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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgcgccctgcatgcagcaattttctgaccgtgcgtgcgtattttatctgctccattccatcaacctgcagGATTCTGCTGGGAAGTGTGACGAACTACGTGCTGTCCAATGCGTCATGCCCCGTGACCGTCGTCAAGTCGAAGTAGTGGCTCTGGCCTTTCATTTCCAGA

Basic information

species Zea mays
transcript GRMZM2G045278_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G045278_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os01g63010.1 (Oryza sativa), 3'ss of exon 3
-----------------------------------------------------------------------------------------------gtacgcgccctgcatgcagca--attttctgaccg-tgcgtgcgtatttta----tctgctccattcc---atcaacct-gcagGATTCTGCTGGGAAGTGTGACGAACTACGTGCTGTCCAATGCGTCATGCCCCGTGACCGTCGTCAAGTCGAAGTAGTGGCT-CTGGCCTTTCATTTCCAGA
                                                                                                |||     |  | || ||||  |||||| ||  | ||  |   |  |  |    | ||||  |||     ||     | ||||||||||||||||||||||||| |||||||||||||| |||||||| ||||| ||||||||||||||| | ||||||| ||| ||       || | | |  
gtgtgtgaatgatacgacggtatagcattgacatgtttctagaaactttcggtctggtttctgtttgagcaaccagagattcatcaggggcagcgatacaatatccccttgtagcatcattttcagaaagctgaatttctgatccagtactttgcttgatttttaaattgtttttgcagGATTCTGCTGGGAAGTGTGACTAACTACGTGCTGTCGAATGCGTCTTGCCCTGTGACCGTCGTCAAGGCAAAGTAGTCGCTACTCTTACAGCAATGCAAA-
















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|7216551|gb|AW562673.1|AW562673
EST:     CAGATGGAGTCGCTCGTCATGGGCAGCCGCGGCCTCGGCCAGATCCAAAG                         GATTCTGCTGGGAAGTGTGACGAACTACGTGCTGTCCAATGCGTCATGCCC
genomic: CAGATCGAGTCGCTCGTCATGGGCAGCCGCGGCCTCGGCCAGATCCAAAGgtacgcgccc ... caacctgcagGATTCTGCTGGGAAGTGTGACGAACTACGTGCTGTCCAATGCGTCATGCCC
EST: gi|50337518|gb|CO532644.1|CO532644
EST:     CAGATCGAGTCGCTCGTCATGGGCAGCCGCGGCCTCGGCCAGATCCAAAG                         GATTCTGCTGGGAAGTGTGACGAACTACGTGCTGTCCAATGCGTCATGCCC
genomic: CAGATCGAGTCGCTCGTCATGGGCAGCCGCGGCCTCGGCCAGATCCAAAGgtacgcgccc ... caacctgcagGATTCTGCTGGGAAGTGTGACGAACTACGTGCTGTCCAATGCGTCATGCCC
EST: gi|101383316|gb|EB813714.1|EB813714
EST:     CAGATCGAGTCGCTCGTCATGGGCAGCCGCGGCCTCGGCCAGATCCAAAG                         GATTTTGTTGGGAAGTGTGACGAACTACGTGCTGTCCAATGCGTCATGCCC
genomic: CAGATCGAGTCGCTCGTCATGGGCAGCCGCGGCCTCGGCCAGATCCAAAGgtacgcgccc ... caacctgcagGATTCTGCTGGGAAGTGTGACGAACTACGTGCTGTCCAATGCGTCATGCCC
EST: gi|87154532|gb|DY399321.1|DY399321
EST:     CAGATCGAGTCGCTCGTCATGGGCAGCCGCGGCCTCGGCCAGATCCAAAG                         GATTCTGCTGGGAAGTGTGACGAACTACGTGCTGTCCAATGCGTCATGCCC
genomic: CAGATCGAGTCGCTCGTCATGGGCAGCCGCGGCCTCGGCCAGATCCAAAGgtacgcgccc ... caacctgcagGATTCTGCTGGGAAGTGTGACGAACTACGTGCTGTCCAATGCGTCATGCCC
EST: gi|26454905|gb|CA826488.1|CA826488
EST:     CAGATCGAGTCGCTCGTCATGGGCAGCCGCGGCCTCGGCCAGATCCAAAG                         GATTCTGCTGGGAAGTGTGACGAACTACGTGCTGTCCAATGCGTCATGCCC
genomic: CAGATCGAGTCGCTCGTCATGGGCAGCCGCGGCCTCGGCCAGATCCAAAGgtacgcgccc ... caacctgcagGATTCTGCTGGGAAGTGTGACGAACTACGTGCTGTCCAATGCGTCATGCCC
EST: gi|21329933|gb|BQ485314.1|BQ485314
EST:     CAGATCGAGTCGCTCGTCATGGGCAGCCGCGGCCTCGGCCAGATCCAAAG                         GATTCTGCTGGGAAGTGTGACGAACTACGTGCTGTCCAATGCGTCATGCCC
genomic: CAGATCGAGTCGCTCGTCATGGGCAGCCGCGGCCTCGGCCAGATCCAAAGgtacgcgccc ... caacctgcagGATTCTGCTGGGAAGTGTGACGAACTACGTGCTGTCCAATGCGTCATGCCC
EST: gi|87154904|gb|DY399693.1|DY399693
EST:     CAGATCGAGTCGCTCGTCATGGGCAGCCGCGGCCTCGGCCAGATCCAAAG                         GATTCTGCTGGGAAGTGTGACGAACTACGTGCTGTCCAATGCGTCATGCCC
genomic: CAGATCGAGTCGCTCGTCATGGGCAGCCGCGGCCTCGGCCAGATCCAAAGgtacgcgccc ... caacctgcagGATTCTGCTGGGAAGTGTGACGAACTACGTGCTGTCCAATGCGTCATGCCC

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 1 RNA-Seqlibrary.


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 38

TGTACTGGGGTGACCCGAGGGAGAAGGTGTGCGACGCGGTGGAGGAGCTCCAGATCGAGTCGCTCGTCATGGGCAGCCGCGGCCTCGGCCAGATCCAAAGgtacgcgccc ... caacctgcagGATTCTGCTGGGAAGTGTGACGAACTACGTGCTGTCCAATGCGTCATGCCCCGTGACCGTCGTCAAGTCGAAGTAGTGGCTCTGGCCTTTCATTTCCAGA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcaattttctgaccgtgcgtgcgtattttatctgctccattccatcaacctgcagGATTCTGCTGGGAAGTGTGACGAACTACGTGCTGTCCAATGCGTCATGCCCCGTGACCGTCGTCAAGTCGAAGTAGTGGCTCTGGCCTTTCATTTCCAGA
      ttctgac  putative branch site (score: 38)
                                       ttccatc  putative PPT
                       tattttatct  TA-rich tract