAAG                         GGGAAGATTATTAATCGACCACTTGCTGGAACTGTTCGAAGGGGCAAGACA
genomic: GCTGTGTATTGGTTGCGTCTAGTCCTGAAATTCTTACACGAGTCAGTAAGgtatatgaat ... atattctcagGGGAAGATTATTAATCGACCACTTGCTGGAACTGTTCGAAGGGGCAAGACA
EST: gi|67024314|gb|CO453063.1|CO453063
EST:     GCTGTGTATTGGTTGCGTCTAGTCCTGAAATTCTTACACGAGTCAGTAAG                         GGGAAGATTATTAATCGACCACTTGCTGGAACTGTTCGAAGGGGCAAGACA
genomic: GCTGTGTATTGGTTGCGTCTAGTCCTGAAATTCTTACACGAGTCAGTAAGgtatatgaat ... atattctcagGGGAAGATTATTAATCGACCACTTGCTGGAACTGTTCGAAGGGGCAAGACA
EST: gi|211282582|gb|FL175928.1|FL175928
EST:     GCTGTGTATTGGTTGCGTCTAGTCCTGAAATTCTTACACGAGTCAGTAAG                         GGGAAGATTATTAATCGACCACTTGCTGGAACTGTTCGAAGGGGCAAGACA
genomic: GCTGTGTATTGGTTGCGTCTAGTCCTGAAATTCTTACACGAGTCAGTAAGgtatatgaat ... atattctcagGGGAAGATTATTAATCGACCACTTGCTGGAACTGTTCGAAGGGGCAAGACA

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: 322

GCAAGAGGCTGTGTATTGGTTGCGTCTAGTCCTGAAATTCTTACACGAGTCAGTAAGgtatatgaat ... atattctcagGGGAAGATTATTAATCGACCACTTGCTGGAACTGTTCGAAGGGGCAAGACAGAGAAGGAAGATCAAATGCAAGAGCAACAACTGTTAAGTGATGAAAAAC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1415

GCAAGAGGCTGTGTATTGGTTGCGTCTAGTCCTGAAATTCTTACACGAGTCAGTAAGgtatatgaat ... atattctcagGGGAAGATTATTAATCGACCACTTGCTGGAACTGTTCGAAGGGGCAAGACAGAGAAGGAAGATCAAATGCAAGAGCAACAACTGTTAAGTGATGAAAAAC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1976

GCAAGAGGCTGTGTATTGGTTGCGTCTAGTCCTGAAATTCTTACACGAGTCAGTAAGgtatatgaat ... atattctcagGGGAAGATTATTAATCGACCACTTGCTGGAACTGTTCGAAGGGGCAAGACAGAGAAGGAAGATCAAATGCAAGAGCAACAACTGTTAAGTGATGAAAAAC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 377

GCAAGAGGCTGTGTATTGGTTGCGTCTAGTCCTGAAATTCTTACACGAGTCAGTAAGgtatatgaat ... atattctcagGGGAAGATTATTAATCGACCACTTGCTGGAACTGTTCGAAGGGGCAAGACAGAGAAGGAAGATCAAATGCAAGAGCAACAACTGTTAAGTGATGAAAAAC