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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgaatgcccggcctttacatgctttgctcagctccgatgcagtcactgccatgatatcgccatcctcgcactcgcgctggtctctacgaacagagacctgaaatggtggatatgcctgatgtgtcctgttctgacttgtgacttcaactgcagGTGGAGAACGCCAGGGCGAGGCTGGACAAGTGGGACGACAAGAAGCAGCCCCTCCTAGCCTAGAAGAAGACTGATTGAAGGTCACTGTAGCGCGCGCTGA

Basic information

species Zea mays
transcript GRMZM2G470075_T02
intron # 4
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|71767622|gb|DR965559.1|DR965559
EST:     AGACGCTCATCCTGCTCTGGGTCACCTTCAGAACAGACTGGACCAAGGAG                         GTGGAGAACGCCAGGGCGAGGCTGGACAAGTGGGACGACAAGAAGCAGCCC
genomic: AGACGCTCATCCTGCTCTGGGTCACCTTCAGAACAGACTGGACCAAGGAGgtgaatgccc ... tcaactgcagGTGGAGAACGCCAGGGCGAGGCTGGACAAGTGGGACGACAAGAAGCAGCCC
EST: gi|211218506|gb|FL448111.1|FL448111
EST:     AGACGCTCATCCTGCTCTGGGTCACCTTCAGAACAGACTGGACCAAGGAG                         GTGGAGAACGCCAGGGCGAGGCTGGACAAGTGGGACGACAAGAAGCAGCCC
genomic: AGACGCTCATCCTGCTCTGGGTCACCTTCAGAACAGACTGGACCAAGGAGgtgaatgccc ... tcaactgcagGTGGAGAACGCCAGGGCGAGGCTGGACAAGTGGGACGACAAGAAGCAGCCC
EST: gi|211320998|gb|FL255479.1|FL255479
EST:     AGACGCTCATCCTGCTCTGGGTCACCTTCAGAACAGACTGGACNTAGGAG                         GTGGAGAACGCCAGGGCGAGGCTGGACAAGTGGGACGACAAGAAGCAGCCC
genomic: AGACGCTCATCCTGCTCTGGGTCACCTTCAGAACAGACTGGACCAAGGAGgtgaatgccc ... tcaactgcagGTGGAGAACGCCAGGGCGAGGCTGGACAAGTGGGACGACAAGAAGCAGCCC
EST: gi|76287403|gb|DV026971.1|DV026971
EST:     AGACGCTCATCCTGCTCTGGGTCACCTTCAGAACAGACTGGACCAAGGAG                         GTGGAGAACGCCAGGGCGAGGCTGGACAAGTGGGACGACAAGAAGCAGCCC
genomic: AGACGCTCATCCTGCTCTGGGTCACCTTCAGAACAGACTGGACCAAGGAGgtgaatgccc ... tcaactgcagGTGGAGAACGCCAGGGCGAGGCTGGACAAGTGGGACGACAAGAAGCAGCCC
EST: gi|211320997|gb|FL255478.1|FL255478
EST:     TCTGGGTCACCTTCAGAACAGACTGGACCAAGGAG                         GTGGAGAATGCCAGGGCGAGGCTGGACAAG
genomic: TCTGGGTCACCTTCAGAACAGACTGGACCAAGGAGgtgaatgccc ... tcaactgcagGTGGAGAACGCCAGGGCGAGGCTGGACAAG
EST: gi|211194008|gb|FL255457.1|FL255457
EST:     ANACGCTCATCCTGCTCTGGGTCACCTTCAGAACAGACTGGACCAAGGAG                         GTGGAGAACGCCAGGGCGAGGCTGGACAAGTGGGACGACAAGAAGCAGCCC
genomic: AGACGCTCATCCTGCTCTGGGTCACCTTCAGAACAGACTGGACCAAGGAGgtgaatgccc ... tcaactgcagGTGGAGAACGCCAGGGCGAGGCTGGACAAGTGGGACGACAAGAAGCAGCCC

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: 30 (upstream exon), 49 (downstream exon)
Score: 12

GGCATTTGGAGCGGCATGGTCATCGGGGGAACCATGATGCAGACGCTCATCCTGCTCTGGGTCACCTTCAGAACAGACTGGACCAAGGAGgtgaatgccc ... tcaactgcagGTGGAGAACGCCAGGGCGAGGCTGGACAAGTGGGACGACAAGAAGCAGCCCCTCCTAGCCTAGAAGAAGACTGATTGAAGGTCACTGTAGCGCGCGCTGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 35

GGCATTTGGAGCGGCATGGTCATCGGGGGAACCATGATGCAGACGCTCATCCTGCTCTGGGTCACCTTCAGAACAGACTGGACCAAGGAGgtgaatgccc ... tcaactgcagGTGGAGAACGCCAGGGCGAGGCTGGACAAGTGGGACGACAAGAAGCAGCCCCTCCTAGCCTAGAAGAAGACTGATTGAAGGTCACTGTAGCGCGCGCTGA


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 22

GGCATTTGGAGCGGCATGGTCATCGGGGGAACCATGATGCAGACGCTCATCCTGCTCTGGGTCACCTTCAGAACAGACTGGACCAAGGAGgtgaatgccc ... tcaactgcagGTGGAGAACGCCAGGGCGAGGCTGGACAAGTGGGACGACAAGAAGCAGCCCCTCCTAGCCTAGAAGAAGACTGATTGAAGGTCACTGTAGCGCGCGCTGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 51

GGCATTTGGAGCGGCATGGTCATCGGGGGAACCATGATGCAGACGCTCATCCTGCTCTGGGTCACCTTCAGAACAGACTGGACCAAGGAGgtgaatgccc ... tcaactgcagGTGGAGAACGCCAGGGCGAGGCTGGACAAGTGGGACGACAAGAAGCAGCCCCTCCTAGCCTAGAAGAAGACTGATTGAAGGTCACTGTAGCGCGCGCTGA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgaaatggtggatatgcctgatgtgtcctgttctgacttgtgacttcaactgcagGTGGAGAACGCCAGGGCGAGGCTGGACAAGTGGGACGACAAGAAGCAGCCCCTCCTAGCCTAGAAGAAGACTGATTGAAGGTCACTGTAGCGCGCGCTGA
                              ttctgac  putative branch site (score: 51)
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgaatgcccggcctttacatgctttgctcagctccgatgcagtcactgccatgatatcgccatcctcgcactcgcgctggtctctacgaacagagacctgaaatggtggatatgcctgatgtgtcctgttctgacttgtgacttcaactgcagGTGGAGAACGCCAGGGCGAGGCTGGACAAGTGGGACGACAAGAAGCAGCCCCTCCTAGCCTAGAAGAAGACTGATTGAAGGTCACTGTAGCGCGCGCTGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG