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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagactagagaattctacctcatttttaatggcaatcttgtgtgcttgctttctgaaatttgttatttttgtatcctgttagTCTACTGCATCTGTTGCACCTCACCTGTGGCAACCTGCAAATGGGATTCTGATGACAAATGACACGAATGATGGCAACCCAGAAGAAGCAACCGCCTGCA

Basic information

species Zea mays
transcript GRMZM2G042992_T01
intron # 19
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|211316880|gb|FL253816.1|FL253816
EST:     TTCATAAGTTGTGGAAATGGCAACGGAGCGACAGAAATCCTAGCGGCAAG                         TCTACTGCATCTGTTGCACCTCACCTGTGGCAACCTGCAAATGGGATTCTG
genomic: TTCATAAGTTGTGGAAATGGCAACGGAGCGACAGAAATCCTAGCGGCAAGgttagactag ... atcctgttagTCTACTGCATCTGTTGCACCTCACCTGTGGCAACCTGCAAATGGGATTCTG
EST: gi|76280738|gb|DV020306.1|DV020306
EST:     TTCATAAGTTGTGGAAATGGCAACGGAGCGACAGAAATCCTAGCGGCAAG                         TCTACTGCATCTGTTGCACCTCACCTGTGGCAACCTGCAAATGGGATTCTG
genomic: TTCATAAGTTGTGGAAATGGCAACGGAGCGACAGAAATCCTAGCGGCAAGgttagactag ... atcctgttagTCTACTGCATCTGTTGCACCTCACCTGTGGCAACCTGCAAATGGGATTCTG
EST: gi|211316878|gb|FL253814.1|FL253814
EST:     TTCATAAGTTGTGGAAATGGCAACGGAGCGACAGAAATCCTAGCGGCAAG                         TCTACTGCATCTGTTGCACCTCACCTGTGGCAACCTGCAAATGGGATTCTG
genomic: TTCATAAGTTGTGGAAATGGCAACGGAGCGACAGAAATCCTAGCGGCAAGgttagactag ... atcctgttagTCTACTGCATCTGTTGCACCTCACCTGTGGCAACCTGCAAATGGGATTCTG
EST: gi|211316882|gb|FL253818.1|FL253818
EST:     TTCATAAGTTGTGGAAATGGCAACGGAGCGACAGAAATCCTAGCGGCAAG                         TCTACTGCATCTGTTGCACCTCACCTGTGGCAACCTGCAAATGGGATTCTG
genomic: TTCATAAGTTGTGGAAATGGCAACGGAGCGACAGAAATCCTAGCGGCAAGgttagactag ... atcctgttagTCTACTGCATCTGTTGCACCTCACCTGTGGCAACCTGCAAATGGGATTCTG
EST: gi|211014474|gb|FL291774.1|FL291774
EST:     TTCATAAGTTGTGGAAATGGCAACGGAGCGACAGAAATCCTAGCGGCAAG                         TCTACTGCATCTGTTGCACCTCACCTGTGGCAACCTGCAAATGGGATTCTG
genomic: TTCATAAGTTGTGGAAATGGCAACGGAGCGACAGAAATCCTAGCGGCAAGgttagactag ... atcctgttagTCTACTGCATCTGTTGCACCTCACCTGTGGCAACCTGCAAATGGGATTCTG
EST: gi|211316883|gb|FL253819.1|FL253819
EST:     TTCATAAGTTGTGGAAATGGCAACGGAGCGACAGAAATCCTAGCGGCAAG                         TCTACTGCATCTGTTGCACCTCACCTGTGGCAACCTGCAAATGGGATTCTG
genomic: TTCATAAGTTGTGGAAATGGCAACGGAGCGACAGAAATCCTAGCGGCAAGgttagactag ... atcctgttagTCTACTGCATCTGTTGCACCTCACCTGTGGCAACCTGCAAATGGGATTCTG
EST: gi|89764406|gb|DY691228.1|DY691228
EST:     GGAGCGACAGAAATCCTAGCGGCAAG                         TCTACTGCATCTGTTGCACCTCACCTGTGGCAACCTGCAAATGGGATTCTG
genomic: GGAGCGACAGAAATCCTAGCGGCAAGgttagactag ... atcctgttagTCTACTGCATCTGTTGCACCTCACCTGTGGCAACCTGCAAATGGGATTCTG
EST: gi|93014018|gb|EB639538.1|EB639538
EST:     TTCATAAGTTGTGGAAATGGCAACGGAGCGACAGAAATCCTAGCGGCAAG                         TCTACTGCATCTGTTGCACCTCACCTGTGGCAACCCTGCAAATGGGATTCT
genomic: TTCATAAGTTGTGGAAATGGCAACGGAGCGACAGAAATCCTAGCGGCAAGgttagactag ... atcctgttagTCTACTGCATCTGTTGCACCTCACCTGTGGCAACC-TGCAAATGGGATTCT
EST: gi|76929334|gb|DV171965.1|DV171965
EST:     TTCATAAGTTGTGGAAATGGCAACGGAGCGACAGAAATCCTAGCGGCAAG                         TCTACTGCATCTGTTGCACCTCACCTGTGGCAACCTGCAAATGGGATTCTG
genomic: TTCATAAGTTGTGGAAATGGCAACGGAGCGACAGAAATCCTAGCGGCAAGgttagactag ... atcctgttagTCTACTGCATCTGTTGCACCTCACCTGTGGCAACCTGCAAATGGGATTCTG
EST: gi|5499066|gb|AI854933.1|AI854933
EST:     TTCATAAGTTGTGGAAATGGCAACGGAGCGACAGAAATCCTAGCGGCAAG                         TCTACTGCATCTGTTGCACCTCACCTGTGGCAACCTGCAAATGGGATTCTG
genomic: TTCATAAGTTGTGGAAATGGCAACGGAGCGACAGAAATCCTAGCGGCAAGgttagactag ... atcctgttagTCTACTGCATCTGTTGCACCTCACCTGTGGCAACCTGCAAATGGGATTCTG
EST: gi|211316881|gb|FL253817.1|FL253817
EST:     TTCATAAGTTGTGGAAATGGCAACGGAGCGACAGAAATCCTAGCGGCAAG                         TCTACTGCATCTGTTGCA
genomic: TTCATAAGTTGTGGAAATGGCAACGGAGCGACAGAAATCCTAGCGGCAAGgttagactag ... atcctgttagTCTACTGCATCTGTTGCA
EST: gi|211316879|gb|FL253815.1|FL253815
EST:     TTCATAAGTTGTGGAAATGGCAACGGAGCGACAGAAATCCTAGCGGCAAG                         TCTACTGCATCTGTTGCACCTCACCTGTGGCAACCTGCAAATGGGATTCTG
genomic: TTCATAAGTTGTGGAAATGGCAACGGAGCGACAGAAATCCTAGCGGCAAGgttagactag ... atcctgttagTCTACTGCATCTGTTGCACCTCACCTGTGGCAACCTGCAAATGGGATTCTG

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), 48 (downstream exon)
Score: 458

GTTATATACAAATAATGGGGTTGCACTCTTGGCTCTTGGCTCCAATGCTGTTCATAAGTTGTGGAAATGGCAACGGAGCGACAGAAATCCTAGCGGCAAGgttagactag ... atcctgttagTCTACTGCATCTGTTGCACCTCACCTGTGGCAACCTGCAAATGGGATTCTGATGACAAATGACACGAATGATGGCAACCCAGAAGAAGCAACCGCCTGCA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 175

GTTATATACAAATAATGGGGTTGCACTCTTGGCTCTTGGCTCCAATGCTGTTCATAAGTTGTGGAAATGGCAACGGAGCGACAGAAATCCTAGCGGCAAGgttagactag ... atcctgttagTCTACTGCATCTGTTGCACCTCACCTGTGGCAACCTGCAAATGGGATTCTGATGACAAATGACACGAATGATGGCAACCCAGAAGAAGCAACCGCCTGCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 204

GTTATATACAAATAATGGGGTTGCACTCTTGGCTCTTGGCTCCAATGCTGTTCATAAGTTGTGGAAATGGCAACGGAGCGACAGAAATCCTAGCGGCAAGgttagactag ... atcctgttagTCTACTGCATCTGTTGCACCTCACCTGTGGCAACCTGCAAATGGGATTCTGATGACAAATGACACGAATGATGGCAACCCAGAAGAAGCAACCGCCTGCA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 174

GTTATATACAAATAATGGGGTTGCACTCTTGGCTCTTGGCTCCAATGCTGTTCATAAGTTGTGGAAATGGCAACGGAGCGACAGAAATCCTAGCGGCAAGgttagactag ... atcctgttagTCTACTGCATCTGTTGCACCTCACCTGTGGCAACCTGCAAATGGGATTCTGATGACAAATGACACGAATGATGGCAACCCAGAAGAAGCAACCGCCTGCA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatggcaatcttgtgtgcttgctttctgaaatttgttatttttgtatcctgttagTCTACTGCATCTGTTGCACCTCACCTGTGGCAACCTGCAAATGGGATTCTGATGACAAATGACACGAATGATGGCAACCCAGAAGAAGCAACCGCCTGCA
 ttttaat  putative branch site (score: 174)
                                              tcctgtt  putative PPT
                      tttctgaaatttgtta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagactagagaattctacctcatttttaatggcaatcttgtgtgcttgctttctgaaatttgttatttttgtatcctgttagTCTACTGCATCTGTTGCACCTCACCTGTGGCAACCTGCAAATGGGATTCTGATGACAAATGACACGAATGATGGCAACCCAGAAGAAGCAACCGCCTGCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA