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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgaggcaaatccgacctctccgcggttctcttctccgcgcgcgctctttcgccgcattttttttaactgtcgcgtcgacctgatctgcgagcggtgagacaaagggggattccgatctgaccccgattcgaattgcagGGCCGGCACGCGGACGGTGCTTGGACTGCCCTTGTCATGGATCGCGCCGAGCTCACCACGGAGCAG

Basic information

species Zea mays
transcript GRMZM2G163233_T04
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|32864578|gb|CF004260.1|CF004260
EST:     CGTCGCCGGGAGCCTCCCGATCCTTCTTCCACCTTGCACGGTCGTGCCAG                         GGCCGGCACGCGGACGGTGCTTGGACTGCCCTTGTCATGGATCGCGCCGAG
genomic: CGTCGCCGGGAGCCTCCCGATCCTTCTTCCACCTTGCACGGTCGTGCCAGgtgaggcaaa ... cgaattgcagGGCCGGCACGCGGACGGTGCTTGGACTGCCCTTGTCATGGATCGCGCCGAG
EST: gi|211500670|gb|FL332346.1|FL332346
EST:     CGTCGCCGGGAGCCTCCCGATCCTTCTTCCACCCCGCCCGGTCGTGCCAG                         GGCCGGCACGCGGACGGTACTTGGACTGCCCTTGTCATGGATCGCGCCGAG
genomic: CGTCGCCGGGAGCCTCCCGATCCTTCTTCCACCTTGCACGGTCGTGCCAGgtgaggcaaa ... cgaattgcagGGCCGGCACGCGGACGGTGCTTGGACTGCCCTTGTCATGGATCGCGCCGAG
EST: gi|211404953|gb|FL354748.1|FL354748
EST:     CGTCGCCGGGAGCCTCCCGATCCTTCTTCCACCTTGCACGGTCGTGCCAG                         GGCCGGCACGCGGACGGTGCTTGGACTGCCCTTGTCATGGATCGCGCCGAG
genomic: CGTCGCCGGGAGCCTCCCGATCCTTCTTCCACCTTGCACGGTCGTGCCAGgtgaggcaaa ... cgaattgcagGGCCGGCACGCGGACGGTGCTTGGACTGCCCTTGTCATGGATCGCGCCGAG
EST: gi|211253216|gb|FL346295.1|FL346295
EST:     CGTCGCCGGGAGCCTCCCGATCCTTCTTCCACCTTGCACGGTCGTGCCAG                         GGCCGGCACGCGGACGGTGCTTGGACTGCCCTTGTCATGGATCGCGCCGAG
genomic: CGTCGCCGGGAGCCTCCCGATCCTTCTTCCACCTTGCACGGTCGTGCCAGgtgaggcaaa ... cgaattgcagGGCCGGCACGCGGACGGTGCTTGGACTGCCCTTGTCATGGATCGCGCCGAG
EST: gi|211378522|gb|FL350956.1|FL350956
EST:     CGTCGCCGGGAGCCTCCCGATCCTTCTTCCACCTTGCACGGTCGTGCCAG                         GGCCGGCACGCGGACGGTGCTTGGACTGCCCTTGTCATGGATCGCGCCGAG
genomic: CGTCGCCGGGAGCCTCCCGATCCTTCTTCCACCTTGCACGGTCGTGCCAGgtgaggcaaa ... cgaattgcagGGCCGGCACGCGGACGGTGCTTGGACTGCCCTTGTCATGGATCGCGCCGAG
EST: gi|71757599|gb|DR955536.1|DR955536
EST:     CGTCGCCGGGAGCCTCCCGATCCTTCTTCCACCTTGCACGGTCGTGCCAG                         GGCCGGCACGCGGACGGTGCTTGGACTGCCCTTGTCATGGATCGCGCCGAG
genomic: CGTCGCCGGGAGCCTCCCGATCCTTCTTCCACCTTGCACGGTCGTGCCAGgtgaggcaaa ... cgaattgcagGGCCGGCACGCGGACGGTGCTTGGACTGCCCTTGTCATGGATCGCGCCGAG
EST: gi|211460866|gb|FL363678.1|FL363678
EST:     CGTCGCCGGGAGCCTCCCGATCCTTCTTCCACCTTGCACGGTCGTGCCAG                         GGCCGGCACGCGGACGGTGCTTGGACTGCCCTTGTCATGGATCGCGCCGAG
genomic: CGTCGCCGGGAGCCTCCCGATCCTTCTTCCACCTTGCACGGTCGTGCCAGgtgaggcaaa ... cgaattgcagGGCCGGCACGCGGACGGTGCTTGGACTGCCCTTGTCATGGATCGCGCCGAG
EST: gi|211207688|gb|FL307218.1|FL307218
EST:     CGTCGCCGGGAGCCTCCCGATCCTTCTTCCACCTTGCACGGTCGTGCCAG                         GGCCGGCACGCGGACGGTGCTTGGACTGCCCTTGTCATGGATCGCGCCGAG
genomic: CGTCGCCGGGAGCCTCCCGATCCTTCTTCCACCTTGCACGGTCGTGCCAGgtgaggcaaa ... cgaattgcagGGCCGGCACGCGGACGGTGCTTGGACTGCCCTTGTCATGGATCGCGCCGAG
EST: gi|211155631|gb|FL334256.1|FL334256
EST:     CGTCGCCGGGAGCCTCCCGATCCTTCTTCCACCTTGCACGGTCGTGCCAG                         GGCCGGCACGCGGACGGTGCTTGGACTGCCCTTGTCATGGATCGCGCCGAG
genomic: CGTCGCCGGGAGCCTCCCGATCCTTCTTCCACCTTGCACGGTCGTGCCAGgtgaggcaaa ... cgaattgcagGGCCGGCACGCGGACGGTGCTTGGACTGCCCTTGTCATGGATCGCGCCGAG
EST: gi|211432573|gb|FL331494.1|FL331494
EST:     CGTCGCCGGGAGCCTCCCGATCCTTCTTCCACCCCGCCCGGTCGTGCCAG                         GGCCGGCACGCGGACGGTACTTGGACTGCCCTTGTCATGGATCGCGCCGAG
genomic: CGTCGCCGGGAGCCTCCCGATCCTTCTTCCACCTTGCACGGTCGTGCCAGgtgaggcaaa ... cgaattgcagGGCCGGCACGCGGACGGTGCTTGGACTGCCCTTGTCATGGATCGCGCCGAG
EST: gi|211220146|gb|FL315335.1|FL315335
EST:     CGTCGCCGGGAGCCTCCCGATCCTTCTTCCACCCCGCCCGGTCGTGCCAG                         GGCCGGCACGCGGACGGTACTTGGACTGCCCTTGTCATGGATCGCGCCGAG
genomic: CGTCGCCGGGAGCCTCCCGATCCTTCTTCCACCTTGCACGGTCGTGCCAGgtgaggcaaa ... cgaattgcagGGCCGGCACGCGGACGGTGCTTGGACTGCCCTTGTCATGGATCGCGCCGAG

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), 47 (downstream exon)
Score: 116

GTCCCTCTCCTCTCAGATCGCTTCCTTGTTCTCGCCTCGTCTTCCCCGATCGTCGCCGGGAGCCTCCCGATCCTTCTTCCACCTTGCACGGTCGTGCCAGgtgaggcaaa ... cgaattgcagGGCCGGCACGCGGACGGTGCTTGGACTGCCCTTGTCATGGATCGCGCCGAGCTCACCACGGAGCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 184

GTCCCTCTCCTCTCAGATCGCTTCCTTGTTCTCGCCTCGTCTTCCCCGATCGTCGCCGGGAGCCTCCCGATCCTTCTTCCACCTTGCACGGTCGTGCCAGgtgaggcaaa ... cgaattgcagGGCCGGCACGCGGACGGTGCTTGGACTGCCCTTGTCATGGATCGCGCCGAGCTCACCACGGAGCAG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 104

GTCCCTCTCCTCTCAGATCGCTTCCTTGTTCTCGCCTCGTCTTCCCCGATCGTCGCCGGGAGCCTCCCGATCCTTCTTCCACCTTGCACGGTCGTGCCAGgtgaggcaaa ... cgaattgcagGGCCGGCACGCGGACGGTGCTTGGACTGCCCTTGTCATGGATCGCGCCGAGCTCACCACGGAGCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 180

GTCCCTCTCCTCTCAGATCGCTTCCTTGTTCTCGCCTCGTCTTCCCCGATCGTCGCCGGGAGCCTCCCGATCCTTCTTCCACCTTGCACGGTCGTGCCAGgtgaggcaaa ... cgaattgcagGGCCGGCACGCGGACGGTGCTTGGACTGCCCTTGTCATGGATCGCGCCGAGCTCACCACGGAGCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctgcgagcggtgagacaaagggggattccgatctgaccccgattcgaattgcagGGCCGGCACGCGGACGGTGCTTGGACTGCCCTTGTCATGGATCGCGCCGAGCTCACCACGGAGCAG
                               atctgac  putative branch site (score: 180)
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgaggcaaatccgacctctccgcggttctcttctccgcgcgcgctctttcgccgcattttttttaactgtcgcgtcgacctgatctgcgagcggtgagacaaagggggattccgatctgaccccgattcgaattgcagGGCCGGCACGCGGACGGTGCTTGGACTGCCCTTGTCATGGATCGCGCCGAGCTCACCACGGAGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG