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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aataacacaattcttgtttgctcgtgaatttcctaaaggctcatgcggatatatcgttttgcccttactaatccatcttcatttttaatcttattcacagGACAAGCCCTGAACTTCTGCTGAATCCG

Basic information

species Zea mays
transcript GRMZM2G118586_T01
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|85152679|gb|DW587816.1|DW587816
EST:     TTCCCTTGCCAAGAAGTCGAGAGGCACAACAAACCGGAGGTGGAGCTCAA                         GACAAGCCCTGAACTTCTGCTGAATCCG
genomic: TTCCCTTGCCAAGAAGTCGAGAGGCACAACAAACCGGAGGTGGAGCTCAAgtaagtcatg ... ttattcacagGACAAGCCCTGAACTTCTGCTGAATCCG
EST: gi|28188265|gb|CB179875.1|CB179875
EST:     TTCCCTTGCCAAGAAGTCGAGAGGCACAACAAACCGGAGGTGGAGCTCAA                         GACAAGCCCTGAACTTCTGCTGAATCCG
genomic: TTCCCTTGCCAAGAAGTCGAGAGGCACAACAAACCGGAGGTGGAGCTCAAgtaagtcatg ... ttattcacagGACAAGCCCTGAACTTCTGCTGAATCCG
EST: gi|32925177|gb|CF029989.1|CF029989
EST:     TTCCCTTGCCAAGAAGTCGAGAGGCACAACAAACCGGAGGTGGAGCTCAA                         GACAAGCCCTGAACTTCTGCTGAATCCG
genomic: TTCCCTTGCCAAGAAGTCGAGAGGCACAACAAACCGGAGGTGGAGCTCAAgtaagtcatg ... ttattcacagGACAAGCCCTGAACTTCTGCTGAATCCG
EST: gi|21432169|gb|BQ547659.1|BQ547659
EST:     TTCCCTTGCCAAGAAGTCGAGAGGCACAACAAACCGGAGGTGGAGCTCAA                         GACAAGCCCTGAACTTCTGCTGAATCCG
genomic: TTCCCTTGCCAAGAAGTCGAGAGGCACAACAAACCGGAGGTGGAGCTCAAgtaagtcatg ... ttattcacagGACAAGCCCTGAACTTCTGCTGAATCCG
EST: gi|60346160|gb|DN213133.1|DN213133
EST:     TTCCCTTGCCAAGAAGTCGAGAGGCACAACAAACCGGAGGTGGAGCTCAA                         GACAAGCCCTGAACTTCTGCTGAATCCG
genomic: TTCCCTTGCCAAGAAGTCGAGAGGCACAACAAACCGGAGGTGGAGCTCAAgtaagtcatg ... ttattcacagGACAAGCCCTGAACTTCTGCTGAATCCG
EST: gi|211438327|gb|FL007592.1|FL007592
EST:     TTCCCTTGCCAAGAAGTCGAGAGGCACAACAAACCGGAGGTGGAGCTCAA                         GACAAGCCCTGAACTTCTGCTGAATCCG
genomic: TTCCCTTGCCAAGAAGTCGAGAGGCACAACAAACCGGAGGTGGAGCTCAAgtaagtcatg ... ttattcacagGACAAGCCCTGAACTTCTGCTGAATCCG
EST: gi|32925995|gb|CF030807.1|CF030807
EST:     TTCCCTTGCCAAGAAGTCGAGAGGCACAACAAACCGGAGGTGGAGCTCAA                         GACAAGCCCTGAACTTCTGCTGAATCCG
genomic: TTCCCTTGCCAAGAAGTCGAGAGGCACAACAAACCGGAGGTGGAGCTCAAgtaagtcatg ... ttattcacagGACAAGCCCTGAACTTCTGCTGAATCCG
EST: gi|211435743|gb|FL007591.1|FL007591
EST:     TTCCCTTGCCAAGAAGTCGAGAGGCACAACAAACCGGAGGTGGAGCTCAA                         GACAAGCCCTGAACTTCTGCTGAATCCG
genomic: TTCCCTTGCCAAGAAGTCGAGAGGCACAACAAACCGGAGGTGGAGCTCAAgtaagtcatg ... ttattcacagGACAAGCCCTGAACTTCTGCTGAATCCG
EST: gi|37376615|gb|CF624854.1|CF624854
EST:     TTCCCTTGCCAAGAAGTCGAGAGGCACAACAAACCGGAGGTGGAGCTCAA                         GACAAGCCCTGAACTTCTGCTGAATCCG
genomic: TTCCCTTGCCAAGAAGTCGAGAGGCACAACAAACCGGAGGTGGAGCTCAAgtaagtcatg ... ttattcacagGACAAGCCCTGAACTTCTGCTGAATCCG

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), 47 (downstream exon)
Score: 108

AATTTCCCTTGCCAAGAAGTCGAGAGGCACAACAAACCGGAGGTGGAGCTCAAgtaagtcatg ... ttattcacagGACAAGCCCTGAACTTCTGCTGAATCCG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 124

AATTTCCCTTGCCAAGAAGTCGAGAGGCACAACAAACCGGAGGTGGAGCTCAAgtaagtcatg ... ttattcacagGACAAGCCCTGAACTTCTGCTGAATCCG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 103

AATTTCCCTTGCCAAGAAGTCGAGAGGCACAACAAACCGGAGGTGGAGCTCAAgtaagtcatg ... ttattcacagGACAAGCCCTGAACTTCTGCTGAATCCG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 128

AATTTCCCTTGCCAAGAAGTCGAGAGGCACAACAAACCGGAGGTGGAGCTCAAgtaagtcatg ... ttattcacagGACAAGCCCTGAACTTCTGCTGAATCCG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cggatatatcgttttgcccttactaatccatcttcatttttaatcttattcacagGACAAGCCCTGAACTTCTGCTGAATCCG
                                           tcttattc  CT-rich tract
                             atcttcatttttaatc  TA-rich tract