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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgttgatcctgtgaatatgttgcaataaaatccaccgagtttcagactttttgtatattttgtcttgtcgatatattttaagaagttttgaaatttaatgcagGGTGCTTTCAAGATCTCGGCAAACAAAACCCACTAAGTATGATGGGGATTTCTCTGATGTTGCGCATCAACATCACCTGCAATCACTTCAAAAGGCTATG

Basic information

species Zea mays
transcript GRMZM2G348675_T02
intron # 16
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|71441451|gb|DR822501.1|DR822501
EST:     TTCTCATCTGATAATGTATCCAAGGCTTGTTTTGAAGAGATCATCGAGAG                         GGTGCTTTCAAGATCTCGGCAAACAAAACCCACTAAGTATGATGGGGATTT
genomic: TTCTCATCTGATAATGTATCCAAGGCTTGTTTTGAAGAGATCATCGAGAGgtttgttgat ... tttaatgcagGGTGCTTTCAAGATCTCGGCAAACAAAACCCACTAAGTATGATGGGGATTT
EST: gi|6526616|gb|AW215913.1|AW215913
EST:     TTCTCATCTGATAATGTATCCAAGGCTTGGTTTGAAGAGATCATCGAGAG                         GGTGCTTTCAAGATCTCGGCAAACAAAACCCACTAAGTATGATGGGGATTT
genomic: TTCTCATCTGATAATGTATCCAAGGCTTGTTTTGAAGAGATCATCGAGAGgtttgttgat ... tttaatgcagGGTGCTTTCAAGATCTCGGCAAACAAAACCCACTAAGTATGATGGGGATTT
EST: gi|21432148|gb|BQ547638.1|BQ547638
EST:     TTCTCATCTGATAATGTATCCAAGGCTTGTTTTGAAGAGATCATCGAGAG                         GGTGCTTTCAAGATCTCGGCAAACAAAACCCACTAAGTATGATGGGGATTT
genomic: TTCTCATCTGATAATGTATCCAAGGCTTGTTTTGAAGAGATCATCGAGAGgtttgttgat ... tttaatgcagGGTGCTTTCAAGATCTCGGCAAACAAAACCCACTAAGTATGATGGGGATTT
EST: gi|5555477|gb|AI881428.1|AI881428
EST:     GAAGAGATCATCGAGAG                         GGTGCTTTCAAGATCTCGGCAAACAAAACCCACTAAGTATGATGGGGATTT
genomic: GAAGAGATCATCGAGAGgtttgttgat ... tttaatgcagGGTGCTTTCAAGATCTCGGCAAACAAAACCCACTAAGTATGATGGGGATTT
EST: gi|21843368|gb|BQ703949.1|BQ703949
EST:     TTCTCATCTGATAATGTATCCAAGGCTTGTTTTGAAGAGATCATCGAGAG                         GGTGCTTTCAAGATCTCGGCAAACAAAACCCACTAAGTATGATGGGGATTT
genomic: TTCTCATCTGATAATGTATCCAAGGCTTGTTTTGAAGAGATCATCGAGAGgtttgttgat ... tttaatgcagGGTGCTTTCAAGATCTCGGCAAACAAAACCCACTAAGTATGATGGGGATTT
EST: gi|86467221|gb|DY233591.1|DY233591
EST:     TTCTCATCTGATAATGTATCCAAGGCTTGTTTTGAAGAGATCATCGAGAG                         GGTGTTTTCAAGATCTCGGCAAACAAAACCCACTAAGTATGATGGGGATTT
genomic: TTCTCATCTGATAATGTATCCAAGGCTTGTTTTGAAGAGATCATCGAGAGgtttgttgat ... tttaatgcagGGTGCTTTCAAGATCTCGGCAAACAAAACCCACTAAGTATGATGGGGATTT

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: 317

TTTGCATACTATGTACAAGCTCTTCCTTTCTGCTGTGGAGTATCTGCCATTCTCATCTGATAATGTATCCAAGGCTTGTTTTGAAGAGATCATCGAGAGgtttgttgat ... tttaatgcagGGTGCTTTCAAGATCTCGGCAAACAAAACCCACTAAGTATGATGGGGATTTCTCTGATGTTGCGCATCAACATCACCTGCAATCACTTCAAAAGGCTATG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 108

TTTGCATACTATGTACAAGCTCTTCCTTTCTGCTGTGGAGTATCTGCCATTCTCATCTGATAATGTATCCAAGGCTTGTTTTGAAGAGATCATCGAGAGgtttgttgat ... tttaatgcagGGTGCTTTCAAGATCTCGGCAAACAAAACCCACTAAGTATGATGGGGATTTCTCTGATGTTGCGCATCAACATCACCTGCAATCACTTCAAAAGGCTATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 136

TTTGCATACTATGTACAAGCTCTTCCTTTCTGCTGTGGAGTATCTGCCATTCTCATCTGATAATGTATCCAAGGCTTGTTTTGAAGAGATCATCGAGAGgtttgttgat ... tttaatgcagGGTGCTTTCAAGATCTCGGCAAACAAAACCCACTAAGTATGATGGGGATTTCTCTGATGTTGCGCATCAACATCACCTGCAATCACTTCAAAAGGCTATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 134

TTTGCATACTATGTACAAGCTCTTCCTTTCTGCTGTGGAGTATCTGCCATTCTCATCTGATAATGTATCCAAGGCTTGTTTTGAAGAGATCATCGAGAGgtttgttgat ... tttaatgcagGGTGCTTTCAAGATCTCGGCAAACAAAACCCACTAAGTATGATGGGGATTTCTCTGATGTTGCGCATCAACATCACCTGCAATCACTTCAAAAGGCTATG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttgtatattttgtcttgtcgatatattttaagaagttttgaaatttaatgcagGGTGCTTTCAAGATCTCGGCAAACAAAACCCACTAAGTATGATGGGGATTTCTCTGATGTTGCGCATCAACATCACCTGCAATCACTTCAAAAGGCTATG
                                            atttaat  putative branch site (score: 134)
                      atatattttaagaagt  TA-rich tract