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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATGCCGCCAAGGGTGGGGATGATGAGGATGATGACCTAGAGgtcagcattgcaccttcatattcttcatgggccattacgtttcatatatgcagctcaaatgatctaataaataaattgtacatgtatcggtctcag

Basic information

species Zea mays
transcript GRMZM2G358059_T01
intron # 12
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|148931875|gb|EC877339.2|EC877339
EST:     GATGCCGCCAAGGGTGGGGATGATGAGGATGATGACCTAGAG                         GATGAGGAAGACGATGAGAAGGCAGACGAGGACAAGGCCGACTCTGATGCC
genomic: GATGCCGCCAAGGGTGGGGATGATGAGGATGATGACCTAGAGgtcagcattg ... tcggtctcagGATGAGGAAGACGATGAGAAGGCAGACGAGGACAAGGCCGACTCTGATGCC
EST: gi|84980101|gb|DW530450.1|DW530450
EST:     GATGCCGCCAAGGGTGGGGATGATGAGGATGATGACCTAGAG                         GATGAGGAAGACGATGAGAAGGCAGACGAGGACAAGGCCGACTCTGATGCC
genomic: GATGCCGCCAAGGGTGGGGATGATGAGGATGATGACCTAGAGgtcagcattg ... tcggtctcagGATGAGGAAGACGATGAGAAGGCAGACGAGGACAAGGCCGACTCTGATGCC
EST: gi|86467986|gb|DY234356.1|DY234356
EST:     GATGCCGCCAAGGGTGGGGATGATGAGGATGATGACCTAGAG                         GATGAGGAAGACGATGAGAAGGCAGACGAGGACAAGGCCGACTCTGATGCC
genomic: GATGCCGCCAAGGGTGGGGATGATGAGGATGATGACCTAGAGgtcagcattg ... tcggtctcagGATGAGGAAGACGATGAGAAGGCAGACGAGGACAAGGCCGACTCTGATGCC
EST: gi|149074502|gb|EE162898.2|EE162898
EST:     GATGCCGCCAAGGGTGGGGATGATGAGGATGATGACCTAGAG                         GATGAGGAAGACGATGAGAAGGCAGACGAGGACAAGGCCGACTCTGATGCC
genomic: GATGCCGCCAAGGGTGGGGATGATGAGGATGATGACCTAGAGgtcagcattg ... tcggtctcagGATGAGGAAGACGATGAGAAGGCAGACGAGGACAAGGCCGACTCTGATGCC
EST: gi|14190892|gb|BG833122.1|BG833122
EST:     GATGCCGCCAAGGGCTGGGGATGATGAGGATGATGACCTAGAG                         GATGCAGGAAGACGATGAGAAGGCAGACGAGGCACAAGGCCGACTCTGATG
genomic: GATGCCGCCAAGGG-TGGGGATGATGAGGATGATGACCTAGAGgtcagcattg ... tcggtctcagGATG-AGGAAGACGATGAGAAGGCAGACGAGG-ACAAGGCCGACTCTGATG
EST: gi|7162446|gb|AW520068.1|AW520068
EST:     GATGCCGCCAAGGGTGGGGATGATGAGGATGATGACCTAGAG                         GATGAGGAAGACGATGAGAAGGCAGACGAGGACAAGGCCGACTCTGATGCC
genomic: GATGCCGCCAAGGGTGGGGATGATGAGGATGATGACCTAGAGgtcagcattg ... tcggtctcagGATGAGGAAGACGATGAGAAGGCAGACGAGGACAAGGCCGACTCTGATGCC
EST: gi|14190894|gb|BG833124.1|BG833124
EST:     GATGCCGCCAAGGGTGGGGATGATGAGGATGATGACCTAGAG                         GATGAGGAAGACGATGAGAAGGCAGACGAGGACAAGGCCGACTCTGATGCC
genomic: GATGCCGCCAAGGGTGGGGATGATGAGGATGATGACCTAGAGgtcagcattg ... tcggtctcagGATGAGGAAGACGATGAGAAGGCAGACGAGGACAAGGCCGACTCTGATGCC
EST: gi|37377946|gb|CF625620.1|CF625620
EST:     GATGCCGCCAAGGGTGGGGATGATGAGGATGATGACCTAGAG                         GATGAGGAAGACGATGAGAAGGCAGACGAGGACAAGGCCGACTCTGATGCC
genomic: GATGCCGCCAAGGGTGGGGATGATGAGGATGATGACCTAGAGgtcagcattg ... tcggtctcagGATGAGGAAGACGATGAGAAGGCAGACGAGGACAAGGCCGACTCTGATGCC
EST: gi|33096251|gb|CF056245.1|CF056245
EST:     GATGCCGCCAAGGGTGGGGATGATGAGGATGATGACCTAGAG                         GATGAGGAAGACGATGAGAAGGCAGACGAGGACAAGGCCGACTCT
genomic: GATGCCGCCAAGGGTGGGGATGATGAGGATGATGACCTAGAGgtcagcattg ... tcggtctcagGATGAGGAAGACGATGAGAAGGCAGACGAGGACAAGGCCGACTCT
EST: gi|149074540|gb|EE162939.2|EE162939
EST:     GATGCCGCCAAGGGTGGGGATGATGAGGATGATGACCTAGAG                         GATGAGGAAGACGATGAGAAGGCAGACGAGGACAAGGCCGACTCTGATGCC
genomic: GATGCCGCCAAGGGTGGGGATGATGAGGATGATGACCTAGAGgtcagcattg ... tcggtctcagGATGAGGAAGACGATGAGAAGGCAGACGAGGACAAGGCCGACTCTGATGCC
EST: gi|86470502|gb|DY236872.1|DY236872
EST:     GATGCCGCCAAGGGTGGGGATGATGAGGATGATGACCTAGAG                         GATGAGGAAGACGATGAGAAGGCAGACGAGGACAAGGCCGACTCTGATGCC
genomic: GATGCCGCCAAGGGTGGGGATGATGAGGATGATGACCTAGAGgtcagcattg ... tcggtctcagGATGAGGAAGACGATGAGAAGGCAGACGAGGACAAGGCCGACTCTGATGCC
EST: gi|71442155|gb|DR823205.1|DR823205
EST:     GATGCCGCCAAGGGTGGGGATGATGAGGATGATGACCTAGAG                         GATGAGGAAGACGATGAGAAGGCAGACGAGGACAAGGCCGACTCTGATGCC
genomic: GATGCCGCCAAGGGTGGGGATGATGAGGATGATGACCTAGAGgtcagcattg ... tcggtctcagGATGAGGAAGACGATGAGAAGGCAGACGAGGACAAGGCCGACTCTGATGCC
EST: gi|37374548|gb|CF623645.1|CF623645
EST:     GATGCCGCCAAGGGTGGGGATGATGAGGATGATGACCTAGAG                         GATGAGGAAGACGATGAGAAGGCAGACGAGGACAAGGCCGACTCTGATGCC
genomic: GATGCCGCCAAGGGTGGGGATGATGAGGATGATGACCTAGAGgtcagcattg ... tcggtctcagGATGAGGAAGACGATGAGAAGGCAGACGAGGACAAGGCCGACTCTGATGCC
EST: gi|14190893|gb|BG833123.1|BG833123
EST:     GATGCCGCCAAGGGTGGGGATGATGAGGATGATGACCTAGAG                         GATGAGGAAGACGATGAGAAGGCAGACGAGGACAAGGCCGACTCTG
genomic: GATGCCGCCAAGGGTGGGGATGATGAGGATGATGACCTAGAGgtcagcattg ... tcggtctcagGATGAGGAAGACGATGAGAAGGCAGACGAGGACAAGGCCGACTCTG
EST: gi|84980095|gb|DW530444.1|DW530444
EST:     GATGCCGCCAAGGGTGGGGATGATGAGGATGATGACCTAGAG                         GATGAGGAAGACGATGAGAAGGCAGACGAGGACAAGGCCGACTCTGATGCC
genomic: GATGCCGCCAAGGGTGGGGATGATGAGGATGATGACCTAGAGgtcagcattg ... tcggtctcagGATGAGGAAGACGATGAGAAGGCAGACGAGGACAAGGCCGACTCTGATGCC
EST: gi|15590491|gb|BI675107.1|BI675107
EST:     GATGCCGCCAAGGGTGGGGATGATGAGGATGATGACCTAGAG                         GATGAGGAAGACGATGAGAAGGCAGACGAGGACAAGGCCGACTCTGATGCC
genomic: GATGCCGCCAAGGGTGGGGATGATGAGGATGATGACCTAGAGgtcagcattg ... tcggtctcagGATGAGGAAGACGATGAGAAGGCAGACGAGGACAAGGCCGACTCTGATGCC
EST: gi|166646465|gb|EG211254.1|EG211254
EST:     CGCCAAGGGTGGGGATGATGAGGATGATGACCTAGAG                         GATGAGGAAGACGATGAGAAGGCAGACGAGGACAAGGCCGACTCTGATGCC
genomic: CGCCAAGGGTGGGGATGATGAGGATGATGACCTAGAGgtcagcattg ... tcggtctcagGATGAGGAAGACGATGAGAAGGCAGACGAGGACAAGGCCGACTCTGATGCC
EST: gi|5268655|gb|AI770619.1|AI770619
EST:     GATGCCGCCAAGGGTGGGGATGATGAGGATGATGACCTAGAG                         GATGAGGAAGACGATGAGAAGGCAGACGAGGACCAGGCCGACTCTGATGCC
genomic: GATGCCGCCAAGGGTGGGGATGATGAGGATGATGACCTAGAGgtcagcattg ... tcggtctcagGATGAGGAAGACGATGAGAAGGCAGACGAGGACAAGGCCGACTCTGATGCC
EST: gi|33093443|gb|CF053437.1|CF053437
EST:     GATGCCGCCAAGGGTGGGGATGATGAGGATGATGACCTAGAG                         GATGAGGAAGACGATGAGAAGGCAGACGAGGACAAGGCCGACTCTGATGCC
genomic: GATGCCGCCAAGGGTGGGGATGATGAGGATGATGACCTAGAGgtcagcattg ... tcggtctcagGATGAGGAAGACGATGAGAAGGCAGACGAGGACAAGGCCGACTCTGATGCC
EST: gi|148937046|gb|EC881219.2|EC881219
EST:     GATGCCGCCAAGGGTGGGGATGATGAGGATGATGACCTAGAG                         GATGAGGAAGACGATGAGAAGGCAGACGAGGACAAGGCCGACTCTGATGCC
genomic: GATGCCGCCAAGGGTGGGGATGATGAGGATGATGACCTAGAGgtcagcattg ... tcggtctcagGATGAGGAAGACGATGAGAAGGCAGACGAGGACAAGGCCGACTCTGATGCC
EST: gi|211100469|gb|FL191950.1|FL191950
EST:     GATGCCGCCAAGGGTGGGGATGATGAGGATGATGACCTAGAG                         GATGAGGAAGACGATGAGAAGGCAGACGAGGACAAGG
genomic: GATGCCGCCAAGGGTGGGGATGATGAGGATGATGACCTAGAGgtcagcattg ... tcggtctcagGATGAGGAAGACGATGAGAAGGCAGACGAGGACAAGG
EST: gi|84980708|gb|DW531057.1|DW531057
EST:     GATGCCGCCAAGGGTGGGGATGATGAGGATGATGACCTAGAG                         GATGAGGAAGACGATGAGAAGGCAGACGAGGACAAGGCCGACTCTGATGCC
genomic: GATGCCGCCAAGGGTGGGGATGATGAGGATGATGACCTAGAGgtcagcattg ... tcggtctcagGATGAGGAAGACGATGAGAAGGCAGACGAGGACAAGGCCGACTCTGATGCC
EST: gi|29544799|gb|CB605407.1|CB605407
EST:     GATGCCGCCAAGGGTGGGGATGATGAGGATGATGACCTAGAG                         GATGAGGAAGACGATGAGAAGGCAGACGAGGACAAGGCCGACTCTGATGCC
genomic: GATGCCGCCAAGGGTGGGGATGATGAGGATGATGACCTAGAGgtcagcattg ... tcggtctcagGATGAGGAAGACGATGAGAAGGCAGACGAGGACAAGGCCGACTCTGATGCC
EST: gi|113615087|gb|DW779890.1|DW779890
EST:     ATGACCTAGAG                         GATGAGGAAGACGATGAGAAGGCAGACGAGGACAAGGCCGACTCTGATGCC
genomic: ATGACCTAGAGgtcagcattg ... tcggtctcagGATGAGGAAGACGATGAGAAGGCAGACGAGGACAAGGCCGACTCTGATGCC
EST: gi|37382092|gb|CF627969.1|CF627969
EST:     GATGCCGCCAAGGGTGGGGATGATGAGGATGATGACCTAGAG                         GATGAGGAAGACGATGAGAAGGCAGACGAGGACAAGGCCGACTCTGATGCC
genomic: GATGCCGCCAAGGGTGGGGATGATGAGGATGATGACCTAGAGgtcagcattg ... tcggtctcagGATGAGGAAGACGATGAGAAGGCAGACGAGGACAAGGCCGACTCTGATGCC
EST: gi|88750940|gb|DY535081.1|DY535081
EST:     GATGCCGCCAAGGGTGGGGATGATGAGGATGATGACCTAGAG                         GATGAGGAAGACGATGAGAAGGCAGACGAGGACAAGGCCGACTCTGATGCC
genomic: GATGCCGCCAAGGGTGGGGATGATGAGGATGATGACCTAGAGgtcagcattg ... tcggtctcagGATGAGGAAGACGATGAGAAGGCAGACGAGGACAAGGCCGACTCTGATGCC
EST: gi|71759740|gb|DR957677.1|DR957677
EST:     GATGCCGCCAAGGGTGGGGATGATGAGGATGATGACCTAGAG                         GATGAGGAAGACGATGAGAAGGCAGACGAGGACAAGGCCGACTCTGATGCC
genomic: GATGCCGCCAAGGGTGGGGATGATGAGGATGATGACCTAGAGgtcagcattg ... tcggtctcagGATGAGGAAGACGATGAGAAGGCAGACGAGGACAAGGCCGACTCTGATGCC
EST: gi|7162466|gb|AW520088.1|AW520088
EST:     GATGCCGCCAAGGGTGGGGATGATGAGGATGATGACCTAGAG                         GATGAGGAAGACGATGAGAAGGCAGACGAGGACAAGGCCGACTCTGATGCC
genomic: GATGCCGCCAAGGGTGGGGATGATGAGGATGATGACCTAGAGgtcagcattg ... tcggtctcagGATGAGGAAGACGATGAGAAGGCAGACGAGGACAAGGCCGACTCTGATGCC
EST: gi|148963936|gb|EE015057.2|EE015057
EST:     GATGCCGCCAAGGGTGGGGATGATGAGGATGATGACCTAGAG                         GATGAGGAAGACGATGAGAAGGCAGACGAGGACAAGGCCGACTCTGATGCC
genomic: GATGCCGCCAAGGGTGGGGATGATGAGGATGATGACCTAGAGgtcagcattg ... tcggtctcagGATGAGGAAGACGATGAGAAGGCAGACGAGGACAAGGCCGACTCTGATGCC
EST: gi|71432522|gb|DR813572.1|DR813572
EST:     GATGCCGCCAAGGGTGGGGATGATGAGGATGATGACCTAGAG                         GATGAGGAAGACGATGAGAAGGCAGACGAGGACAAGGCCGACTCTGATGCC
genomic: GATGCCGCCAAGGGTGGGGATGATGAGGATGATGACCTAGAGgtcagcattg ... tcggtctcagGATGAGGAAGACGATGAGAAGGCAGACGAGGACAAGGCCGACTCTGATGCC

