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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttcaatctctaccgtccgtttcgctgcttctttcttgccaatggttcaactcactccaataatgtcattctgtttttgttagcagAAAAGAAGATACTAGTGACGTTGACACAAGCTCTAGATTCCCAAGCCAAGGAGTTAAAATCCTTGACCGATTCAATCGGTCATACCAGGGAACCCATAAA

Basic information

species Zea mays
transcript GRMZM2G363460_T05
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|31354170|gb|CD438527.1|CD438527
EST:     TTCTGCTATTGCCAAAACAAACCAACAACTGCTTGCTTCAAAGGATGAAG                         AAAAGAAGATACTAGTGACGTTGACACAAGCTCTAGATTCCCAAGCCAAGG
genomic: TTCTGCTATTGCCAAAACAAACCAACAACTGCTTGCTTCAAAGGATGAAGgtttcaatct ... ttgttagcagAAAAGAAGATACTAGTGACGTTGACACAAGCTCTAGATTCCCAAGCCAAGG
EST: gi|20300876|gb|BQ163819.1|BQ163819
EST:     TTCTGCTATTGCCAAAACAAACCAACAACTGCTTGCTTCAAAGGATGAAG                         AAAAGAAGATACTAGTGACGTTGACACAAGCTCTAGATTCCCAAGCCAAGG
genomic: TTCTGCTATTGCCAAAACAAACCAACAACTGCTTGCTTCAAAGGATGAAGgtttcaatct ... ttgttagcagAAAAGAAGATACTAGTGACGTTGACACAAGCTCTAGATTCCCAAGCCAAGG
EST: gi|148946560|gb|EC885619.2|EC885619
EST:     TTCTGCTATTGCCAAAACAAACCAACAACTGCTTGCTTCAAAGTATGAAG                         AAAAGAAGATACTAGTGACGTTGACACAAGCTCTAGATTCCCAAGCCAAGG
genomic: TTCTGCTATTGCCAAAACAAACCAACAACTGCTTGCTTCAAAGGATGAAGgtttcaatct ... ttgttagcagAAAAGAAGATACTAGTGACGTTGACACAAGCTCTAGATTCCCAAGCCAAGG
EST: gi|67019556|gb|CO448305.1|CO448305
EST:     TCTGCTATTGCCAAAACAAACCAACAACTGCTTGCTTCAAAGGATGAAAG                         AAA-GAAGATACTAGTGACGTTGACACAAGCTCTAGATTCCCA-GCCNAG
genomic: TCTGCTATTGCCAAAACAAACCAACAACTGCTTGCTTCAAAGGATGAA-Ggtttcaatct ... ttgttagcagAAAAGAAGATACTAGTGACGTTGACACAAGCTCTAGATTCCCAAGCCAAG
EST: gi|148941345|gb|EC886254.2|EC886254
EST:     TTCTGCTATTGCCAAAACAAACCAACAACTGCTTGCTTCAAAGGATGAAG                         AAAAGAAGATACTAGTGACGTTGACANCA-GCTCTAGATTCCCAAGCCAAG
genomic: TTCTGCTATTGCCAAAACAAACCAACAACTGCTTGCTTCAAAGGATGAAGgtttcaatct ... ttgttagcagAAAAGAAGATACTAGTGACGTTGACA-CAAGCTCTAGATTCCCAAGCCAAG
EST: gi|149085990|gb|EE175517.2|EE175517
EST:     TTCTGCTATTGCCAAAACAAACCAACAACTGCTTGCTTCAAAGGATGAAG                         AAAAGAAGATACTAGTGACGTTGACACAAGCTCTAGATTCCCAAGCCAAGG
genomic: TTCTGCTATTGCCAAAACAAACCAACAACTGCTTGCTTCAAAGGATGAAGgtttcaatct ... ttgttagcagAAAAGAAGATACTAGTGACGTTGACACAAGCTCTAGATTCCCAAGCCAAGG
EST: gi|31355282|gb|CD439639.1|CD439639
EST:     TTCTGCTATTGCCAAAACAAACCAACAACTGCTTGCTTCAAAGGATGAAGCAG                       
genomic: TTCTGCTATTGCCAAAACAAACCAACAACTGCTTGCTTCAAAGGATG-A--AGgtttcaatct ... ttgttagc
EST: gi|76913179|gb|DV165031.1|DV165031
EST:     TTCTGCTATTGCCAAAACAAACCAACAACTGCTTGCTTCAAAGGATGAAG                         AAAAGAAGATACTAGTGACGTTGACACAAGCTCTAGATTCTCAAGCCAAGG
genomic: TTCTGCTATTGCCAAAACAAACCAACAACTGCTTGCTTCAAAGGATGAAGgtttcaatct ... ttgttagcagAAAAGAAGATACTAGTGACGTTGACACAAGCTCTAGATTCCCAAGCCAAGG

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: 45 (upstream exon), 48 (downstream exon)
Score: 73

AGGATTGATGATGAAACGGCTGATGCTGTAAAGGCTTCTGCTTCGGCTGTTTCTGCTATTGCCAAAACAAACCAACAACTGCTTGCTTCAAAGGATGAAGgtttcaatct ... ttgttagcagAAAAGAAGATACTAGTGACGTTGACACAAGCTCTAGATTCCCAAGCCAAGGAGTTAAAATCCTTGACCGATTCAATCGGTCATACCAGGGAACCCATAAA


Block sizes: 32 (upstream exon), 49 (downstream exon)
Score: 199

AGGATTGATGATGAAACGGCTGATGCTGTAAAGGCTTCTGCTTCGGCTGTTTCTGCTATTGCCAAAACAAACCAACAACTGCTTGCTTCAAAGGATGAAGgtttcaatct ... ttgttagcagAAAAGAAGATACTAGTGACGTTGACACAAGCTCTAGATTCCCAAGCCAAGGAGTTAAAATCCTTGACCGATTCAATCGGTCATACCAGGGAACCCATAAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 200

AGGATTGATGATGAAACGGCTGATGCTGTAAAGGCTTCTGCTTCGGCTGTTTCTGCTATTGCCAAAACAAACCAACAACTGCTTGCTTCAAAGGATGAAGgtttcaatct ... ttgttagcagAAAAGAAGATACTAGTGACGTTGACACAAGCTCTAGATTCCCAAGCCAAGGAGTTAAAATCCTTGACCGATTCAATCGGTCATACCAGGGAACCCATAAA


Block sizes: 32 (upstream exon), 48 (downstream exon)
Score: 102

AGGATTGATGATGAAACGGCTGATGCTGTAAAGGCTTCTGCTTCGGCTGTTTCTGCTATTGCCAAAACAAACCAACAACTGCTTGCTTCAAAGGATGAAGgtttcaatct ... ttgttagcagAAAAGAAGATACTAGTGACGTTGACACAAGCTCTAGATTCCCAAGCCAAGGAGTTAAAATCCTTGACCGATTCAATCGGTCATACCAGGGAACCCATAAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttcttgccaatggttcaactcactccaataatgtcattctgtttttgttagcagAAAAGAAGATACTAGTGACGTTGACACAAGCTCTAGATTCCCAAGCCAAGGAGTTAAAATCCTTGACCGATTCAATCGGTCATACCAGGGAACCCATAAA
                 aactcac  putative branch site (score: 102)
                                     ttctgttttt  putative PPT
                                          tttttgtta  TA-rich tract