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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatatattacataacttttttattttgaactaagtgacatcactatattttcctatgaaatatagGTACCAGTGGAGGTCGGGCATGGATTGCAACTGGAAGTGAAG

Basic information

species Zea mays
transcript GRMZM2G028307_T02
intron # 12
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|211332968|gb|FL315995.1|FL315995
EST:     GAGCAGCTATTCAAGATTATGTGCCACAGTGGAATCAAGGGACGAAGGAG                         GTACCAGTGGAGGTCGGGCATGGATTGCAACTGGAAGTGAAG
genomic: GAGCAGCTATTCAAGGTTATGTGCCACAGTGGAATCAAGGGACGAAGGAGgtatatatta ... tgaaatatagGTACCAGTGGAGGTCGGGCATGGATTGCAACTGGAAGTGAAG
EST: gi|50328270|gb|CO523396.1|CO523396
EST:     AGTGGAATCAAGGGACGAAGGAG                         GTACCAGTGGAGGTCGGGCATGGATTGCAACTGGAAGTGAAG
genomic: AGTGGAATCAAGGGACGAAGGAGgtatatatta ... tgaaatatagGTACCAGTGGAGGTCGGGCATGGATTGCAACTGGAAGTGAAG
EST: gi|74237283|gb|DT645197.1|DT645197
EST:     GAGCAGCTATTCAAGGTTATGTGCCACAGTGGAATCAAGGGACGAAGGAG                         GTACCAGTGGAGGTCGGGCATGGATTGCAACTGGAAGTGAAG
genomic: GAGCAGCTATTCAAGGTTATGTGCCACAGTGGAATCAAGGGACGAAGGAGgtatatatta ... tgaaatatagGTACCAGTGGAGGTCGGGCATGGATTGCAACTGGAAGTGAAG
EST: gi|211028161|gb|FL322650.1|FL322650
EST:     GAGCAGCTATTCAAGATTATGTGCCACAGTGGAATCAAGGGACGAAGGAG                         GTACCAGTGGAGGTCGGGCATGGATTGCAACTGGAAGTGAAG
genomic: GAGCAGCTATTCAAGGTTATGTGCCACAGTGGAATCAAGGGACGAAGGAGgtatatatta ... tgaaatatagGTACCAGTGGAGGTCGGGCATGGATTGCAACTGGAAGTGAAG
EST: gi|211010841|gb|FL363378.1|FL363378
EST:     GAGCAGCTATTCAAGATTATGTGCCACAGTGGAATCAAGGGACGAAGGAG                         GTACCAGTGGAGGTCGGGCATGGATTGCAACTGGAAGTGAAG
genomic: GAGCAGCTATTCAAGGTTATGTGCCACAGTGGAATCAAGGGACGAAGGAGgtatatatta ... tgaaatatagGTACCAGTGGAGGTCGGGCATGGATTGCAACTGGAAGTGAAG
EST: gi|89760464|gb|DY688865.1|DY688865
EST:     GAGCAGCTATTCAAGGTTATGTGCCACAGTGGAATCAAGGGACGAAGGAG                         GTACCAGTGGAGGTCGGGCATGGATTGCAACTGGAAGTGAAG
genomic: GAGCAGCTATTCAAGGTTATGTGCCACAGTGGAATCAAGGGACGAAGGAGgtatatatta ... tgaaatatagGTACCAGTGGAGGTCGGGCATGGATTGCAACTGGAAGTGAAG
EST: gi|211483893|gb|FL352028.1|FL352028
EST:     GAGCAGCTATTCAAGATTATGTGCCACAGTGGAATCAAGGGACGAAGGAG                         GTACCAGTGGAGGTCGGGCATGGATTGCAACTGGAAGTGAAG
genomic: GAGCAGCTATTCAAGGTTATGTGCCACAGTGGAATCAAGGGACGAAGGAGgtatatatta ... tgaaatatagGTACCAGTGGAGGTCGGGCATGGATTGCAACTGGAAGTGAAG

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: 47 (upstream exon), 42 (downstream exon)
Score: 138

ATGTGGGAGTTAAATGCGAATGGAAATCTTGTGAGCAGCTATTCAAGGTTATGTGCCACAGTGGAATCAAGGGACGAAGGAGgtatatatta ... tgaaatatagGTACCAGTGGAGGTCGGGCATGGATTGCAACTGGAAGTGAAG


Block sizes: 47 (upstream exon), 42 (downstream exon)
Score: 46

ATGTGGGAGTTAAATGCGAATGGAAATCTTGTGAGCAGCTATTCAAGGTTATGTGCCACAGTGGAATCAAGGGACGAAGGAGgtatatatta ... tgaaatatagGTACCAGTGGAGGTCGGGCATGGATTGCAACTGGAAGTGAAG


Block sizes: 49 (upstream exon), 42 (downstream exon)
Score: 46

ATGTGGGAGTTAAATGCGAATGGAAATCTTGTGAGCAGCTATTCAAGGTTATGTGCCACAGTGGAATCAAGGGACGAAGGAGgtatatatta ... tgaaatatagGTACCAGTGGAGGTCGGGCATGGATTGCAACTGGAAGTGAAG


Block sizes: 49 (upstream exon), 42 (downstream exon)
Score: 131

ATGTGGGAGTTAAATGCGAATGGAAATCTTGTGAGCAGCTATTCAAGGTTATGTGCCACAGTGGAATCAAGGGACGAAGGAGgtatatatta ... tgaaatatagGTACCAGTGGAGGTCGGGCATGGATTGCAACTGGAAGTGAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ataacttttttattttgaactaagtgacatcactatattttcctatgaaatatagGTACCAGTGGAGGTCGGGCATGGATTGCAACTGGAAGTGAAG
 acataac  putative branch site (score: 131)
                                     ttttcctat  putative PPT
                                 tatattttcctatgaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatatattacataacttttttattttgaactaagtgacatcactatattttcctatgaaatatagGTACCAGTGGAGGTCGGGCATGGATTGCAACTGGAAGTGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG