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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gcggaggagagctacgggtccggcgggtacggctctggctacggcggtcagacccggccggaggagagctatgggtcagcagggtatggatctgccaatccgcaggctgagacatacggctctggctacgggaggaagccacagGTAGAGGAGAGCTACGGATCGGAGTATGGGTCTGGGTTCGGGAGGAAGCCGCAGATTGAGGAGAGCTATGGATCGGGGTACGGGAGGACGCCGCAGGTTG

Basic information

species Zea mays
transcript GRMZM2G701082_T05
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|211080379|gb|FL084284.1|FL084284
EST:     AGAAGCAGGAGGAGGAGAGCTACGGCTCTGGATATGGGAGGAAACCGCAG                         GCGGAGGAGAGCTACGG
genomic: AGAAGCAGGAGGAGGAGAGCTACGGCTCTGGATATGGGAGGAAACCGCAGgcggaggaga ... gaagccacagGTAGAGGAGAGCTACGG
EST: gi|149037208|gb|EE155294.2|EE155294
EST:     AGAAGCAGGAGGAGGAGAGCTACGGCTCTGGATATGGGAGGAAACCGCAG                         GTAGAGGAGAGCTACGGATCGGAGTATGGGTCTGGGTTCGGGAGGAAGCCG
genomic: AGAAGCAGGAGGAGGAGAGCTACGGCTCTGGATATGGGAGGAAACCGCAGgcggaggaga ... gaagccacagGTAGAGGAGAGCTACGGATCGGAGTATGGGTCTGGGTTCGGGAGGAAGCCG
EST: gi|211077653|gb|FL084280.1|FL084280
EST:     AGAAGCAGGAGGAGGAGAGCTACGGCTCTGGATATGGGAGGAAACCGCAG                         GCGGAGGAGAGCTACGG
genomic: AGAAGCAGGAGGAGGAGAGCTACGGCTCTGGATATGGGAGGAAACCGCAGgcggaggaga ... gaagccacagGTAGAGGAGAGCTACGG
EST: gi|211080383|gb|FL084288.1|FL084288
EST:     AGAAGCAGGAGGAGGAGAGCTACGGCTCTGGATATGGGAGGAAACCGCAG                         GCGGARGAGAGCTACGG
genomic: AGAAGCAGGAGGAGGAGAGCTACGGCTCTGGATATGGGAGGAAACCGCAGgcggaggaga ... gaagccacagGTAGAGGAGAGCTACGG
EST: gi|71441598|gb|DR822648.1|DR822648
EST:     GGAGGAAGCCACAG                         GTAGAGGAGAGCTACGGATCGGAGTATGGGTCTGGGTTCGGGAGGAAGCCG
genomic: GGAGGAAACCGCAGgcggaggaga ... gaagccacagGTAGAGGAGAGCTACGGATCGGAGTATGGGTCTGGGTTCGGGAGGAAGCCG
EST: gi|211080386|gb|FL084291.1|FL084291
EST:     AGAAGCAGGAGGAGGAGAGCTACGGCTCTGGATATGGGAGGAAACCGCAG                         GCGGAGGAGAGCTACGG
genomic: AGAAGCAGGAGGAGGAGAGCTACGGCTCTGGATATGGGAGGAAACCGCAGgcggaggaga ... gaagccacagGTAGAGGAGAGCTACGG
EST: gi|211080388|gb|FL084293.1|FL084293
EST:     AGAAGCAGGAGGAGGAGAGCTACGGCTCTGGATATGGGAGGAAACCGCAG                         GCGGAGGAGAGCTACGGGTCGG
genomic: AGAAGCAGGAGGAGGAGAGCTACGGCTCTGGATATGGGAGGAAACCGCAGgcggaggaga ... gaagccacagGTAGAGGAGAGCTACGGATCGG
EST: gi|211080378|gb|FL084283.1|FL084283
EST:     AGAAGCAAGAGGAGGAGAGCTACGGCTCTGGATATGGGAGGAAACCGCAG                         GCGGAGGAGAGCTA
genomic: AGAAGCAGGAGGAGGAGAGCTACGGCTCTGGATATGGGAGGAAACCGCAGgcggaggaga ... gaagccacagGTAGAGGAGAGCTA

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: 418

GGAGGAGGGCGGTGGCTATGGATCTGGCTTCGGATCCGGGTATGGGAGGAAGAAGCAGGAGGAGGAGAGCTACGGCTCTGGATATGGGAGGAAACCGCAGgcggaggaga ... gaagccacagGTAGAGGAGAGCTACGGATCGGAGTATGGGTCTGGGTTCGGGAGGAAGCCGCAGATTGAGGAGAGCTATGGATCGGGGTACGGGAGGACGCCGCAGGTTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 788

GGAGGAGGGCGGTGGCTATGGATCTGGCTTCGGATCCGGGTATGGGAGGAAGAAGCAGGAGGAGGAGAGCTACGGCTCTGGATATGGGAGGAAACCGCAGgcggaggaga ... gaagccacagGTAGAGGAGAGCTACGGATCGGAGTATGGGTCTGGGTTCGGGAGGAAGCCGCAGATTGAGGAGAGCTATGGATCGGGGTACGGGAGGACGCCGCAGGTTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1021

GGAGGAGGGCGGTGGCTATGGATCTGGCTTCGGATCCGGGTATGGGAGGAAGAAGCAGGAGGAGGAGAGCTACGGCTCTGGATATGGGAGGAAACCGCAGgcggaggaga ... gaagccacagGTAGAGGAGAGCTACGGATCGGAGTATGGGTCTGGGTTCGGGAGGAAGCCGCAGATTGAGGAGAGCTATGGATCGGGGTACGGGAGGACGCCGCAGGTTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 560

GGAGGAGGGCGGTGGCTATGGATCTGGCTTCGGATCCGGGTATGGGAGGAAGAAGCAGGAGGAGGAGAGCTACGGCTCTGGATATGGGAGGAAACCGCAGgcggaggaga ... gaagccacagGTAGAGGAGAGCTACGGATCGGAGTATGGGTCTGGGTTCGGGAGGAAGCCGCAGATTGAGGAGAGCTATGGATCGGGGTACGGGAGGACGCCGCAGGTTG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcggaggagagctacgggtccggcgggtacggctctggctacggcggtcagacccggccggaggagagctatgggtcagcagggtatggatctgccaatccgcaggctgagacatacggctctggctacgggaggaagccacagGTAGAGGAGAGCTACGGATCGGAGTATGGGTCTGGGTTCGGGAGGAAGCCGCAGATTGAGGAGAGCTATGGATCGGGGTACGGGAGGACGCCGCAGGTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA