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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTCTCAAAGGGCCAGTACCACTGTGACGGATGTGGAATATGTAGgtaagcaccaccacgctgatggctacgtctaaagacttgacgcgcagaagtgtaaaacttctgtcagccgttcaaaactgataaattcgggttcctcgtcttcttgttgtttatgcag

Basic information

species Zea mays
transcript GRMZM2G144782_T03
intron # 6
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|71424311|gb|DR806292.1|DR806292
EST:     GGGCCAGTACCACTGTGACGGATGTGGAATATGTAG                         AACCGGCGGCGTGGAGAACTTTTTCCACTGTGATAAATGTG
genomic: GGGCCAGTACCACTGTGACGGATGTGGAATATGTAGgtaagcacca ... gtttatgcagAACCGGCGGCGTGGAGAACTTTTTCCACTGTGATAAATGTG
EST: gi|18649707|gb|BM498526.1|BM498526
EST:     GTCTCAAAGGGCCAGTACCACTGTGACGGATGTGGAATATGTAG                         AACTGGCGGCGTGGAGAACTTTTTCCACTGTGATAAATGTG
genomic: GTCTCAAAGGGCCAGTACCACTGTGACGGATGTGGAATATGTAGgtaagcacca ... gtttatgcagAACCGGCGGCGTGGAGAACTTTTTCCACTGTGATAAATGTG
EST: gi|61236803|gb|DN586530.1|DN586530
EST:     GTCTCAAAGGGCCAGTACCACTGTGACGGATGCGGAATATGTAG                         AACCGGCGGCGTGGAGAACTTTTTCCACTGTGATAAATGTG
genomic: GTCTCAAAGGGCCAGTACCACTGTGACGGATGTGGAATATGTAGgtaagcacca ... gtttatgcagAACCGGCGGCGTGGAGAACTTTTTCCACTGTGATAAATGTG

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: 44 (upstream exon), 41 (downstream exon)
Score: 89

GTCTCAAAGGGCCAGTACCACTGTGACGGATGTGGAATATGTAGgtaagcacca ... gtttatgcagAACCGGCGGCGTGGAGAACTTTTTCCACTGTGATAAATGTG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 744

GTCTCAAAGGGCCAGTACCACTGTGACGGATGTGGAATATGTAGgtaagcacca ... gtttatgcagAACCGGCGGCGTGGAGAACTTTTTCCACTGTGATAAATGTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1167

GTCTCAAAGGGCCAGTACCACTGTGACGGATGTGGAATATGTAGgtaagcacca ... gtttatgcagAACCGGCGGCGTGGAGAACTTTTTCCACTGTGATAAATGTG


Block sizes: 47 (upstream exon), 41 (downstream exon)
Score: 35

GTCTCAAAGGGCCAGTACCACTGTGACGGATGTGGAATATGTAGgtaagcacca ... gtttatgcagAACCGGCGGCGTGGAGAACTTTTTCCACTGTGATAAATGTG