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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tatgtgtaactctgcttattaattgttgcatacatttcattttgtaattctgtccttttagatacgagaatttatttatattcctttttttttgtaatagGGAGCTTTACAGCAACAAAATAAGTGGGGCAATACCCCCTGAACTGGGGAACCTGACTAACCTTGTCAGTTTGGATCTGTATATGAACAACTTCTCTGGC

Basic information

species Zea mays
transcript GRMZM2G150024_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|26456609|gb|CA828192.1|CA828192
EST:     GGCGTCCTAGTGCCACAGCTTGGTCAGCTGAAAAATCTCCAATATTT                         GGAGCTTTACAGCAACAAAATAAG-GGGGCAATACCCCCTGAACTGGGGAA
genomic: GGCGTCCTAGTGCCACAGCTTGGTCAGCTGAAAAATCTCCAATATTTgtaagttctg ... tttgtaatagGGAGCTTTACAGCAACAAAATAAGTGGGGCAATACCCCCTGAACTGGGGAA
EST: gi|148934569|gb|EC878617.2|EC878617
EST:     TCTGGCGTCCTAGTGCCACAGCTTGGTCAGCTGAAAAATCTCCAATATTT                         GGAGCTTTACAGCAACAAAATAAGTGGGGCAATACCCCCTGAACTGGGGAA
genomic: TCTGGCGTCCTAGTGCCACAGCTTGGTCAGCTGAAAAATCTCCAATATTTgtaagttctg ... tttgtaatagGGAGCTTTACAGCAACAAAATAAGTGGGGCAATACCCCCTGAACTGGGGAA
EST: gi|87156676|gb|DY401465.1|DY401465
EST:     GGCGTCCTAGTGCCACAGCTTGGTCAGCTGAAAAATCTCCAATATTT                         GGAGCTTTACAGCAACAAAATAAGTGGGGCAATACCCCCTGAACTGGGGAA
genomic: GGCGTCCTAGTGCCACAGCTTGGTCAGCTGAAAAATCTCCAATATTTgtaagttctg ... tttgtaatagGGAGCTTTACAGCAACAAAATAAGTGGGGCAATACCCCCTGAACTGGGGAA

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: 282

TGACCTTGGAAATGCACAATTATCTGGCGTCCTAGTGCCACAGCTTGGTCAGCTGAAAAATCTCCAATATTTgtaagttctg ... tttgtaatagGGAGCTTTACAGCAACAAAATAAGTGGGGCAATACCCCCTGAACTGGGGAACCTGACTAACCTTGTCAGTTTGGATCTGTATATGAACAACTTCTCTGGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 396

TGACCTTGGAAATGCACAATTATCTGGCGTCCTAGTGCCACAGCTTGGTCAGCTGAAAAATCTCCAATATTTgtaagttctg ... tttgtaatagGGAGCTTTACAGCAACAAAATAAGTGGGGCAATACCCCCTGAACTGGGGAACCTGACTAACCTTGTCAGTTTGGATCTGTATATGAACAACTTCTCTGGC


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 436

TGACCTTGGAAATGCACAATTATCTGGCGTCCTAGTGCCACAGCTTGGTCAGCTGAAAAATCTCCAATATTTgtaagttctg ... tttgtaatagGGAGCTTTACAGCAACAAAATAAGTGGGGCAATACCCCCTGAACTGGGGAACCTGACTAACCTTGTCAGTTTGGATCTGTATATGAACAACTTCTCTGGC


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 162

TGACCTTGGAAATGCACAATTATCTGGCGTCCTAGTGCCACAGCTTGGTCAGCTGAAAAATCTCCAATATTTgtaagttctg ... tttgtaatagGGAGCTTTACAGCAACAAAATAAGTGGGGCAATACCCCCTGAACTGGGGAACCTGACTAACCTTGTCAGTTTGGATCTGTATATGAACAACTTCTCTGGC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aattctgtccttttagatacgagaatttatttatattcctttttttttgtaatagGGAGCTTTACAGCAACAAAATAAGTGGGGCAATACCCCCTGAACTGGGGAACCTGACTAACCTTGTCAGTTTGGATCTGTATATGAACAACTTCTCTGGC
                         tttatttatattcctt  CT-rich tract
                     agaatttatttatatt  TA-rich tract