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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGTGAGGGTGATCCTACATTTCGAGAAGAGCTTCTTAACTTTACACAAAGGGGGCGTATTCTGCAACTTTCAAACTTTAAGGATGACTCCAGTCCAATTGgttagaatttctgtcttggtagaagattgccctgaccctgcttatcacctcatgattttcttgttttctgataccaagttctctgcag

Basic information

species Zea mays
transcript GRMZM2G114513_T02
intron # 4
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|211097837|gb|FL067788.1|FL067788
EST:     GGGGCGTATTCTGCAACTTTCAAACTTTAAGGATGACTCCAGTCCAATTG                         CTTGGGATTGTTCTGCC
genomic: GGGGCGTATTCTGCAACTTTCAAACTTTAAGGATGACTCCAGTCCAATTGgttagaattt ... ttctctgcagCTTGGGATTGTTCTGCC
EST: gi|211079577|gb|FL056323.1|FL056323
EST:     GGGGCGTATTCTGCAACTTTCAAACTTTAAGGATGACTCCAGTCCAATTG                         CTTGGGATTGT
genomic: GGGGCGTATTCTGCAACTTTCAAACTTTAAGGATGACTCCAGTCCAATTGgttagaattt ... ttctctgcagCTTGGGATTGT
EST: gi|21760018|gb|BQ635559.1|BQ635559
EST:     GGGGCGTATTCTGCAACTTTCAAACTTTAAGGATGACTCCAGTCCAATTG                         CTTGGGATTGTTCTGCCTGGGTGCGCACATATGGTTTGTTTTTGGAAGAAA
genomic: GGGGCGTATTCTGCAACTTTCAAACTTTAAGGATGACTCCAGTCCAATTGgttagaattt ... ttctctgcagCTTGGGATTGTTCTGCCTGGGTGCGCACATATGGTTTGTTTTTGGAAGAAA
EST: gi|211050621|gb|FL256688.1|FL256688
EST:     GGGGCGTATTCTGCAACTTTCAAACTTTAAGGATGACTCCAGTCCAATTG                         CTTGGGGTTGTTCTGCCTGGGTGCGCACATATGGNTTGTTTTTGGAAGAAA
genomic: GGGGCGTATTCTGCAACTTTCAAACTTTAAGGATGACTCCAGTCCAATTGgttagaattt ... ttctctgcagCTTGGGATTGTTCTGCCTGGGTGCGCACATATGGTTTGTTTTTGGAAGAAA
EST: gi|33099286|gb|CF059246.1|CF059246
EST:     GGGGCGTATTCTGCAACTTTCAAACTTTAAGGATGACTCAAGTCCAATTG                         CTTGGGATTGTT
genomic: GGGGCGTATTCTGCAACTTTCAAACTTTAAGGATGACTCCAGTCCAATTGgttagaattt ... ttctctgcagCTTGGGATTGTT
EST: gi|211092899|gb|FL067769.1|FL067769
EST:     GGGGCGTATTCTGCAACTTTCAAACTTTAAGGATGACTCCAGTCCAATTG                         CTTGGGATTGTTCTGCCTGGGTGCGCACATATGGTTTGTTTTTGGAAGAAA
genomic: GGGGCGTATTCTGCAACTTTCAAACTTTAAGGATGACTCCAGTCCAATTGgttagaattt ... ttctctgcagCTTGGGATTGTTCTGCCTGGGTGCGCACATATGGTTTGTTTTTGGAAGAAA
EST: gi|211053572|gb|FL256699.1|FL256699
EST:     GGGGCGTATTCTGCAACTTTCAAACTTTAAGGATGACTCCAGTCCAATTG                         CTTGGGGTTGTTCTGCCTGGGNGCGCACATATGGTTTGTTTTTGGAA
genomic: GGGGCGTATTCTGCAACTTTCAAACTTTAAGGATGACTCCAGTCCAATTGgttagaattt ... ttctctgcagCTTGGGATTGTTCTGCCTGGGTGCGCACATATGGTTTGTTTTTGGAA
EST: gi|211095366|gb|FL067775.1|FL067775
EST:     GGGGCGTATTCTGCAACTTTCAAACTTTAAGGATGACTCCAGTCCAATTG                         CTTGGGATTGTTCTGCCTGGGTGCGCACATATGGTTTGTTTTTGGAAGAAA
genomic: GGGGCGTATTCTGCAACTTTCAAACTTTAAGGATGACTCCAGTCCAATTGgttagaattt ... ttctctgcagCTTGGGATTGTTCTGCCTGGGTGCGCACATATGGTTTGTTTTTGGAAGAAA

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: 260

CGTGAGGGTGATCCTACATTTCGAGAAGAGCTTCTTAACTTTACACAAAGGGGGCGTATTCTGCAACTTTCAAACTTTAAGGATGACTCCAGTCCAATTGgttagaattt ... ttctctgcagCTTGGGATTGTTCTGCCTGGGTGCGCACATATGGTTTGTTTTTGGAAGAAAGGTTGGAGTGCTTCAGAGTTCTGAAGTATGATGTTGAAGCTGAGCGTTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 223

CGTGAGGGTGATCCTACATTTCGAGAAGAGCTTCTTAACTTTACACAAAGGGGGCGTATTCTGCAACTTTCAAACTTTAAGGATGACTCCAGTCCAATTGgttagaattt ... ttctctgcagCTTGGGATTGTTCTGCCTGGGTGCGCACATATGGTTTGTTTTTGGAAGAAAGGTTGGAGTGCTTCAGAGTTCTGAAGTATGATGTTGAAGCTGAGCGTTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 208

CGTGAGGGTGATCCTACATTTCGAGAAGAGCTTCTTAACTTTACACAAAGGGGGCGTATTCTGCAACTTTCAAACTTTAAGGATGACTCCAGTCCAATTGgttagaattt ... ttctctgcagCTTGGGATTGTTCTGCCTGGGTGCGCACATATGGTTTGTTTTTGGAAGAAAGGTTGGAGTGCTTCAGAGTTCTGAAGTATGATGTTGAAGCTGAGCGTTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 249

CGTGAGGGTGATCCTACATTTCGAGAAGAGCTTCTTAACTTTACACAAAGGGGGCGTATTCTGCAACTTTCAAACTTTAAGGATGACTCCAGTCCAATTGgttagaattt ... ttctctgcagCTTGGGATTGTTCTGCCTGGGTGCGCACATATGGTTTGTTTTTGGAAGAAAGGTTGGAGTGCTTCAGAGTTCTGAAGTATGATGTTGAAGCTGAGCGTTT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CGTGAGGGTGATCCTACATTTCGAGAAGAGCTTCTTAACTTTACACAAAGGGGGCGTATTCTGCAACTTTCAAACTTTAAGGATGACTCCAGTCCAATTGgttagaatttctgtcttggtagaagattgccctgaccctgcttatcacctcatgattttcttgttttctgataccaagttctctgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG