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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaatcttttcatggcagtactggaattttcatataaatattgtccctagcaagggccaaatggcaattactgatctcattaagttgtgcagATGCTTCCATTGAAAGTGAGCGTGGTAAGTCTGCCATGTCACCAAGCAGCAGGCCACCTGCAGTGGAAAATGACAAACAGCATGAGGCCAGGGCCATGGC

Basic information

species Zea mays
transcript GRMZM2G059015_T01
intron # 10
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|32924440|gb|CF029252.1|CF029252
EST:     TGGCCGGCAATATGCTACAAAGAATGTTACTGATTCGAACAAATATGAAG                         ATGCTTCCATTGAAGGTGAGCGTGGTAAGTGTGCCATGTCACCAAGCAGCA
genomic: TGGCCGGCAATATACTGCAAAGAATGTTACTGATTCGAACAAATATGAAGgtaaatcttt ... agttgtgcagATGCTTCCATTGAAAGTGAGCGTGGTAAGTCTGCCATGTCACCAAGCAGCA
EST: gi|32923626|gb|CF028438.1|CF028438
EST:     TGGCCGGCAATATACTGCAAAGAATGTTACTGATTCGAACAAATATGAAG                         ATGCTTCCATTGAAGGTGAGCGTGGTAAGTCTGCCATGTCACCAAGCAGCA
genomic: TGGCCGGCAATATACTGCAAAGAATGTTACTGATTCGAACAAATATGAAGgtaaatcttt ... agttgtgcagATGCTTCCATTGAAAGTGAGCGTGGTAAGTCTGCCATGTCACCAAGCAGCA
EST: gi|32923668|gb|CF028480.1|CF028480
EST:     TGGCCGGCAATATACTGCAAAGAATGTTACTGATTCGAACAAATATGAAG                         ATGCTTCCATTGAAGGTGAGCGTGGTAAGTCTGCCATGTCACCAAGCAGCA
genomic: TGGCCGGCAATATACTGCAAAGAATGTTACTGATTCGAACAAATATGAAGgtaaatcttt ... agttgtgcagATGCTTCCATTGAAAGTGAGCGTGGTAAGTCTGCCATGTCACCAAGCAGCA
EST: gi|32924617|gb|CF029429.1|CF029429
EST:     TGGCCGGCAATATACTGCAAAGAATGTTACTGATTCGAACAAATATGAAG                         ATGCTTCCATTGAAGGTGAGCGTGGTAAGTCTGCCATGTCGCCAAGCAGCA
genomic: TGGCCGGCAATATACTGCAAAGAATGTTACTGATTCGAACAAATATGAAGgtaaatcttt ... agttgtgcagATGCTTCCATTGAAAGTGAGCGTGGTAAGTCTGCCATGTCACCAAGCAGCA
EST: gi|32924484|gb|CF029296.1|CF029296
EST:     TGGCCGGCAATATACTACAAAGAATGTTACTGATTCGAACAAATATGAAG                         ATGCTTCCATTGAAGGTGAGCGTGGTAAGTCTGCCATGTCACCAAGCAGCA
genomic: TGGCCGGCAATATACTGCAAAGAATGTTACTGATTCGAACAAATATGAAGgtaaatcttt ... agttgtgcagATGCTTCCATTGAAAGTGAGCGTGGTAAGTCTGCCATGTCACCAAGCAGCA
EST: gi|32923688|gb|CF028500.1|CF028500
EST:     TGGCCGGCAATATACTGTAAAGAATGTTACTGATTCGAACAAATATGAAG                         ATGCTTCCATTGAAGGTGAGCGTGGTAAGTCTGCCATGTCACCAAGCAGCA
genomic: TGGCCGGCAATATACTGCAAAGAATGTTACTGATTCGAACAAATATGAAGgtaaatcttt ... agttgtgcagATGCTTCCATTGAAAGTGAGCGTGGTAAGTCTGCCATGTCACCAAGCAGCA
EST: gi|211139803|gb|FL319394.1|FL319394
EST:     TGGCCGGCAATATACTGCAAAGAATGTTACTGATTCGAACAAATATGAAG                         ATGCTTCCATTGAAAGTGAGCGTGGTAAGTCTGCCATGTCACCAAGCAGCA
genomic: TGGCCGGCAATATACTGCAAAGAATGTTACTGATTCGAACAAATATGAAGgtaaatcttt ... agttgtgcagATGCTTCCATTGAAAGTGAGCGTGGTAAGTCTGCCATGTCACCAAGCAGCA
EST: gi|32924174|gb|CF028986.1|CF028986
EST:     TGGCCGGCAATATACTGCAAAGAATGTTACTGATTCGAACAAATATGAAG                         ATGCTTCCATTGAAGGTGAGCGTGGTAAGTCTGCCATGTCACCAAGCAGCA
