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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CACCTAAAAGGACGACCTCTGGCCGCCCTTGTCCCGCCCCGACGCCTCGGTTTCCACTGCATAGGCGTGGTGCGGCGATCCGTCCGGGCCTAGGGTTGCGgtaaggaaccctaacttgcttcgatgtttttttcctctgagatttatttgtcgtgggagatctctcgctcgccatgggcaatcagatcctaattctccgggggagaagcgggggagctctactcttgactgcgccctggtactgtgcag

Basic information

species Zea mays
transcript GRMZM2G030422_T01
intron # 1
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|18655046|gb|BM499851.1|BM499851
EST:     TTTCCACTGCATAGGCGTGGTGCGGCGATCCGTCCGGGCCTAGGGTTGCG                         AGAGACACTATAGGGTACGACCCTAGGAGCATCCGCCTCCACGTGGGTGAG
genomic: TTTCCACTGCATAGGCGTGGTGCGGCGATCCGTCCGGGCCTAGGGTTGCGgtaaggaacc ... tactgtgcagAGAGACACTATAGGGTACGACCCTAGGAGCATCCGCCTCCACGTGGGTGAG
EST: gi|18662061|gb|BM501725.1|BM501725
EST:     TTTCCACTGCATAGGCGTGGTGCGGCGATCCGTCCGGGCCTAGGGTTGCG                         AGAGACACTATAGGGTACGACCCTAGGAGCATCCGCCTCCACGTGGGTGAG
genomic: TTTCCACTGCATAGGCGTGGTGCGGCGATCCGTCCGGGCCTAGGGTTGCGgtaaggaacc ... tactgtgcagAGAGACACTATAGGGTACGACCCTAGGAGCATCCGCCTCCACGTGGGTGAG
EST: gi|71766923|gb|DR964860.1|DR964860
EST:     TTTCCACTGCATAGGCGTGGTGCGGCGATCCGTCCGGGCCTAGGGTTGCG                         AGAGACACTATAGGGTACGACCCTAGGAGCATCCGCCTCCACGTGGGTGAG
genomic: TTTCCACTGCATAGGCGTGGTGCGGCGATCCGTCCGGGCCTAGGGTTGCGgtaaggaacc ... tactgtgcagAGAGACACTATAGGGTACGACCCTAGGAGCATCCGCCTCCACGTGGGTGAG
EST: gi|18662063|gb|BM501726.1|BM501726
EST:     GCATAGGTCGTGGTGCGGCGATCCGCTCCGGGCCTAGGGTTGCG                         AGTAGACACTATAGGGTACGACCCTAGGAGCATCCGCCTCCACGTGGGTGA
genomic: GCATAGG-CGTGGTGCGGCGATCCG-TCCGGGCCTAGGGTTGCGgtaaggaacc ... tactgtgcagAG-AGACACTATAGGGTACGACCCTAGGAGCATCCGCCTCCACGTGGGTGA
EST: gi|18655047|gb|BM499852.1|BM499852
EST:     TTTCCACTGCATAGGCGTGG-GCGGCGATCCG-CCGGGCCTAGGGTTGCG                         AGAGACACTATAGGGTACGACCCTAGGAGCATCCGCCTCCACGTGGGTGAG
genomic: TTTCCACTGCATAGGCGTGGTGCGGCGATCCGTCCGGGCCTAGGGTTGCGgtaaggaacc ... tactgtgcagAGAGACACTATAGGGTACGACCCTAGGAGCATCCGCCTCCACGTGGGTGAG

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: 265

CACCTAAAAGGACGACCTCTGGCCGCCCTTGTCCCGCCCCGACGCCTCGGTTTCCACTGCATAGGCGTGGTGCGGCGATCCGTCCGGGCCTAGGGTTGCGgtaaggaacc ... tactgtgcagAGAGACACTATAGGGTACGACCCTAGGAGCATCCGCCTCCACGTGGGTGAGGCGGAAGAGGGAGGATGACATCGCTCAGCCGTGAGCTGGTCTTCCTCAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 147

CACCTAAAAGGACGACCTCTGGCCGCCCTTGTCCCGCCCCGACGCCTCGGTTTCCACTGCATAGGCGTGGTGCGGCGATCCGTCCGGGCCTAGGGTTGCGgtaaggaacc ... tactgtgcagAGAGACACTATAGGGTACGACCCTAGGAGCATCCGCCTCCACGTGGGTGAGGCGGAAGAGGGAGGATGACATCGCTCAGCCGTGAGCTGGTCTTCCTCAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 227

CACCTAAAAGGACGACCTCTGGCCGCCCTTGTCCCGCCCCGACGCCTCGGTTTCCACTGCATAGGCGTGGTGCGGCGATCCGTCCGGGCCTAGGGTTGCGgtaaggaacc ... tactgtgcagAGAGACACTATAGGGTACGACCCTAGGAGCATCCGCCTCCACGTGGGTGAGGCGGAAGAGGGAGGATGACATCGCTCAGCCGTGAGCTGGTCTTCCTCAT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 187

CACCTAAAAGGACGACCTCTGGCCGCCCTTGTCCCGCCCCGACGCCTCGGTTTCCACTGCATAGGCGTGGTGCGGCGATCCGTCCGGGCCTAGGGTTGCGgtaaggaacc ... tactgtgcagAGAGACACTATAGGGTACGACCCTAGGAGCATCCGCCTCCACGTGGGTGAGGCGGAAGAGGGAGGATGACATCGCTCAGCCGTGAGCTGGTCTTCCTCAT