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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagattctatttactttgctactagctcaaatttttgccgcttaactagctcacccggcctgcaaccgtgcagGCTCTTGTGACATGAAGCCATGGCTGCGGCGTATTCTCCAATTTTTGAGAAACTTATATCAGCATTCCAAACTCTAGAATGCCATCATAATGTTTTCATT

Basic information

species Zea mays
transcript GRMZM2G034143_T01
intron # 15
splice site 3'
intron type U2

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|211032140|gb|FL160201.1|FL160201
EST:     GATTATCAGTCATCGACGCCATTCTTTTGTGACGATAAAAATCGTGTCAG                         GCTCTTGTGACATGAAGCCATGGCTGCGGCGTATTCTCCAATTTTTGAGAA
genomic: GATTATCAGTCATCGACGCCATTCTTTTGTGACGATAAAAATCGTGTCAGgtgagattct ... aaccgtgcagGCTCTTGTGACATGAAGCCATGGCTGCGGCGTATTCTCCAATTTTTGAGAA
EST: gi|211032141|gb|FL160202.1|FL160202
EST:     GATTATCAGTCATCGACGCCATTCTTTTGTGACGATAAAAATCGTGTCAG                         GCTCTTGTGACATGAAGCCATGGCTGCGGCGTATTCTCCAATTTTTGAGAA
genomic: GATTATCAGTCATCGACGCCATTCTTTTGTGACGATAAAAATCGTGTCAGgtgagattct ... aaccgtgcagGCTCTTGTGACATGAAGCCATGGCTGCGGCGTATTCTCCAATTTTTGAGAA
EST: gi|14311434|gb|BG901189.1|BG901189
EST:     GATTATCAGTCATCGACGCCATTCTTTTGTGACGATAAAAATCGTGTCAG                         GCTCTTGTGACATGAAGCCATGGCTGCGGCGTATTCTGCAATTTTTGAGAA
genomic: GATTATCAGTCATCGACGCCATTCTTTTGTGACGATAAAAATCGTGTCAGgtgagattct ... aaccgtgcagGCTCTTGTGACATGAAGCCATGGCTGCGGCGTATTCTCCAATTTTTGAGAA
EST: gi|148943393|gb|EC888452.2|EC888452
EST:     GATTATCAGTCATCGACGCCATTCTTTTGTGACGATAAAAATCGTGTCAG                         GCTCTTGTGACATGAAGCCATGGCTGCGGCGTATTCTCCAATTTTTGAGAA
genomic: GATTATCAGTCATCGACGCCATTCTTTTGTGACGATAAAAATCGTGTCAGgtgagattct ... aaccgtgcagGCTCTTGTGACATGAAGCCATGGCTGCGGCGTATTCTCCAATTTTTGAGAA
EST: gi|211032143|gb|FL160204.1|FL160204
EST:     GATTATCAGTCATCGACGCCATTCTTTTGTGACGATAAAAATCGTGTCAG                         GCTCTTGTGACATGAAGCCATGGCTGSGGCGTATTCTCCAATTTTTGAGA
genomic: GATTATCAGTCATCGACGCCATTCTTTTGTGACGATAAAAATCGTGTCAGgtgagattct ... aaccgtgcagGCTCTTGTGACATGAAGCCATGGCTGCGGCGTATTCTCCAATTTTTGAGA
EST: gi|37385350|gb|CF629812.1|CF629812
EST:     GATTATCAGTCATCGACGCCATTCTTTTGTGACGATAAAAATCGTGTCAG                         GCTCTTGTGACATGAAGCCATGGCTGCGGCGTATTCTCCAATTTTTGAGAA
genomic: GATTATCAGTCATCGACGCCATTCTTTTGTGACGATAAAAATCGTGTCAGgtgagattct ... aaccgtgcagGCTCTTGTGACATGAAGCCATGGCTGCGGCGTATTCTCCAATTTTTGAGAA
EST: gi|60340284|gb|DN207257.1|DN207257
EST:     GATTATCAGTCATCGACGCCATTCTTTTGTGACGATAAAAATCGTGTCAG                         GCTCTTGTGACATGAAGCCATGGCTGCGGCGTATTCTCCAATTTTTGAGAA
genomic: GATTATCAGTCATCGACGCCATTCTTTTGTGACGATAAAAATCGTGTCAGgtgagattct ... aaccgtgcagGCTCTTGTGACATGAAGCCATGGCTGCGGCGTATTCTCCAATTTTTGAGAA
EST: gi|110957674|gb|EE177726.1|EE177726
EST:     GATTATCAGTCATCGACGCCATTCTTTTGTGACGATAAAAATCGTGTCAG                         GCTCTTGTGACATGAAGCCATGGCTGCGGCGTATTCTCCAATTTTTGAGAA
genomic: GATTATCAGTCATCGACGCCATTCTTTTGTGACGATAAAAATCGTGTCAGgtgagattct ... aaccgtgcagGCTCTTGTGACATGAAGCCATGGCTGCGGCGTATTCTCCAATTTTTGAGAA
EST: gi|24766852|gb|CA401999.1|CA401999
EST:     GATTATCAGTCATCGACGCCACTCTTTTGTGACGATAAAAATCGTGTCAG                         GCTCTTGTGACATGAAGCCATGGCTGCGGCGTATTCTCCAATTTTTGAGAA
genomic: GATTATCAGTCATCGACGCCATTCTTTTGTGACGATAAAAATCGTGTCAGgtgagattct ... aaccgtgcagGCTCTTGTGACATGAAGCCATGGCTGCGGCGTATTCTCCAATTTTTGAGAA
EST: gi|67012645|gb|CO441394.1|CO441394
EST:     GATTATCAGTCATCGACGCCATTCTTTTGTGACGATAAAAATCGTGTCAG                         GCTCTTGTGACATGAAGCCATGGCTGCGGCGTATTCTCCAATTTTTGAGAA
genomic: GATTATCAGTCATCGACGCCATTCTTTTGTGACGATAAAAATCGTGTCAGgtgagattct ... aaccgtgcagGCTCTTGTGACATGAAGCCATGGCTGCGGCGTATTCTCCAATTTTTGAGAA
EST: gi|78113248|gb|DV531642.1|DV531642
EST:     GATTATCAGTCATCGACGCCATTCTTTTGTGACGATAAAAATCGTGTCAG                         GCTCTTGTGACATGAAGCCATGGCTGCGGCGTATTCTCCAATTTTTGAGAA
genomic: GATTATCAGTCATCGACGCCATTCTTTTGTGACGATAAAAATCGTGTCAGgtgagattct ... aaccgtgcagGCTCTTGTGACATGAAGCCATGGCTGCGGCGTATTCTCCAATTTTTGAGAA
EST: gi|211032142|gb|FL160203.1|FL160203
EST:     GATTATCAGTCATCGACGCCATTCTTTTGTGACGATAAAAATCGTGTCAG                         GCTCTTGTGACATGAAGCCATGGCTGCGGCGTATTCTCCAATTTTTGAGAA
genomic: GATTATCAGTCATCGACGCCATTCTTTTGTGACGATAAAAATCGTGTCAGgtgagattct ... aaccgtgcagGCTCTTGTGACATGAAGCCATGGCTGCGGCGTATTCTCCAATTTTTGAGAA

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: 47 (upstream exon), 49 (downstream exon)
Score: 50

GTGTTGTGCCTGGGATGGGCGAATTTGGAGACAGATACTTTGGAACAGATGATTATCAGTCATCGACGCCATTCTTTTGTGACGATAAAAATCGTGTCAGgtgagattct ... aaccgtgcagGCTCTTGTGACATGAAGCCATGGCTGCGGCGTATTCTCCAATTTTTGAGAAACTTATATCAGCATTCCAAACTCTAGAATGCCATCATAATGTTTTCATT


Block sizes: 48 (upstream exon), 40 (downstream exon)
Score: 12

GTGTTGTGCCTGGGATGGGCGAATTTGGAGACAGATACTTTGGAACAGATGATTATCAGTCATCGACGCCATTCTTTTGTGACGATAAAAATCGTGTCAGgtgagattct ... aaccgtgcagGCTCTTGTGACATGAAGCCATGGCTGCGGCGTATTCTCCAATTTTTGAGAAACTTATATCAGCATTCCAAACTCTAGAATGCCATCATAATGTTTTCATT


Block sizes: 46 (upstream exon), 36 (downstream exon)
Score: 17

GTGTTGTGCCTGGGATGGGCGAATTTGGAGACAGATACTTTGGAACAGATGATTATCAGTCATCGACGCCATTCTTTTGTGACGATAAAAATCGTGTCAGgtgagattct ... aaccgtgcagGCTCTTGTGACATGAAGCCATGGCTGCGGCGTATTCTCCAATTTTTGAGAAACTTATATCAGCATTCCAAACTCTAGAATGCCATCATAATGTTTTCATT


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 75

GTGTTGTGCCTGGGATGGGCGAATTTGGAGACAGATACTTTGGAACAGATGATTATCAGTCATCGACGCCATTCTTTTGTGACGATAAAAATCGTGTCAGgtgagattct ... aaccgtgcagGCTCTTGTGACATGAAGCCATGGCTGCGGCGTATTCTCCAATTTTTGAGAAACTTATATCAGCATTCCAAACTCTAGAATGCCATCATAATGTTTTCATT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctactagctcaaatttttgccgcttaactagctcacccggcctgcaaccgtgcagGCTCTTGTGACATGAAGCCATGGCTGCGGCGTATTCTCCAATTTTTGAGAAACTTATATCAGCATTCCAAACTCTAGAATGCCATCATAATGTTTTCATT
                             agctcac  putative branch site (score: 75)
        tcaaattttt  TA-rich tract