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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtacctgttttctgtttctatttcttgtgacttattctctctttctgtgtcttctgtcaatctacctaacaccttttattttctgatgcagATGCTGAATTGTATGACTTCGATGATGAGAAG

Basic information

species Zea mays
transcript GRMZM2G010085_T01
intron # 11
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|87155727|gb|DY400516.1|DY400516
EST:     GAAAATGAAAAAGTTCACTGAGGATGCCATCAAATTTAAGATGGATGATA                         ATGCTGAATTGTATGACTTCGATGATGAGAAG
genomic: GAAAATGAAAAAGTTCACTGAGGATGCCATCAAATTTAAGATGGATGATAgtatgtacct ... tctgatgcagATGCTGAATTGTATGACTTCGATGATGAGAAG
EST: gi|32930781|gb|CF035593.1|CF035593
EST:     GAAAATGAAAAAGTTCACTGAGGATGCCATCAAATTTAAGATGGATGATA                         ATGCTGAATTGTATGACTTCGATGATGAGAAG
genomic: GAAAATGAAAAAGTTCACTGAGGATGCCATCAAATTTAAGATGGATGATAgtatgtacct ... tctgatgcagATGCTGAATTGTATGACTTCGATGATGAGAAG
EST: gi|31351381|gb|CD435738.1|CD435738
EST:     GAAAATGAAAAAGTTCACTGAGGATGCCATCAAATTTAAGATGGATGATA                         ATGCTGAATTGTATGACTTCGATGATGAGAAG
genomic: GAAAATGAAAAAGTTCACTGAGGATGCCATCAAATTTAAGATGGATGATAgtatgtacct ... tctgatgcagATGCTGAATTGTATGACTTCGATGATGAGAAG
EST: gi|6194488|gb|AW146592.1|AW146592
EST:     CAAATTTAAGATGGATGATA                         ATGCTGAATTGTATGACTTCGATGATGAGAAG
genomic: CAAATTTAAGATGGATGATAgtatgtacct ... tctgatgcagATGCTGAATTGTATGACTTCGATGATGAGAAG
EST: gi|32930784|gb|CF035596.1|CF035596
EST:     GAAAATGAAAAAGTTCACTGAGGATGCCATCAAATTTAAGATGGATGATA                         ATGCTGAATTGTATGACTTCGATGATGAGAAG
genomic: GAAAATGAAAAAGTTCACTGAGGATGCCATCAAATTTAAGATGGATGATAgtatgtacct ... tctgatgcagATGCTGAATTGTATGACTTCGATGATGAGAAG
EST: gi|22546162|gb|BU098473.1|BU098473
EST:     GAAAATGAAAAAGTTCACTGAGGATGCCATCAAATTTAAGATGGATGATA                         ATGCTGAATTGTATGACTTCGATGATGAGAAG
genomic: GAAAATGAAAAAGTTCACTGAGGATGCCATCAAATTTAAGATGGATGATAgtatgtacct ... tctgatgcagATGCTGAATTGTATGACTTCGATGATGAGAAG

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), 32 (downstream exon)
Score: 356

ATTGACCGTATTATAGCTAAAGGAGAGGAGACAACAGCAGAACTTGATGCGAAAATGAAAAAGTTCACTGAGGATGCCATCAAATTTAAGATGGATGATAgtatgtacct ... tctgatgcagATGCTGAATTGTATGACTTCGATGATGAGAAG


Block sizes: 47 (upstream exon), 32 (downstream exon)
Score: 73

ATTGACCGTATTATAGCTAAAGGAGAGGAGACAACAGCAGAACTTGATGCGAAAATGAAAAAGTTCACTGAGGATGCCATCAAATTTAAGATGGATGATAgtatgtacct ... tctgatgcagATGCTGAATTGTATGACTTCGATGATGAGAAG


Block sizes: 49 (upstream exon), 32 (downstream exon)
Score: 72

ATTGACCGTATTATAGCTAAAGGAGAGGAGACAACAGCAGAACTTGATGCGAAAATGAAAAAGTTCACTGAGGATGCCATCAAATTTAAGATGGATGATAgtatgtacct ... tctgatgcagATGCTGAATTGTATGACTTCGATGATGAGAAG


Block sizes: 49 (upstream exon), 32 (downstream exon)
Score: 113

ATTGACCGTATTATAGCTAAAGGAGAGGAGACAACAGCAGAACTTGATGCGAAAATGAAAAAGTTCACTGAGGATGCCATCAAATTTAAGATGGATGATAgtatgtacct ... tctgatgcagATGCTGAATTGTATGACTTCGATGATGAGAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctctctttctgtgtcttctgtcaatctacctaacaccttttattttctgatgcagATGCTGAATTGTATGACTTCGATGATGAGAAG
                                 caccttttattttct  CT-rich tract
                                     ttttattttctgat  TA-rich tract