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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgtggatttttcatgcctcttatgaccttttttttccttttcgttttattgggtgtattaccattggtcagtgaccaaaggacaattcgctcactaccgttatgttaacaaacctgtcgatgtttttgccagGCAACTCCTCATGGTGTCTCAAATTACGTTGCTAGTAGGCATTATCTTCAGCTTCAAAGTCACGAGCACATACTATGTCGTCCAGTATGTTGTCTCAGCA

Basic information

species Zea mays
transcript GRMZM2G050329_T01
intron # 9
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|37374852|gb|CF623821.1|CF623821
EST:     CCTGTAAACGCTGTNGTTGGAACATACATCAGCAATATGTTTGAGGACAG                         GCAACTCCTCATGGTGTCTCAAATTACGTTGCTAGTAGGCATTATCTTCAG
genomic: CCTGTAAACGCTGTTGTTGGAACATACATCAGCAATATGTTTGAGGACAGgtttgtggat ... tttttgccagGCAACTCCTCATGGTGTCTCAAATTACGTTGCTAGTAGGCATTATCTTCAG
EST: gi|211027210|gb|FL160163.1|FL160163
EST:     CCTGTAAACGCTGTTGTTGGAACATACATCAGCAATATGTTTGAGGACAG                         GCAACTCCTCATGGTGTCTCAAATTACGTTGCTAGTAGGCATTATCTTC
genomic: CCTGTAAACGCTGTTGTTGGAACATACATCAGCAATATGTTTGAGGACAGgtttgtggat ... tttttgccagGCAACTCCTCATGGTGTCTCAAATTACGTTGCTAGTAGGCATTATCTTC
EST: gi|14191326|gb|BG833556.1|BG833556
EST:     ACGCTGTTGTTGGAACATACATCAGCAATATGTTTGAGGACAG                         GCAACTCCTCATGGTGTCTCAAATTACGTTGTTAGTAGGCATTATCTTCAG
genomic: ACGCTGTTGTTGGAACATACATCAGCAATATGTTTGAGGACAGgtttgtggat ... tttttgccagGCAACTCCTCATGGTGTCTCAAATTACGTTGCTAGTAGGCATTATCTTCAG

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), 33 (downstream exon)
Score: 113

ATACAAGCGCAGTGGCAATATTTCTAGCAATCCTAGGGTTGACAGTCCTTCCTGTAAACGCTGTTGTTGGAACATACATCAGCAATATGTTTGAGGACAGgtttgtggat ... tttttgccagGCAACTCCTCATGGTGTCTCAAATTACGTTGCTAGTAGGCATTATCTTCAGCTTCAAAGTCACGAGCACATACTATGTCGTCCAGTATGTTGTCTCAGCA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 201

ATACAAGCGCAGTGGCAATATTTCTAGCAATCCTAGGGTTGACAGTCCTTCCTGTAAACGCTGTTGTTGGAACATACATCAGCAATATGTTTGAGGACAGgtttgtggat ... tttttgccagGCAACTCCTCATGGTGTCTCAAATTACGTTGCTAGTAGGCATTATCTTCAGCTTCAAAGTCACGAGCACATACTATGTCGTCCAGTATGTTGTCTCAGCA


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 127

ATACAAGCGCAGTGGCAATATTTCTAGCAATCCTAGGGTTGACAGTCCTTCCTGTAAACGCTGTTGTTGGAACATACATCAGCAATATGTTTGAGGACAGgtttgtggat ... tttttgccagGCAACTCCTCATGGTGTCTCAAATTACGTTGCTAGTAGGCATTATCTTCAGCTTCAAAGTCACGAGCACATACTATGTCGTCCAGTATGTTGTCTCAGCA


Block sizes: 48 (upstream exon), 35 (downstream exon)
Score: 142

ATACAAGCGCAGTGGCAATATTTCTAGCAATCCTAGGGTTGACAGTCCTTCCTGTAAACGCTGTTGTTGGAACATACATCAGCAATATGTTTGAGGACAGgtttgtggat ... tttttgccagGCAACTCCTCATGGTGTCTCAAATTACGTTGCTAGTAGGCATTATCTTCAGCTTCAAAGTCACGAGCACATACTATGTCGTCCAGTATGTTGTCTCAGCA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaggacaattcgctcactaccgttatgttaacaaacctgtcgatgtttttgccagGCAACTCCTCATGGTGTCTCAAATTACGTTGCTAGTAGGCATTATCTTCAGCTTCAAAGTCACGAGCACATACTATGTCGTCCAGTATGTTGTCTCAGCA
                         tgttaac  putative branch site (score: 142)
                                             tttttgcc  putative PPT
                      ttatgttaa  TA-rich tract