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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatctggtcttgctactagtgttgatttgaatgttgtagattcaaaaataagttgtgtagtgtcagaaatcaaagtgacagaacatacacgaaaccatccacacaacatttacagtgcccataacaacagttgacataatttcttttcctcttcagagttgacatgattcctttggtgttccatatgtgtagTTTGATCCAGTAAAGCTGAAGAAACTTGGGCCAACTTTTAAGACGAATGGTTCTGTAACGGCTGGCAATTCTTCTAGTATAAG

Basic information

species Zea mays
transcript GRMZM5G860137_T01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G860137_T01 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os01g02020.1 (Oryza sativa), 3'ss of exon 6
gtaatctggtcttgctactagtgttgatttgaatgttgtagattcaaaaataagttgtgtagtgtcagaaatcaaagtgacagaacatacacgaaaccatccacacaacatttacagtgcccataacaacagttgacataatttcttttcctcttcagagttgacatgattcctttggtgt-tccatatgtgtagTTTGATCCAGTAAAGCTGAAGAAACTTGGGCCAACTTTTAAGACGAATGGTTCTGTAACGGCTGGCAATTCTTCTAGTATAAG
                                                                                   | || | |   ||  ||  | |    |||   |||||  | ||||||| || |    | || ||| ||     |||  ||||||| ||| || ||||| || || ||   ||||  || |||  ||||||| |||||||||||| ||||| |||| ||||||||||||||| || ||||||||||||||||||||
-----------------------------------------------------------------------------------accaaaaaaataaaaataaaaattgaatt---agtgcaaacaacaacaattaa----acttttttccc-----agacctgacatgtttctttgggtgtgtctatttgcacagTTCAATTCAGCGAAGCTGAGGAAACTTGGGCCGACTTTCAAGAAGAATGGTTCTGTAACTGCCGGCAATTCTTCTAGTATAAG
















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|78180536|gb|DV551029.1|DV551029
EST:     GTAGAGGGAAACCACCAGTTGTTGTTGACAAGGATGAGAGTCTTGCAAAG                         TTTGATCCAGTAAAGCTGAAGAAACTTGGGCCAACTTTTAAGACGAATGGT
genomic: GTAGAGGGAAACCACCAGTTGTTGTTGACAAGGATGAGAGTCTTGCAAAGgtaatctggt ... atatgtgtagTTTGATCCAGTAAAGCTGAAGAAACTTGGGCCAACTTTTAAGACGAATGGT
EST: gi|71298332|gb|DR785147.1|DR785147
EST:     GACAAGGATGAGAGTCTTGCAAAG                         TTTGATCCAGTAAAGCTGAAGAAACTTGGGCCAACTTTTAAGACGAATGGT
genomic: GACAAGGATGAGAGTCTTGCAAAGgtaatctggt ... atatgtgtagTTTGATCCAGTAAAGCTGAAGAAACTTGGGCCAACTTTTAAGACGAATGGT
EST: gi|6994169|gb|AW453383.1|AW453383
EST:     GTAGAGGGAAACCACCAGTTGTTGTTGACAAGGATGAGAGTCTTGCAAAG                         TTTGATCCAGTAAAGCTGAAGAAACTTGGGCCAACTTTTAAGACGAATGGT
genomic: GTAGAGGGAAACCACCAGTTGTTGTTGACAAGGATGAGAGTCTTGCAAAGgtaatctggt ... atatgtgtagTTTGATCCAGTAAAGCTGAAGAAACTTGGGCCAACTTTTAAGACGAATGGT
EST: gi|12047245|gb|BF729384.1|BF729384
EST:     GTAGAGGGAAACCACCAGTTGTTGTTGACAAGGATGAGAGTCTTGCAAAG                         TTTGATCCAGTAAAGCTGAAGAAACTTGGGCCAACTTTTAAGACGAATGGT
genomic: GTAGAGGGAAACCACCAGTTGTTGTTGACAAGGATGAGAGTCTTGCAAAGgtaatctggt ... atatgtgtagTTTGATCCAGTAAAGCTGAAGAAACTTGGGCCAACTTTTAAGACGAATGGT

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: 45 (upstream exon), 49 (downstream exon)
Score: 68

GTTGAAATTTCTTCTGGTAGAGGGAAACCACCAGTTGTTGTTGACAAGGATGAGAGTCTTGCAAAGgtaatctggt ... atatgtgtagTTTGATCCAGTAAAGCTGAAGAAACTTGGGCCAACTTTTAAGACGAATGGTTCTGTAACGGCTGGCAATTCTTCTAGTATAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 190

GTTGAAATTTCTTCTGGTAGAGGGAAACCACCAGTTGTTGTTGACAAGGATGAGAGTCTTGCAAAGgtaatctggt ... atatgtgtagTTTGATCCAGTAAAGCTGAAGAAACTTGGGCCAACTTTTAAGACGAATGGTTCTGTAACGGCTGGCAATTCTTCTAGTATAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 116

GTTGAAATTTCTTCTGGTAGAGGGAAACCACCAGTTGTTGTTGACAAGGATGAGAGTCTTGCAAAGgtaatctggt ... atatgtgtagTTTGATCCAGTAAAGCTGAAGAAACTTGGGCCAACTTTTAAGACGAATGGTTCTGTAACGGCTGGCAATTCTTCTAGTATAAG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 67

GTTGAAATTTCTTCTGGTAGAGGGAAACCACCAGTTGTTGTTGACAAGGATGAGAGTCTTGCAAAGgtaatctggt ... atatgtgtagTTTGATCCAGTAAAGCTGAAGAAACTTGGGCCAACTTTTAAGACGAATGGTTCTGTAACGGCTGGCAATTCTTCTAGTATAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatttcttttcctcttcagagttgacatgattcctttggtgttccatatgtgtagTTTGATCCAGTAAAGCTGAAGAAACTTGGGCCAACTTTTAAGACGAATGGTTCTGTAACGGCTGGCAATTCTTCTAGTATAAG
                   agttgac  putative branch site (score: 67)