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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaggatctgtgttcacctcatcagatgttaaatgcttattatgaatccgtgaggctaaagcatgctttcattgtagACCTATATTCTACCTTGCGCGTGCTTTTTAGCAATTCTTAGGAGAAAAGTGAGCTGGCACCAG

Basic information

species Zea mays
transcript GRMZM2G105192_T05
intron # 9
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|16926851|gb|BM079919.1|BM079919
EST:     GACTTGTGATGGCCTTAGTTGGTTCTTTACTTACGATGCTTGTG                         ACCTATATTCTACCTTGCGCGTGCTTTTTAGCAATTCTTAGGAGAAAAGTG
genomic: GACTTGTGATGGCCTTAGTTGGTTCTTTACTTACGATGCTTGTGgtaaggatct ... ttcattgtagACCTATATTCTACCTTGCGCGTGCTTTTTAGCAATTCTTAGGAGAAAAGTG
EST: gi|16922011|gb|BM075387.1|BM075387
EST:     GACTTGTGATGGCCTTAGTTGGTTCTTTACTTACGATGCTTGTG                         ACCTATATTCTACCTTGCGCGTGCTTTTTAGCAATTCTTAGGAGAAAAGTG
genomic: GACTTGTGATGGCCTTAGTTGGTTCTTTACTTACGATGCTTGTGgtaaggatct ... ttcattgtagACCTATATTCTACCTTGCGCGTGCTTTTTAGCAATTCTTAGGAGAAAAGTG
EST: gi|17929411|gb|BM266371.1|BM266371
EST:     GACTTGTGATGGCATTAGTTGGTTCTTTACTTACGATGCTTGTG                         ACCTATATTCTACCTTGCGCGTGCTTTTTAGCAATTCTTAGGAGAAAAGTG
genomic: GACTTGTGATGGCCTTAGTTGGTTCTTTACTTACGATGCTTGTGgtaaggatct ... ttcattgtagACCTATATTCTACCTTGCGCGTGCTTTTTAGCAATTCTTAGGAGAAAAGTG
EST: gi|110220376|gb|EC902274.1|EC902274
EST:     GACTTGGGATGGCCTTAGTTGGTTCTTTACTTACGATGCTTGTG                         ACCTATATTTTACCTTGCGCGTGCTTTTTAGCAATTCTTAGGAGAAAAGTG
genomic: GACTTGTGATGGCCTTAGTTGGTTCTTTACTTACGATGCTTGTGgtaaggatct ... ttcattgtagACCTATATTCTACCTTGCGCGTGCTTTTTAGCAATTCTTAGGAGAAAAGTG
EST: gi|18162838|gb|BM332677.1|BM332677
EST:     GACTTGTGATGGCCTTAGTTGGTTCTTTACTTACGATGCTTGTG                         ACCTATATTCTACCTTGCGCGTGCTTTTTAGCAATTCTTAGGAGAAAAGTG
genomic: GACTTGTGATGGCCTTAGTTGGTTCTTTACTTACGATGCTTGTGgtaaggatct ... ttcattgtagACCTATATTCTACCTTGCGCGTGCTTTTTAGCAATTCTTAGGAGAAAAGTG
EST: gi|29544356|gb|CB604736.1|CB604736
EST:     GACTTGTGATGGCCTTAGTTGGTTCTTTACTTACGATGCTTGTG                         ACCTATATTCTACCTTGCGCGTGCTTTTTAGCAATTCTTAGGAGAAAAGTG
genomic: GACTTGTGATGGCCTTAGTTGGTTCTTTACTTACGATGCTTGTGgtaaggatct ... ttcattgtagACCTATATTCTACCTTGCGCGTGCTTTTTAGCAATTCTTAGGAGAAAAGTG
EST: gi|17932564|gb|BM269524.1|BM269524
EST:     GACTTGTGATGGCCTTAGTTGGTTCTTTACTTACGATGCTTGTG                         ACCTATATTCTACCTTGCGCGTGCTTTTTAGCAATTCTTAGGAGAAAAGTG
genomic: GACTTGTGATGGCCTTAGTTGGTTCTTTACTTACGATGCTTGTGgtaaggatct ... ttcattgtagACCTATATTCTACCTTGCGCGTGCTTTTTAGCAATTCTTAGGAGAAAAGTG
EST: gi|18173199|gb|BM348587.1|BM348587
EST:     GACTTGTGATGGCCTTAGTTGGTTCTTTACTTACGATGCTTGTG                         ACCTATATTCTACCTTGCGCGTGCTTTTTAGCAATTCTTAGGAGAAAAGTG
genomic: GACTTGTGATGGCCTTAGTTGGTTCTTTACTTACGATGCTTGTGgtaaggatct ... ttcattgtagACCTATATTCTACCTTGCGCGTGCTTTTTAGCAATTCTTAGGAGAAAAGTG
EST: gi|113700925|gb|EE678429.1|EE678429
