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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtgccgaacgaggctttacctccgtgggtttctgatcgcctcgcgatgttcgatctgtaacggtctttttttttgtcacggtgtgcagATGCTGGGACAGGTTTTGCGAAGACTCCGACCAGCGGTGGCGGCTGAGGTGGCGAGGGGCTACTCCGCCGCGGCGAAGGAG

Basic information

species Zea mays
transcript GRMZM2G097226_T01
intron # 1
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|78122124|gb|DV540508.1|DV540508
EST:     CGACGACGAGGATGCTGGGCGCAGCGAGGAGGCAGCTTGGATCCGGTCCC                         ATGCTGGGACAGGTTTTGCGAAGACTCCGACCAGCGGTGGCGGCTGAGGTG
genomic: CGACGACGAGGATGCTGGGCGCAGCGAGGAGGCAGCTTGGATCCGGTCCCgtgagtgccg ... cggtgtgcagATGCTGGGACAGGTTTTGCGAAGACTCCGACCAGCGGTGGCGGCTGAGGTG
EST: gi|211069303|gb|FL193602.1|FL193602
EST:     CGACGACGAGGATGCTGGGCGCAGCGAGGAGGCAGCTTGGATCCGGTCCC                         ATGCTGGGACAGATTTTGCGAAGGCTCCGACCAGCGGTGGCGGCTGAGGTG
genomic: CGACGACGAGGATGCTGGGCGCAGCGAGGAGGCAGCTTGGATCCGGTCCCgtgagtgccg ... cggtgtgcagATGCTGGGACAGGTTTTGCGAAGACTCCGACCAGCGGTGGCGGCTGAGGTG
EST: gi|32799904|gb|CD952140.1|CD952140
EST:     GATCCGGTCCC                         ATGCTGGGACAGGTTTTGCGAAGACTCCGACCAGCGGTGGCGGCTGAGGTG
genomic: GATCCGGTCCCgtgagtgccg ... cggtgtgcagATGCTGGGACAGGTTTTGCGAAGACTCCGACCAGCGGTGGCGGCTGAGGTG
EST: gi|91057168|gb|EB167586.1|EB167586
EST:     CGACGACGAGGATGCTGGGCGCAGCGAGGAGGCAGCTTGGATCCGGTCCC                         ATGCTGGGACAGGTTTTGCGAAGACTCCGACCAGCGGTGGCGGCTGAGGTG
genomic: CGACGACGAGGATGCTGGGCGCAGCGAGGAGGCAGCTTGGATCCGGTCCCgtgagtgccg ... cggtgtgcagATGCTGGGACAGGTTTTGCGAAGACTCCGACCAGCGGTGGCGGCTGAGGTG

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: 44 (upstream exon), 45 (downstream exon)
Score: 138

TCCATCTCCAGGCCGCGTCGAATTCTTCCATCCACCGCACCGGTCGACGACGACGACGAGGATGCTGGGCGCAGCGAGGAGGCAGCTTGGATCCGGTCCCgtgagtgccg ... cggtgtgcagATGCTGGGACAGGTTTTGCGAAGACTCCGACCAGCGGTGGCGGCTGAGGTGGCGAGGGGCTACTCCGCCGCGGCGAAGGAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 205

TCCATCTCCAGGCCGCGTCGAATTCTTCCATCCACCGCACCGGTCGACGACGACGACGAGGATGCTGGGCGCAGCGAGGAGGCAGCTTGGATCCGGTCCCgtgagtgccg ... cggtgtgcagATGCTGGGACAGGTTTTGCGAAGACTCCGACCAGCGGTGGCGGCTGAGGTGGCGAGGGGCTACTCCGCCGCGGCGAAGGAG


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 136

TCCATCTCCAGGCCGCGTCGAATTCTTCCATCCACCGCACCGGTCGACGACGACGACGAGGATGCTGGGCGCAGCGAGGAGGCAGCTTGGATCCGGTCCCgtgagtgccg ... cggtgtgcagATGCTGGGACAGGTTTTGCGAAGACTCCGACCAGCGGTGGCGGCTGAGGTGGCGAGGGGCTACTCCGCCGCGGCGAAGGAG


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 183

TCCATCTCCAGGCCGCGTCGAATTCTTCCATCCACCGCACCGGTCGACGACGACGACGAGGATGCTGGGCGCAGCGAGGAGGCAGCTTGGATCCGGTCCCgtgagtgccg ... cggtgtgcagATGCTGGGACAGGTTTTGCGAAGACTCCGACCAGCGGTGGCGGCTGAGGTGGCGAGGGGCTACTCCGCCGCGGCGAAGGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatcgcctcgcgatgttcgatctgtaacggtctttttttttgtcacggtgtgcagATGCTGGGACAGGTTTTGCGAAGACTCCGACCAGCGGTGGCGGCTGAGGTGGCGAGGGGCTACTCCGCCGCGGCGAAGGAG
                     ctgtaac  putative branch site (score: 183)
                              tctttttttttgtcac  putative PPT
                              tcttttttttt  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtgccgaacgaggctttacctccgtgggtttctgatcgcctcgcgatgttcgatctgtaacggtctttttttttgtcacggtgtgcagATGCTGGGACAGGTTTTGCGAAGACTCCGACCAGCGGTGGCGGCTGAGGTGGCGAGGGGCTACTCCGCCGCGGCGAAGGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG