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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tatccccatatatttttgtacttcactaattgaggcactttcaattactatattctttttagtataagactcaactctgaaataactgtaattttggcagATCTCTGGGCAAGACAAACCCTCATTAAATGGCAATATCCCTGTAACTCCTAGGTTAAACTCTGTACCACAGCCAAAGCCTCATCAACCTATGAGGTCTA

Basic information

species Zea mays
transcript GRMZM2G175676_T06
intron # 2
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|211020295|gb|FL072145.1|FL072145
EST:     TGGGATGAACAAGGTTCCTGGAGAGGGTTCTGTATGAAATTCTTATTCAG                         ATCTCTGGGCAAGACAAACCCTCATTAAATGGCAATATCCCTGTAACTCCT
genomic: TGG-ATGA-CAAGGTTCCTG-AGAGGGTTCTGTATGAAATTCTTATTCAGgtaggtcgtg ... attttggcagATCTCTGGGCAAGACAAACCCTCATTAAATGGCAATATCCCTGTAACTCCT
EST: gi|211020294|gb|FL072144.1|FL072144
EST:     ACTTGGATGACAAGGTTCCTGAGAGGGTTCTGTATGAAATTCTTATTCAG                         ATCTCTGGGCAAGACAAACCCTCATTAAATGGCAATATCCCTGTAACTCCT
genomic: ACTTGGATGACAAGGTTCCTGAGAGGGTTCTGTATGAAATTCTTATTCAGgtaggtcgtg ... attttggcagATCTCTGGGCAAGACAAACCCTCATTAAATGGCAATATCCCTGTAACTCCT
EST: gi|211020297|gb|FL072147.1|FL072147
EST:     ACTTGGATGACAAGGTTCCTGAGAGGGTTCTGTATGAAATTCTTATTCAG                         ATCTCTGGGCAAGACAAACCCTCATTAAATGGCAATATCCCTGTAACTCCT
genomic: ACTTGGATGACAAGGTTCCTGAGAGGGTTCTGTATGAAATTCTTATTCAGgtaggtcgtg ... attttggcagATCTCTGGGCAAGACAAACCCTCATTAAATGGCAATATCCCTGTAACTCCT
EST: gi|211020291|gb|FL072141.1|FL072141
EST:     ACTTGGATGACAAGGTTCCTGAGAGGGTTCTGTATGAAATTCTTATTCAG                         ATCTCTGGGCAAGACAAACCCTCATTAAATGGCAATATCCCTGTAACTCCT
genomic: ACTTGGATGACAAGGTTCCTGAGAGGGTTCTGTATGAAATTCTTATTCAGgtaggtcgtg ... attttggcagATCTCTGGGCAAGACAAACCCTCATTAAATGGCAATATCCCTGTAACTCCT
EST: gi|211020292|gb|FL072142.1|FL072142
EST:     ACTTGGATGACAAGGTTCCTGAGAGGGTTCTGTATGAAATTCTTATTCAG                         ATCTCTGGGCAAGACAAACCCTCATTAAATGGCAATATCCCTGTAACTCCT
genomic: ACTTGGATGACAAGGTTCCTGAGAGGGTTCTGTATGAAATTCTTATTCAGgtaggtcgtg ... attttggcagATCTCTGGGCAAGACAAACCCTCATTAAATGGCAATATCCCTGTAACTCCT

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), 49 (downstream exon)
Score: 105

GTAACTTGGATGACAAGGTTCCTGAGAGGGTTCTGTATGAAATTCTTATTCAGgtaggtcgtg ... attttggcagATCTCTGGGCAAGACAAACCCTCATTAAATGGCAATATCCCTGTAACTCCTAGGTTAAACTCTGTACCACAGCCAAAGCCTCATCAACCTATGAGGTCTA


Block sizes: 44 (upstream exon), 49 (downstream exon)
Score: 131

GTAACTTGGATGACAAGGTTCCTGAGAGGGTTCTGTATGAAATTCTTATTCAGgtaggtcgtg ... attttggcagATCTCTGGGCAAGACAAACCCTCATTAAATGGCAATATCCCTGTAACTCCTAGGTTAAACTCTGTACCACAGCCAAAGCCTCATCAACCTATGAGGTCTA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 79

GTAACTTGGATGACAAGGTTCCTGAGAGGGTTCTGTATGAAATTCTTATTCAGgtaggtcgtg ... attttggcagATCTCTGGGCAAGACAAACCCTCATTAAATGGCAATATCCCTGTAACTCCTAGGTTAAACTCTGTACCACAGCCAAAGCCTCATCAACCTATGAGGTCTA


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 68

GTAACTTGGATGACAAGGTTCCTGAGAGGGTTCTGTATGAAATTCTTATTCAGgtaggtcgtg ... attttggcagATCTCTGGGCAAGACAAACCCTCATTAAATGGCAATATCCCTGTAACTCCTAGGTTAAACTCTGTACCACAGCCAAAGCCTCATCAACCTATGAGGTCTA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tactatattctttttagtataagactcaactctgaaataactgtaattttggcagATCTCTGGGCAAGACAAACCCTCATTAAATGGCAATATCCCTGTAACTCCTAGGTTAAACTCTGTACCACAGCCAAAGCCTCATCAACCTATGAGGTCTA
                                  aaataac  putative branch site (score: 68)
     tattctttttagtata  TA-rich tract