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: 2227

GATGCCGCCAAGGGTGGGGATGATGAGGATGATGACCTAGAGgtcagcattg ... tcggtctcagGATGAGGAAGACGATGAGAAGGCAGACGAGGACAAGGCCGACTCTGATGCCGAGGATGGCAAGGATTCTGATGATGAGAAGCAC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1313

GATGCCGCCAAGGGTGGGGATGATGAGGATGATGACCTAGAGgtcagcattg ... tcggtctcagGATGAGGAAGACGATGAGAAGGCAGACGAGGACAAGGCCGACTCTGATGCCGAGGATGGCAAGGATTCTGATGATGAGAAGCAC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1141

GATGCCGCCAAGGGTGGGGATGATGAGGATGATGACCTAGAGgtcagcattg ... tcggtctcagGATGAGGAAGACGATGAGAAGGCAGACGAGGACAAGGCCGACTCTGATGCCGAGGATGGCAAGGATTCTGATGATGAGAAGCAC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 6620

GATGCCGCCAAGGGTGGGGATGATGAGGATGATGACCTAGAGgtcagcattg ... tcggtctcagGATGAGGAAGACGATGAGAAGGCAGACGAGGACAAGGCCGACTCTGATGCCGAGGATGGCAAGGATTCTGATGATGAGAAGCAC


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GATGCCGCCAAGGGTGGGGATGATGAGGATGATGACCTAGAGgtcagcattgcaccttcatattcttcatgggccattacgtttcatatatgcagctcaaatgatctaataaataaattgtacatgtatcggtctcag

- - - - - - - - - - - - GAGGAT
- - - - - - - - - - - -  AGGATG