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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgtcctctgtagttccgtttgtctatatgttgtttcatagtaaaggcttctttgacttaaaaagcacattttgcactgcagATGCTTCTGAAGATGCTCCCAGCTTATTACAATCATGTCCGGGCATTTGAGAATACTCTAGTAACCAAGTTTTTTGGTCTACACTGTGTCAAGTTAGCTG

Basic information

species Zea mays
transcript GRMZM2G036113_T02
intron # 3
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|74238324|gb|DT646238.1|DT646238
EST:     CAAACGATGATCGGTACATGATAAAGACGATGAAGAAATCTGAAGTGAAG                         ATGCTTCTGAAGATGCTCCCAGCTTATTACAATCATGTCCGGGCATTTGAG
genomic: CAAACGATGATCGGTACATGATAAAGACGATGAAGAAATCTGAAGTGAAGgtttgtcctc ... tgcactgcagATGCTTCTGAAGATGCTCCCAGCTTATTACAATCATGTCCGGGCATTTGAG




















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: 31

TCTCAGAGAGCTTTCATCTCCTGGTAAGAGTGGAAGCTTTTTCTACCTGACAAACGATGATCGGTACATGATAAAGACGATGAAGAAATCTGAAGTGAAGgtttgtcctc ... tgcactgcagATGCTTCTGAAGATGCTCCCAGCTTATTACAATCATGTCCGGGCATTTGAGAATACTCTAGTAACCAAGTTTTTTGGTCTACACTGTGTCAAGTTAGCTG


Block sizes: 44 (upstream exon), 45 (downstream exon)
Score: 19

TCTCAGAGAGCTTTCATCTCCTGGTAAGAGTGGAAGCTTTTTCTACCTGACAAACGATGATCGGTACATGATAAAGACGATGAAGAAATCTGAAGTGAAGgtttgtcctc ... tgcactgcagATGCTTCTGAAGATGCTCCCAGCTTATTACAATCATGTCCGGGCATTTGAGAATACTCTAGTAACCAAGTTTTTTGGTCTACACTGTGTCAAGTTAGCTG


Block sizes: 48 (upstream exon), 43 (downstream exon)
Score: 10

TCTCAGAGAGCTTTCATCTCCTGGTAAGAGTGGAAGCTTTTTCTACCTGACAAACGATGATCGGTACATGATAAAGACGATGAAGAAATCTGAAGTGAAGgtttgtcctc ... tgcactgcagATGCTTCTGAAGATGCTCCCAGCTTATTACAATCATGTCCGGGCATTTGAGAATACTCTAGTAACCAAGTTTTTTGGTCTACACTGTGTCAAGTTAGCTG


Block sizes: 47 (upstream exon), 45 (downstream exon)
Score: 39

TCTCAGAGAGCTTTCATCTCCTGGTAAGAGTGGAAGCTTTTTCTACCTGACAAACGATGATCGGTACATGATAAAGACGATGAAGAAATCTGAAGTGAAGgtttgtcctc ... tgcactgcagATGCTTCTGAAGATGCTCCCAGCTTATTACAATCATGTCCGGGCATTTGAGAATACTCTAGTAACCAAGTTTTTTGGTCTACACTGTGTCAAGTTAGCTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgttgtttcatagtaaaggcttctttgacttaaaaagcacattttgcactgcagATGCTTCTGAAGATGCTCCCAGCTTATTACAATCATGTCCGGGCATTTGAGAATACTCTAGTAACCAAGTTTTTTGGTCTACACTGTGTCAAGTTAGCTG
                       ctttgac  putative branch site (score: 39)
                            acttaaaaa  TA-rich tract