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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagaacttggacttgctgtgattagcattgtgtgatattctgtactgctaatgaaaccttttcctttcccccttctttgtatatagGTCAAAGATTTTCACATATGATCAAGTCGTGGAAAAAGTAGCTGAAAAACTTGGCGTGGATGACCCATCGAAAATTCGTCTTACATCACATAATTGTTAT

Basic information

species Zea mays
transcript GRMZM5G864266_T01
intron # 25
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|76909980|gb|DV163634.1|DV163634
EST:     CACTTCCGTTCATTGGAGAAGCCCAAGGACGACGAATTTTGCCTTGAGAT                         GTCAAAGATTTTCACATATGATCAAGTCGTGGAAAAAGTAGCTGAAAAACT
genomic: CACTTCCGTTCATTGGAGAAGCCCAAGGACGACGAATTTTGCCTTGAGATgtaagaactt ... ttgtatatagGTCAAAGATTTTCACATATGATCAAGTCGTGGAAAAAGTAGCTGAAAAACT
EST: gi|32836874|gb|CD976552.1|CD976552
EST:     CACTTCCGTTCATTGGAGAAGCCCAAGGACGACGAATTTTGCCTTGAGAT                         GTCAAAGATTTTCACATATGATCAAGTCGTGGAAAAAGTAGCTGAAAAACT
genomic: CACTTCCGTTCATTGGAGAAGCCCAAGGACGACGAATTTTGCCTTGAGATgtaagaactt ... ttgtatatagGTCAAAGATTTTCACATATGATCAAGTCGTGGAAAAAGTAGCTGAAAAACT

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: 48 (upstream exon), 48 (downstream exon)
Score: 198

GTGGTGCACTTCCGTTCATTGGAGAAGCCCAAGGACGACGAATTTTGCCTTGAGATgtaagaactt ... ttgtatatagGTCAAAGATTTTCACATATGATCAAGTCGTGGAAAAAGTAGCTGAAAAACTTGGCGTGGATGACCCATCGAAAATTCGTCTTACATCACATAATTGTTAT


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 74

GTGGTGCACTTCCGTTCATTGGAGAAGCCCAAGGACGACGAATTTTGCCTTGAGATgtaagaactt ... ttgtatatagGTCAAAGATTTTCACATATGATCAAGTCGTGGAAAAAGTAGCTGAAAAACTTGGCGTGGATGACCCATCGAAAATTCGTCTTACATCACATAATTGTTAT


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 82

GTGGTGCACTTCCGTTCATTGGAGAAGCCCAAGGACGACGAATTTTGCCTTGAGATgtaagaactt ... ttgtatatagGTCAAAGATTTTCACATATGATCAAGTCGTGGAAAAAGTAGCTGAAAAACTTGGCGTGGATGACCCATCGAAAATTCGTCTTACATCACATAATTGTTAT


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 145

GTGGTGCACTTCCGTTCATTGGAGAAGCCCAAGGACGACGAATTTTGCCTTGAGATgtaagaactt ... ttgtatatagGTCAAAGATTTTCACATATGATCAAGTCGTGGAAAAAGTAGCTGAAAAACTTGGCGTGGATGACCCATCGAAAATTCGTCTTACATCACATAATTGTTAT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgatattctgtactgctaatgaaaccttttcctttcccccttctttgtatatagGTCAAAGATTTTCACATATGATCAAGTCGTGGAAAAAGTAGCTGAAAAACTTGGCGTGGATGACCCATCGAAAATTCGTCTTACATCACATAATTGTTAT
              tgctaat  putative branch site (score: 145)
                         ccttttcctttccccc  putative PPT
                                            tttgtatata  TA-rich tract