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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaattaattgatcagcaactgaattatttcctccatatttctattttttgtgttttgtttttaacggctcaagatatttggtttgctcaattctgatttgttttgcagGATGCTGACTCAAAGCGCAGTGCATTGGAAGAGCAGGGGAAAAAATTGGATGAGAGAGAGGCAAAGGTCACTAATAGAGAAAAG

Basic information

species Zea mays
transcript GRMZM2G015875_T01
intron # 5
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|18964673|gb|BM661140.1|BM661140
EST:     AAGAGGATGATATTAACAAAAGACTAAATGAATTGCATTTACAGGAAAAG                         GATGCTGACTCAAAGCGTAGTGCATTGGAAGAGCAGGGGAAAAAATTGGAT
genomic: AAGAGGATGATATTAACAAAAGACTAAATGAATTACATTTACAGGAAAAGgtaattaatt ... tgttttgcagGATGCTGACTCAAAGCGCAGTGCATTGGAAGAGCAGGGGAAAAAATTGGAT
EST: gi|18963745|gb|BM660606.1|BM660606
EST:     AAGAGGATGATATTAACAAAAGACTAAATGAATTGCATTTACAGGAAAAG                         GATGCTGACTCAAAGCGTAGTGCATTGGAAGAGCAGGGGAAAAAATTGGAT
genomic: AAGAGGATGATATTAACAAAAGACTAAATGAATTACATTTACAGGAAAAGgtaattaatt ... tgttttgcagGATGCTGACTCAAAGCGCAGTGCATTGGAAGAGCAGGGGAAAAAATTGGAT
EST: gi|18963743|gb|BM660605.1|BM660605
EST:     AAGAGGATGATATTAACAAAAGACTAAATGAATTGCATTTACAGGAAAAG                         GATGCTGACTCAAAGCGTAGTGCATTGGAAGAGCAGGGGAAAAAATTGGAT
genomic: AAGAGGATGATATTAACAAAAGACTAAATGAATTACATTTACAGGAAAAGgtaattaatt ... tgttttgcagGATGCTGACTCAAAGCGCAGTGCATTGGAAGAGCAGGGGAAAAAATTGGAT
EST: gi|87153938|gb|DY398727.1|DY398727
EST:     AAGAGGATGATATTAACAAAAGACTAAATGAATTGCATTTACAGGAAAAG                         GATGCTGACTCAAAGCGTAGTGCATTGGAAGAGCAGGGGAAAAAATTGGAT
genomic: AAGAGGATGATATTAACAAAAGACTAAATGAATTACATTTACAGGAAAAGgtaattaatt ... tgttttgcagGATGCTGACTCAAAGCGCAGTGCATTGGAAGAGCAGGGGAAAAAATTGGAT
EST: gi|18171138|gb|BM340978.1|BM340978
EST:     AAGAGGATGATATTAACAAAAGACTAAATGAATTACATTTACAGGAAAAG                         GATGCTGACTCAAAGCGCAGTGCATTGGAAGAGCAGGGGAAAAAATTGGAT
genomic: AAGAGGATGATATTAACAAAAGACTAAATGAATTACATTTACAGGAAAAGgtaattaatt ... tgttttgcagGATGCTGACTCAAAGCGCAGTGCATTGGAAGAGCAGGGGAAAAAATTGGAT

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: 198

GGAGGAGGCACGAAGGACAGTGGAGGCCGCTAAAGTTACTCTGAAAGTCAAAGAGGATGATATTAACAAAAGACTAAATGAATTACATTTACAGGAAAAGgtaattaatt ... tgttttgcagGATGCTGACTCAAAGCGCAGTGCATTGGAAGAGCAGGGGAAAAAATTGGATGAGAGAGAGGCAAAGGTCACTAATAGAGAAAAG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 77

GGAGGAGGCACGAAGGACAGTGGAGGCCGCTAAAGTTACTCTGAAAGTCAAAGAGGATGATATTAACAAAAGACTAAATGAATTACATTTACAGGAAAAGgtaattaatt ... tgttttgcagGATGCTGACTCAAAGCGCAGTGCATTGGAAGAGCAGGGGAAAAAATTGGATGAGAGAGAGGCAAAGGTCACTAATAGAGAAAAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 93

GGAGGAGGCACGAAGGACAGTGGAGGCCGCTAAAGTTACTCTGAAAGTCAAAGAGGATGATATTAACAAAAGACTAAATGAATTACATTTACAGGAAAAGgtaattaatt ... tgttttgcagGATGCTGACTCAAAGCGCAGTGCATTGGAAGAGCAGGGGAAAAAATTGGATGAGAGAGAGGCAAAGGTCACTAATAGAGAAAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 119

GGAGGAGGCACGAAGGACAGTGGAGGCCGCTAAAGTTACTCTGAAAGTCAAAGAGGATGATATTAACAAAAGACTAAATGAATTACATTTACAGGAAAAGgtaattaatt ... tgttttgcagGATGCTGACTCAAAGCGCAGTGCATTGGAAGAGCAGGGGAAAAAATTGGATGAGAGAGAGGCAAAGGTCACTAATAGAGAAAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgtttttaacggctcaagatatttggtttgctcaattctgatttgttttgcagGATGCTGACTCAAAGCGCAGTGCATTGGAAGAGCAGGGGAAAAAATTGGATGAGAGAGAGGCAAAGGTCACTAATAGAGAAAAG
                                           tttgtttt  CT-rich tract
                 aagatattt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaattaattgatcagcaactgaattatttcctccatatttctattttttgtgttttgtttttaacggctcaagatatttggtttgctcaattctgatttgttttgcagGATGCTGACTCAAAGCGCAGTGCATTGGAAGAGCAGGGGAAAAAATTGGATGAGAGAGAGGCAAAGGTCACTAATAGAGAAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG