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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgggtgtggatatgccgcatcgaaacattactgttcttggttgagctgaggctgctccatcctgtccgagatatttaatgatgggttgtttcagGACAGTGGCGCTTACATGGAGCACCGTCTGGCCGGCGTGGACAGGGTGCAGATCACGGGCCTGAACGCGGGCACGCTGGACCTGACGAATAACGGCTGGG

Basic information

species Zea mays
transcript GRMZM2G175779_T01
intron # 11
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|78179084|gb|DV549457.1|DV549457
EST:     AGAAGGGCGTGAACCACGTCGCCGTCTTGGCATCGTCGATGGGAATGACG                         GACAGTGGCGCTTACATGGAGCACCGTCTGGCCGGCGTGGACAGGGTGCAG
genomic: AGAAGGGCGTGAACCACGTCGCCGTCTTGGCATCGTCGATGGGAATGACGgtgggtgtgg ... gttgtttcagGACAGTGGCGCTTACATGGAGCACCGTCTGGCCGGCGTGGACAGGGTGCAG
EST: gi|21390502|gb|BQ528551.1|BQ528551
EST:     GGCGTGAACCACGTCGCCGTCTTGGCATCGTCGATGGGAATGACG                         GACAGTGGCGCTTACATGGAGCACCGTCTGGCCGGCGTGGACAGGGTGCAG
genomic: GGCGTGAACCACGTCGCCGTCTTGGCATCGTCGATGGGAATGACGgtgggtgtgg ... gttgtttcagGACAGTGGCGCTTACATGGAGCACCGTCTGGCCGGCGTGGACAGGGTGCAG
EST: gi|89761736|gb|DY689632.1|DY689632
EST:     AGAAGGGCGTGAACCACGTCGCCGTCTTGGCATCGTCGATGGGAATGACG                         GACAGTGGCGCTTACATGGAGCACCGTCTGGCCGGCGTGGACAGGGTGCAG
genomic: AGAAGGGCGTGAACCACGTCGCCGTCTTGGCATCGTCGATGGGAATGACGgtgggtgtgg ... gttgtttcagGACAGTGGCGCTTACATGGAGCACCGTCTGGCCGGCGTGGACAGGGTGCAG
EST: gi|76920516|gb|DV168211.1|DV168211
EST:     AGAAGGGCGTGAACCACGTCGCCGTCTTGGCATCGTCGATGGGAATGACG                         GACAGTGGCGCTTACATGGAGCACCGTCTGGCCGGCGTGGACAGGGTGCAG
genomic: AGAAGGGCGTGAACCACGTCGCCGTCTTGGCATCGTCGATGGGAATGACGgtgggtgtgg ... gttgtttcagGACAGTGGCGCTTACATGGAGCACCGTCTGGCCGGCGTGGACAGGGTGCAG
EST: gi|8551676|gb|BE128847.1|BE128847
EST:     AGAAGGGCGTGAACCACGTCGCCGTCTTGGCATCGTCGATGGGAATGACG                         GACAGTGGCGCTTACATGGAGCACCGTCTGGCCGGCGTGGACAGGGTGCAG
genomic: AGAAGGGCGTGAACCACGTCGCCGTCTTGGCATCGTCGATGGGAATGACGgtgggtgtgg ... gttgtttcagGACAGTGGCGCTTACATGGAGCACCGTCTGGCCGGCGTGGACAGGGTGCAG
EST: gi|12047076|gb|BF729215.1|BF729215
EST:     AGAAGGGCGTGAACCACGTCGCCGTCTTGGCATCGTCGATGGGAATGACG                         GACAGTGGCGCTTACATGGAGCACCGTCTGGCCGGCGTGGACAGGGTGCAG
genomic: AGAAGGGCGTGAACCACGTCGCCGTCTTGGCATCGTCGATGGGAATGACGgtgggtgtgg ... gttgtttcagGACAGTGGCGCTTACATGGAGCACCGTCTGGCCGGCGTGGACAGGGTGCAG
EST: gi|78080986|gb|DV509398.1|DV509398
EST:     AGAAGGGCGTGAACCACGTCGCCGTCTTGGCATCGTCGATGGGAATGACG                         GACAGTGGCGCTTACATGGAGCACCGTCTGGCCGGCGTGGACAGGGTGCAG
genomic: AGAAGGGCGTGAACCACGTCGCCGTCTTGGCATCGTCGATGGGAATGACGgtgggtgtgg ... gttgtttcagGACAGTGGCGCTTACATGGAGCACCGTCTGGCCGGCGTGGACAGGGTGCAG
EST: gi|76281440|gb|DV021008.1|DV021008
EST:     AGAAGGGCGTGAACCACGTCGCCGTCTTGGCATCGTCGATGGGAATGACG                         GACAGTGGCGCTTACATGGAGCACCGTCTGGCCGGCGTGGACAGGGTGCAG
genomic: AGAAGGGCGTGAACCACGTCGCCGTCTTGGCATCGTCGATGGGAATGACGgtgggtgtgg ... gttgtttcagGACAGTGGCGCTTACATGGAGCACCGTCTGGCCGGCGTGGACAGGGTGCAG

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), 48 (downstream exon)
Score: 56

CGGGACCAAGATGAACAAGGCGTTCACGCTCGAGAAGCCCATGGACCTGAAGAAGGGCGTGAACCACGTCGCCGTCTTGGCATCGTCGATGGGAATGACGgtgggtgtgg ... gttgtttcagGACAGTGGCGCTTACATGGAGCACCGTCTGGCCGGCGTGGACAGGGTGCAGATCACGGGCCTGAACGCGGGCACGCTGGACCTGACGAATAACGGCTGGG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttgagctgaggctgctccatcctgtccgagatatttaatgatgggttgtttcagGACAGTGGCGCTTACATGGAGCACCGTCTGGCCGGCGTGGACAGGGTGCAGATCACGGGCCTGAACGCGGGCACGCTGGACCTGACGAATAACGGCTGGG
                                 atttaat  putative branch site (score: 56)
                                              ttgtttc  putative PPT
                             agatatttaatgat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgggtgtggatatgccgcatcgaaacattactgttcttggttgagctgaggctgctccatcctgtccgagatatttaatgatgggttgtttcagGACAGTGGCGCTTACATGGAGCACCGTCTGGCCGGCGTGGACAGGGTGCAGATCACGGGCCTGAACGCGGGCACGCTGGACCTGACGAATAACGGCTGGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA