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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAGGAAGAAATAATAGGTTTGGCTCCCCATCCGACCGAACAATCCTGTATTTGTGACCCTTCTGAGGAAAAACCATGTTCAGCGCAGAAACAACTGTCTGgtgagtttattcatatagctaaagtaaatgaaaatggttggataattgatttgcatatattagttctttgtaagttagattctgatttgttctgcaatct...

Basic information

species Zea mays
transcript GRMZM2G065496_T01
intron # 3
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|91054726|gb|EB165144.1|EB165144
EST:     TTGTGACCCTTCTGAGGAAAAACCATGTTCAGCGCAGAAACAACTGTCTG                         ATCATCCCAAGCAAGTTTGCTGCTGATCATCTTGGGGAAAGAGCGCACAAC
genomic: TTGTGACCCTTCTGAGGAAAAACCATGTTCAGCGCAGAAACAACTGTCTGgtgagtttat ... tattgtgcagATCATCCCAAGCAAGTTTGCTGCTGATCATCTTGGGGAAAGAGCGCACAAC
EST: gi|89760968|gb|DY689168.1|DY689168
EST:     TTGTGACCCTTCTGAGGAAAAACCATGTTCAGCGCAGAAACAACTGTCTG                         ATCATCCCAAGCAAGTTTGCTGCTGATCATCTTGGGGAAAGAGCGCACAAC
genomic: TTGTGACCCTTCTGAGGAAAAACCATGTTCAGCGCAGAAACAACTGTCTGgtgagtttat ... tattgtgcagATCATCCCAAGCAAGTTTGCTGCTGATCATCTTGGGGAAAGAGCGCACAAC
EST: gi|78108961|gb|DV527378.1|DV527378
EST:     TTGTGACCCTTCTGAGGAAAAACCATGTTCAGCGCAGAAACAACTGTCTG                         ATCATCCCAAGCAAGTTTGCTGCTGATCATCTTGGGGAAAGAGCGCACAAC
genomic: TTGTGACCCTTCTGAGGAAAAACCATGTTCAGCGCAGAAACAACTGTCTGgtgagtttat ... tattgtgcagATCATCCCAAGCAAGTTTGCTGCTGATCATCTTGGGGAAAGAGCGCACAAC
EST: gi|71308093|gb|DR790262.1|DR790262
EST:     TTGTGACCCTTCTGAGGAAAAACCATGTTCAGCGCAGAAACAACTGTCTG                         ATCATCCCAAGCAAGTTTGCTGCTGATCATCTTGGGGAAAGAGCGCACAAC
genomic: TTGTGACCCTTCTGAGGAAAAACCATGTTCAGCGCAGAAACAACTGTCTGgtgagtttat ... tattgtgcagATCATCCCAAGCAAGTTTGCTGCTGATCATCTTGGGGAAAGAGCGCACAAC
EST: gi|74232418|gb|DT640332.1|DT640332
EST:     TTGTGACCCTTCTGAGGAAAAACCATGTTCAGCGCAGAAACAACTGTCTG                         ATCATCCCAAGCAAGTTTGCTGCTGATCATCTTGGGGAAAGAGCGCACAAC
genomic: TTGTGACCCTTCTGAGGAAAAACCATGTTCAGCGCAGAAACAACTGTCTGgtgagtttat ... tattgtgcagATCATCCCAAGCAAGTTTGCTGCTGATCATCTTGGGGAAAGAGCGCACAAC
EST: gi|101399910|gb|EB821802.1|EB821802
EST:     TTGTGACCCTTCTGAGGAAAAACCATGTTCAGCGCAGAAACAACTGTCTG                         TTCTTCCCAAGCAAGTTTGTTGCTGATCATCTTGGGGAAAGAGCGCACAAC
genomic: TTGTGACCCTTCTGAGGAAAAACCATGTTCAGCGCAGAAACAACTGTCTGgtgagtttat ... tattgtgcagATCATCCCAAGCAAGTTTGCTGCTGATCATCTTGGGGAAAGAGCGCACAAC
EST: gi|71428131|gb|DR809181.1|DR809181
EST:     TTGTGACCCTTCTGAGGAAAAACCATGTTCAGCGCAGAAACAACTGTCTG                         ATCATCCCAAGCAAGTTTGCTGCTGATCATCTTGGGGAAAGAGCGCACAAC
genomic: TTGTGACCCTTCTGAGGAAAAACCATGTTCAGCGCAGAAACAACTGTCTGgtgagtttat ... tattgtgcagATCATCCCAAGCAAGTTTGCTGCTGATCATCTTGGGGAAAGAGCGCACAAC
EST: gi|71444231|gb|DR825281.1|DR825281
EST:     TCAGCGCAGAAACAACTGTCTG                         ATCATCCCAAGCAAGTTTGCTGCTGATCATCTTGGGGAAAGAGCGCACAAC
genomic: TCAGCGCAGAAACAACTGTCTGgtgagtttat ... tattgtgcagATCATCCCAAGCAAGTTTGCTGCTGATCATCTTGGGGAAAGAGCGCACAAC
EST: gi|211012995|gb|FL456827.1|FL456827
EST:     GAAAAACCATGTTCAGCGCAGAAACAACTGTCTG                         ATCATCCCAAGCAAGTTTGCTGCTGATCATCTTGGGGAAAGAGCGCACAAC
genomic: GAAAAACCATGTTCAGCGCAGAAACAACTGTCTGgtgagtttat ... tattgtgcagATCATCCCAAGCAAGTTTGCTGCTGATCATCTTGGGGAAAGAGCGCACAAC
EST: gi|76286535|gb|DV026103.1|DV026103
EST:     TTGTGACCCTTCTGAGGAAAAACCATGTTCAGCGCAGAAACAACTGTCTG                         ATCATCCCAAGCAAGTTTGCTGCTGATCATCTTGGGGAAAGAGCGCACAAC
genomic: TTGTGACCCTTCTGAGGAAAAACCATGTTCAGCGCAGAAACAACTGTCTGgtgagtttat ... tattgtgcagATCATCCCAAGCAAGTTTGCTGCTGATCATCTTGGGGAAAGAGCGCACAAC

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: 48 (upstream exon), 48 (downstream exon)
Score: 100

AAGGAAGAAATAATAGGTTTGGCTCCCCATCCGACCGAACAATCCTGTATTTGTGACCCTTCTGAGGAAAAACCATGTTCAGCGCAGAAACAACTGTCTGgtgagtttat ... tattgtgcagATCATCCCAAGCAAGTTTGCTGCTGATCATCTTGGGGAAAGAGCGCACAACATCATACTTCGTAGGCCGAACAGGAAGGAGAAATGGCATGTCAGCTACT


Block sizes: 13 (upstream exon), 37 (downstream exon)
Score: 2

AAGGAAGAAATAATAGGTTTGGCTCCCCATCCGACCGAACAATCCTGTATTTGTGACCCTTCTGAGGAAAAACCATGTTCAGCGCAGAAACAACTGTCTGgtgagtttat ... tattgtgcagATCATCCCAAGCAAGTTTGCTGCTGATCATCTTGGGGAAAGAGCGCACAACATCATACTTCGTAGGCCGAACAGGAAGGAGAAATGGCATGTCAGCTACT


Block sizes: 46 (upstream exon), 41 (downstream exon)
Score: 11

AAGGAAGAAATAATAGGTTTGGCTCCCCATCCGACCGAACAATCCTGTATTTGTGACCCTTCTGAGGAAAAACCATGTTCAGCGCAGAAACAACTGTCTGgtgagtttat ... tattgtgcagATCATCCCAAGCAAGTTTGCTGCTGATCATCTTGGGGAAAGAGCGCACAACATCATACTTCGTAGGCCGAACAGGAAGGAGAAATGGCATGTCAGCTACT