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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggatgatcagagaattacatttccttcttaaatcatagccttttattttactgaaatatgtgttgtgtgttctaactggttcatacataattttctgcagAAAGATCCACTTTTGGTGAAGGTGAATAAGCTGACATCCACGAAGACGCAACTTCCCTACTCATATTACTCTCTTCCTTTCTGTAAACCAAACACGATAG

Basic information

species Zea mays
transcript GRMZM2G180575_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|28361644|gb|CB240000.1|CB240000
EST:     CGGCCGCCGCGTTCTATCTACCCGGCGTGGCGCCCAACGACTTCCATAAG                         AAAGATCCACTTTTGGTGAAGGTGAATAAGCTGACATCCACGAAGACGCAA
genomic: CGGCCGCCGCGTTTTACCTACCCGGCGTGGCGCCCAACGACTTCCATAAGgtccaaattc ... ttttctgcagAAAGATCCACTTTTGGTGAAGGTGAATAAGCTGACATCCACGAAGACGCAA
EST: gi|160481645|gb|EY254215.1|EY254215
EST:     CGCCGCGTTCTATCTACCCGGCGTGGCGCCCAACGACTTCCATAAG                         AAAGATCCACTTTTGGTGAAGGTGAATAAGCTGACATCCACGAAGACGCAA
genomic: CGCCGCGTTTTACCTACCCGGCGTGGCGCCCAACGACTTCCATAAGgtccaaattc ... ttttctgcagAAAGATCCACTTTTGGTGAAGGTGAATAAGCTGACATCCACGAAGACGCAA

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: 48 (upstream exon), 49 (downstream exon)
Score: 962

GATGCTCCGCTGGGCCGCGGCGGCGCTCGCGGCGCTCCTCGCCGCCTCACCGGCCGCCGCGTTTTACCTACCCGGCGTGGCGCCCAACGACTTCCATAAGgtccaaattc ... ttttctgcagAAAGATCCACTTTTGGTGAAGGTGAATAAGCTGACATCCACGAAGACGCAACTTCCCTACTCATATTACTCTCTTCCTTTCTGTAAACCAAACACGATAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 414

GATGCTCCGCTGGGCCGCGGCGGCGCTCGCGGCGCTCCTCGCCGCCTCACCGGCCGCCGCGTTTTACCTACCCGGCGTGGCGCCCAACGACTTCCATAAGgtccaaattc ... ttttctgcagAAAGATCCACTTTTGGTGAAGGTGAATAAGCTGACATCCACGAAGACGCAACTTCCCTACTCATATTACTCTCTTCCTTTCTGTAAACCAAACACGATAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 434

GATGCTCCGCTGGGCCGCGGCGGCGCTCGCGGCGCTCCTCGCCGCCTCACCGGCCGCCGCGTTTTACCTACCCGGCGTGGCGCCCAACGACTTCCATAAGgtccaaattc ... ttttctgcagAAAGATCCACTTTTGGTGAAGGTGAATAAGCTGACATCCACGAAGACGCAACTTCCCTACTCATATTACTCTCTTCCTTTCTGTAAACCAAACACGATAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 802

GATGCTCCGCTGGGCCGCGGCGGCGCTCGCGGCGCTCCTCGCCGCCTCACCGGCCGCCGCGTTTTACCTACCCGGCGTGGCGCCCAACGACTTCCATAAGgtccaaattc ... ttttctgcagAAAGATCCACTTTTGGTGAAGGTGAATAAGCTGACATCCACGAAGACGCAACTTCCCTACTCATATTACTCTCTTCCTTTCTGTAAACCAAACACGATAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttactgaaatatgtgttgtgtgttctaactggttcatacataattttctgcagAAAGATCCACTTTTGGTGAAGGTGAATAAGCTGACATCCACGAAGACGCAACTTCCCTACTCATATTACTCTCTTCCTTTCTGTAAACCAAACACGATAG
                        ttctaac  putative branch site (score: 802)
                                             ttttctgc  putative PPT
                                  ttcatacataatttt  TA-rich tract