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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtgatggattattcaggatggaaatcacatcattttttggttcatttgtcttaacactggcacatggaactgtttttatttgaatttacagACAGCCTGATTTAGGATTCATGAAACGGTTACAACAGATACTAGGTCGGAAGCATAAAAAAAATCTTCAT

Basic information

species Zea mays
transcript GRMZM2G100707_T01
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G100707_T01 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os03g05660.1 (Oryza sativa), 3'ss of exon 10
gtaag--tgatggattattcaggatggaaatcacatcattttttggttcatttgtcttaacactggcacatggaactgtttttatttgaatttacagACAGCCTGATTTAGGATTCATGAAACGGTTACAACAGATACTAGGTCGGAAGCATAAAAAAAATCTTCAT------------------------
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gtaagattcatgaataagt-aggttgagaaggacattgcaatcc--tttctaaaacttggtgcatgtaacacgagctgttttaatt-gattttgcagGCGACCAGATTTAGGATTCATGAAGCGGTTGCAACAAATATTAGGTCGGAAGCATCAGCGCAATCTTCATGTCGGTATCTCATATGATCACACT
















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|32933286|gb|CF038098.1|CF038098
EST:     CAGAAGCCTTACACAATTGTCTATTTCCACTCTGTGGCATCATTACAACC                         GCAGCCTGATTTAGGATTCATGAAACGGTTACAACAGATACTAGGTCGGAA
genomic: CAGAAGCCTTACACAATTGTCTATTTCCACTCTGTGGCATCATTACAACCgtaagtgatg ... gaatttacagACAGCCTGATTTAGGATTCATGAAACGGTTACAACAGATACTAGGTCGGAA
EST: gi|93015870|gb|EB641390.1|EB641390
EST:     CAGAAGCCTTACACAATTGTCTATTTCCACTCTGTGGCATCATTACAACC                         ACAGCCTGATTTAGGATTCATGAAACGGTTACAACAGATACTAGGTCGGAA
genomic: CAGAAGCCTTACACAATTGTCTATTTCCACTCTGTGGCATCATTACAACCgtaagtgatg ... gaatttacagACAGCCTGATTTAGGATTCATGAAACGGTTACAACAGATACTAGGTCGGAA
EST: gi|211442681|gb|FL456308.1|FL456308
EST:     AATTGTCTATTTCCACTCTGTGGCATCATTACAACC                         MCAGCYTGATTTAGGATTCATGAAACGGTTACAACAGATACTAGGTCGGAA
genomic: AATTGTCTATTTCCACTCTGTGGCATCATTACAACCgtaagtgatg ... gaatttacagACAGCCTGATTTAGGATTCATGAAACGGTTACAACAGATACTAGGTCGGAA
EST: gi|37398356|gb|CF636490.1|CF636490
EST:     CAGAAGCCTTACACAATTGTCTATTTCCACTCTGTGGCATCATTACAACC                         ACAGCCTGATTTAGGATTCATGAAACGGTTACAACAGATANTAGGTCGGAA
genomic: CAGAAGCCTTACACAATTGTCTATTTCCACTCTGTGGCATCATTACAACCgtaagtgatg ... gaatttacagACAGCCTGATTTAGGATTCATGAAACGGTTACAACAGATACTAGGTCGGAA
EST: gi|5915101|gb|AW052742.1|AW052742
EST:     CAGAAGCCTTACACAATTGTCTATTTCCACTCTGTGGCATCATTACAACC                         ACAGCCTGATTTAGGATTCATGAAACGGTTACAACAGATACTAGGTCGGAA
genomic: CAGAAGCCTTACACAATTGTCTATTTCCACTCTGTGGCATCATTACAACCgtaagtgatg ... gaatttacagACAGCCTGATTTAGGATTCATGAAACGGTTACAACAGATACTAGGTCGGAA
EST: gi|149097072|gb|EE182879.2|EE182879
EST:     CAGAAGCCTTACACAATTGTCTATTTCCACTCTGTGGCATCATTACAACC                         ACAGCCTGATTTAGGATTCATGAAACGGTTACAACAGATACTAGGTCGGAA
genomic: CAGAAGCCTTACACAATTGTCTATTTCCACTCTGTGGCATCATTACAACCgtaagtgatg ... gaatttacagACAGCCTGATTTAGGATTCATGAAACGGTTACAACAGATACTAGGTCGGAA

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), 48 (downstream exon)
Score: 90

GAATTTGAATCTCTGATTCAGAAGCCTTACACAATTGTCTATTTCCACTCTGTGGCATCATTACAACCgtaagtgatg ... gaatttacagACAGCCTGATTTAGGATTCATGAAACGGTTACAACAGATACTAGGTCGGAAGCATAAAAAAAATCTTCAT


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 99

GAATTTGAATCTCTGATTCAGAAGCCTTACACAATTGTCTATTTCCACTCTGTGGCATCATTACAACCgtaagtgatg ... gaatttacagACAGCCTGATTTAGGATTCATGAAACGGTTACAACAGATACTAGGTCGGAAGCATAAAAAAAATCTTCAT


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 93

GAATTTGAATCTCTGATTCAGAAGCCTTACACAATTGTCTATTTCCACTCTGTGGCATCATTACAACCgtaagtgatg ... gaatttacagACAGCCTGATTTAGGATTCATGAAACGGTTACAACAGATACTAGGTCGGAAGCATAAAAAAAATCTTCAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 90

GAATTTGAATCTCTGATTCAGAAGCCTTACACAATTGTCTATTTCCACTCTGTGGCATCATTACAACCgtaagtgatg ... gaatttacagACAGCCTGATTTAGGATTCATGAAACGGTTACAACAGATACTAGGTCGGAAGCATAAAAAAAATCTTCAT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttggttcatttgtcttaacactggcacatggaactgtttttatttgaatttacagACAGCCTGATTTAGGATTCATGAAACGGTTACAACAGATACTAGGTCGGAAGCATAAAAAAAATCTTCAT
            tcttaac  putative branch site (score: 90)
                               aactgtttttatttga  TA-rich tract