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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAATTTGTCACTTTGAAGGCTATATTTAAATCACATGTGCTGAGGGTGCACAAATCCAAATTTGCACAGgttaaggattaaccttttctcctctaaagtagactcacaatgtttagtacctaagttgtattttcagttgctttctgcctcaccctcttggattgacacatttattttgacttttgcag

Basic information

species Zea mays
transcript GRMZM2G415846_T01
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G415846_T01 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os06g47350.2 (Oryza sativa), 5'ss of exon 10
GAATTTGTCACTTTGAAGGCTATATTTAAATCACATGTGCTGAGGGTGCACAAATCCAAATTTGCACAGgttaaggattaaccttttctcctctaaagtagactcacaatgttt-----agtac-ctaagttgtatt----------------ttcagttgctttctgcctcaccctcttggattgacacatttattttgacttttgcag
|| |||| || | ||||| |||| |||  | ||  |||||| |||||||||||||||||||||||||||||||||  | | | |||| |  | | || |||| |||| ||  ||     ||| | | | ||  ||||                |||  | ||| ||||| ||   ||  |    |||  | | |  | | | ||| ||||
GAGTTTGACATTCTGAAGACTATCTTTCGAGCATCTGTGCTAAGGGTGCACAAATCCAAATTTGCACAGgttaagattaaccttttttttgtgttaactagattcactataattttgtgagtgcaccatgtgctattcagcattatatatttattccatcgctctctgcttcgttcttgttatctgattcttctgctgtaaattt-gcag
















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|101383979|gb|EB814044.1|EB814044
EST:     CTATATTTAAATCACATGTGCTGAGGGTGCACAAATCCAAATTTGCACAG                         TTTATCATGTTTTATGCTTGTTCCCTGCATCCTGAGATTGGCGATGGCTTT
genomic: CTATATTTAAATCACATGTGCTGAGGGTGCACAAATCCAAATTTGCACAGgttaaggatt ... acttttgcagTTTATCATGTTTTATGCTTGTTCCCTGCATCCTGAGATTGGCGATGGCTTT
EST: gi|93283859|gb|EB676123.1|EB676123
EST:     CTATATTTAAATCACATGTGCTGAGGGTGCACAAATCCAAATTTGCACAG                         TTTATCATGTTTTATGCTTGTTCCCTGCATCCTGAGATTGGCGATGGCTTT
genomic: CTATATTTAAATCACATGTGCTGAGGGTGCACAAATCCAAATTTGCACAGgttaaggatt ... acttttgcagTTTATCATGTTTTATGCTTGTTCCCTGCATCCTGAGATTGGCGATGGCTTT
EST: gi|21843184|gb|BQ703750.1|BQ703750
EST:     CTATATTTAAATCACATGTGCTGAGGGTGCACAAATCCAAATTTGCACAG                         TTTATCATGTTTTATGCTTGTTCCCTGCATCCTGAGATTGGCGATGGCTTT
genomic: CTATATTTAAATCACATGTGCTGAGGGTGCACAAATCCAAATTTGCACAGgttaaggatt ... acttttgcagTTTATCATGTTTTATGCTTGTTCCCTGCATCCTGAGATTGGCGATGGCTTT
EST: gi|26457293|gb|CA828876.1|CA828876
EST:     CTATATTTAAATCACATGTGCTGAGGGTGCACAAATCCAAATTTGCACAG                         TTTATCATGTTTTATGCTTGTTCCCTGCATCCTGAGATTGGCGATGGCTTT
genomic: CTATATTTAAATCACATGTGCTGAGGGTGCACAAATCCAAATTTGCACAGgttaaggatt ... acttttgcagTTTATCATGTTTTATGCTTGTTCCCTGCATCCTGAGATTGGCGATGGCTTT
EST: gi|21390134|gb|BQ528183.1|BQ528183
EST:     CTATATTTAAATCACATGTGCTGAGGGTGCACAAATCCAAATTTGCACAG                         TTTATCATGTTTTATGCTTGTTCCCTGCATCCTGAGATTGGCGATGGCTTT
genomic: CTATATTTAAATCACATGTGCTGAGGGTGCACAAATCCAAATTTGCACAGgttaaggatt ... acttttgcagTTTATCATGTTTTATGCTTGTTCCCTGCATCCTGAGATTGGCGATGGCTTT

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: 248

GAATTTGTCACTTTGAAGGCTATATTTAAATCACATGTGCTGAGGGTGCACAAATCCAAATTTGCACAGgttaaggatt ... acttttgcagTTTATCATGTTTTATGCTTGTTCCCTGCATCCTGAGATTGGCGATGGCTTTGCTAATTTTCTTACTGATATTTTTATTGACAAGGACAAAAACGAGGATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 152

GAATTTGTCACTTTGAAGGCTATATTTAAATCACATGTGCTGAGGGTGCACAAATCCAAATTTGCACAGgttaaggatt ... acttttgcagTTTATCATGTTTTATGCTTGTTCCCTGCATCCTGAGATTGGCGATGGCTTTGCTAATTTTCTTACTGATATTTTTATTGACAAGGACAAAAACGAGGATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 181

GAATTTGTCACTTTGAAGGCTATATTTAAATCACATGTGCTGAGGGTGCACAAATCCAAATTTGCACAGgttaaggatt ... acttttgcagTTTATCATGTTTTATGCTTGTTCCCTGCATCCTGAGATTGGCGATGGCTTTGCTAATTTTCTTACTGATATTTTTATTGACAAGGACAAAAACGAGGATG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 158

GAATTTGTCACTTTGAAGGCTATATTTAAATCACATGTGCTGAGGGTGCACAAATCCAAATTTGCACAGgttaaggatt ... acttttgcagTTTATCATGTTTTATGCTTGTTCCCTGCATCCTGAGATTGGCGATGGCTTTGCTAATTTTCTTACTGATATTTTTATTGACAAGGACAAAAACGAGGATG