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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAAACATGCAGTACACAACAAGAACAGATTCGGACATTTCAAAAGCAGCTTGCAGTTGCGACTGAGAAGTTGAAGgttagaagttgaagcatatgctactagcgttctttatgtctttacaaatatatgcactgttccattatttggcatctcaaaactgatacacttattcaattgtgcag

Basic information

species Zea mays
transcript GRMZM2G114861_T01
intron # 7
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|22520949|gb|BU079760.1|BU079760
EST:     AGATTCGGACATTTCAAAAGCAGC-TGCAGTTGCGACTGAGAAGTTGAAG                         CTTGCTGATGTAACTGCGATAGAGGCGATGACTGGATATGAAGAACAGAAG
genomic: AGATTCGGACATTTCAAAAGCAGCTTGCAGTTGCGACTGAGAAGTTGAAGgttagaagtt ... aattgtgcagCTTGCTGATGTAACTGCGATAGAGGCGATGACTGGTTATGAAGAACAGAAG
EST: gi|13198508|gb|BG354356.1|BG354356
EST:     AGATTCGGACATTTCAAAAGCAGCTTGCAGTTGCGACTGAGAAGTTGAAG                         CTTGCTGATGTAACTGCGCATAGAGGCGATGACTGGTTATGAAGAACAGAA
genomic: AGATTCGGACATTTCAAAAGCAGCTTGCAGTTGCGACTGAGAAGTTGAAGgttagaagtt ... aattgtgcagCTTGCTGATGTAACTGCG-ATAGAGGCGATGACTGGTTATGAAGAACAGAA
EST: gi|87155658|gb|DY400447.1|DY400447
EST:     AGATTCGGACATTTCAAAAGCAGCTTGCAGTTGCGACTGAGAAGTTGAAG                         CTTGCTGATGTAACTGCGATAGAGGCGATGACTGGATATGAAGAACAGAAG
genomic: AGATTCGGACATTTCAAAAGCAGCTTGCAGTTGCGACTGAGAAGTTGAAGgttagaagtt ... aattgtgcagCTTGCTGATGTAACTGCGATAGAGGCGATGACTGGTTATGAAGAACAGAAG
EST: gi|32942682|gb|CF047501.1|CF047501
EST:     AGATTCGGACATTTCAAAAGCAGCTTGCAGTTGCGACTGAGAAGTTGAAG                         CTTGCTGATGTAACTGCGATAGAGGCGATGACTGGTTATGAAGAACAGAAG
genomic: AGATTCGGACATTTCAAAAGCAGCTTGCAGTTGCGACTGAGAAGTTGAAGgttagaagtt ... aattgtgcagCTTGCTGATGTAACTGCGATAGAGGCGATGACTGGTTATGAAGAACAGAAG
EST: gi|32942760|gb|CF047579.1|CF047579
EST:     AGATTCGGACATTTCAAAAGCAGCTTGTAGTTGCGACTGAGAAGTTGAAG                         CTTGCTGATGTAACTGCGATAGAGGCGATGACTGGTTATGAAGAACAGAAG
genomic: AGATTCGGACATTTCAAAAGCAGCTTGCAGTTGCGACTGAGAAGTTGAAGgttagaagtt ... aattgtgcagCTTGCTGATGTAACTGCGATAGAGGCGATGACTGGTTATGAAGAACAGAAG
EST: gi|32928735|gb|CF033547.1|CF033547
EST:     AGATTCGGACATTTCAAAAGCAGCTTGCAGTTGCGACTGAGAAGTTGAAG                         CTTGCTGATGTAACTGCGATAGAGGCGATGACTGGTTATGAAGAACGGAAG
genomic: AGATTCGGACATTTCAAAAGCAGCTTGCAGTTGCGACTGAGAAGTTGAAGgttagaagtt ... aattgtgcagCTTGCTGATGTAACTGCGATAGAGGCGATGACTGGTTATGAAGAACAGAAG
EST: gi|26559172|gb|CA831407.1|CA831407
EST:     AGATTCGGACATTTCAAAAGCAGCTTGCAGTTGCGACTGAGAAGTTGAAG                         CTTGCTGATGTAACTGCGATAGAGGCGATGACTGGATATGAAGAACAGAAG
genomic: AGATTCGGACATTTCAAAAGCAGCTTGCAGTTGCGACTGAGAAGTTGAAGgttagaagtt ... aattgtgcagCTTGCTGATGTAACTGCGATAGAGGCGATGACTGGTTATGAAGAACAGAAG

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: 123

GAAACATGCAGTACACAACAAGAACAGATTCGGACATTTCAAAAGCAGCTTGCAGTTGCGACTGAGAAGTTGAAGgttagaagtt ... aattgtgcagCTTGCTGATGTAACTGCGATAGAGGCGATGACTGGTTATGAAGAACAGAAGGAGAAAATAAAATACCTTGAGGAGCGTTTAGCACAGGCAGAGTCTCAAA


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 48

GAAACATGCAGTACACAACAAGAACAGATTCGGACATTTCAAAAGCAGCTTGCAGTTGCGACTGAGAAGTTGAAGgttagaagtt ... aattgtgcagCTTGCTGATGTAACTGCGATAGAGGCGATGACTGGTTATGAAGAACAGAAGGAGAAAATAAAATACCTTGAGGAGCGTTTAGCACAGGCAGAGTCTCAAA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 41

GAAACATGCAGTACACAACAAGAACAGATTCGGACATTTCAAAAGCAGCTTGCAGTTGCGACTGAGAAGTTGAAGgttagaagtt ... aattgtgcagCTTGCTGATGTAACTGCGATAGAGGCGATGACTGGTTATGAAGAACAGAAGGAGAAAATAAAATACCTTGAGGAGCGTTTAGCACAGGCAGAGTCTCAAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 216

GAAACATGCAGTACACAACAAGAACAGATTCGGACATTTCAAAAGCAGCTTGCAGTTGCGACTGAGAAGTTGAAGgttagaagtt ... aattgtgcagCTTGCTGATGTAACTGCGATAGAGGCGATGACTGGTTATGAAGAACAGAAGGAGAAAATAAAATACCTTGAGGAGCGTTTAGCACAGGCAGAGTCTCAAA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAAACATGCAGTACACAACAAGAACAGATTCGGACATTTCAAAAGCAGCTTGCAGTTGCGACTGAGAAGTTGAAGgttagaagttgaagcatatgctactagcgttctttatgtctttacaaatatatgcactgttccattatttggcatctcaaaactgatacacttattcaattgtgcag

- - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG