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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACAGGCAGACACCGTGGTAAAATCTCTGATGGCCAGCCAAAGCCTTCTTACAAGGGTTTTCCAAATGTTTAACAAGATAGAGCCTCCTATTCTTCTTAAGgtaaaagtctaaaacatttagtctgctctgctatatgttcatgtgattcaatttctttgtatttgtgtttgtttggttatggaagtattcattttttttttgtgcag

Basic information

species Zea mays
transcript GRMZM2G017654_T01
intron # 20
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G017654_T01 (Zea mays), 5'ss of exon 20
lower sequence: LOC_Os04g56530.1 (Oryza sativa), 5'ss of exon 20
ACAGGCAGACACCGTGGTAAAATCTCTGATGGCCAGCCAAAGCCTTCTTACAAGGGTTTTCCAAATGTTTAACAAGATAGAGCCTCCTATTCTTCTTAAGgtaaaagtctaaaacatttagtctgctctgctatatgttcatgtgattcaatttctttgtatttgtgtttgtttggttatggaagtattcattttttttttgtgcag
||| |||||||| || ||||||||||| ||| | ||||||||||||||| || || ||||||| ||||||||||||||||| || ||||||||||||||||||||| |  ||    ||||||   ||  |   |       ||||| |  |||| ||||| ||| ||||| |   ||| | |||  ||    |||  |||| |||||
ACAAGCAGACACTGTCGTAAAATCTCTCATGTCTAGCCAAAGCCTTCTTGCACGGCTTTTCCAGATGTTTAACAAGATAGAACCGCCTATTCTTCTTAAGgtaaaacttcaagcattttagtg-acttagtgttgctactttgtgact-gatttgtttgtgtttctgtttct---gttcttgaaccatc---tttccttttctgcag
















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|211147060|gb|FL256812.1|FL256812
EST:     CAAGGGTTTTCCAAATGTTTAACAAGATAGAGCCTCCTATTCTTCTTAAG                         ATTCTTAGGTGCATTAATCATTTGTCGGGTGATCCTAATTGTCTTGAGACA
genomic: CAAGGGTTTTCCAAATGTTTAACAAGATAGAGCCTCCTATTCTTCTTAAGgtaaaagtct ... ttttgtgcagATTCTTAGGTGCATTAATCATTTGTCGGGTGATCCTAATTGTCTTGAGACA
EST: gi|67013249|gb|CO441998.1|CO441998
EST:     C-AGGGTTTTCCAAATGTTTAACAAGATAGAGCCTCCTATTCTTCTTAAG                         ATTCTTAGGTGCATTAATCATTTGTCGGGTGATCCTAATTGTCTTGAGACA
genomic: CAAGGGTTTTCCAAATGTTTAACAAGATAGAGCCTCCTATTCTTCTTAAGgtaaaagtct ... ttttgtgcagATTCTTAGGTGCATTAATCATTTGTCGGGTGATCCTAATTGTCTTGAGACA
EST: gi|67014005|gb|CO442754.1|CO442754
EST:     CAAGGGTTTTCCAAATGTTTAACAAGATAGAGCCTCCTATTCTTCTTAAG                         ATTCTTAGGTGCATTAATCATTTGTCGGGTGATCCTAATTGTCTTGAGACA
genomic: CAAGGGTTTTCCAAATGTTTAACAAGATAGAGCCTCCTATTCTTCTTAAGgtaaaagtct ... ttttgtgcagATTCTTAGGTGCATTAATCATTTGTCGGGTGATCCTAATTGTCTTGAGACA
EST: gi|91878211|gb|EB408168.1|EB408168
EST:     CAAGGGTTTTCCAAATGTTTAACAAGATAGAGCCTCCTATTCTTCTTAAG                         ATTCTTAGGTGCATTAATCATTTGTCGGGTGATCCTAATTGTCTTGAGACA
genomic: CAAGGGTTTTCCAAATGTTTAACAAGATAGAGCCTCCTATTCTTCTTAAGgtaaaagtct ... ttttgtgcagATTCTTAGGTGCATTAATCATTTGTCGGGTGATCCTAATTGTCTTGAGACA

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: 191

ACAGGCAGACACCGTGGTAAAATCTCTGATGGCCAGCCAAAGCCTTCTTACAAGGGTTTTCCAAATGTTTAACAAGATAGAGCCTCCTATTCTTCTTAAGgtaaaagtct ... ttttgtgcagATTCTTAGGTGCATTAATCATTTGTCGGGTGATCCTAATTGTCTTGAGACACTTCAACGCACAGATGCAATCAAACATCTGATACCGATTCTGGAGCTTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 173

ACAGGCAGACACCGTGGTAAAATCTCTGATGGCCAGCCAAAGCCTTCTTACAAGGGTTTTCCAAATGTTTAACAAGATAGAGCCTCCTATTCTTCTTAAGgtaaaagtct ... ttttgtgcagATTCTTAGGTGCATTAATCATTTGTCGGGTGATCCTAATTGTCTTGAGACACTTCAACGCACAGATGCAATCAAACATCTGATACCGATTCTGGAGCTTC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 166

ACAGGCAGACACCGTGGTAAAATCTCTGATGGCCAGCCAAAGCCTTCTTACAAGGGTTTTCCAAATGTTTAACAAGATAGAGCCTCCTATTCTTCTTAAGgtaaaagtct ... ttttgtgcagATTCTTAGGTGCATTAATCATTTGTCGGGTGATCCTAATTGTCTTGAGACACTTCAACGCACAGATGCAATCAAACATCTGATACCGATTCTGGAGCTTC


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 202

ACAGGCAGACACCGTGGTAAAATCTCTGATGGCCAGCCAAAGCCTTCTTACAAGGGTTTTCCAAATGTTTAACAAGATAGAGCCTCCTATTCTTCTTAAGgtaaaagtct ... ttttgtgcagATTCTTAGGTGCATTAATCATTTGTCGGGTGATCCTAATTGTCTTGAGACACTTCAACGCACAGATGCAATCAAACATCTGATACCGATTCTGGAGCTTC