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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGAGAGCGACTACCAGGACCTGCTGCGCAACACGGACGCCAACCAGACGGCGCTCGACAAGAACATGTTCGGTGGCCAACGGCTGCACGTCTGTGGCGAGgtattggtaacccagatgtcctgctcccagcctattgaggtcaatggaactgggagcggagcacactgttcactcatcgcttgggttggaacctaatctgtcacttgcag

Basic information

species Zea mays
transcript GRMZM2G089259_T01
intron # 3
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|74237070|gb|DT644984.1|DT644984
EST:     CGCTCGACAAGAACATGTTCGGTGGCCAACGGCTGCACGTCTGTGGCGAG                         GGCCATGAACCTTTTGTTTCGTACGAGGGCCTTGAGCAGCTGCACCGGTTT
genomic: CGCTCGACAAGAACATGTTCGGTGGCCAACGGCTGCACGTCTGTGGCGAGgtattggtaa ... tcacttgcagGGCCATGAACCTTTTGTTTCGTACGAGGGCCTTGAGCAGCTGCACCGGTTT
EST: gi|211183324|gb|FK979377.1|FK979377
EST:     CGCTCGACAAGAACATGTTCGGTGGCCAACGGCTGCACGTCTGTGGCGAG                         GGCCATGAACCTTTTGTTTCGTACGAGGGCCTTGAGCAGCTGCACCTGTTT
genomic: CGCTCGACAAGAACATGTTCGGTGGCCAACGGCTGCACGTCTGTGGCGAGgtattggtaa ... tcacttgcagGGCCATGAACCTTTTGTTTCGTACGAGGGCCTTGAGCAGCTGCACCGGTTT
EST: gi|87157614|gb|DY402403.1|DY402403
EST:     CGCTCGACAAGAACATGTTCGGTGGCCAACGGCTGCACGTCTGTGGCGAG                         GGCCATGAACCTTTTGTTTCGTACGAGGGCCTTGAGCAGCTGCACCGGTTT
genomic: CGCTCGACAAGAACATGTTCGGTGGCCAACGGCTGCACGTCTGTGGCGAGgtattggtaa ... tcacttgcagGGCCATGAACCTTTTGTTTCGTACGAGGGCCTTGAGCAGCTGCACCGGTTT
EST: gi|71428557|gb|DR809607.1|DR809607
EST:     CGCTCGACAAGAACATGTTCGGTGGCCAACGGCTGCACGTCTGTGGCGAG                         GGCCATGAACCTTTTGTTTCGTACGAGGGCCTTGAGCAGCTGCACCGGTTT
genomic: CGCTCGACAAGAACATGTTCGGTGGCCAACGGCTGCACGTCTGTGGCGAGgtattggtaa ... tcacttgcagGGCCATGAACCTTTTGTTTCGTACGAGGGCCTTGAGCAGCTGCACCGGTTT
EST: gi|94475718|gb|EB704676.1|EB704676
EST:     CGCTCGACAAGAACATGTTCGGTGGCCAACGGCTGCACGTCTGTGGCGAG                         GGCCATGAACCTTTTGTTTCGTACGAGGGCCTTGAGCAGCTGCACCGGTTT
genomic: CGCTCGACAAGAACATGTTCGGTGGCCAACGGCTGCACGTCTGTGGCGAGgtattggtaa ... tcacttgcagGGCCATGAACCTTTTGTTTCGTACGAGGGCCTTGAGCAGCTGCACCGGTTT
EST: gi|50336816|gb|CO531942.1|CO531942
EST:     CGCTCGACAAGAACATGTTCGGTGGCCAACGGCTGCACGTCTGTGGCGAG                         GGCCATGAACCTTTTGTTTCGTACGAGGGCCTTGAGCAGCTGCACCGGTTT
genomic: CGCTCGACAAGAACATGTTCGGTGGCCAACGGCTGCACGTCTGTGGCGAGgtattggtaa ... tcacttgcagGGCCATGAACCTTTTGTTTCGTACGAGGGCCTTGAGCAGCTGCACCGGTTT
EST: gi|211180923|gb|FK979371.1|FK979371
EST:     CGCTCGACAAGAACATGTTCGGTGGCCAACGGCTGCACGTCTGTGGCGAG                         GGCCATGAACCTTTTGTTTCGTACGAGGGCCTTGAGCAGCTGCACCGGTTT
genomic: CGCTCGACAAGAACATGTTCGGTGGCCAACGGCTGCACGTCTGTGGCGAGgtattggtaa ... tcacttgcagGGCCATGAACCTTTTGTTTCGTACGAGGGCCTTGAGCAGCTGCACCGGTTT
EST: gi|22546168|gb|BU098479.1|BU098479
EST:     CGCTCGACAAGAACATGTTCGGTGGCCAACGGCTGCACGTCTGTGGCGAG                         GGCCATGAACCTTTTGTTTCGTACGA
genomic: CGCTCGACAAGAACATGTTCGGTGGCCAACGGCTGCACGTCTGTGGCGAGgtattggtaa ... tcacttgcagGGCCATGAACCTTTTGTTTCGTACGA
EST: gi|71321201|gb|DR797302.1|DR797302
EST:     CGCTCGACAAGAACATGTTCGGTGGCCAACGGCTGCACGTCTGTGGCGAG                         GGCCATGAACCTTTTGTTTCGTACGAGGGCCTTGAGCAGCTGCACCGGTTT
genomic: CGCTCGACAAGAACATGTTCGGTGGCCAACGGCTGCACGTCTGTGGCGAGgtattggtaa ... tcacttgcagGGCCATGAACCTTTTGTTTCGTACGAGGGCCTTGAGCAGCTGCACCGGTTT
EST: gi|71329466|gb|DR801453.1|DR801453
EST:     CGCTCGACAAGAACATGTTCGGTGGCCAACGGCTGCACGTCTGTGGCGAG                         GGCCATGAACCTTTTGTTTCGTACGAGGGCCTTGAGCAGCTGCACCGGTTT
genomic: CGCTCGACAAGAACATGTTCGGTGGCCAACGGCTGCACGTCTGTGGCGAGgtattggtaa ... tcacttgcagGGCCATGAACCTTTTGTTTCGTACGAGGGCCTTGAGCAGCTGCACCGGTTT
EST: gi|87157722|gb|DY402511.1|DY402511
EST:     CGCTCGACAAGAACATGTTCGGTGGCCAACGGCTGCACGTCTGTGGCGAG                         GGCCATGAACCTTTTGTTTCGTACGAGGGCCTTGAGCAGCTGCACCGGTTT
genomic: CGCTCGACAAGAACATGTTCGGTGGCCAACGGCTGCACGTCTGTGGCGAGgtattggtaa ... tcacttgcagGGCCATGAACCTTTTGTTTCGTACGAGGGCCTTGAGCAGCTGCACCGGTTT
EST: gi|148957093|gb|EC903064.2|EC903064
EST:     CGCTCGACAAGAACATGTTCGGTGGCCAACGGCTGCACGTCTGTGGCGAG                         GGGCCATGAACCTTTTTGTTTCGTACGAGGGCCTTGAGCAGCTGCACCCGG
genomic: CGCTCGACAAGAACATGTTCGGTGGCCAACGGCTGCACGTCTGTGGCGAGgtattggtaa ... tcacttgcagGG-CCATGAACCTTTT-GTTTCGTACGAGGGCCTTGAGCAGCTGCACC-GG
EST: gi|22819833|gb|BU499923.1|BU499923
EST:     CGCTCGACAAGAACATGTTCGGTGGCCAACGGCTGCACGTCTGTGGCGAG                         GGCCATGAACCTTTTGTTTCGTACGAGGGCCTTGAGCAGCTGCACCGGTTT
genomic: CGCTCGACAAGAACATGTTCGGTGGCCAACGGCTGCACGTCTGTGGCGAGgtattggtaa ... tcacttgcagGGCCATGAACCTTTTGTTTCGTACGAGGGCCTTGAGCAGCTGCACCGGTTT
EST: gi|37421156|gb|CF648275.1|CF648275
EST:     CGCTCGACAAGAACATGTTCGGTGGCCAACGGCTGCACGTCTGTGGCGAG                         GGCCATGAACCTTTTGTTTCGTACGATGGCCTTGAGCAGCTGCACCGGTTT
genomic: CGCTCGACAAGAACATGTTCGGTGGCCAACGGCTGCACGTCTGTGGCGAGgtattggtaa ... tcacttgcagGGCCATGAACCTTTTGTTTCGTACGAGGGCCTTGAGCAGCTGCACCGGTTT
EST: gi|71428023|gb|DR809073.1|DR809073
EST:     CGCTCGACAAGAACATGTTCGGTGGCCAACGGCTGCACGTCTGTGGCGAG                         GGCCATGAACCTTTTGTTTCGTACGAGGGCCTTGAGCAGCTGCACCGGTTT
genomic: CGCTCGACAAGAACATGTTCGGTGGCCAACGGCTGCACGTCTGTGGCGAGgtattggtaa ... tcacttgcagGGCCATGAACCTTTTGTTTCGTACGAGGGCCTTGAGCAGCTGCACCGGTTT
EST: gi|76012907|gb|DT940077.1|DT940077
EST:     CGCTCGACAAGAACATGTTCGGTGGCCAACGGCTGCACGTCTGTGGCGAG                         GGCCATGAACCTTTTGTTTCGTACGAGGGCCTTGAGCAGCTGCACCGGTTT
genomic: CGCTCGACAAGAACATGTTCGGTGGCCAACGGCTGCACGTCTGTGGCGAGgtattggtaa ... tcacttgcagGGCCATGAACCTTTTGTTTCGTACGAGGGCCTTGAGCAGCTGCACCGGTTT
EST: gi|26558674|gb|CA830909.1|CA830909
EST:     CGCTCGACAAGAACATGTTCGGTGGCCAACGGCTGCACGTCTGTGGCGAG                         GGCCATGAACCTTTTGTTTCGTACGAGGGCCTTGAGCAGCTGCACCGGTTT
genomic: CGCTCGACAAGAACATGTTCGGTGGCCAACGGCTGCACGTCTGTGGCGAGgtattggtaa ... tcacttgcagGGCCATGAACCTTTTGTTTCGTACGAGGGCCTTGAGCAGCTGCACCGGTTT
EST: gi|33466850|gb|CF243899.1|CF243899
EST:     CGCTCGACAAGAACATGTTCGGTGGCCAACGGCTGCACGTCTGTGGCGAG                         GGCCATGAACCTTTTGTTTCGTACGAGGGCCTTGAGCAGCTGCACCGGTTT
genomic: CGCTCGACAAGAACATGTTCGGTGGCCAACGGCTGCACGTCTGTGGCGAGgtattggtaa ... tcacttgcagGGCCATGAACCTTTTGTTTCGTACGAGGGCCTTGAGCAGCTGCACCGGTTT
EST: gi|148994788|gb|EE034233.2|EE034233
EST:     CGCTCGACAAGAACATGTTCGGTGGCCAACGGCTGCACGTCTGTGGCGAG                         GGCCATGAACCTTTTGTTTCGTACGAGGGCCTTGAGCAGCTGCACCGGTTT
genomic: CGCTCGACAAGAACATGTTCGGTGGCCAACGGCTGCACGTCTGTGGCGAGgtattggtaa ... tcacttgcagGGCCATGAACCTTTTGTTTCGTACGAGGGCCTTGAGCAGCTGCACCGGTTT

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: 86

CGAGAGCGACTACCAGGACCTGCTGCGCAACACGGACGCCAACCAGACGGCGCTCGACAAGAACATGTTCGGTGGCCAACGGCTGCACGTCTGTGGCGAGgtattggtaa ... tcacttgcagGGCCATGAACCTTTTGTTTCGTACGAGGGCCTTGAGCAGCTGCACCGGTTTCTCTTCATCCTTGGTATCACTCATGTGTTGTACAGTTTTGTAACAGTGG


Block sizes: 45 (upstream exon), 48 (downstream exon)
Score: 28

CGAGAGCGACTACCAGGACCTGCTGCGCAACACGGACGCCAACCAGACGGCGCTCGACAAGAACATGTTCGGTGGCCAACGGCTGCACGTCTGTGGCGAGgtattggtaa ... tcacttgcagGGCCATGAACCTTTTGTTTCGTACGAGGGCCTTGAGCAGCTGCACCGGTTTCTCTTCATCCTTGGTATCACTCATGTGTTGTACAGTTTTGTAACAGTGG


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 15

CGAGAGCGACTACCAGGACCTGCTGCGCAACACGGACGCCAACCAGACGGCGCTCGACAAGAACATGTTCGGTGGCCAACGGCTGCACGTCTGTGGCGAGgtattggtaa ... tcacttgcagGGCCATGAACCTTTTGTTTCGTACGAGGGCCTTGAGCAGCTGCACCGGTTTCTCTTCATCCTTGGTATCACTCATGTGTTGTACAGTTTTGTAACAGTGG


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

CGAGAGCGACTACCAGGACCTGCTGCGCAACACGGACGCCAACCAGACGGCGCTCGACAAGAACATGTTCGGTGGCCAACGGCTGCACGTCTGTGGCGAGgtattggtaa ... tcacttgcagGGCCATGAACCTTTTGTTTCGTACGAGGGCCTTGAGCAGCTGCACCGGTTTCTCTTCATCCTTGGTATCACTCATGTGTTGTACAGTTTTGTAACAGTGG


Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CGAGAGCGACTACCAGGACCTGCTGCGCAACACGGACGCCAACCAGACGGCGCTCGACAAGAACATGTTCGGTGGCCAACGGCTGCACGTCTGTGGCGAGgtattggtaacccagatgtcctgctcccagcctattgaggtcaatggaactgggagcggagcacactgttcactcatcgcttgggttggaacctaatctgtcacttgcag

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