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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatctttgtcatgtctgtgtgagcaactgagcatgcacaaggggattcacacaactaatttgactattggtgcatccgtgtagGTTGATCCAAGGAAGTTTGGTTTGCTAGCGAACTGGCAGCGGGACTACACGATGGAGAACATCCTCACCCAGCTCAAGAAAGAGATGGCTGCCTCGCAGA

Basic information

species Zea mays
transcript GRMZM2G071010_T02
intron # 2
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|33092413|gb|CF052407.1|CF052407
EST:     GATTCCACTCAAGAATCAACATGACATGCGTTAATCCCGAGACAGGAATG                         GTTGATCCAAGGAAGTTTGGTTTGCTAGCGAACTGGCAGCGGGACTACACG
genomic: GATTCCACTCAAGAATCAACATGACATGCGTTAATCACGAGACAGGAATGgtaatctttg ... atccgtgtagGTTGATCCAAGGAAGTTTGGTTTGCTAGCGAACTGGCAGCGGGACTACACG
EST: gi|32805334|gb|CD957570.1|CD957570
EST:     TAATTACGAGACAGGAATG                         GTTGATCCAAGGAAGTTTGGTTTGCTAGCGAACTGGCAGCGGGACTACACG
genomic: TAATCACGAGACAGGAATGgtaatctttg ... atccgtgtagGTTGATCCAAGGAAGTTTGGTTTGCTAGCGAACTGGCAGCGGGACTACACG
EST: gi|32908045|gb|CF012858.1|CF012858
EST:     GATTCCACTCAAGAATCAACATGACATGCGTTAATCACGAGACAGGAATG                         GTTGATCCAAGGAAGTTTGGTTTGCTAGCGAACTGGCAGCGGGACTACACG
genomic: GATTCCACTCAAGAATCAACATGACATGCGTTAATCACGAGACAGGAATGgtaatctttg ... atccgtgtagGTTGATCCAAGGAAGTTTGGTTTGCTAGCGAACTGGCAGCGGGACTACACG
EST: gi|5650118|gb|AI920478.1|AI920478
EST:     GATTCCACTCAAGAATCAACATGACATGCGTTAATCNCGAGACAGGAATG                         GTTGATCCAAGGAAGTTTGGTTTGCTAGCGAACTGGCAGCGGGGCTACNCG
genomic: GATTCCACTCAAGAATCAACATGACATGCGTTAATCACGAGACAGGAATGgtaatctttg ... atccgtgtagGTTGATCCAAGGAAGTTTGGTTTGCTAGCGAACTGGCAGCGGGACTACACG
EST: gi|5895802|gb|AW037048.1|AW037048
EST:     AACATGACATGCGTTAATCACGAGACAGGAGTG                         GGTGATCCAAGGAAGTTTGGTTTGCTAGCGAACTGGCAGCGGGACTACACG
genomic: AACATGACATGCGTTAATCACGAGACAGGAATGgtaatctttg ... atccgtgtagGTTGATCCAAGGAAGTTTGGTTTGCTAGCGAACTGGCAGCGGGACTACACG
EST: gi|93013912|gb|EB639432.1|EB639432
EST:     GATTCCACTCAAGAATCAACATGACATGCGTTAATCACGAGACAGGAATG                         GTTGATCCAAGGAAGTTTGGTTTGCTAGCGAACTGGCAGCGGGACTACACG
genomic: GATTCCACTCAAGAATCAACATGACATGCGTTAATCACGAGACAGGAATGgtaatctttg ... atccgtgtagGTTGATCCAAGGAAGTTTGGTTTGCTAGCGAACTGGCAGCGGGACTACACG

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: 753

GCTGAAGTTGTTTTGTGACAAGGACTATCCGGAGAAGCCACCATCTGTCAGATTCCACTCAAGAATCAACATGACATGCGTTAATCACGAGACAGGAATGgtaatctttg ... atccgtgtagGTTGATCCAAGGAAGTTTGGTTTGCTAGCGAACTGGCAGCGGGACTACACGATGGAGAACATCCTCACCCAGCTCAAGAAAGAGATGGCTGCCTCGCAGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1005

GCTGAAGTTGTTTTGTGACAAGGACTATCCGGAGAAGCCACCATCTGTCAGATTCCACTCAAGAATCAACATGACATGCGTTAATCACGAGACAGGAATGgtaatctttg ... atccgtgtagGTTGATCCAAGGAAGTTTGGTTTGCTAGCGAACTGGCAGCGGGACTACACGATGGAGAACATCCTCACCCAGCTCAAGAAAGAGATGGCTGCCTCGCAGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1113

GCTGAAGTTGTTTTGTGACAAGGACTATCCGGAGAAGCCACCATCTGTCAGATTCCACTCAAGAATCAACATGACATGCGTTAATCACGAGACAGGAATGgtaatctttg ... atccgtgtagGTTGATCCAAGGAAGTTTGGTTTGCTAGCGAACTGGCAGCGGGACTACACGATGGAGAACATCCTCACCCAGCTCAAGAAAGAGATGGCTGCCTCGCAGA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 642

GCTGAAGTTGTTTTGTGACAAGGACTATCCGGAGAAGCCACCATCTGTCAGATTCCACTCAAGAATCAACATGACATGCGTTAATCACGAGACAGGAATGgtaatctttg ... atccgtgtagGTTGATCCAAGGAAGTTTGGTTTGCTAGCGAACTGGCAGCGGGACTACACGATGGAGAACATCCTCACCCAGCTCAAGAAAGAGATGGCTGCCTCGCAGA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gagcatgcacaaggggattcacacaactaatttgactattggtgcatccgtgtagGTTGATCCAAGGAAGTTTGGTTTGCTAGCGAACTGGCAGCGGGACTACACGATGGAGAACATCCTCACCCAGCTCAAGAAAGAGATGGCTGCCTCGCAGA
                        aactaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatctttgtcatgtctgtgtgagcaactgagcatgcacaaggggattcacacaactaatttgactattggtgcatccgtgtagGTTGATCCAAGGAAGTTTGGTTTGCTAGCGAACTGGCAGCGGGACTACACGATGGAGAACATCCTCACCCAGCTCAAGAAAGAGATGGCTGCCTCGCAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG