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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgtgatcactaccagtctaccacataactatcatttcacaatttttagagagagcttaaattactcacctgttctttgtacagGTCACTTTGTGGTGTACAGATTCTCTGAACCCTAAATCTTATCTGGAAGAGCACTCGTTTCTTATCACTGATGTTAGATTTAGCCCAAGCATGTCACGCC

Basic information

species Zea mays
transcript GRMZM2G425377_T01
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|21760225|gb|BQ635766.1|BQ635766
EST:     ACTTCTCAGCTGATGGTAAACTGCTTGCTACTGGTGGTCATGATAAAAAG                         GTCACTTTGTGGTGTACAGATTCTCTGAACCCTAAATCTTATCTGGAAGAG
genomic: ACTTCTCAGCTGATGGTAAACTGCTTGCTACTGGTGGTCATGATAAAAAGgtgtgatcac ... ctttgtacagGTCACTTTGTGGTGTACAGATTCTCTGAACCCTAAATCTTATCTGGAAGAG
EST: gi|26457484|gb|CA829067.1|CA829067
EST:     ACTTCTCAGCTGATGGTAAACTGCTTGCTACTGGTGGTCATGATAAAAAG                         GTCACTTTGTGGTGTACAGATTCTCTGAACCCTAAATCTTATCTGGAAGAG
genomic: ACTTCTCAGCTGATGGTAAACTGCTTGCTACTGGTGGTCATGATAAAAAGgtgtgatcac ... ctttgtacagGTCACTTTGTGGTGTACAGATTCTCTGAACCCTAAATCTTATCTGGAAGAG
EST: gi|160481508|gb|EY254340.1|EY254340
EST:     ACTTCTCAGCTGATGGTAAACTGCTTGCTACTGGTGGTCATGATAAAAAG                         GTCACTTTGTGGTGTACAGATTCTCTGAACCCTAAATCTTATCTGGAAGAG
genomic: ACTTCTCAGCTGATGGTAAACTGCTTGCTACTGGTGGTCATGATAAAAAGgtgtgatcac ... ctttgtacagGTCACTTTGTGGTGTACAGATTCTCTGAACCCTAAATCTTATCTGGAAGAG
EST: gi|160481532|gb|EY254364.1|EY254364
EST:     ACTTCTCAGCTGATGGTAAACTGCTTGCTACTGGTGGTCATGATAAAAAG                         GTCACTTTGTGGTGTACAGATTCTCTGAACCCTAAATCTTATCTGGAAGAG
genomic: ACTTCTCAGCTGATGGTAAACTGCTTGCTACTGGTGGTCATGATAAAAAGgtgtgatcac ... ctttgtacagGTCACTTTGTGGTGTACAGATTCTCTGAACCCTAAATCTTATCTGGAAGAG

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: 211

TTCTGAGGTTGCCAAAGCACGCGCAAGCACAGCCAAAGTTGTCTGTTGCCACTTCTCAGCTGATGGTAAACTGCTTGCTACTGGTGGTCATGATAAAAAGgtgtgatcac ... ctttgtacagGTCACTTTGTGGTGTACAGATTCTCTGAACCCTAAATCTTATCTGGAAGAGCACTCGTTTCTTATCACTGATGTTAGATTTAGCCCAAGCATGTCACGCC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 114

TTCTGAGGTTGCCAAAGCACGCGCAAGCACAGCCAAAGTTGTCTGTTGCCACTTCTCAGCTGATGGTAAACTGCTTGCTACTGGTGGTCATGATAAAAAGgtgtgatcac ... ctttgtacagGTCACTTTGTGGTGTACAGATTCTCTGAACCCTAAATCTTATCTGGAAGAGCACTCGTTTCTTATCACTGATGTTAGATTTAGCCCAAGCATGTCACGCC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 176

TTCTGAGGTTGCCAAAGCACGCGCAAGCACAGCCAAAGTTGTCTGTTGCCACTTCTCAGCTGATGGTAAACTGCTTGCTACTGGTGGTCATGATAAAAAGgtgtgatcac ... ctttgtacagGTCACTTTGTGGTGTACAGATTCTCTGAACCCTAAATCTTATCTGGAAGAGCACTCGTTTCTTATCACTGATGTTAGATTTAGCCCAAGCATGTCACGCC


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 205

TTCTGAGGTTGCCAAAGCACGCGCAAGCACAGCCAAAGTTGTCTGTTGCCACTTCTCAGCTGATGGTAAACTGCTTGCTACTGGTGGTCATGATAAAAAGgtgtgatcac ... ctttgtacagGTCACTTTGTGGTGTACAGATTCTCTGAACCCTAAATCTTATCTGGAAGAGCACTCGTTTCTTATCACTGATGTTAGATTTAGCCCAAGCATGTCACGCC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatcatttcacaatttttagagagagcttaaattactcacctgttctttgtacagGTCACTTTGTGGTGTACAGATTCTCTGAACCCTAAATCTTATCTGGAAGAGCACTCGTTTCTTATCACTGATGTTAGATTTAGCCCAAGCATGTCACGCC
                                 tactcac  putative branch site (score: 205)
                                   ctcacctgttcttt  CT-rich tract
     tttcacaattttta  TA-rich tract