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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaggccgcccttaactgtctttttgcaaatctccatagcaaatgtctcagttctgataatcctatgccacattcttttgcagGGTTTGTGCATGTATGCAG

Basic information

species Zea mays
transcript GRMZM2G060564_T04
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|71768983|gb|DR966920.1|DR966920
EST:     TCAGAGGCTTCCCAGATCCTTAATTGTCTGTCTGATTTGGTCTACTGGAC                         GGTTTGTGCATGTATGCAG
genomic: TCAGAGGCTTCCCAGATCCTTAATTGTCTGTCTGATTTGGTCTACTGGACgtaaggccgc ... tcttttgcagGGTTTGTGCATGTATGCAG




















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), 45 (downstream exon)
Score: 65

TTGCTTGCATCTTCTCTATAGTTGCAGCTATTGTTGGTAGCGAGGAGCTTTCAGAGGCTTCCCAGATCCTTAATTGTCTGTCTGATTTGGTCTACTGGACgtaaggccgc ... tcttttgcagGGTTTGTGCATGTATGCAG


Block sizes: 49 (upstream exon), 19 (downstream exon)
Score: 124

TTGCTTGCATCTTCTCTATAGTTGCAGCTATTGTTGGTAGCGAGGAGCTTTCAGAGGCTTCCCAGATCCTTAATTGTCTGTCTGATTTGGTCTACTGGACgtaaggccgc ... tcttttgcagGGTTTGTGCATGTATGCAG


Block sizes: 49 (upstream exon), 19 (downstream exon)
Score: 144

TTGCTTGCATCTTCTCTATAGTTGCAGCTATTGTTGGTAGCGAGGAGCTTTCAGAGGCTTCCCAGATCCTTAATTGTCTGTCTGATTTGGTCTACTGGACgtaaggccgc ... tcttttgcagGGTTTGTGCATGTATGCAG


Block sizes: 49 (upstream exon), 19 (downstream exon)
Score: 185

TTGCTTGCATCTTCTCTATAGTTGCAGCTATTGTTGGTAGCGAGGAGCTTTCAGAGGCTTCCCAGATCCTTAATTGTCTGTCTGATTTGGTCTACTGGACgtaaggccgc ... tcttttgcagGGTTTGTGCATGTATGCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatctccatagcaaatgtctcagttctgataatcctatgccacattcttttgcagGGTTTGTGCATGTATGCAG
                       ttctgat  putative branch site (score: 185)
                                          cattctttt  putative PPT
                                           attctttt  TA-rich tract