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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTCAGAGACCTGGTCCACAAGAAGAGCAAATTCCAGTACAAGCCCAACTGGATCAATGTTCTTGAGGGGTCTCAGGAAGCATCCTACCTATGGgtatgagttagcagtgacacaactacaaattcttctatgctcttgcttactttatctttacactaccacatacatatatatctgtatgctctgtaaggtcgtcggtgtaacttcagtgtagaagtagaaccttagcctgtgcatgccctgagatgtattgtag

Basic information

species Zea mays
transcript GRMZM2G085711_T02
intron # 4
splice site 5'
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|71757183|gb|DR955120.1|DR955120
EST:     CCAACTGGATCAATGTTCTTGAGGGGTCTCAGGAAGCATCCTACCTATGG                         GTCGCTCTGAATTACTTGCTGGATAAACTGGGAGGGGAGTATTCCCAGACG
genomic: CCAACTGGATCAATGTTCTTGAGGGGTCTCAGGAAGCATCCTACCTATGGgtatgagtta ... tgtattgtagGTCGCTCTGAATTACTTGCTGGATAAACTGGGAGGGGAGTATTCCCAGACG
EST: gi|78120186|gb|DV538570.1|DV538570
EST:     CCAACTGGATCAATGTTCTTGAGGGGTCTCAGGAAGCATCCTACCTATGG                         GTCGCTCTGAATTACTTGCTGGATAAACTGGGAGGGGAGTATTCCCAGACG
genomic: CCAACTGGATCAATGTTCTTGAGGGGTCTCAGGAAGCATCCTACCTATGGgtatgagtta ... tgtattgtagGTCGCTCTGAATTACTTGCTGGATAAACTGGGAGGGGAGTATTCCCAGACG
EST: gi|211540961|gb|FL453890.1|FL453890
EST:     CCAACTGGATCAATGTTCTTGAGGGGTCTCAGGAAGCATCCTACCTATGG                         GTCGCTCTGAATTACTTGCTGGATAAACTGGGAGGGGAGTATTCCCAGACG
genomic: CCAACTGGATCAATGTTCTTGAGGGGTCTCAGGAAGCATCCTACCTATGGgtatgagtta ... tgtattgtagGTCGCTCTGAATTACTTGCTGGATAAACTGGGAGGGGAGTATTCCCAGACG
EST: gi|93012636|gb|EB638156.1|EB638156
EST:     CCAACTGGATCAATGTTCTTGAGGGGTCTCAGGAAGCATCCTACCTATGG                         GTCGCTCTGAATTACTTGCTGGATAAACTGGGAGGGGAGTATTCCCAGACG
genomic: CCAACTGGATCAATGTTCTTGAGGGGTCTCAGGAAGCATCCTACCTATGGgtatgagtta ... tgtattgtagGTCGCTCTGAATTACTTGCTGGATAAACTGGGAGGGGAGTATTCCCAGACG
EST: gi|76013368|gb|DT940538.1|DT940538
EST:     CCAACTGGATCAATGTTCTTGAGGGGTCTCAGGAAGCATCCTACCTATGG                         GTCGCTCTGAATTACTTGCTGGATAAACTGGGAGGGGAGTATTCCCAGACG
genomic: CCAACTGGATCAATGTTCTTGAGGGGTCTCAGGAAGCATCCTACCTATGGgtatgagtta ... tgtattgtagGTCGCTCTGAATTACTTGCTGGATAAACTGGGAGGGGAGTATTCCCAGACG
EST: gi|93283843|gb|EB676107.1|EB676107
EST:     GGAAGCATCCTACCTATGG                         GTCGCTCTGAATTACTTGCTGGATAAACTGGGAGGGGAGTATTCCCAGACG
genomic: GGAAGCATCCTACCTATGGgtatgagtta ... tgtattgtagGTCGCTCTGAATTACTTGCTGGATAAACTGGGAGGGGAGTATTCCCAGACG
EST: gi|32847046|gb|CD986727.1|CD986727
EST:     CCAACTGGATCAATGTTCTTGAGGGGTCTCAGGAAGCATCCTACCTATGG                         GTCGCTCTGAATTACTTGCTGGATAAACTGGGAGGGGAGTATTCCCAGACG
genomic: CCAACTGGATCAATGTTCTTGAGGGGTCTCAGGAAGCATCCTACCTATGGgtatgagtta ... tgtattgtagGTCGCTCTGAATTACTTGCTGGATAAACTGGGAGGGGAGTATTCCCAGACG
EST: gi|71323603|gb|DR798474.1|DR798474
EST:     CCAACTGGATCAATGTTCTTGAGGGGTCTCAGGAAGCATCCTACCTATGG                         GTCGCTCTGAATTACTTGCTGGATAAACTGGGAGGGGAGTATTCCCAGACG
genomic: CCAACTGGATCAATGTTCTTGAGGGGTCTCAGGAAGCATCCTACCTATGGgtatgagtta ... tgtattgtagGTCGCTCTGAATTACTTGCTGGATAAACTGGGAGGGGAGTATTCCCAGACG
EST: gi|91876116|gb|EB406073.1|EB406073
EST:     CCAACTGGATCAATGTTCTTGAGGGGTCTCAGGAAGCATCCTACCTATGG                         GTCGCTCTGAATTACTTGCTGGATAAACTGGGAGGGGAGTATTCCCAGACG
genomic: CCAACTGGATCAATGTTCTTGAGGGGTCTCAGGAAGCATCCTACCTATGGgtatgagtta ... tgtattgtagGTCGCTCTGAATTACTTGCTGGATAAACTGGGAGGGGAGTATTCCCAGACG
EST: gi|78120472|gb|DV538856.1|DV538856
EST:     CCAACTGGATCAATGTTCTTGAGGGGTCTCAGGAAGCATCCTACCTATGG                         GTCGCTCTGAATTACTTGCTGGATAAACTGGGAGGGGAGTATTCCCAGACG
genomic: CCAACTGGATCAATGTTCTTGAGGGGTCTCAGGAAGCATCCTACCTATGGgtatgagtta ... tgtattgtagGTCGCTCTGAATTACTTGCTGGATAAACTGGGAGGGGAGTATTCCCAGACG
EST: gi|76011901|gb|DT939071.1|DT939071
EST:     CCAACTGGATCAATGTTCTTGAGGGGTCTCAGGAAGCATCCTACCTATGG                         GTCGCTCTGAATTACTTGCTGGATAAACTGGGAGGGGAGTATTCCCAGACG
genomic: CCAACTGGATCAATGTTCTTGAGGGGTCTCAGGAAGCATCCTACCTATGGgtatgagtta ... tgtattgtagGTCGCTCTGAATTACTTGCTGGATAAACTGGGAGGGGAGTATTCCCAGACG
EST: gi|94472194|gb|EB701152.1|EB701152
EST:     CCAACTGGATCAATGTTCTTGAGGGGTCTCAGGAAGCATCCTACCTATGG                         GTCGCTCTGAATTACTTGCTGGATAAACTGGGAGGGGAGTATTCCCAGACG
genomic: CCAACTGGATCAATGTTCTTGAGGGGTCTCAGGAAGCATCCTACCTATGGgtatgagtta ... tgtattgtagGTCGCTCTGAATTACTTGCTGGATAAACTGGGAGGGGAGTATTCCCAGACG
EST: gi|71329501|gb|DR801472.1|DR801472
EST:     CCAACTGGATCAATGTTCTTGAGGGGTCTCAGGAAGCATCCTACCTATGG                         GTCGCTCTGAATTACTTGCTGGATAAACTGGGAGGGGAGTATTCCCAGACG
genomic: CCAACTGGATCAATGTTCTTGAGGGGTCTCAGGAAGCATCCTACCTATGGgtatgagtta ... tgtattgtagGTCGCTCTGAATTACTTGCTGGATAAACTGGGAGGGGAGTATTCCCAGACG
EST: gi|78120622|gb|DV539006.1|DV539006
EST:     CCAACTGGATCAATGTTCTTGAGGGGTCTCAGGAAGCATCCTACCTATGG                         GTCGCTCTGAATTACTTGCTGGATAAACTGGGAGGGGAGTATTCCCAGACG
genomic: CCAACTGGATCAATGTTCTTGAGGGGTCTCAGGAAGCATCCTACCTATGGgtatgagtta ... tgtattgtagGTCGCTCTGAATTACTTGCTGGATAAACTGGGAGGGGAGTATTCCCAGACG

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 3 RNA-Seq libraries.


Block sizes: 21 (upstream exon), 41 (downstream exon)
Score: 2

GTCAGAGACCTGGTCCACAAGAAGAGCAAATTCCAGTACAAGCCCAACTGGATCAATGTTCTTGAGGGGTCTCAGGAAGCATCCTACCTATGGgtatgagtta ... tgtattgtagGTCGCTCTGAATTACTTGCTGGATAAACTGGGAGGGGAGTATTCCCAGACGGTAGGCGTGATTGATTTGGGTGGCGGGTCGGTGCAAATGGCGTACGCTG


Block sizes: 37 (upstream exon), 45 (downstream exon)
Score: 5

GTCAGAGACCTGGTCCACAAGAAGAGCAAATTCCAGTACAAGCCCAACTGGATCAATGTTCTTGAGGGGTCTCAGGAAGCATCCTACCTATGGgtatgagtta ... tgtattgtagGTCGCTCTGAATTACTTGCTGGATAAACTGGGAGGGGAGTATTCCCAGACGGTAGGCGTGATTGATTTGGGTGGCGGGTCGGTGCAAATGGCGTACGCTG


Block sizes: 45 (upstream exon), 46 (downstream exon)
Score: 11

GTCAGAGACCTGGTCCACAAGAAGAGCAAATTCCAGTACAAGCCCAACTGGATCAATGTTCTTGAGGGGTCTCAGGAAGCATCCTACCTATGGgtatgagtta ... tgtattgtagGTCGCTCTGAATTACTTGCTGGATAAACTGGGAGGGGAGTATTCCCAGACGGTAGGCGTGATTGATTTGGGTGGCGGGTCGGTGCAAATGGCGTACGCTG