EST:     GACTTGTGATGGCCTTAGTTGGTTCTTTACTTACGATGCTTGTG                         ACCTATATTCTACCTTGCGCGTGCTTTTTAGCAATTCTTAGGAGAAAAGTG
genomic: GACTTGTGATGGCCTTAGTTGGTTCTTTACTTACGATGCTTGTGgtaaggatct ... ttcattgtagACCTATATTCTACCTTGCGCGTGCTTTTTAGCAATTCTTAGGAGAAAAGTG
EST: gi|18166790|gb|BM336629.1|BM336629
EST:     GACTTGTGATGGCCTTAGTTGGTTCTTTACTTACGATGCTTGTG                         ACCTATATTCTACCTTGCGCGTGCTTTTTAGCAATTCTTAGGAGAAAAGTG
genomic: GACTTGTGATGGCCTTAGTTGGTTCTTTACTTACGATGCTTGTGgtaaggatct ... ttcattgtagACCTATATTCTACCTTGCGCGTGCTTTTTAGCAATTCTTAGGAGAAAAGTG
EST: gi|71426676|gb|DR807726.1|DR807726
EST:     GACTTGTGATGGCCTTAGTTGGTTCTTTACTTACGATGCTTGTG                         ACCTATATTCTACCTTGCGCGTGCTTTTTAGCAATTCTTAGGAGAAAAGTG
genomic: GACTTGTGATGGCCTTAGTTGGTTCTTTACTTACGATGCTTGTGgtaaggatct ... ttcattgtagACCTATATTCTACCTTGCGCGTGCTTTTTAGCAATTCTTAGGAGAAAAGTG
EST: gi|67019146|gb|CO447895.1|CO447895
EST:     GACTTTTGATGGCCTTAGTTGGTTCTTTACTTACGATGCTTGTG                         ACCTATATTCTACCTTGCGCGTGCTTTTTAGCAATTCTTAGGAGAAAAGTG
genomic: GACTTGTGATGGCCTTAGTTGGTTCTTTACTTACGATGCTTGTGgtaaggatct ... ttcattgtagACCTATATTCTACCTTGCGCGTGCTTTTTAGCAATTCTTAGGAGAAAAGTG
EST: gi|110522223|gb|EE026407.1|EE026407
EST:     GACTTGTGATGGCCTTAGTTGGTTCTTTACTTACGATGCTTGTG                         ACCTATATTTTACCTTGCGCGTGCTTTTTAGCAATTTTTAGGAGAAAAGTG
genomic: GACTTGTGATGGCCTTAGTTGGTTCTTTACTTACGATGCTTGTGgtaaggatct ... ttcattgtagACCTATATTCTACCTTGCGCGTGCTTTTTAGCAATTCTTAGGAGAAAAGTG
EST: gi|91876287|gb|EB406244.1|EB406244
EST:     GACTTGTGATGGCCTTAGTTGGTTCTTTACTTACGATGCTTGTG                         ACCTATATTTTACCTTGCGCGTGCTTTTTAGCAATTTTTAGGAGAAAAGTG
genomic: GACTTGTGATGGCCTTAGTTGGTTCTTTACTTACGATGCTTGTGgtaaggatct ... ttcattgtagACCTATATTCTACCTTGCGCGTGCTTTTTAGCAATTCTTAGGAGAAAAGTG
EST: gi|76288379|gb|DV027947.1|DV027947
EST:     GACTTGTGATGGCCTTAGTTGGTTCTTTACTTACGATGCTTGTG                         ACCTATATTCTACCTTGCGCGTGCTTTTTAGCAATTCTTAGGAGAAAAGTG
genomic: GACTTGTGATGGCCTTAGTTGGTTCTTTACTTACGATGCTTGTGgtaaggatct ... ttcattgtagACCTATATTCTACCTTGCGCGTGCTTTTTAGCAATTCTTAGGAGAAAAGTG
EST: gi|71446062|gb|DR827112.1|DR827112
EST:     GACTTGTGATGGCCTTAGTTGGTTCTTTACTTACGATGCTTGTG                         ACCTATATTTTACCTTGCGCGTGCTTTTTAGCAATTTTTAGGAGAAAAGTG
genomic: GACTTGTGATGGCCTTAGTTGGTTCTTTACTTACGATGCTTGTGgtaaggatct ... ttcattgtagACCTATATTCTACCTTGCGCGTGCTTTTTAGCAATTCTTAGGAGAAAAGTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cagatgttaaatgcttattatgaatccgtgaggctaaagcatgctttcattgtagACCTATATTCTACCTTGCGCGTGCTTTTTAGCAATTCTTAGGAGAAAAGTGAGCTGGCACCAG
                               ggctaaa  putative branch site (score: 3)
                                           ctttcatt  putative PPT
      ttaaatgcttattat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaggatctgtgttcacctcatcagatgttaaatgcttattatgaatccgtgaggctaaagcatgctttcattgtagACCTATATTCTACCTTGCGCGTGCTTTTTAGCAATTCTTAGGAGAAAAGTGAGCTGGCACCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA