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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATCAGAGATGATTTTGAGAAAGAGGACTCGTTTCATGGATTGTGTGCAATGgtatatccagacctcctggttatggactgggtgatttttgttctgaaatcttatttggttacttacaccag

Basic information

species Zea mays
transcript GRMZM5G869572_T01
intron # 6
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|211163358|gb|FK967901.1|FK967901
EST:     TCAGAGATGATTTTGAGAAAGAGGACTCGTTTCATGGATTGTGTGCAATG                         GTGGCAGCAAACCCTACAGGAGGCGCCGGTTCATTAGCTTACATCTGCCAG
genomic: TCAGAGATGATTTTGAGAAAGAGGACTCGTTTCATGGATTGTGTGCAATGgtatatccag ... cttacaccagGTGGCAGCAAACCCTACAGGAGGCGCCGGTTCATTAGCTTACATCTGCCAG
EST: gi|31363389|gb|CD447746.1|CD447746
EST:     TCAGAGATGATTTTGAGAAAGAGGACTCGTTTCATGGATTGTGTGCAATG                         GTGGCAGCAAACCCTACAGGAGGCGCCGGTTCATTAGCTTACATCTGCCAG
genomic: TCAGAGATGATTTTGAGAAAGAGGACTCGTTTCATGGATTGTGTGCAATGgtatatccag ... cttacaccagGTGGCAGCAAACCCTACAGGAGGCGCCGGTTCATTAGCTTACATCTGCCAG
EST: gi|89250982|gb|DY622768.1|DY622768
EST:     TCAGAGATGATTTTGAGAAAGAGGACTCGTTTCATGGATTGTGTGCAATG                         GTGGCAGCAAACCCTACAGGAGGCGCCGGTTCATTAGCTTACATCTGCCAG
genomic: TCAGAGATGATTTTGAGAAAGAGGACTCGTTTCATGGATTGTGTGCAATGgtatatccag ... cttacaccagGTGGCAGCAAACCCTACAGGAGGCGCCGGTTCATTAGCTTACATCTGCCAG
EST: gi|6918339|gb|AW399869.1|AW399869
EST:     TCAGAGATGATTTTGAGAAAGAGGACTCGTTTCATGGACTGTGTGCAATG                         GTGGCAGCAAACCCTACAGGAGGCGCCGGTTCATTAGCTTACATCTGCCAG
genomic: TCAGAGATGATTTTGAGAAAGAGGACTCGTTTCATGGATTGTGTGCAATGgtatatccag ... cttacaccagGTGGCAGCAAACCCTACAGGAGGCGCCGGTTCATTAGCTTACATCTGCCAG
EST: gi|211163359|gb|FK967902.1|FK967902
EST:     TCAGAGATGATTTTGAGAAAGAGGACTCGTTTCATGGATTGTGTGCAATG                         GTGGCAGCAAACCCTACAGGAGGCGCCGGTTCATTAGCTTACATCTGCCAG
genomic: TCAGAGATGATTTTGAGAAAGAGGACTCGTTTCATGGATTGTGTGCAATGgtatatccag ... cttacaccagGTGGCAGCAAACCCTACAGGAGGCGCCGGTTCATTAGCTTACATCTGCCAG
EST: gi|6918594|gb|AW400124.1|AW400124
EST:     TCAGAGATGATTTTGAGAAAGAGGACTCGTTTCATGGACTGTGTGCAATG                         GTGGCAGCAAACCCTACAGGAGGCGCCGGTTCATTAGCTTACATCTGGCAG
genomic: TCAGAGATGATTTTGAGAAAGAGGACTCGTTTCATGGATTGTGTGCAATGgtatatccag ... cttacaccagGTGGCAGCAAACCCTACAGGAGGCGCCGGTTCATTAGCTTACATCTGCCAG
EST: gi|60338787|gb|DN205760.1|DN205760
EST:     TCAGAGATGATTTTGAGAAAGAGGACTCGTTTCATGGATTGTGTGCAATG                         GTGGCAGCAAACCCTACAGGAGGCGCCGGTTCATTAGCTTACATCTGCCAG
genomic: TCAGAGATGATTTTGAGAAAGAGGACTCGTTTCATGGATTGTGTGCAATGgtatatccag ... cttacaccagGTGGCAGCAAACCCTACAGGAGGCGCCGGTTCATTAGCTTACATCTGCCAG

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: 72

GATCAGAGATGATTTTGAGAAAGAGGACTCGTTTCATGGATTGTGTGCAATGgtatatccag ... cttacaccagGTGGCAGCAAACCCTACAGGAGGCGCCGGTTCATTAGCTTACATCTGCCAGGCCTGTGCGAGTTGGACT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 64

GATCAGAGATGATTTTGAGAAAGAGGACTCGTTTCATGGATTGTGTGCAATGgtatatccag ... cttacaccagGTGGCAGCAAACCCTACAGGAGGCGCCGGTTCATTAGCTTACATCTGCCAGGCCTGTGCGAGTTGGACT


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

GATCAGAGATGATTTTGAGAAAGAGGACTCGTTTCATGGATTGTGTGCAATGgtatatccag ... cttacaccagGTGGCAGCAAACCCTACAGGAGGCGCCGGTTCATTAGCTTACATCTGCCAGGCCTGTGCGAGTTGGACT


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

GATCAGAGATGATTTTGAGAAAGAGGACTCGTTTCATGGATTGTGTGCAATGgtatatccag ... cttacaccagGTGGCAGCAAACCCTACAGGAGGCGCCGGTTCATTAGCTTACATCTGCCAGGCCTGTGCGAGTTGGACT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GATCAGAGATGATTTTGAGAAAGAGGACTCGTTTCATGGATTGTGTGCAATGgtatatccagacctcctggttatggactgggtgatttttgttctgaaatcttatttggttacttacaccag

- -  GAGATG
- - - - - - - - - - AAGAGG
- - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - CATGGA