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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tattagatttccattatcccccgtaaaccaaacacagcctatagatgagctaacaagctttagttctcttgcgtattttcctgatatcgatatgtgttagGCTTTTAACTGGGAATCCAATAAGCACAACTGGTGGAGTATTTTGGAGGAAAAAGTAACCGATCTTGCGGAATCTGGGTTTACGTCAGTGTGGCTTCCTC

Basic information

species Zea mays
transcript GRMZM2G422938_T01
intron # 3
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|149104327|gb|EE289772.2|EE289772
EST:     ATGGAATCATCAAGAATGGAAGGGAAATCCTATTTCAC                         GCTTTTAACTGGGAATCCAATAAGCACAACTGGTGGAGTATTTTGGAGGAA
genomic: ATGGAATCATCAAGAATGGAAGGGAAATCCTATTTCAGgtgagaattt ... tatgtgttagGCTTTTAACTGGGAATCCAATAAGCACAACTGGTGGAGTATTTTGGAGGAA
EST: gi|149089899|gb|EE179185.2|EE179185
EST:     ATGGAATCATCAAGAATGGAAGGGAAATCCTATTTCAG                         GCTTTTAACTGGGAATCCAATAAGCACAACTGGTGGAGTATTTTGGAGGAA
genomic: ATGGAATCATCAAGAATGGAAGGGAAATCCTATTTCAGgtgagaattt ... tatgtgttagGCTTTTAACTGGGAATCCAATAAGCACAACTGGTGGAGTATTTTGGAGGAA
EST: gi|148947022|gb|EC892319.2|EC892319
EST:     ATGGAATCATCAAGAATGGAAGGGAAATCCTATTTCAG                         GCTTTTAACTGGGAATCCAATAAGCACAACTGGTGGAGTATTTTGGAGGAA
genomic: ATGGAATCATCAAGAATGGAAGGGAAATCCTATTTCAGgtgagaattt ... tatgtgttagGCTTTTAACTGGGAATCCAATAAGCACAACTGGTGGAGTATTTTGGAGGAA
EST: gi|211338713|gb|FL158147.1|FL158147
EST:     ATGGAATCATCAAGAATGGAAGGGAAATCCTATTTCAG                         GCTTTTAACTGGGAATCCAATAAGCACAACTGGGTGGAGTATTTTGGAGGA
genomic: ATGGAATCATCAAGAATGGAAGGGAAATCCTATTTCAGgtgagaattt ... tatgtgttagGCTTTTAACTGGGAATCCAATAAGCACAACTGG-TGGAGTATTTTGGAGGA
EST: gi|47962573|gb|CN845282.1|CN845282
EST:     ATGGAATCATCAAGAATGGAAGGGAAATCCTATTTCAG                         GCTTTTAACTGGGAATCCAATAAGCACAACTGGTGGAGTATTTTGGAGGAA
genomic: ATGGAATCATCAAGAATGGAAGGGAAATCCTATTTCAGgtgagaattt ... tatgtgttagGCTTTTAACTGGGAATCCAATAAGCACAACTGGTGGAGTATTTTGGAGGAA
EST: gi|93014248|gb|EB639768.1|EB639768
EST:     ATGGAATCCTCAAGAATGGAAGGGAAATCCCATTTCAG                         GCTTTTAACTGGGAATCCAATAAGCACAACTGGGGGAGTATTTTGGAGGAA
genomic: ATGGAATCATCAAGAATGGAAGGGAAATCCTATTTCAGgtgagaattt ... tatgtgttagGCTTTTAACTGGGAATCCAATAAGCACAACTGGTGGAGTATTTTGGAGGAA
EST: gi|89761789|gb|DY689662.1|DY689662
EST:     ATGGAATCATCAAGAATGGAAGGGAAATCCTATTTCAG                         GCTTTTAACTGGGAATCCAATAAGCACAACTGGTGGAGTATTTTGGAGGAA
genomic: ATGGAATCATCAAGAATGGAAGGGAAATCCTATTTCAGgtgagaattt ... tatgtgttagGCTTTTAACTGGGAATCCAATAAGCACAACTGGTGGAGTATTTTGGAGGAA
EST: gi|91051790|gb|EB162208.1|EB162208
EST:     ATGGAATCATCAAGAATGGAAGGGAAATCCTATTTCAG                         GCTTTTAACTGGGAATCCAATAAGCACAACTGGTGGAGTATTTTGGAGGAA
genomic: ATGGAATCATCAAGAATGGAAGGGAAATCCTATTTCAGgtgagaattt ... tatgtgttagGCTTTTAACTGGGAATCCAATAAGCACAACTGGTGGAGTATTTTGGAGGAA
EST: gi|211372983|gb|FL340766.1|FL340766
EST:     ATGGAATCATCAAGAATGGAAGGGAAATCCTATTTCAG                         GCTTTTTACTGGGAATCCAATAAGCACAACTGGTGGAGTATTTTGGAGGAA
genomic: ATGGAATCATCAAGAATGGAAGGGAAATCCTATTTCAGgtgagaattt ... tatgtgttagGCTTTTAACTGGGAATCCAATAAGCACAACTGGTGGAGTATTTTGGAGGAA
EST: gi|31612368|gb|CD568990.1|CD568990
EST:     ATGGAATCATCAAGAATGGAAGGGAAATCCTATTTCAG                         GCTTTTAACTGGGAATCCAATAAGCACAACTGGTGGAGTATTTTGGAGGAA
genomic: ATGGAATCATCAAGAATGGAAGGGAAATCCTATTTCAGgtgagaattt ... tatgtgttagGCTTTTAACTGGGAATCCAATAAGCACAACTGGTGGAGTATTTTGGAGGAA
EST: gi|50331881|gb|CO527007.1|CO527007
EST:     ATGGAATCATCAAGAATGGAAGGGAAATCCTATTTCAG                         GCTTTTAACTGGGAATCCAATAAGCACAACTGGTGGAGTATTTTGGAGGAA
genomic: ATGGAATCATCAAGAATGGAAGGGAAATCCTATTTCAGgtgagaattt ... tatgtgttagGCTTTTAACTGGGAATCCAATAAGCACAACTGGTGGAGTATTTTGGAGGAA
EST: gi|18166002|gb|BM335841.1|BM335841
EST:     ATGGAATCATCAAGAATGGAAGGGAAATCCTATTTCAG                         GCTTTTAACTGGGAATCCAATAAGCACAACTGG-GGAGT
genomic: ATGGAATCATCAAGAATGGAAGGGAAATCCTATTTCAGgtgagaattt ... tatgtgttagGCTTTTAACTGGGAATCCAATAAGCACAACTGGTGGAGT

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: 36 (upstream exon), 49 (downstream exon)
Score: 79

ATGGAATCATCAAGAATGGAAGGGAAATCCTATTTCAGgtgagaattt ... tatgtgttagGCTTTTAACTGGGAATCCAATAAGCACAACTGGTGGAGTATTTTGGAGGAAAAAGTAACCGATCTTGCGGAATCTGGGTTTACGTCAGTGTGGCTTCCTC


Block sizes: 36 (upstream exon), 48 (downstream exon)
Score: 151

ATGGAATCATCAAGAATGGAAGGGAAATCCTATTTCAGgtgagaattt ... tatgtgttagGCTTTTAACTGGGAATCCAATAAGCACAACTGGTGGAGTATTTTGGAGGAAAAAGTAACCGATCTTGCGGAATCTGGGTTTACGTCAGTGTGGCTTCCTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 154

ATGGAATCATCAAGAATGGAAGGGAAATCCTATTTCAGgtgagaattt ... tatgtgttagGCTTTTAACTGGGAATCCAATAAGCACAACTGGTGGAGTATTTTGGAGGAAAAAGTAACCGATCTTGCGGAATCTGGGTTTACGTCAGTGTGGCTTCCTC


Block sizes: 36 (upstream exon), 49 (downstream exon)
Score: 138

ATGGAATCATCAAGAATGGAAGGGAAATCCTATTTCAGgtgagaattt ... tatgtgttagGCTTTTAACTGGGAATCCAATAAGCACAACTGGTGGAGTATTTTGGAGGAAAAAGTAACCGATCTTGCGGAATCTGGGTTTACGTCAGTGTGGCTTCCTC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgagctaacaagctttagttctcttgcgtattttcctgatatcgatatgtgttagGCTTTTAACTGGGAATCCAATAAGCACAACTGGTGGAGTATTTTGGAGGAAAAAGTAACCGATCTTGCGGAATCTGGGTTTACGTCAGTGTGGCTTCCTC
                            tatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tattagatttccattatcccccgtaaaccaaacacagcctatagatgagctaacaagctttagttctcttgcgtattttcctgatatcgatatgtgttagGCTTTTAACTGGGAATCCAATAAGCACAACTGGTGGAGTATTTTGGAGGAAAAAGTAACCGATCTTGCGGAATCTGGGTTTACGTCAGTGTGGCTTCCTC

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