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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aatgaagggaatacatttttgtgaattaaaacactgcactttctgaatgcattgtttcacctgaaataggtaagcattgacatattctgtttgcctgcagATCGCAAGGGTAAGAATGGCAATCAG

Basic information

species Zea mays
transcript GRMZM2G386971_T01
intron # 1
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|71428873|gb|DR809923.1|DR809923
EST:     CGTCGTGCGCAATGACGGTCGCGCCCACGCCCACGTCCACGTAGCCTCCG                         ATCGCAAGGGTAAGAATGGCAATCAG
genomic: CGTCGTGCGCAATGACGGTCGCGCCCACGCCCACGTCCACGTAGCCTCCGgtccgatttg ... ttgcctgcagATCGCAAGGGTAAGAATGGCAATCAG




















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), 48 (downstream exon)
Score: 262

CCCGTGGTGGTCCTCGTGTTCCTCTTCGTGGTCGCGCCTTCGCTCTTCTTCGTCGTGCGCAATGACGGTCGCGCCCACGCCCACGTCCACGTAGCCTCCGgtccgatttg ... ttgcctgcagATCGCAAGGGTAAGAATGGCAATCAG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 132

CCCGTGGTGGTCCTCGTGTTCCTCTTCGTGGTCGCGCCTTCGCTCTTCTTCGTCGTGCGCAATGACGGTCGCGCCCACGCCCACGTCCACGTAGCCTCCGgtccgatttg ... ttgcctgcagATCGCAAGGGTAAGAATGGCAATCAG


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 164

CCCGTGGTGGTCCTCGTGTTCCTCTTCGTGGTCGCGCCTTCGCTCTTCTTCGTCGTGCGCAATGACGGTCGCGCCCACGCCCACGTCCACGTAGCCTCCGgtccgatttg ... ttgcctgcagATCGCAAGGGTAAGAATGGCAATCAG


Block sizes: 44 (upstream exon), 49 (downstream exon)
Score: 236

CCCGTGGTGGTCCTCGTGTTCCTCTTCGTGGTCGCGCCTTCGCTCTTCTTCGTCGTGCGCAATGACGGTCGCGCCCACGCCCACGTCCACGTAGCCTCCGgtccgatttg ... ttgcctgcagATCGCAAGGGTAAGAATGGCAATCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatgcattgtttcacctgaaataggtaagcattgacatattctgtttgcctgcagATCGCAAGGGTAAGAATGGCAATCAG
                             cattgac  putative branch site (score: 236)
                                       ttctgttt  putative PPT
     attgttt  TA-rich tract