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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTGAGTGGGATGAGATAAATGTTGCGTGGGGTCAGGCTGCACTTCTGTTGCATACCATGGCCCATTATTTCACTCCAAAATTCCGgtatccttttgttttctcgcagcagctatagtgctcattctaagtgcatggtgttacttacaattctaactctattgaagtgcataaactgtgataattttaatagtaagcacaaaagaatttttttcttagaagaaatgttgcaatgcatttcttgaacattttcctag

Basic information

species Zea mays
transcript GRMZM2G027857_T01
intron # 7
splice site 5'
intron type U12 (go to U12 genes for details)

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G027857_T01 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os01g48920.1 (Oryza sativa), 5'ss of exon 7
GTTGAGTGGGATGAGATAAATGTTGCGTGGGGTCAGGCTGCACTTCTGTTGCATACCATGGCCCATTATTTCACTCCAAAATTCCGgtatccttttgttttctcgcagcagctatagtgctcattctaagtgcatggtgttacttacaattctaact--ctattgaagtgcataaactgtgataattttaatagtaagcacaaaagaatttttttcttagaagaaatgttgcaatgcatttcttgaacattttcctag
||||| |||||||||||||||| ||| |||||||||||||| ||||| |||||||||||||| || || ||||| ||||||||   ||||||||    | |     |  |  |||  | ||     |||     ||||  | |||   |     | |  | |||||  | |      |    || |                                                                        
GTTGAATGGGATGAGATAAATGCTGCTTGGGGTCAGGCTGCTCTTCTTTTGCATACCATGGCTCAGTACTTCACCCCAAAATTTGAgtatccttgacatattgatgactatttattttactacaattaatccattggtcattcttttgagaaggaattcccattgatcttcccttcatcaactagt------------------------------------------------------------------------

upper sequence: GRMZM2G027857_T01 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os03g44200.1 (Oryza sativa), 5'ss of exon 8
GTTGAGTGGGATGAGATAAATGTTGCGTGGGGTCAGGCTGCACTTCTGTTGCATACCATGGCCCATTATTTCACTCCAAAATTCCGgtatccttttgttttctcgcagcagctatagtgctcattctaagtgcatggtgttacttacaattctaactctattgaagtgcataaactgtgataattttaatagtaagcacaaaagaatttttttcttagaagaaatgttgcaatgcatttcttgaacattttcctag
|| ||||||||||||||||||| ||| ||||| |||||||| |||||||||||||||||||| || || |||   ||||||||   |||||||||  |    |  ||  |  | |  | |  | | ||  |||  |   ||   |  |    ||| ||   |  |  ||||  ||    || |  |   ||                                                                 
GTGGAGTGGGATGAGATAAATGCTGCTTGGGGCCAGGCTGCTCTTCTGTTGCATACCATGGCTCAGTACTTCTTCCCAAAATTTGAgtatccttt-atacagtgacattatttttgctac--agtttatttgctggtcattctcttgagaagtaattca--tacatggcatttacctccatcaactagtta-----------------------------------------------------------------
















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|211072573|gb|FL217254.1|FL217254
EST:     GCTGMACTTCTGTTGCATACCATGGCCCATTATTTCACTCCAAAATTCCG                         ATACCGGATCAAGATTCACCCTATGGGAAGCTATCCAAGAGTCACAGACAT
genomic: GCTGCACTTCTGTTGCATACCATGGCCCATTATTTCACTCCAAAATTCCGgtatcctttt ... attttcctagATACCGGATCAAGATTCACCCTATGGGAAGCTATCCAAGAGTCACAGACAT
EST: gi|60400753|gb|DN233560.1|DN233560
EST:     CTGCACTTCTGTTGCATACCATGGCCCATTATTTCACTCCAAAATTCCG                         ATACCGGATCAAGATTCACCCTATGGGAAGCTATCCAAGAGTCACAGACAT
genomic: CTGCACTTCTGTTGCATACCATGGCCCATTATTTCACTCCAAAATTCCGgtatcctttt ... attttcctagATACCGGATCAAGATTCACCCTATGGGAAGCTATCCAAGAGTCACAGACAT

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: 46 (upstream exon), 47 (downstream exon)
Score: 213

GTTGAGTGGGATGAGATAAATGTTGCGTGGGGTCAGGCTGCACTTCTGTTGCATACCATGGCCCATTATTTCACTCCAAAATTCCGgtatcctttt ... attttcctagATACCGGATCAAGATTCACCCTATGGGAAGCTATCCAAGAGTCACAGACATCCACAATCATACATATGAACT


Block sizes: 47 (upstream exon), 46 (downstream exon)
Score: 235

GTTGAGTGGGATGAGATAAATGTTGCGTGGGGTCAGGCTGCACTTCTGTTGCATACCATGGCCCATTATTTCACTCCAAAATTCCGgtatcctttt ... attttcctagATACCGGATCAAGATTCACCCTATGGGAAGCTATCCAAGAGTCACAGACATCCACAATCATACATATGAACT


Block sizes: 47 (upstream exon), 47 (downstream exon)
Score: 229

GTTGAGTGGGATGAGATAAATGTTGCGTGGGGTCAGGCTGCACTTCTGTTGCATACCATGGCCCATTATTTCACTCCAAAATTCCGgtatcctttt ... attttcctagATACCGGATCAAGATTCACCCTATGGGAAGCTATCCAAGAGTCACAGACATCCACAATCATACATATGAACT


Block sizes: 47 (upstream exon), 46 (downstream exon)
Score: 227

GTTGAGTGGGATGAGATAAATGTTGCGTGGGGTCAGGCTGCACTTCTGTTGCATACCATGGCCCATTATTTCACTCCAAAATTCCGgtatcctttt ... attttcctagATACCGGATCAAGATTCACCCTATGGGAAGCTATCCAAGAGTCACAGACATCCACAATCATACATATGAACT