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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgattaacctacacctatgtctaacgcaacatatttcactgtcctgaagtttattaatatcttacataaggtttataattcatgcagCGAAAGGAAAAGATCCAAGGAACCTTGTGGGAGCTTGAACAAGGGATGCTTGCTAGCAATACCTCATCAGCCAGTTCTGACGTCAAAACATGGCAGGCTT

Basic information

species Zea mays
transcript GRMZM2G026043_T01
intron # 7
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|60350697|gb|DN217670.1|DN217670
EST:     CAAACAAAGTCAGCTCAAGGACACAAGACTCTGGATCTCAG                         CGAAAGGAAAAGATCCAAGGAACCTTGTGGGAGCTTGAACAAGGGATGCTT
genomic: CAAACAAAGTCAGCTCAAGGACACAAGACTCTGGATCTCAGgtgattaacc ... attcatgcagCGAAAGGAAAAGATCCAAGGAACCTTGTGGGAGCTTGAACAAGGGATGCTT
EST: gi|71301414|gb|DR786739.1|DR786739
EST:     CGCCTCCCTCAAACAAAGTCAGCTCAAGGACACAAGACTCTGGATCTCAG                         CGAAAGGAAAAGATCCAAGGAACCTTGTGGGAGCTTGAACAAGGGATGCTT
genomic: CGCCTCCCTCAAACAAAGTCAGCTCAAGGACACAAGACTCTGGATCTCAGgtgattaacc ... attcatgcagCGAAAGGAAAAGATCCAAGGAACCTTGTGGGAGCTTGAACAAGGGATGCTT
EST: gi|83278885|gb|DV942893.1|DV942893
EST:     CAAGGACACAAGACTCTGGATCTCAG                         CGAAAGGAAAAGATCCAAGGAACCTTGTGGGAGCTTGAACAAGGGATGCTT
genomic: CAAGGACACAAGACTCTGGATCTCAGgtgattaacc ... attcatgcagCGAAAGGAAAAGATCCAAGGAACCTTGTGGGAGCTTGAACAAGGGATGCTT
EST: gi|71301413|gb|DR786738.1|DR786738
EST:     CCTCAAACAAAGTCAGCTCAAGGACACAAGACTCTGGATCTCAG                         CGAAAGGAAAAGATCCAAGGAACCTTGTGGGAGCTTGAACAAGGGATGCTT
genomic: CCTCAAACAAAGTCAGCTCAAGGACACAAGACTCTGGATCTCAGgtgattaacc ... attcatgcagCGAAAGGAAAAGATCCAAGGAACCTTGTGGGAGCTTGAACAAGGGATGCTT
EST: gi|60355911|gb|DN222884.1|DN222884
EST:     CAAACAAAGTCAGCTCAAGGACACAAGACTCTGGATCTCAG                         CGAAAGGAAAAGATCCAAGGAACCTTGTGGGAGCTTGAACAAGGGATGCTT
genomic: CAAACAAAGTCAGCTCAAGGACACAAGACTCTGGATCTCAGgtgattaacc ... attcatgcagCGAAAGGAAAAGATCCAAGGAACCTTGTGGGAGCTTGAACAAGGGATGCTT
EST: gi|71332998|gb|DR803526.1|DR803526
EST:     CGCCTCCCTCAAACAAAGTCAGCTCAAGGACACAAGACTCTGGATCTCAG                         CGAAAGGAAAAGATCCAAGGAACCTTGTGGGAGCTTGAACAAGGGATGCTT
genomic: CGCCTCCCTCAAACAAAGTCAGCTCAAGGACACAAGACTCTGGATCTCAGgtgattaacc ... attcatgcagCGAAAGGAAAAGATCCAAGGAACCTTGTGGGAGCTTGAACAAGGGATGCTT

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: 48 (upstream exon), 49 (downstream exon)
Score: 59

ATCACAGCGTCAGGAGATCCAAGAGCTGAAGCGCACCCTTGCTGAGGCAACGCCTCCCTCAAACAAAGTCAGCTCAAGGACACAAGACTCTGGATCTCAGgtgattaacc ... attcatgcagCGAAAGGAAAAGATCCAAGGAACCTTGTGGGAGCTTGAACAAGGGATGCTTGCTAGCAATACCTCATCAGCCAGTTCTGACGTCAAAACATGGCAGGCTT


Block sizes: 48 (upstream exon), 45 (downstream exon)
Score: 63

ATCACAGCGTCAGGAGATCCAAGAGCTGAAGCGCACCCTTGCTGAGGCAACGCCTCCCTCAAACAAAGTCAGCTCAAGGACACAAGACTCTGGATCTCAGgtgattaacc ... attcatgcagCGAAAGGAAAAGATCCAAGGAACCTTGTGGGAGCTTGAACAAGGGATGCTTGCTAGCAATACCTCATCAGCCAGTTCTGACGTCAAAACATGGCAGGCTT


Block sizes: 48 (upstream exon), 45 (downstream exon)
Score: 64

ATCACAGCGTCAGGAGATCCAAGAGCTGAAGCGCACCCTTGCTGAGGCAACGCCTCCCTCAAACAAAGTCAGCTCAAGGACACAAGACTCTGGATCTCAGgtgattaacc ... attcatgcagCGAAAGGAAAAGATCCAAGGAACCTTGTGGGAGCTTGAACAAGGGATGCTTGCTAGCAATACCTCATCAGCCAGTTCTGACGTCAAAACATGGCAGGCTT


Block sizes: 48 (upstream exon), 45 (downstream exon)
Score: 78

ATCACAGCGTCAGGAGATCCAAGAGCTGAAGCGCACCCTTGCTGAGGCAACGCCTCCCTCAAACAAAGTCAGCTCAAGGACACAAGACTCTGGATCTCAGgtgattaacc ... attcatgcagCGAAAGGAAAAGATCCAAGGAACCTTGTGGGAGCTTGAACAAGGGATGCTTGCTAGCAATACCTCATCAGCCAGTTCTGACGTCAAAACATGGCAGGCTT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttcactgtcctgaagtttattaatatcttacataaggtttataattcatgcagCGAAAGGAAAAGATCCAAGGAACCTTGTGGGAGCTTGAACAAGGGATGCTTGCTAGCAATACCTCATCAGCCAGTTCTGACGTCAAAACATGGCAGGCTT
              aagtttattaatatct  TA-rich tract