genomic: TGGCCGGCAATATACTGCAAAGAATGTTACTGATTCGAACAAATATGAAGgtaaatcttt ... agttgtgcagATGCTTCCATTGAAAGTGAGCGTGGTAAGTCTGCCATGTCACCAAGCAGCA
EST: gi|32924327|gb|CF029139.1|CF029139
EST:     TGGCCGGCAATATACTGCAAAGAATGTTACTGATTCGAACAAATATGAAG                         ATGCTTCCATTGAAGGTGAGCGTGGTAAGTCTGCCATGTCACCAAGCAGCA
genomic: TGGCCGGCAATATACTGCAAAGAATGTTACTGATTCGAACAAATATGAAGgtaaatcttt ... agttgtgcagATGCTTCCATTGAAAGTGAGCGTGGTAAGTCTGCCATGTCACCAAGCAGCA
EST: gi|30591508|gb|CD052408.1|CD052408
EST:     CAATATACTGCAAAGAATGTTACTGATTCGAACAAATATGAAG                         ATGCTTCCATTGAAGGTGAGCGTGGCAAGTCTGCCATGTCACCAAGCAGCA
genomic: CAATATACTGCAAAGAATGTTACTGATTCGAACAAATATGAAGgtaaatcttt ... agttgtgcagATGCTTCCATTGAAAGTGAGCGTGGTAAGTCTGCCATGTCACCAAGCAGCA
EST: gi|87152934|gb|DY397723.1|DY397723
EST:     TGGCCGGCAATATACTGCAAAGAATGTTACTGATTCGAACAAATATGAAG                         ATGCTTCCATTGAAGGTGAGCGTGGTAAGTCTGCCATGTCACCAAGCAGCA
genomic: TGGCCGGCAATATACTGCAAAGAATGTTACTGATTCGAACAAATATGAAGgtaaatcttt ... agttgtgcagATGCTTCCATTGAAAGTGAGCGTGGTAAGTCTGCCATGTCACCAAGCAGCA
EST: gi|5928896|gb|AW056188.1|AW056188
EST:     GTTACTGATTCGAACAAATATGAAG                         ATGCTTCCATTGAAAGTGAGCGTGGTAAGTCTGCCATGTCACCAAGCAGCA
genomic: GTTACTGATTCGAACAAATATGAAGgtaaatcttt ... agttgtgcagATGCTTCCATTGAAAGTGAGCGTGGTAAGTCTGCCATGTCACCAAGCAGCA
EST: gi|32923847|gb|CF028659.1|CF028659
EST:     TGGCCGGCAATATACTGCAAAGAATGTTACTGATTCGAACAAATATGAAG                         ATGCTTCCATTGAAGGTGAGCGTGGTAAGTCTGCCATGTCACCAAGCAGCA
genomic: TGGCCGGCAATATACTGCAAAGAATGTTACTGATTCGAACAAATATGAAGgtaaatcttt ... agttgtgcagATGCTTCCATTGAAAGTGAGCGTGGTAAGTCTGCCATGTCACCAAGCAGCA
EST: gi|19058289|gb|BM736956.1|BM736956
EST:     GATTCGAACAAATATGAAG                         ATGCTTCCATTGAAGGTGAGCGTGGTAAGTCTGCCATGTCACCAAGCAGCA
genomic: GATTCGAACAAATATGAAGgtaaatcttt ... agttgtgcagATGCTTCCATTGAAAGTGAGCGTGGTAAGTCTGCCATGTCACCAAGCAGCA
EST: gi|32923892|gb|CF028704.1|CF028704
EST:     TGGCCGGCAATATACTGCAAAGAATGTTACTGATTCGAACAAATATGAAG                         ATGCTTCCATTGAAGGTGAGCGTGGTAAGTCTGCCATGTCACCAAGCAGCA
genomic: TGGCCGGCAATATACTGCAAAGAATGTTACTGATTCGAACAAATATGAAGgtaaatcttt ... agttgtgcagATGCTTCCATTGAAAGTGAGCGTGGTAAGTCTGCCATGTCACCAAGCAGCA
EST: gi|24766578|gb|CA401727.1|CA401727
EST:     CTGCAAAGAATGTTACTGATTCGAACAAATATGAAG                         ATGCTTCCATTGAAAGTGAGCGTGGTAAGTCTGCCATGTCACCAAGCAGCA
genomic: CTGCAAAGAATGTTACTGATTCGAACAAATATGAAGgtaaatcttt ... agttgtgcagATGCTTCCATTGAAAGTGAGCGTGGTAAGTCTGCCATGTCACCAAGCAGCA
EST: gi|32923769|gb|CF028581.1|CF028581
EST:     TGGCCGGCAATATACTGCAAAGAATGTTACTGATTCGAACAAATATGAAG                         ATGCTTCCATTGAAGGTGAGCGTGGTAAGTCTGCCATGTCACCAAGCAGCA
genomic: TGGCCGGCAATATACTGCAAAGAATGTTACTGATTCGAACAAATATGAAGgtaaatcttt ... agttgtgcagATGCTTCCATTGAAAGTGAGCGTGGTAAGTCTGCCATGTCACCAAGCAGCA

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: 416

AGGAACCTGGTAATTCGTCCAATTGAGCAGTGGTCTTCACGGAGAGAAACTGGCCGGCAATATACTGCAAAGAATGTTACTGATTCGAACAAATATGAAGgtaaatcttt ... agttgtgcagATGCTTCCATTGAAAGTGAGCGTGGTAAGTCTGCCATGTCACCAAGCAGCAGGCCACCTGCAGTGGAAAATGACAAACAGCATGAGGCCAGGGCCATGGC


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 259

AGGAACCTGGTAATTCGTCCAATTGAGCAGTGGTCTTCACGGAGAGAAACTGGCCGGCAATATACTGCAAAGAATGTTACTGATTCGAACAAATATGAAGgtaaatcttt ... agttgtgcagATGCTTCCATTGAAAGTGAGCGTGGTAAGTCTGCCATGTCACCAAGCAGCAGGCCACCTGCAGTGGAAAATGACAAACAGCATGAGGCCAGGGCCATGGC


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 293

AGGAACCTGGTAATTCGTCCAATTGAGCAGTGGTCTTCACGGAGAGAAACTGGCCGGCAATATACTGCAAAGAATGTTACTGATTCGAACAAATATGAAGgtaaatcttt ... agttgtgcagATGCTTCCATTGAAAGTGAGCGTGGTAAGTCTGCCATGTCACCAAGCAGCAGGCCACCTGCAGTGGAAAATGACAAACAGCATGAGGCCAGGGCCATGGC


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 216

AGGAACCTGGTAATTCGTCCAATTGAGCAGTGGTCTTCACGGAGAGAAACTGGCCGGCAATATACTGCAAAGAATGTTACTGATTCGAACAAATATGAAGgtaaatcttt ... agttgtgcagATGCTTCCATTGAAAGTGAGCGTGGTAAGTCTGCCATGTCACCAAGCAGCAGGCCACCTGCAGTGGAAAATGACAAACAGCATGAGGCCAGGGCCATGGC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atattgtccctagcaagggccaaatggcaattactgatctcattaagttgtgcagATGCTTCCATTGAAAGTGAGCGTGGTAAGTCTGCCATGTCACCAAGCAGCAGGCCACCTGCAGTGGAAAATGACAAACAGCATGAGGCCAGGGCCATGGC
                               tactgat  putative branch site (score: 216)
                                         attaagtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaatcttttcatggcagtactggaattttcatataaatattgtccctagcaagggccaaatggcaattactgatctcattaagttgtgcagATGCTTCCATTGAAAGTGAGCGTGGTAAGTCTGCCATGTCACCAAGCAGCAGGCCACCTGCAGTGGAAAATGACAAACAGCATGAGGCCAGGGCCATGGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA