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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgcgttatccttaaaagtttaacataagtagtcgtgttctatcacccattaatataaccaattctttgtgtttacagAAAAAGGAGCTGGAAGCAGAGTTGGCAAACGTGTCTGGATTTGCTAAGCCAACTCGAAAAATAAG

Basic information

species Zea mays
transcript GRMZM2G070126_T01
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|148934696|gb|EC878744.2|EC878744
EST:     GCAAAGACCCTGTAAAGTCTATTTTGTTCGAGAAGATGAGGGATACTATG                         AAAAAGGAGCTGGAAGCAGAGTTGGCAAACGTGTCTGGATTTGCTAAGCCA
genomic: GCAAAGACCCTGTAAAGTCTATTTTGTTCGAGAAGATGAGGGATACTATGgtgcgttatc ... gtgtttacagAAAAAGGAGCTGGAAGCAGAGTTGGCAAACGTGTCTGGATTTGCTAAGCCA
EST: gi|211187526|gb|FL410059.1|FL410059
EST:     GGGATACTATG                         AAAAAGGAGCTGGAAGCAGAGTTGGCAAACGTGTCTGGATTTGCTAAGCCA
genomic: GGGATACTATGgtgcgttatc ... gtgtttacagAAAAAGGAGCTGGAAGCAGAGTTGGCAAACGTGTCTGGATTTGCTAAGCCA
EST: gi|211274055|gb|FL438415.1|FL438415
EST:     GGGATACTATG                         AAAAAGGAGCTGGAAGCAGAGTTGGCAAACGTGTCTGGATTTGCTAAGCCA
genomic: GGGATACTATGgtgcgttatc ... gtgtttacagAAAAAGGAGCTGGAAGCAGAGTTGGCAAACGTGTCTGGATTTGCTAAGCCA

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), 48 (downstream exon)
Score: 109

TGTCCGGGCTTCTTCTAAGGGTTTGACACTAGAGCTTTGTCGGTGGATTGGCAAAGACCCTGTAAAGTCTATTTTGTTCGAGAAGATGAGGGATACTATGgtgcgttatc ... gtgtttacagAAAAAGGAGCTGGAAGCAGAGTTGGCAAACGTGTCTGGATTTGCTAAGCCAACTCGAAAAATAAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 30

TGTCCGGGCTTCTTCTAAGGGTTTGACACTAGAGCTTTGTCGGTGGATTGGCAAAGACCCTGTAAAGTCTATTTTGTTCGAGAAGATGAGGGATACTATGgtgcgttatc ... gtgtttacagAAAAAGGAGCTGGAAGCAGAGTTGGCAAACGTGTCTGGATTTGCTAAGCCAACTCGAAAAATAAG


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

TGTCCGGGCTTCTTCTAAGGGTTTGACACTAGAGCTTTGTCGGTGGATTGGCAAAGACCCTGTAAAGTCTATTTTGTTCGAGAAGATGAGGGATACTATGgtgcgttatc ... gtgtttacagAAAAAGGAGCTGGAAGCAGAGTTGGCAAACGTGTCTGGATTTGCTAAGCCAACTCGAAAAATAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 94

TGTCCGGGCTTCTTCTAAGGGTTTGACACTAGAGCTTTGTCGGTGGATTGGCAAAGACCCTGTAAAGTCTATTTTGTTCGAGAAGATGAGGGATACTATGgtgcgttatc ... gtgtttacagAAAAAGGAGCTGGAAGCAGAGTTGGCAAACGTGTCTGGATTTGCTAAGCCAACTCGAAAAATAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cataagtagtcgtgttctatcacccattaatataaccaattctttgtgtttacagAAAAAGGAGCTGGAAGCAGAGTTGGCAAACGTGTCTGGATTTGCTAAGCCAACTCGAAAAATAAG
                             atataac  putative branch site (score: 94)
                                       ttctttgt  putative PPT
                         attaatataaccaatt  TA-rich tract