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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGGAAGCCACGGAGTGGATCGAGGAAGACGAGCCGGGCGTGTGCCTCACCATCCGCGAGCTCGGCGATGGCACTCGCGAACTCCGCCGCATCCGGTTCAGgtatgcatggcactgatcagtcatggacatgcggaagcatacatcactggctcagtaaccaaaatccttcttgatcactcggttcattcatgtgatcatgtctgttccatgtttctgtgatgctgcag

Basic information

species Zea mays
transcript GRMZM2G374203_T01
intron # 5
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|60347677|gb|DN214650.1|DN214650
EST:     ATCCGCGAGCTCGGCGATGGCACTCGCGAACTCCGCCGCATCCGGTTCAG                         CCGGGAGATATTCGGCGAGGATAGGGCCAAGGTGTGGTGGGAGCAGAACAG
genomic: ATCCGCGAGCTCGGCGATGGCACTCGCGAACTCCGCCGCATCCGGTTCAGgtatgcatgg ... gatgctgcagCCGGGAGATATTCGGCGAGGATAGGGCCAAGGTGTGGTGGGAGCAGAACAG
EST: gi|78023790|gb|DV492177.1|DV492177
EST:     ATCCGCGAGCTCGGCGACGGCACTCGCGAGCTCCGCCGCATCCGGTTCAG                         CCGGGAGATATTCGGCGAGGATAGGGCCAAGGTGTGGTGGGAGCAGAACAG
genomic: ATCCGCGAGCTCGGCGATGGCACTCGCGAACTCCGCCGCATCCGGTTCAGgtatgcatgg ... gatgctgcagCCGGGAGATATTCGGCGAGGATAGGGCCAAGGTGTGGTGGGAGCAGAACAG
EST: gi|5456447|gb|AI834137.1|AI834137
EST:     ATCCGCGAGCTCGGCGACGGCACTCGCGAGCTCCGCCGCATCCGGTTCAG                         CCGGGAGATATTCGGCGAGGATAGGGCCAAGGTGTGGTGGGAGCAGAACAG
genomic: ATCCGCGAGCTCGGCGATGGCACTCGCGAACTCCGCCGCATCCGGTTCAGgtatgcatgg ... gatgctgcagCCGGGAGATATTCGGCGAGGATAGGGCCAAGGTGTGGTGGGAGCAGAACAG
EST: gi|5055563|gb|AI734450.1|AI734450
EST:     ATCCGCGAGCTCGGCGACGGCACTCGCGAGCTCCGCCGCATCCGGTTCAG                         CCGGGAGATATTCGGCGAGGATAGGGCCAAGGTGTGGTGGGAGCAGAACAG
genomic: ATCCGCGAGCTCGGCGATGGCACTCGCGAACTCCGCCGCATCCGGTTCAGgtatgcatgg ... gatgctgcagCCGGGAGATATTCGGCGAGGATAGGGCCAAGGTGTGGTGGGAGCAGAACAG

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 2 RNA-Seq libraries.


Block sizes: 33 (upstream exon), 30 (downstream exon)
Score: 2

TGGAAGCCACGGAGTGGATCGAGGAAGACGAGCCGGGCGTGTGCCTCACCATCCGCGAGCTCGGCGATGGCACTCGCGAACTCCGCCGCATCCGGTTCAGgtatgcatgg ... gatgctgcagCCGGGAGATATTCGGCGAGGATAGGGCCAAGGTGTGGTGGGAGCAGAACAGGGAGAGAATACAGGCGGAATATCTGTAGCAAGCGATCAGACACTGAGCT


Block sizes: 25 (upstream exon), 25 (downstream exon)
Score: 1

TGGAAGCCACGGAGTGGATCGAGGAAGACGAGCCGGGCGTGTGCCTCACCATCCGCGAGCTCGGCGATGGCACTCGCGAACTCCGCCGCATCCGGTTCAGgtatgcatgg ... gatgctgcagCCGGGAGATATTCGGCGAGGATAGGGCCAAGGTGTGGTGGGAGCAGAACAGGGAGAGAATACAGGCGGAATATCTGTAGCAAGCGATCAGACACTGAGCT




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