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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgtggttttgattagacactggtggggaaaagagaaactacatctaagctgatactacacctcaacttcttttctgattagtgcagttcattttgtgcagGCTGAGATATTAGCAAAATTCAAACCACATCTGGATACGTCGACTCTAATTACAAACATCAGAAACATCGAGAAGGCCATCAGAGATTGCTTGGACCACT

Basic information

species Zea mays
transcript GRMZM2G055607_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G055607_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os07g44960.2 (Oryza sativa), 3'ss of exon 5
tgtggttttgattagacactggtggggaaaagagaaactac----atctaagctgatactacacctcaacttcttttctgattagtgcagttcattttgtgcagGCTGAGATATTAGCAAAATTCAAACCACATCTGGATACGTCGACTCTAATTACAAACATCAGAAACATCGAGAAGGCCATCAGAGATTGCTTGGACCACT
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--tcctacatatttc-cattccaagagaaatgtaacatcactatcaatcatgttggcaaggaagaaaaaaaaaatgaaatgcttatatatttt-ttctgagcagGCTGAGATATTAGCGAAATTCAAGCCGGTGCTGGATGTGTCAAATCTGATTCCAAACATCAGAAATGCCGAGAAATACATCAGAGATTGCTTGGACCACT
















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|71758717|gb|DR956654.1|DR956654
EST:     CAAAGCAGTTGAATGGAACTCACAAGTCTCATGTTCACTCAAAAGAAGAG                         GGTGAGATATTAGCAAAATTCAAACCACATCTGGATACGTCGACTCTAATT
genomic: CAAAGCAGTTGAATGGAACTCACAAGTCTCATGTTCACTCAAAAGAAGAGgtaccttcga ... ttttgtgcagGCTGAGATATTAGCAAAATTCAAACCACATCTGGATACGTCGACTCTAATT
EST: gi|71305859|gb|DR789055.1|DR789055
EST:     CAAACCAGTTGAATGGAACTCCCAAGTCTCATGTTCACTCAAAAGAAGAG                         GCTGAGATATTAGCAAAATTCAAACCACATCTGGATACGTCGACTCTAATT
genomic: CAAAGCAGTTGAATGGAACTCACAAGTCTCATGTTCACTCAAAAGAAGAGgtaccttcga ... ttttgtgcagGCTGAGATATTAGCAAAATTCAAACCACATCTGGATACGTCGACTCTAATT
EST: gi|76911990|gb|DV164524.1|DV164524
EST:     CAAAGCAGTTGAATGGAACTCACAAGTCTCATGTTCACTCAAAAGAAGAG                         GCTGAGATATTAGCAAAATTCAAACCACATCTGGATACGTCGACTCTAATT
genomic: CAAAGCAGTTGAATGGAACTCACAAGTCTCATGTTCACTCAAAAGAAGAGgtaccttcga ... ttttgtgcagGCTGAGATATTAGCAAAATTCAAACCACATCTGGATACGTCGACTCTAATT
EST: gi|71315790|gb|DR794540.1|DR794540
EST:     CAAAGCAGTTGAATGGAACTCACAAGTCTCATGTTCACTCAAAAGAAGAG                         GCTGAGATATTAGCAAAATTCAAACCACATCTGGATACGTCGACTCTAATT
genomic: CAAAGCAGTTGAATGGAACTCACAAGTCTCATGTTCACTCAAAAGAAGAGgtaccttcga ... ttttgtgcagGCTGAGATATTAGCAAAATTCAAACCACATCTGGATACGTCGACTCTAATT
EST: gi|50330183|gb|CO525309.1|CO525309
EST:     CAAAGCAGTTGAATGGAACTCACAAGTCTCATGTTCACTCAAAAGAAGAG                         GCTGAGATATTAGCAAAATTCAAACCACATCTGGATACGTCGACTCTAATT
genomic: CAAAGCAGTTGAATGGAACTCACAAGTCTCATGTTCACTCAAAAGAAGAGgtaccttcga ... ttttgtgcagGCTGAGATATTAGCAAAATTCAAACCACATCTGGATACGTCGACTCTAATT
EST: gi|71762875|gb|DR960812.1|DR960812
EST:     CAAAGCAGTTGAATGGAACTCACAAGTCTCATGTTCACTCAAAAGAAGAG                         GCTGAGATATTAGCAAAATTCAAACCACATCTGGATACGTCGACTCTAATT
genomic: CAAAGCAGTTGAATGGAACTCACAAGTCTCATGTTCACTCAAAAGAAGAGgtaccttcga ... ttttgtgcagGCTGAGATATTAGCAAAATTCAAACCACATCTGGATACGTCGACTCTAATT

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), 36 (downstream exon)
Score: 50

CACATTGCGCAGGCTTGTATCTGTGCTGGCCAACGACTATGACAAAGATGCAAAGCAGTTGAATGGAACTCACAAGTCTCATGTTCACTCAAAAGAAGAGgtaccttcga ... ttttgtgcagGCTGAGATATTAGCAAAATTCAAACCACATCTGGATACGTCGACTCTAATTACAAACATCAGAAACATCGAGAAGGCCATCAGAGATTGCTTGGACCACT


Block sizes: 38 (upstream exon), 39 (downstream exon)
Score: 18

CACATTGCGCAGGCTTGTATCTGTGCTGGCCAACGACTATGACAAAGATGCAAAGCAGTTGAATGGAACTCACAAGTCTCATGTTCACTCAAAAGAAGAGgtaccttcga ... ttttgtgcagGCTGAGATATTAGCAAAATTCAAACCACATCTGGATACGTCGACTCTAATTACAAACATCAGAAACATCGAGAAGGCCATCAGAGATTGCTTGGACCACT


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 51

CACATTGCGCAGGCTTGTATCTGTGCTGGCCAACGACTATGACAAAGATGCAAAGCAGTTGAATGGAACTCACAAGTCTCATGTTCACTCAAAAGAAGAGgtaccttcga ... ttttgtgcagGCTGAGATATTAGCAAAATTCAAACCACATCTGGATACGTCGACTCTAATTACAAACATCAGAAACATCGAGAAGGCCATCAGAGATTGCTTGGACCACT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 166

CACATTGCGCAGGCTTGTATCTGTGCTGGCCAACGACTATGACAAAGATGCAAAGCAGTTGAATGGAACTCACAAGTCTCATGTTCACTCAAAAGAAGAGgtaccttcga ... ttttgtgcagGCTGAGATATTAGCAAAATTCAAACCACATCTGGATACGTCGACTCTAATTACAAACATCAGAAACATCGAGAAGGCCATCAGAGATTGCTTGGACCACT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aagctgatactacacctcaacttcttttctgattagtgcagttcattttgtgcagGCTGAGATATTAGCAAAATTCAAACCACATCTGGATACGTCGACTCTAATTACAAACATCAGAAACATCGAGAAGGCCATCAGAGATTGCTTGGACCACT
                          ttctgat  putative branch site (score: 166)
                                         ttcatttt  putative PPT
                                         ttcatttt  TA-rich tract