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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagttcatgctatgtactactagatggatgctgttgctttaattctagcgacatggtaatccttcttgcctggttgttccatgcacgtagGACATGAAGACAAGGGAGAAGGAGCTTCTGGCCAAGGAGGCCGAGCTGAACAGGCGTGAGAAG

Basic information

species Zea mays
transcript GRMZM2G011078_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G011078_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os03g38590.1 (Oryza sativa), 3'ss of exon 3
-gtagttca-tgctatgtactactagatggatgctgttgctttaattctagcgacatggtaatccttcttgcctggttgttccatgca-cgtagGACATGAAGACAAGGGAGAAGGAGCTTCTGGCCAAGGAGGCCGAGCTGAACAGGCGTGAGAAG
  || | || | || || |  |   |||| |   ||||  || |  |    |   |  |||||  | | ||| || |   |      |   ||||| ||||| |||||||||||||| ||||| || ||||| |||||||| |||||||| ||||||
gttactacactactctgaatgatgtgatgaaa--tgttatttgacatgattcccaaaagtaatt-tacctgcgtgttaaatatgcataatatagGATATGAAAACAAGGGAGAAGGAACTTCTTGCAAAGGAAGCCGAGCTAAACAGGCGAGAGAAG
















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|76927248|gb|DV171197.1|DV171197
EST:     TCTACAACGACTTCGCTACCCCAGTGGATATCCCCATGGACACAAACAAG                         GACATGAAGACAAGGGAGAAGGAGCTTCTGGCCAAGGAGGCCGAGCTGAAC
genomic: TCTACAACGACTTCGCTACCCCAGTGGATATCCCCATGGACACAAACAAGgtagttcatg ... atgcacgtagGACATGAAGACAAGGGAGAAGGAGCTTCTGGCCAAGGAGGCCGAGCTGAAC
EST: gi|76280658|gb|DV020226.1|DV020226
EST:     TCTACAACGACTTCGCTACCCCAGTGGATATCCCCATGGACACAAACAAG                         GACATGAAGACAAGGGAGAAGGAGCTTCTGGCCAAGGAGGCCGAGCTGAAC
genomic: TCTACAACGACTTCGCTACCCCAGTGGATATCCCCATGGACACAAACAAGgtagttcatg ... atgcacgtagGACATGAAGACAAGGGAGAAGGAGCTTCTGGCCAAGGAGGCCGAGCTGAAC
EST: gi|71440939|gb|DR821989.1|DR821989
EST:     TCTACAACGACTTCGCTACCCCAGTGGATATCCCCATGGACACAAACAAG                         GACATGAAGACAAGGGAGAAGGAGCTTCTGGCCAAGGAGGGCGAGCTGAAC
genomic: TCTACAACGACTTCGCTACCCCAGTGGATATCCCCATGGACACAAACAAGgtagttcatg ... atgcacgtagGACATGAAGACAAGGGAGAAGGAGCTTCTGGCCAAGGAGGCCGAGCTGAAC
EST: gi|76282431|gb|DV021999.1|DV021999
EST:     TCTACAACGACTTCGCTACCCCAGTGGATATCCCCATGGACACAAACAAG                         GACATGAAGACAAGGGAGAAGGAGCTTCTGGCCAAGGAGGCCGAGCTGAAC
genomic: TCTACAACGACTTCGCTACCCCAGTGGATATCCCCATGGACACAAACAAGgtagttcatg ... atgcacgtagGACATGAAGACAAGGGAGAAGGAGCTTCTGGCCAAGGAGGCCGAGCTGAAC
EST: gi|78092064|gb|DV520438.1|DV520438
EST:     TCTACAACGACTTCGCTACCCCAGTGGATATCCCCATGGACACAAACAAG                         GACATGAAGACAAGGGAGAAGGAGCTTCTGGCCAAGGAGGCCGAGCTGAAC
genomic: TCTACAACGACTTCGCTACCCCAGTGGATATCCCCATGGACACAAACAAGgtagttcatg ... atgcacgtagGACATGAAGACAAGGGAGAAGGAGCTTCTGGCCAAGGAGGCCGAGCTGAAC
EST: gi|89760517|gb|DY688893.1|DY688893
EST:     TCTACAACGACTTCGCTACCCCAGTGGATATCCCCATGGACACAAACAAG                         GACATGAAGACAAGGGAGAAGGAGCTTCTGGCCAAGGAGGCCGAGCTGAAC
genomic: TCTACAACGACTTCGCTACCCCAGTGGATATCCCCATGGACACAAACAAGgtagttcatg ... atgcacgtagGACATGAAGACAAGGGAGAAGGAGCTTCTGGCCAAGGAGGCCGAGCTGAAC
EST: gi|78080153|gb|DV508565.1|DV508565
EST:     TCTACAACGACTTCGCTACCCCAGTGGATATCCCCATGGACACAAACAAG                         GACATGAAGACAAGGGAGAAGGAGCTTCTGGCCAAGGAGGCCGAGCTGAAC
genomic: TCTACAACGACTTCGCTACCCCAGTGGATATCCCCATGGACACAAACAAGgtagttcatg ... atgcacgtagGACATGAAGACAAGGGAGAAGGAGCTTCTGGCCAAGGAGGCCGAGCTGAAC
EST: gi|76928466|gb|DV171634.1|DV171634
EST:     TCTACAACGACTTCGCTACCCCGGTGGATATCCCCATGGACACAAACAAG                         GACATGAAGACAAGGGAGAAGGAGCTTCTGGCCAAGGAGGCCGAGCTGAAC
genomic: TCTACAACGACTTCGCTACCCCAGTGGATATCCCCATGGACACAAACAAGgtagttcatg ... atgcacgtagGACATGAAGACAAGGGAGAAGGAGCTTCTGGCCAAGGAGGCCGAGCTGAAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gctttaattctagcgacatggtaatccttcttgcctggttgttccatgcacgtagGACATGAAGACAAGGGAGAAGGAGCTTCTGGCCAAGGAGGCCGAGCTGAACAGGCGTGAGAAG
 ctttaat  putative branch site (score: 4)
     aattcta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtagttcatgctatgtactactagatggatgctgttgctttaattctagcgacatggtaatccttcttgcctggttgttccatgcacgtagGACATGAAGACAAGGGAGAAGGAGCTTCTGGCCAAGGAGGCCGAGCTGAACAGGCGTGAGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA