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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gcaagatcatcaaaagagcagttcgctagaggtttgctggtccagtttccaaagcaacagataaactgatgcccagatcgatcacctgcagTGTGTCCGGCGGGAAGAAAGTCAGCGGCCGGCTGAACTTCGACGTCGTCAGCGATCTGGTCGTGGCCAGTAGCCTCGGCAGTGACCGTGACGCCAAGCCT

Basic information

species Zea mays
transcript GRMZM2G033828_T01
intron # 18
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|76933781|gb|DV173583.1|DV173583
EST:     TTCCAGAGCCCCTCCAAGGACCTGAAGGCTATCAACAACCGCCTAAACAG                         TGTGTCCGGCGGGAAGAAAGTCAGCGGCCGGCTGAACTTCGACGTCGTCAG
genomic: TTCCAGAGCCCCTCCAAGGACCTGAAGGCTATCAACAACCGCCTAAACAGgcaagatcat ... tcacctgcagTGTGTCCGGCGGGAAGAAAGTCAGCGGCCGGCTGAACTTCGACGTCGTCAG
EST: gi|30088298|gb|CB886503.1|CB886503
EST:     TTCCAGAGCCCCTCCAAGGACCTGAAGGCTATCAACAACCGCCTAAACAG                         TGTGTCCGGCGGGAAGAAAGTCAGCGGCCGGCTGAACTTCGACGTCGTCAG
genomic: TTCCAGAGCCCCTCCAAGGACCTGAAGGCTATCAACAACCGCCTAAACAGgcaagatcat ... tcacctgcagTGTGTCCGGCGGGAAGAAAGTCAGCGGCCGGCTGAACTTCGACGTCGTCAG
EST: gi|27522004|gb|CA989110.1|CA989110
EST:     TTCCAGAGCCCCTCCAAGGACCTGAAGGCTATCAACAACCGCCTAAACAG                         TGTGTCCGGCGGGAAGAAAGTCAGCGGCCGGCTGAACTTCGACGTCGTCAG
genomic: TTCCAGAGCCCCTCCAAGGACCTGAAGGCTATCAACAACCGCCTAAACAGgcaagatcat ... tcacctgcagTGTGTCCGGCGGGAAGAAAGTCAGCGGCCGGCTGAACTTCGACGTCGTCAG
EST: gi|30087032|gb|CB885240.1|CB885240
EST:     TTCCAGAGCCCCTCCAAGGACCTGAAGGCTATCAACAACCGCCTAAACAG                         TGTGTCCGGCGGGAAGAAAGTCAGCGGCCGGCTGAACTTCGACGTCGTCAG
genomic: TTCCAGAGCCCCTCCAAGGACCTGAAGGCTATCAACAACCGCCTAAACAGgcaagatcat ... tcacctgcagTGTGTCCGGCGGGAAGAAAGTCAGCGGCCGGCTGAACTTCGACGTCGTCAG
EST: gi|30031776|gb|CB833627.1|CB833627
EST:     TTCCAGAGCCCCTCCAAGGACCTGAAGGCTATCAACAACCGCCTAAACAG                         TGTGTCCGGCGGGAAGAAAGTCAGCGGCCGGCTGAACTTCGACGTCGTCAG
genomic: TTCCAGAGCCCCTCCAAGGACCTGAAGGCTATCAACAACCGCCTAAACAGgcaagatcat ... tcacctgcagTGTGTCCGGCGGGAAGAAAGTCAGCGGCCGGCTGAACTTCGACGTCGTCAG
EST: gi|29544714|gb|CB605094.1|CB605094
EST:     TTCCAGAGCCCCTCCAAGGACCTGAAGGCTATCAACAACCGCCTAAACAG                         TGTGTCCGGCGGGAAGAAAGTCAGCGGCCGGCTGAACTTCGACGTCGTCAG
genomic: TTCCAGAGCCCCTCCAAGGACCTGAAGGCTATCAACAACCGCCTAAACAGgcaagatcat ... tcacctgcagTGTGTCCGGCGGGAAGAAAGTCAGCGGCCGGCTGAACTTCGACGTCGTCAG
EST: gi|30086964|gb|CB885172.1|CB885172
EST:     TTCCAGAGCCCCTCCAAGGACCTGAAGGCTATCAACAACCGCCTAAACAG                         TGTGTCCGGCGGGAAGAAAGTCAGCGGCCGGCTGAACTTCGACGTCGTCAG
genomic: TTCCAGAGCCCCTCCAAGGACCTGAAGGCTATCAACAACCGCCTAAACAGgcaagatcat ... tcacctgcagTGTGTCCGGCGGGAAGAAAGTCAGCGGCCGGCTGAACTTCGACGTCGTCAG
EST: gi|30032038|gb|CB833889.1|CB833889
EST:     TTCCAGAGCCCCTCCAAGGACCTGAAGGCTATCAACAACCGCCTAAACAG                         TGTGTCCGGCGGGAAGAAAGTCAGCGGCCGGCTGAACTTCGACGTCGTCAG
genomic: TTCCAGAGCCCCTCCAAGGACCTGAAGGCTATCAACAACCGCCTAAACAGgcaagatcat ... tcacctgcagTGTGTCCGGCGGGAAGAAAGTCAGCGGCCGGCTGAACTTCGACGTCGTCAG
EST: gi|30088299|gb|CB886504.1|CB886504
EST:     TTCCAGAGCCCCTCCAAGGACCTGAAGGCTATCAACAACCGCCTAAACAG                         TGTGTCCGGCGGGAAGAAAGTCAGCGGCCGGCTGAACTTCGACGTCGTCAG
genomic: TTCCAGAGCCCCTCCAAGGACCTGAAGGCTATCAACAACCGCCTAAACAGgcaagatcat ... tcacctgcagTGTGTCCGGCGGGAAGAAAGTCAGCGGCCGGCTGAACTTCGACGTCGTCAG
EST: gi|22935543|gb|BU571818.1|BU571818
EST:     TTCCAGAGCCCCTCCAAGGACCTGAAGGCTATCAACAACCGCCTAAACAG                         TGTGTCCGGCGGGAAGAAAGTCAGCGGCCGGCTGAACTTCGACGTGGTCAG
genomic: TTCCAGAGCCCCTCCAAGGACCTGAAGGCTATCAACAACCGCCTAAACAGgcaagatcat ... tcacctgcagTGTGTCCGGCGGGAAGAAAGTCAGCGGCCGGCTGAACTTCGACGTCGTCAG
EST: gi|27575967|gb|CA998661.1|CA998661
EST:     TTCCAGAGCCCCTCCAAGGACCTGAAGGCTATCAACAACCGCCTAAACAG                         TGTGTCCGGCGGGAAGAAAGTCAGCGGCCGGCTGAACTTCGACGTCGTCAG
genomic: TTCCAGAGCCCCTCCAAGGACCTGAAGGCTATCAACAACCGCCTAAACAGgcaagatcat ... tcacctgcagTGTGTCCGGCGGGAAGAAAGTCAGCGGCCGGCTGAACTTCGACGTCGTCAG
EST: gi|30031712|gb|CB833563.1|CB833563
EST:     TTCCAGAGCCCCTCCAAGGACCTGAAGGCTATCAACAACCGCCTAAACAG                         TGTGTCCGGCGGGAAGAAAGTCAGCG
genomic: TTCCAGAGCCCCTCCAAGGACCTGAAGGCTATCAACAACCGCCTAAACAGgcaagatcat ... tcacctgcagTGTGTCCGGCGGGAAGAAAGTCAGCG
EST: gi|166639923|gb|EG092619.1|EG092619
EST:     TTCCAGAGCCCCTCCAAGGACCTGAAGGCTATCAACAACCGCCTAAACAG                         TGTGTCCGGCGGGAAGAAAGT
genomic: TTCCAGAGCCCCTCCAAGGACCTGAAGGCTATCAACAACCGCCTAAACAGgcaagatcat ... tcacctgcagTGTGTCCGGCGGGAAGAAAGT

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: 40

CCCCGAGCTCCAAGAGCTACTACGCGTGCGTCGGCGAGAGCACCTACGCGTTCCAGAGCCCCTCCAAGGACCTGAAGGCTATCAACAACCGCCTAAACAGgcaagatcat ... tcacctgcagTGTGTCCGGCGGGAAGAAAGTCAGCGGCCGGCTGAACTTCGACGTCGTCAGCGATCTGGTCGTGGCCAGTAGCCTCGGCAGTGACCGTGACGCCAAGCCT


Block sizes: 32 (upstream exon), 49 (downstream exon)
Score: 5

CCCCGAGCTCCAAGAGCTACTACGCGTGCGTCGGCGAGAGCACCTACGCGTTCCAGAGCCCCTCCAAGGACCTGAAGGCTATCAACAACCGCCTAAACAGgcaagatcat ... tcacctgcagTGTGTCCGGCGGGAAGAAAGTCAGCGGCCGGCTGAACTTCGACGTCGTCAGCGATCTGGTCGTGGCCAGTAGCCTCGGCAGTGACCGTGACGCCAAGCCT


Block sizes: 49 (upstream exon), 43 (downstream exon)
Score: 5

CCCCGAGCTCCAAGAGCTACTACGCGTGCGTCGGCGAGAGCACCTACGCGTTCCAGAGCCCCTCCAAGGACCTGAAGGCTATCAACAACCGCCTAAACAGgcaagatcat ... tcacctgcagTGTGTCCGGCGGGAAGAAAGTCAGCGGCCGGCTGAACTTCGACGTCGTCAGCGATCTGGTCGTGGCCAGTAGCCTCGGCAGTGACCGTGACGCCAAGCCT


Block sizes: 49 (upstream exon), 43 (downstream exon)
Score: 2

CCCCGAGCTCCAAGAGCTACTACGCGTGCGTCGGCGAGAGCACCTACGCGTTCCAGAGCCCCTCCAAGGACCTGAAGGCTATCAACAACCGCCTAAACAGgcaagatcat ... tcacctgcagTGTGTCCGGCGGGAAGAAAGTCAGCGGCCGGCTGAACTTCGACGTCGTCAGCGATCTGGTCGTGGCCAGTAGCCTCGGCAGTGACCGTGACGCCAAGCCT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctggtccagtttccaaagcaacagataaactgatgcccagatcgatcacctgcagTGTGTCCGGCGGGAAGAAAGTCAGCGGCCGGCTGAACTTCGACGTCGTCAGCGATCTGGTCGTGGCCAGTAGCCTCGGCAGTGACCGTGACGCCAAGCCT
                           aactgat  putative branch site (score: 2)
                      agataaa  TA-rich tract