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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acagttttgcatttctacattcaatgtatttgtagcacttgttgtcaggcaacatatatctgcttcgttgtcttaaagcatctgtttctcctttttacagGTAGATGTCCCACAAAACCGAGGCAACAAAAGGATGCACAAGTGGCTCTTCAAATCAACTAAAACAACTATCGCCCGCGTCTGGTCTTCTTGGTTAGTGC

Basic information

species Zea mays
transcript GRMZM2G096169_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|31612016|gb|CD568638.1|CD568638
EST:     GGGGATTCAGTTGCTCGGAATCAGATGGAGTCCCTCCTTTGCATTCTGTG                         GCAAGTAGATGTCCCACAAAACCGAGGCAACAAAAGGATGCACAAGTGGCT
genomic: GGGGATTCAGTTGCTCGGAATCAGATGGAGTCCCTCCTTTGCATTCTGTGgcaagtgaga ... ctttttacagG----TAGATGTCCCACAAAACCGAGGCAACAAAAGGATGCACAAGTGGCT
EST: gi|60354175|gb|DN221148.1|DN221148
EST:     GGGGATTCAGTTGCTCGGAATCAGATGGAGTCCCTCCTTTGCATTCTGTG                         GTAGATGTCCCACAAAACCGAGGCAACAAAAGGATGCACAAGTGGCTCTTC
genomic: GGGGATTCAGTTGCTCGGAATCAGATGGAGTCCCTCCTTTGCATTCTGTGgcaagtgaga ... ctttttacagGTAGATGTCCCACAAAACCGAGGCAACAAAAGGATGCACAAGTGGCTCTTC
EST: gi|60350385|gb|DN217358.1|DN217358
EST:     GGGGATTCAGTTGCTCGGAATCAGATGGAGTCCCTCCTTTGCATTCTGTG                         GTAGATGTCCCACAAAACCGAGGCAACAAAAGGATGCACAAGTGGCTCTTC
genomic: GGGGATTCAGTTGCTCGGAATCAGATGGAGTCCCTCCTTTGCATTCTGTGgcaagtgaga ... ctttttacagGTAGATGTCCCACAAAACCGAGGCAACAAAAGGATGCACAAGTGGCTCTTC
EST: gi|60354170|gb|DN221143.1|DN221143
EST:     GGGGATTCAGTTGCTCGGAATCAGATGGAGTCCCTCCTTTGCATTCTGTG                         GTAGATGTCCCACAAAACCGAGGCAACAAAAGGATGCACAAGTGGCTCTTC
genomic: GGGGATTCAGTTGCTCGGAATCAGATGGAGTCCCTCCTTTGCATTCTGTGgcaagtgaga ... ctttttacagGTAGATGTCCCACAAAACCGAGGCAACAAAAGGATGCACAAGTGGCTCTTC

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), 45 (downstream exon)
Score: 4

ATGCAAGGAAGTTCTTGGAGTTGATGAGAGGCAAGACACTTGCGTTCGTTGGGGATTCAGTTGCTCGGAATCAGATGGAGTCCCTCCTTTGCATTCTGTGgcaagtgaga ... ctttttacagGTAGATGTCCCACAAAACCGAGGCAACAAAAGGATGCACAAGTGGCTCTTCAAATCAACTAAAACAACTATCGCCCGCGTCTGGTCTTCTTGGTTAGTGC


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 10

ATGCAAGGAAGTTCTTGGAGTTGATGAGAGGCAAGACACTTGCGTTCGTTGGGGATTCAGTTGCTCGGAATCAGATGGAGTCCCTCCTTTGCATTCTGTGgcaagtgaga ... ctttttacagGTAGATGTCCCACAAAACCGAGGCAACAAAAGGATGCACAAGTGGCTCTTCAAATCAACTAAAACAACTATCGCCCGCGTCTGGTCTTCTTGGTTAGTGC


Block sizes: 21 (upstream exon), 49 (downstream exon)
Score: 7

ATGCAAGGAAGTTCTTGGAGTTGATGAGAGGCAAGACACTTGCGTTCGTTGGGGATTCAGTTGCTCGGAATCAGATGGAGTCCCTCCTTTGCATTCTGTGgcaagtgaga ... ctttttacagGTAGATGTCCCACAAAACCGAGGCAACAAAAGGATGCACAAGTGGCTCTTCAAATCAACTAAAACAACTATCGCCCGCGTCTGGTCTTCTTGGTTAGTGC


Block sizes: 20 (upstream exon), 41 (downstream exon)
Score: 6

ATGCAAGGAAGTTCTTGGAGTTGATGAGAGGCAAGACACTTGCGTTCGTTGGGGATTCAGTTGCTCGGAATCAGATGGAGTCCCTCCTTTGCATTCTGTGgcaagtgaga ... ctttttacagGTAGATGTCCCACAAAACCGAGGCAACAAAAGGATGCACAAGTGGCTCTTCAAATCAACTAAAACAACTATCGCCCGCGTCTGGTCTTCTTGGTTAGTGC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caggcaacatatatctgcttcgttgtcttaaagcatctgtttctcctttttacagGTAGATGTCCCACAAAACCGAGGCAACAAAAGGATGCACAAGTGGCTCTTCAAATCAACTAAAACAACTATCGCCCGCGTCTGGTCTTCTTGGTTAGTGC
                                 catctgtttctccttt  CT-rich tract
     aacatatat  TA-rich tract