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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACTATTGAAGCACTTTCTTGTGTTCCTTCTCCAGAGTTAGCTCTGAGACTATATTTGCAGTGTGCAGAGgtatgtttgtgatactgcgtattttcataattcttcatcttactctctgattatgtttttaatttag

Basic information

species Zea mays
transcript GRMZM5G844195_T02
intron # 18
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G844195_T02 (Zea mays), 5'ss of exon 18
lower sequence: LOC_Os03g58700.1 (Oryza sativa), 5'ss of exon 17
ACTATTGAAGCACTTTCTTGTGTTCCTTCTCCAGAGTTAGCTCTGAGACTATATTTGCAGTGTGCAGAGgtatgtttgtgatactgcgta-----ttttcataattcttcatcttactctctgattatgtttt-taatttag
|| |||||||| || || |||||||||||||| ||  | ||||| ||| ||||| ||||||||||||||||||   ||| | | |   |      ||| ||||| ||| ||| | |   | | | ||  |||  || |  ||
ACCATTGAAGCTCTCTCATGTGTTCCTTCTCCTGAACTGGCTCTCAGATTATATCTGCAGTGTGCAGAGgtattgctgtaacaattgatttatgctttccataactctgcatatca---tgtaactacctttcatattacag
















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|9952706|gb|BE639169.1|BE639169
EST:     GTGTTCCTTCCCCAGAGGTAGCTCTGAGACTATATTTGCAGTGTGCAGAG                         GCTGCCAATGACTGTGATTTGGAACCAGTTGCTTATGAGTTCTTTACTCAA
genomic: GTGTTCCTTCTCCAGAGTTAGCTCTGAGACTATATTTGCAGTGTGCAGAGgtatgtttgt ... tttaatttagGCTGCCAATGACTGTGATTTGGAACCAGTTGCTTATGAGTTCTTTACTCAA
EST: gi|31355991|gb|CD440348.1|CD440348
EST:     GTGTTCCTTCCCCAGAGTTAGCTCTGAGACTATATTTGCAGTGTGCAGAG                         GCTGCCAATGACTGTGATTTGGAACCAGTTGCTTATGAGTTCTTTACTCAA
genomic: GTGTTCCTTCTCCAGAGTTAGCTCTGAGACTATATTTGCAGTGTGCAGAGgtatgtttgt ... tttaatttagGCTGCCAATGACTGTGATTTGGAACCAGTTGCTTATGAGTTCTTTACTCAA
EST: gi|31353910|gb|CD438267.1|CD438267
EST:     GTGTTCCTTCCCCAGAGTTAGCTCTGAGACTATATTTGCAGTGTGCAGAG                         GCTGCCAATGACTGTGATTTGGAACCAGTTGCTTATGAGTTCTTTACTCAA
genomic: GTGTTCCTTCTCCAGAGTTAGCTCTGAGACTATATTTGCAGTGTGCAGAGgtatgtttgt ... tttaatttagGCTGCCAATGACTGTGATTTGGAACCAGTTGCTTATGAGTTCTTTACTCAA
EST: gi|31355451|gb|CD439808.1|CD439808
EST:     GTGTTCCTTCCCCAGAGTTAGCTCTGAGACTATATTTGCAGTGTGCAGAG                         GCTGCCAATGACTGTGATTTGGAACCAGTTGCTTATGAGTTCTTTACTCAA
genomic: GTGTTCCTTCTCCAGAGTTAGCTCTGAGACTATATTTGCAGTGTGCAGAGgtatgtttgt ... tttaatttagGCTGCCAATGACTGTGATTTGGAACCAGTTGCTTATGAGTTCTTTACTCAA
EST: gi|78088719|gb|DV517112.1|DV517112
EST:     GTGTTCCTTCTCCAGAGTTAGCTCTGAGACTATATTTGCAGTGTGCAGAG                         GCTGCCAATGACTGTGATTTGGAACCAGTTGCTTATGAGTTCTTTACTCAA
genomic: GTGTTCCTTCTCCAGAGTTAGCTCTGAGACTATATTTGCAGTGTGCAGAGgtatgtttgt ... tttaatttagGCTGCCAATGACTGTGATTTGGAACCAGTTGCTTATGAGTTCTTTACTCAA

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), 47 (downstream exon)
Score: 190

ACTATTGAAGCACTTTCTTGTGTTCCTTCTCCAGAGTTAGCTCTGAGACTATATTTGCAGTGTGCAGAGgtatgtttgt ... tttaatttagGCTGCCAATGACTGTGATTTGGAACCAGTTGCTTATGAGTTCTTTACTCAAGCGTTCATTTTATATGAAGAAGAAATCACG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 146

ACTATTGAAGCACTTTCTTGTGTTCCTTCTCCAGAGTTAGCTCTGAGACTATATTTGCAGTGTGCAGAGgtatgtttgt ... tttaatttagGCTGCCAATGACTGTGATTTGGAACCAGTTGCTTATGAGTTCTTTACTCAAGCGTTCATTTTATATGAAGAAGAAATCACG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 149

ACTATTGAAGCACTTTCTTGTGTTCCTTCTCCAGAGTTAGCTCTGAGACTATATTTGCAGTGTGCAGAGgtatgtttgt ... tttaatttagGCTGCCAATGACTGTGATTTGGAACCAGTTGCTTATGAGTTCTTTACTCAAGCGTTCATTTTATATGAAGAAGAAATCACG


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

ACTATTGAAGCACTTTCTTGTGTTCCTTCTCCAGAGTTAGCTCTGAGACTATATTTGCAGTGTGCAGAGgtatgtttgt ... tttaatttagGCTGCCAATGACTGTGATTTGGAACCAGTTGCTTATGAGTTCTTTACTCAAGCGTTCATTTTATATGAAGAAGAAATCACG