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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagaggcagtaaattctggatgcaatgctcttcttctatttgtaatctaattagcaaataataatcgattgatggataatcccatattgttttcccagAACTTTGACAAGATTACACACCGTGTTCAGAGTAAAAACAAGGATCAG

Basic information

species Zea mays
transcript GRMZM2G085427_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|29946837|gb|CB816350.1|CB816350
EST:     CACACCAAGAGGAGGAGANNNNNNNCAATGCGCTGCGGCAAGTAGGAAAA                         AACTTTGACAAGATTACACACCGTGTTCAGAGTAAAAACAAGGATCAG
genomic: CACACCAAGAGGAGGAGATTTTTTTCAATGCGCTGCGGCAAGTAGGAAAAgtaagaggca ... gttttcccagAACTTTGACAAGATTACACACCGTGTTCAGAGTAAAAACAAGGATCAG
EST: gi|78119579|gb|DV537963.1|DV537963
EST:     CACACCAAGAGGAGGAGANNNNNNNCAATGCGCTGCGGCAAGTAGGAAAA                         AACTTTGACAAGATTACACACCGTGTTCAGAGTAAAAACAAGGATCAG
genomic: CACACCAAGAGGAGGAGATTTTTTTCAATGCGCTGCGGCAAGTAGGAAAAgtaagaggca ... gttttcccagAACTTTGACAAGATTACACACCGTGTTCAGAGTAAAAACAAGGATCAG
EST: gi|211048831|gb|FL187591.1|FL187591
EST:     CACACCAAGAGGAGGAGANNNNNNNCAATGCGCTGCGGCAAGTAGGAAAA                         AACTTTGACAAGATTACACACCGTGTTCAGAGTAAAAACAAGGATCAG
genomic: CACACCAAGAGGAGGAGATTTTTTTCAATGCGCTGCGGCAAGTAGGAAAAgtaagaggca ... gttttcccagAACTTTGACAAGATTACACACCGTGTTCAGAGTAAAAACAAGGATCAG

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: 91

CAAAAAAGCAGACTCGACAATGGGCTGCGTGGACACACCAAGAGGAGGAGATTTTTTTCAATGCGCTGCGGCAAGTAGGAAAAgtaagaggca ... gttttcccagAACTTTGACAAGATTACACACCGTGTTCAGAGTAAAAACAAGGATCAG


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 64

CAAAAAAGCAGACTCGACAATGGGCTGCGTGGACACACCAAGAGGAGGAGATTTTTTTCAATGCGCTGCGGCAAGTAGGAAAAgtaagaggca ... gttttcccagAACTTTGACAAGATTACACACCGTGTTCAGAGTAAAAACAAGGATCAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 79

CAAAAAAGCAGACTCGACAATGGGCTGCGTGGACACACCAAGAGGAGGAGATTTTTTTCAATGCGCTGCGGCAAGTAGGAAAAgtaagaggca ... gttttcccagAACTTTGACAAGATTACACACCGTGTTCAGAGTAAAAACAAGGATCAG


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 102

CAAAAAAGCAGACTCGACAATGGGCTGCGTGGACACACCAAGAGGAGGAGATTTTTTTCAATGCGCTGCGGCAAGTAGGAAAAgtaagaggca ... gttttcccagAACTTTGACAAGATTACACACCGTGTTCAGAGTAAAAACAAGGATCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatctaattagcaaataataatcgattgatggataatcccatattgttttcccagAACTTTGACAAGATTACACACCGTGTTCAGAGTAAAAACAAGGATCAG
                                           ttgttttccc  CT-rich tract
     aattagcaaataataa  TA-rich tract