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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGTAAAACTCTGGTTAGACTTGGGAGAAGTAAGGAGGCAATCAGCACTTGTACGGAAGCACTGATCATAGACAGTGAACTTGTTGATGCGCTTACACAGgtaacttgcctgcctggaatcatgcagaacatcagtgtaaaattcagaatgcaaactcaaggtttctagacctgatcttacaactttgacactagtttct...

Basic information

species Zea mays
transcript GRMZM2G341404_T01
intron # 7
splice site 5'
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|60394505|gb|DN227375.1|DN227375
EST:     AAGCACTGATCATAGACAGTGAACTTGTTGATGCGCTTACACAG                         AGAGGTGAAGCTAAACTTCTCTCAGAAGATTGGGAAGGAGCAGTTCAGGAT
genomic: AAGCACTGATCATAGACAGTGAACTTGTTGATGCGCTTACACAGgtaacttgcc ... cttgctgcagAGAGGTGAAGCTAAACTTCTCTCAGAAGATTGGGAAGGAGCAGTTCAGGAT
EST: gi|19770415|gb|BQ035136.1|BQ035136
EST:     GTACGGAAGCACTGATCATAGACAGTGAACTTGTTGATGCGCTTACACAG                         AGAGGTGAAGCTAAACTTCTCTCAGAAGATTGGGAAGGAGCAGTTCAGGAT
genomic: GTACGGAAGCACTGATCATAGACAGTGAACTTGTTGATGCGCTTACACAGgtaacttgcc ... cttgctgcagAGAGGTGAAGCTAAACTTCTCTCAGAAGATTGGGAAGGAGCAGTTCAGGAT
EST: gi|26456221|gb|CA827804.1|CA827804
EST:     GTACGGAAGCACTGATCATAGACAGTGAACTTGTTGATGCGCTTACACAG                         AGAGGTGAAGCTAAACTTCTCTCAGAAGATTGGGAAGGAGCAGTTCAGGAT
genomic: GTACGGAAGCACTGATCATAGACAGTGAACTTGTTGATGCGCTTACACAGgtaacttgcc ... cttgctgcagAGAGGTGAAGCTAAACTTCTCTCAGAAGATTGGGAAGGAGCAGTTCAGGAT
EST: gi|71323580|gb|DR798458.1|DR798458
EST:     GTACGGAAGCACTGATCATAGACAGTGAACTTGTTGATGCGCTTACACAG                         AGAGGTGAAGCTAAACTTCTCTCAGAAGATTGGGAAGGAGCAGTTCAGGAT
genomic: GTACGGAAGCACTGATCATAGACAGTGAACTTGTTGATGCGCTTACACAGgtaacttgcc ... cttgctgcagAGAGGTGAAGCTAAACTTCTCTCAGAAGATTGGGAAGGAGCAGTTCAGGAT
EST: gi|32791567|gb|CD943803.1|CD943803
EST:     GTACGGAAGCACTGATCATAGACAGTGAACTTGTTGATGCGCTTACACAG                         AGAGGTGAAGCTAAACTTCTCTCAGAAGATTGGGAAGGAGCAGTTCAGGAT
genomic: GTACGGAAGCACTGATCATAGACAGTGAACTTGTTGATGCGCTTACACAGgtaacttgcc ... cttgctgcagAGAGGTGAAGCTAAACTTCTCTCAGAAGATTGGGAAGGAGCAGTTCAGGAT
EST: gi|78104564|gb|DV522982.1|DV522982
EST:     GTACGGAAGCACTGATCATAGACAGTGAACTTGTTGATGCGCTTGCACAG                         AGAGGTGAAGCTAAACTTCTCTCAGAAGATTGGGAAGGAGCAGTTCAGGAT
genomic: GTACGGAAGCACTGATCATAGACAGTGAACTTGTTGATGCGCTTACACAGgtaacttgcc ... cttgctgcagAGAGGTGAAGCTAAACTTCTCTCAGAAGATTGGGAAGGAGCAGTTCAGGAT
EST: gi|32805133|gb|CD957369.1|CD957369
EST:     GTACGGAAGCACTGATCATAGACAGTGAACTTGTTGATGCGCTTACACAG                         AGAGGTGAAGCTAAACTTCTCTCAGAAGATTGGGAAGGAGCAGTTCAGGA
genomic: GTACGGAAGCACTGATCATAGACAGTGAACTTGTTGATGCGCTTACACAGgtaacttgcc ... cttgctgcagAGAGGTGAAGCTAAACTTCTCTCAGAAGATTGGGAAGGAGCAGTTCAGGA
EST: gi|7227648|gb|AW566289.1|AW566289
EST:     GTACGGAAGCACTGATCATAGACAGTGAACTTGTTGATGCGCTTACACAG                         AGAGGTGAAGCTAAACTTCTCTCAGAAGA
genomic: GTACGGAAGCACTGATCATAGACAGTGAACTTGTTGATGCGCTTACACAGgtaacttgcc ... cttgctgcagAGAGGTGAAGCTAAACTTCTCTCAGAAGA
EST: gi|32799442|gb|CD951678.1|CD951678
EST:     GTACGGAAGCACTGATCATAGACAGTGAACTTGTTGATGCGCTTACACAG                         AGAGGTGAAGCTAAACTTCTCTCAGAAGATTGGGAAGGAGCAGTTCAGGAT
genomic: GTACGGAAGCACTGATCATAGACAGTGAACTTGTTGATGCGCTTACACAGgtaacttgcc ... cttgctgcagAGAGGTGAAGCTAAACTTCTCTCAGAAGATTGGGAAGGAGCAGTTCAGGAT
EST: gi|78080723|gb|DV509135.1|DV509135
EST:     GTACGGAAGCACTGATCATAGACAGTGAACTTGTTGATGCGCTTACACAG                         AGAGGTGAAGCTAAACTTCTCTCAGCAGATTGGGAAGGAGCAGTTCAGGAT
genomic: GTACGGAAGCACTGATCATAGACAGTGAACTTGTTGATGCGCTTACACAGgtaacttgcc ... cttgctgcagAGAGGTGAAGCTAAACTTCTCTCAGAAGATTGGGAAGGAGCAGTTCAGGAT
EST: gi|91875153|gb|EB405110.1|EB405110
EST:     GTACGGAAGCACTGATCATAGACAGTGAACTTGTTGATGCGCTTACACAG                         AGAGGTGAAGCTAAACTTCTCTCAGAAGATTGGGAAGGAGCAGTTCAGGAT
genomic: GTACGGAAGCACTGATCATAGACAGTGAACTTGTTGATGCGCTTACACAGgtaacttgcc ... cttgctgcagAGAGGTGAAGCTAAACTTCTCTCAGAAGATTGGGAAGGAGCAGTTCAGGAT
EST: gi|32796833|gb|CD949069.1|CD949069
EST:     GTACGGAAGCACTGATCATAGACAGTGAACTTGTTGATGCGCTTACACAG                         AGAGGTGAAGCTAAACTTCTCTCAGAAGATTGGGAAGGAGCAGTTCAGGGT
genomic: GTACGGAAGCACTGATCATAGACAGTGAACTTGTTGATGCGCTTACACAGgtaacttgcc ... cttgctgcagAGAGGTGAAGCTAAACTTCTCTCAGAAGATTGGGAAGGAGCAGTTCAGGAT
EST: gi|26456078|gb|CA827661.1|CA827661
EST:     GTACGGAAGCACTGATCATAGACAGTGAACTTGTTGATGCGCTTACACAG                         AGAGGTGAAGCTAAACTTCTCTCAGAAGATTGGGAAGGAGCAGTTCAGGAT
genomic: GTACGGAAGCACTGATCATAGACAGTGAACTTGTTGATGCGCTTACACAGgtaacttgcc ... cttgctgcagAGAGGTGAAGCTAAACTTCTCTCAGAAGATTGGGAAGGAGCAGTTCAGGAT
EST: gi|32799460|gb|CD951696.1|CD951696
EST:     GTACGGAAGCACTGATCATAGACAGTGAACTTGTTGATGCGCTTACACAG                         AGAGGTGAAGCTAAACTTCTCTCAGAAGATTGGGAAGGAGCAGTTCAGGAT
genomic: GTACGGAAGCACTGATCATAGACAGTGAACTTGTTGATGCGCTTACACAGgtaacttgcc ... cttgctgcagAGAGGTGAAGCTAAACTTCTCTCAGAAGATTGGGAAGGAGCAGTTCAGGAT
EST: gi|32799713|gb|CD951949.1|CD951949
EST:     GTACGGAAGCACTGATCATAGACAGTGAACTTGTTGATGCGCTTACACAG                         AGAGGTGAAGCTAAACTTCTCTCAGAAGATTGGGAAGGAGCAGTTCAGGAT
genomic: GTACGGAAGCACTGATCATAGACAGTGAACTTGTTGATGCGCTTACACAGgtaacttgcc ... cttgctgcagAGAGGTGAAGCTAAACTTCTCTCAGAAGATTGGGAAGGAGCAGTTCAGGAT
EST: gi|67016841|gb|CO445590.1|CO445590
EST:     GTACGGAAGCACTGATCATAGACAGTGAACTTGTTGATGCGCTTACACAG                         AGAGGTGAAGCTAAACTTCTCTCAGAAGATTGNGAANGAGCAGTTCAGGAT
genomic: GTACGGAAGCACTGATCATAGACAGTGAACTTGTTGATGCGCTTACACAGgtaacttgcc ... cttgctgcagAGAGGTGAAGCTAAACTTCTCTCAGAAGATTGGGAAGGAGCAGTTCAGGAT

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: 48 (upstream exon), 49 (downstream exon)
Score: 245

GTGTAAAACTCTGGTTAGACTTGGGAGAAGTAAGGAGGCAATCAGCACTTGTACGGAAGCACTGATCATAGACAGTGAACTTGTTGATGCGCTTACACAGgtaacttgcc ... cttgctgcagAGAGGTGAAGCTAAACTTCTCTCAGAAGATTGGGAAGGAGCAGTTCAGGATTTAAAAGAGGCCGCCCAGAAATCTCCACAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 354

GTGTAAAACTCTGGTTAGACTTGGGAGAAGTAAGGAGGCAATCAGCACTTGTACGGAAGCACTGATCATAGACAGTGAACTTGTTGATGCGCTTACACAGgtaacttgcc ... cttgctgcagAGAGGTGAAGCTAAACTTCTCTCAGAAGATTGGGAAGGAGCAGTTCAGGATTTAAAAGAGGCCGCCCAGAAATCTCCACAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 239

GTGTAAAACTCTGGTTAGACTTGGGAGAAGTAAGGAGGCAATCAGCACTTGTACGGAAGCACTGATCATAGACAGTGAACTTGTTGATGCGCTTACACAGgtaacttgcc ... cttgctgcagAGAGGTGAAGCTAAACTTCTCTCAGAAGATTGGGAAGGAGCAGTTCAGGATTTAAAAGAGGCCGCCCAGAAATCTCCACAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 495

GTGTAAAACTCTGGTTAGACTTGGGAGAAGTAAGGAGGCAATCAGCACTTGTACGGAAGCACTGATCATAGACAGTGAACTTGTTGATGCGCTTACACAGgtaacttgcc ... cttgctgcagAGAGGTGAAGCTAAACTTCTCTCAGAAGATTGGGAAGGAGCAGTTCAGGATTTAAAAGAGGCCGCCCAGAAATCTCCACAG