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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTCAATTATCTCAGAGAGGAGCTACAAATGTTGTCTAAATCAAATCATGTTGCTATTGTCACTGTTGATGGTAGACCTGgttagtgctttctatgatttgctatcatgtttcttacaagctaacttatactgtgctttatcttctacatgctgtgatcttttaactgctggccttcatc...

Basic information

species Zea mays
transcript GRMZM2G078711_T01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G078711_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os01g01070.3 (Oryza sativa), 5'ss of exon 4
GTCAATTATCTCAGAGAGGAGCTACAAATGTTGTCTAAATCAAATCATGTTGCTATTGTCACTGTTGATGGTAGACCTGgttagtgctttctatgatttgctatcatgtttcttacaagctaacttatactgtgctttatcttctacatgctgt-gatcttttaactgctg-gccttcatc
|||||| ||||||||||||| || ||| | ||||| |  |||||||| |||||||||||||| || ||||||||||| |||   | |  |   |  | || | |  ||| |||  ||   |   || | |   |  ||||   | | |  || |  | ||  | |    |  |  ||| | 
GTCAATCATCTCAGAGAGGACCTCCAACTTTTGTCCAGGTCAAATCAAGTTGCTATTGTCACCGTCGATGGTAGACCAGgtctctcccattcttc-tctgttctgttgtatct-gcagtgtgcttttttcctggaattattaaccataacctattaacctagtgatatttatgttttcttt
















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|32840160|gb|CD979841.1|CD979841
EST:     GTTGTCTAAATCAAATCATGTTGCTATTGTCACTGTTGATGGTAGACCTG                         GGCCTGGTGCATATGGTATTACAGCTGTTATTATTGGAGCTATTGGCTATT
genomic: GTTGTCTAAATCAAATCATGTTGCTATTGTCACTGTTGATGGTAGACCTGgttagtgctt ... catgttgcagGGCCTGGTGCATATGGTATTACAGCTGTTATTATTGGAGCTATTGGCTATT
EST: gi|32838724|gb|CD978405.1|CD978405
EST:     GTTGTCTAAATCAAATCATGTTGCTATTGTCACTGTTGATGGTAGACCTG                         GGCCTGGTGCATATGGTATTACAGCTGTTATTATTGGAGCTATTGGCTATT
genomic: GTTGTCTAAATCAAATCATGTTGCTATTGTCACTGTTGATGGTAGACCTGgttagtgctt ... catgttgcagGGCCTGGTGCATATGGTATTACAGCTGTTATTATTGGAGCTATTGGCTATT
EST: gi|78105202|gb|DV523620.1|DV523620
EST:     GTTGTCTAAATCAAATCATGTTGCTATTGTCACTGTTGATGGTAGACCTG                         GGCCTGGTGCATATGGTATTACAGCTGTTATTATTGGAGCTATTGGCTATT
genomic: GTTGTCTAAATCAAATCATGTTGCTATTGTCACTGTTGATGGTAGACCTGgttagtgctt ... catgttgcagGGCCTGGTGCATATGGTATTACAGCTGTTATTATTGGAGCTATTGGCTATT
EST: gi|76017583|gb|DT944753.1|DT944753
EST:     GTTGTCTAAATCAAATCATGTTGCTATTGTCACTGTTGATGGTAGACCTG                         GGCCTGGTGCATATGGTATTACAGCTGTTATTATTGGAGCTATTGGCTATT
genomic: GTTGTCTAAATCAAATCATGTTGCTATTGTCACTGTTGATGGTAGACCTGgttagtgctt ... catgttgcagGGCCTGGTGCATATGGTATTACAGCTGTTATTATTGGAGCTATTGGCTATT
EST: gi|76015767|gb|DT942937.1|DT942937
EST:     GTTGTCTAAATCAAATCATGTTGCTATTGTCACTGTTGATGGTAGACCTG                         GGCCTGGTGCATATGGTATTACAGCTGTTATTATTGGAGCTATTGGCTATT
genomic: GTTGTCTAAATCAAATCATGTTGCTATTGTCACTGTTGATGGTAGACCTGgttagtgctt ... catgttgcagGGCCTGGTGCATATGGTATTACAGCTGTTATTATTGGAGCTATTGGCTATT
EST: gi|211421421|gb|FL071937.1|FL071937
EST:     GTTGTCTAAATCAAATCATGTTGCTATTGTCACTGTTGATGGTAGACCTG                         GGCCTGGTGCATATGGTATTACAGCTGTTATTATTGGAGCTATTGGCTATT
genomic: GTTGTCTAAATCAAATCATGTTGCTATTGTCACTGTTGATGGTAGACCTGgttagtgctt ... catgttgcagGGCCTGGTGCATATGGTATTACAGCTGTTATTATTGGAGCTATTGGCTATT

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: 48 (upstream exon), 33 (downstream exon)
Score: 148

GTCAATTATCTCAGAGAGGAGCTACAAATGTTGTCTAAATCAAATCATGTTGCTATTGTCACTGTTGATGGTAGACCTGgttagtgctt ... catgttgcagGGCCTGGTGCATATGGTATTACAGCTGTTATTATTGGAGCTATTGGCTATTTATTCATAAGATGGAAG


Block sizes: 47 (upstream exon), 33 (downstream exon)
Score: 142

GTCAATTATCTCAGAGAGGAGCTACAAATGTTGTCTAAATCAAATCATGTTGCTATTGTCACTGTTGATGGTAGACCTGgttagtgctt ... catgttgcagGGCCTGGTGCATATGGTATTACAGCTGTTATTATTGGAGCTATTGGCTATTTATTCATAAGATGGAAG


Block sizes: 47 (upstream exon), 33 (downstream exon)
Score: 197

GTCAATTATCTCAGAGAGGAGCTACAAATGTTGTCTAAATCAAATCATGTTGCTATTGTCACTGTTGATGGTAGACCTGgttagtgctt ... catgttgcagGGCCTGGTGCATATGGTATTACAGCTGTTATTATTGGAGCTATTGGCTATTTATTCATAAGATGGAAG


Block sizes: 48 (upstream exon), 33 (downstream exon)
Score: 117

GTCAATTATCTCAGAGAGGAGCTACAAATGTTGTCTAAATCAAATCATGTTGCTATTGTCACTGTTGATGGTAGACCTGgttagtgctt ... catgttgcagGGCCTGGTGCATATGGTATTACAGCTGTTATTATTGGAGCTATTGGCTATTTATTCATAAGATGGAAG