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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtgatagatcccaagtcccaacaacacattcctgcctgccaaggacttccaggattcgttcggtttcgaggactgaactctctctgcatctctctctctcgataaaccgcagGTCGTCTCCAGCATGCGGACCAAGATGATCGAGGGCTCGTCGAGCAGCCCGTCGGCGCACGACGACATCAACTCGTTCCTGCTAGACGATGACTTCAG

Basic information

species Zea mays
transcript GRMZM5G852338_T02
intron # 5
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|76289318|gb|DV028886.1|DV028886
EST:     GCACGATGTACTGCGACGACAAGTTTGGGACCCTGGGCATTCCATCAGAA                         GTCGTCTCCAGCATGCGGACCAAGATGATCGAGGGCTCGTCGAGCAGCCCG
genomic: GCACGATGTACTGCGACGACAAGTTTGGGACCCTGGGCATTCCATCAGAAgtgagtgata ... taaaccgcagGTCGTCTCCAGCATGCGGACCAAGATGATCGAGGGCTCGTCGAGCAGCCCG
EST: gi|211128089|gb|FL016621.1|FL016621
EST:     GCACGATGTACTGCGACGACAAGTTTGGGACCCTGGGCATTCCATCAGAA                         GTCGTCTCCAGCATGCGGACCAAGATGATCGAGGGCTCGTCGAGCAGCCCG
genomic: GCACGATGTACTGCGACGACAAGTTTGGGACCCTGGGCATTCCATCAGAAgtgagtgata ... taaaccgcagGTCGTCTCCAGCATGCGGACCAAGATGATCGAGGGCTCGTCGAGCAGCCCG
EST: gi|161588827|gb|EY961989.1|EY961989
EST:     GCACGATGTACTGCGACGACAAGTTTGGGACCCTGGGCATTCCATCAGAA                         GTCGTCTCCAGCATGCGGAACCAAGATGATCGAGGG
genomic: GCACGATGTACTGCGACGACAAGTTTGGGACCCTGGGCATTCCATCAGAAgtgagtgata ... taaaccgcagGTCGTCTCCAGCATGCGGA-CCAAGATGATCGAGGG
EST: gi|88750549|gb|DY534690.1|DY534690
EST:     GCACGATGTACTGCGACGACAAGTTTGGGACCCTGGGCATTCCATCAGAA                         GTCGTCTCCAGCATGCGGACCAAGATGATCGAGGGCTCGTCGAGCAGCCCG
genomic: GCACGATGTACTGCGACGACAAGTTTGGGACCCTGGGCATTCCATCAGAAgtgagtgata ... taaaccgcagGTCGTCTCCAGCATGCGGACCAAGATGATCGAGGGCTCGTCGAGCAGCCCG
EST: gi|16925511|gb|BM078579.1|BM078579
EST:     GCACGATGTACTGCGACGACAAGTTTGGGACCCTGGGCATTCCATCAGAA                         GTCGTCTCCAGCATGCGGACCAAGATGATCGAGGGCTCGTCGAGCAGCCCG
genomic: GCACGATGTACTGCGACGACAAGTTTGGGACCCTGGGCATTCCATCAGAAgtgagtgata ... taaaccgcagGTCGTCTCCAGCATGCGGACCAAGATGATCGAGGGCTCGTCGAGCAGCCCG
EST: gi|28983818|gb|BQ538836.2|BQ538836
EST:     GCACGATGTACTGCGACGACAAGTTTGGGACCCTGGGCATTCCATCAGAA                         GTCGTCTCCAGCATGCGGACCAAGATGATCGAGGGCTCGTCGAGCAGCCCG
genomic: GCACGATGTACTGCGACGACAAGTTTGGGACCCTGGGCATTCCATCAGAAgtgagtgata ... taaaccgcagGTCGTCTCCAGCATGCGGACCAAGATGATCGAGGGCTCGTCGAGCAGCCCG

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: 47 (upstream exon), 31 (downstream exon)
Score: 16

GTGCTGAGCATGCAGCAACTGTACCGGATCAGCACGATGTACTGCGACGACAAGTTTGGGACCCTGGGCATTCCATCAGAAgtgagtgata ... taaaccgcagGTCGTCTCCAGCATGCGGACCAAGATGATCGAGGGCTCGTCGAGCAGCCCGTCGGCGCACGACGACATCAACTCGTTCCTGCTAGACGATGACTTCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 138

GTGCTGAGCATGCAGCAACTGTACCGGATCAGCACGATGTACTGCGACGACAAGTTTGGGACCCTGGGCATTCCATCAGAAgtgagtgata ... taaaccgcagGTCGTCTCCAGCATGCGGACCAAGATGATCGAGGGCTCGTCGAGCAGCCCGTCGGCGCACGACGACATCAACTCGTTCCTGCTAGACGATGACTTCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 295

GTGCTGAGCATGCAGCAACTGTACCGGATCAGCACGATGTACTGCGACGACAAGTTTGGGACCCTGGGCATTCCATCAGAAgtgagtgata ... taaaccgcagGTCGTCTCCAGCATGCGGACCAAGATGATCGAGGGCTCGTCGAGCAGCCCGTCGGCGCACGACGACATCAACTCGTTCCTGCTAGACGATGACTTCAG


Block sizes: 47 (upstream exon), 45 (downstream exon)
Score: 85

GTGCTGAGCATGCAGCAACTGTACCGGATCAGCACGATGTACTGCGACGACAAGTTTGGGACCCTGGGCATTCCATCAGAAgtgagtgata ... taaaccgcagGTCGTCTCCAGCATGCGGACCAAGATGATCGAGGGCTCGTCGAGCAGCCCGTCGGCGCACGACGACATCAACTCGTTCCTGCTAGACGATGACTTCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttcggtttcgaggactgaactctctctgcatctctctctctcgataaaccgcagGTCGTCTCCAGCATGCGGACCAAGATGATCGAGGGCTCGTCGAGCAGCCCGTCGGCGCACGACGACATCAACTCGTTCCTGCTAGACGATGACTTCAG
                               tctctctctctcgat  CT-rich tract
                                            ataaa  TA-rich tract