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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctgaagaaaagagttacttccttgaagtctatagagttagttattaaggtatattgagtattgcaaactgttactgacatatacttctgctgtgatttagTGTACTCATTAGACCACATCCTGCCATTTGGAGGCTAGTTCATGGGATGGCAGTTGTTTACCTTGTCGCCCTCACTTTCTTGCTTTTCCAG

Basic information

species Zea mays
transcript GRMZM2G110834_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G110834_T02 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os01g02890.1 (Oryza sativa), 3'ss of exon 3
--ctgaagaaaagagttacttccttgaagtctatagagttagttattaaggtatattgagtattgca-aactgttactgacatatacttctgctgtgatttagTGTACTCATTAGACCACATCCTGCCATTTGGAGGCTAGTTCATGGGATGGCAGTTGTTTACCTTGTCGCCCTCACTTTCTTGCTTTTCCAG
   ||| | |  |    | |||||  || | ||   |  |  ||       | | |  | | |||   |||  ||||| | || || || | || ||||| |||||||| |||||||||||||||||||||||| |||| || || ||||||||||||||||||||||| || || ||||| ||||||||||||
aagtgaggcactgttccatttcctaaaaatata---acctcattgggggcttctctgtaattttgtttaacatttacttatatttatttatactatgattcagTGTACTTATTAGACCACATCCTGCCATTTGGCGGCTGGTCCACGGGATGGCAGTTGTTTACCTTGTTGCTCTAACTTTTTTGCTTTTCCAG

upper sequence: GRMZM2G110834_T02 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA20G25830.2 (Glycine max), 3'ss of exon 6
-ctgaagaaaagagttacttccttgaagtctatagagttagttattaaggtatattgagtattgcaaactgttactgacatatacttctgctgtgatttagTGTACTCATTAGACCACATCCTGCCATTTGGAGGCTAGTTCATGGGATGGCAGTTGTTTACCTTGTCGCCCTCACTTTCTTGCTTTTCCAG
  | |  | |  ||||   |  || |  ||    ||  |  |  | ||  |    |    | |   | |||    |    | |  |  || | | ||| || || || ||||| ||||||||||| |||||| |  | |||||||| ||||| ||||| ||||| || |||||||| || |||||||| |||
agtaataatattagttgagttttt-agttcagctgaagttatagtaaattttctcttgagaatattacctgaatatatttttttttcatgttttcattcagGGTTCTTATTAGGCCACATCCTGCAATTTGGCGCTTGGTTCATGGCATGGCTGTTGTATACCTAGTTGCCCTCACATTTTTGCTTTTTCAG

upper sequence: GRMZM2G110834_T02 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA10G41430.1 (Glycine max), 3'ss of exon 4
ctgaagaaaagagttacttccttgaagtctatagagttagttattaaggtatattgagtattgcaaactgttactgacatatacttctgctgtgattt------agTGTACTCATTAGACCACATCCTGCCATTTGGAGGCTAGTTCATGGGATGGCAGTTGTTTACCTTGTCGCCCTCACTTTCTTGCTTTTCCAG
    |||  |    || ||  ||||  | ||        |   ||   ||  |||   | ||| | ||| ||||    ||||  || |  | | ||||      || || || ||||| ||||||||||| |||||| |  | |||||||| ||||| |||||||||||||| |||||||| || |||||||| |||
----agagtaataata-ttagttgagttttagttcagctgaagttgtagtgaattttctcttg-agactattacctgaatatttttttcttattattttcattcagGGTTCTTATTAGGCCACATCCTGCAATTTGGCGCTTGGTTCATGGAATGGCTGTTGTTTACCTTGTTGCCCTCACATTTTTGCTTTTTCAG

upper sequence: GRMZM2G110834_T02 (Zea mays), 3'ss of exon 3
lower sequence: Vv01s0011g04370.t01 (Vitis vinifera), 3'ss of exon 4
--ctga----agaaaagagttacttccttgaagtctatagagttagttattaaggtatattgagtattgcaaactgttactgacatatacttctgctgtgatttagTGTACTCATTAGACCACATCCTGCCATTTGGAGGCTAGTTCATGGGATGGCAGTTGTTTACCTTGTCGCCCTCACTTTCTTGCTTTTCCAG
  ||||    ||||  |  ||      ||||      |  ||||  | |  |       ||  | | || ||| | ||   |   | |  || |  |       || ||||| ||||| |||||||| || |||||| | ||||||||||||||||| ||  ||||||||||    ||||| || ||||||||||||
tgctgacaccagaatgggattttgatgttgatactactgaagttcataaacatttccagttatgcactgtaaaat-ttgtagttgtcttttttttttac-----agGGTACTTATTAGGCCACATCCAGCAATTTGGCGACTAGTTCATGGGATGGCGGTCATTTACCTTGTTTGTCTCACATTTTTGCTTTTCCAG

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|74240999|gb|DT648913.1|DT648913
EST:     GCGATGATTGCTGNNNNNNNGGCTTACTCTTTTCTTCAGGCGCCTTCAAC                         TGTACTCATTAGACCACATCCTGCCATTTGGAGGCTAGTTCATGGGATGGC
genomic: GCGATGATTGCTGTTTTTTTGGCTTACTCTTTTCTTCAGGCGCCTTCAACgtgagttaca ... tgtgatttagTGTACTCATTAGACCACATCCTGCCATTTGGAGGCTAGTTCATGGGATGGC
EST: gi|76910093|gb|DV163697.1|DV163697
EST:     GCGATGATTGCTGNNNNNNNGGCTTACTCTTTTCTTCAGGCGCCTTCAAC                         TGTACTCATTAGACCACATCCTGCCATTTGGAGGCTAGTTCATGGGATGGC
genomic: GCGATGATTGCTGTTTTTTTGGCTTACTCTTTTCTTCAGGCGCCTTCAACgtgagttaca ... tgtgatttagTGTACTCATTAGACCACATCCTGCCATTTGGAGGCTAGTTCATGGGATGGC
EST: gi|211102605|gb|FL400863.1|FL400863
EST:     TTTTTTGGCTTACTCTTTTCTTCAGGCGCCTTCAAC                         TGTACTCATTAGACCACATCCTGCCATTTGGAGGCTAGTTCATGGGATGGC
genomic: TTTTTTGGCTTACTCTTTTCTTCAGGCGCCTTCAACgtgagttaca ... tgtgatttagTGTACTCATTAGACCACATCCTGCCATTTGGAGGCTAGTTCATGGGATGGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaggtatattgagtattgcaaactgttactgacatatacttctgctgtgatttagTGTACTCATTAGACCACATCCTGCCATTTGGAGGCTAGTTCATGGGATGGCAGTTGTTTACCTTGTCGCCCTCACTTTCTTGCTTTTCCAG
                          tactgac  putative branch site (score: 1)
                                      cttctgct  putative PPT
                                 atatactt  TA-rich tract