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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgatgactgcacaaccttattacctttttatcttaatatgtggtttaattcttcatactgaaatattgataggatggcctttaatgtcctcagcttttgagagatgtatttaatttgatatatggggggttgaactgtgtctgacatttcttttgttgtaccagGAGCTATGTTGGATCTAGCAAACCGTGCCAAGG

Basic information

species Zea mays
transcript GRMZM2G023073_T01
intron # 5
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|87151830|gb|DY396619.1|DY396619
EST:     CTTGAATCTGAAG                         GAGCTATGTTGGATCTAGCAAACCGTGCCAAGG
genomic: CTTGAATCTGAAGgtgatgactg ... gttgtaccagGAGCTATGTTGGATCTAGCAAACCGTGCCAAGG
EST: gi|89763664|gb|DY690763.1|DY690763
EST:     AGAAGGGAAAAAGACTGCCCAGATCCTTGAATCTGAAG                         GAGCTATGTTGGATCTAGCAAACCGTGCCAAGG
genomic: AGAAGGGAAAAAGACTGCCCAGATCCTTGAATCTGAAGgtgatgactg ... gttgtaccagGAGCTATGTTGGATCTAGCAAACCGTGCCAAGG

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: 49 (upstream exon), 49 (downstream exon)
Score: 123

AGGAAAAAACGCGCTCAAATCCTTGAGTCAGAAGGGATGAAACAGGCCCAAATCCTTGAATCAGAAGGGAAAAAGACTGCCCAGATCCTTGAATCTGAAGgtgatgactg ... gttgtaccagGAGCTATGTTGGATCTAGCAAACCGTGCCAAGG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 73

AGGAAAAAACGCGCTCAAATCCTTGAGTCAGAAGGGATGAAACAGGCCCAAATCCTTGAATCAGAAGGGAAAAAGACTGCCCAGATCCTTGAATCTGAAGgtgatgactg ... gttgtaccagGAGCTATGTTGGATCTAGCAAACCGTGCCAAGG


Block sizes: 48 (upstream exon), 44 (downstream exon)
Score: 70

AGGAAAAAACGCGCTCAAATCCTTGAGTCAGAAGGGATGAAACAGGCCCAAATCCTTGAATCAGAAGGGAAAAAGACTGCCCAGATCCTTGAATCTGAAGgtgatgactg ... gttgtaccagGAGCTATGTTGGATCTAGCAAACCGTGCCAAGG


Block sizes: 49 (upstream exon), 43 (downstream exon)
Score: 160

AGGAAAAAACGCGCTCAAATCCTTGAGTCAGAAGGGATGAAACAGGCCCAAATCCTTGAATCAGAAGGGAAAAAGACTGCCCAGATCCTTGAATCTGAAGgtgatgactg ... gttgtaccagGAGCTATGTTGGATCTAGCAAACCGTGCCAAGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttaatttgatatatggggggttgaactgtgtctgacatttcttttgttgtaccagGAGCTATGTTGGATCTAGCAAACCGTGCCAAGG
                             gtctgac  putative branch site (score: 160)
                                     tttcttttgtt  CT-rich tract
     ttgatatat  TA-rich tract