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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gcaagttgcttcattttttaactcataagtacttttcatatattgtggtctagtctggtcatattatgctactataagcagGAACTGTTGACAAGGCATAAAGCAACCGTGGCTGAATTTCTCTCCAACAATTATGATTGG

Basic information

species Zea mays
transcript GRMZM2G066051_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G066051_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os07g39630.1 (Oryza sativa), 3'ss of exon 5
-----------------gcaagttgcttcat-tttttaactcataagtacttttcatatat-tgtggtctagtctggtcatattatgctactataagcagGAACTGTTGACAAGGCATAAAGCAACCGTGGCTGAATTTCTCTCCAACAATTATGATTGG
                      |||  | || ||||| |  |    || | |||   |||  |||  ||| || || |||||||    ||||  || ||||||||  |||||||||||||||| |||||||| |||||||| || || |||||||| |||
gtgcaggagcacacttgctttcttggctaatatttttcatccccttgttcctttttcatacgtgtcttcttgtgtgatcatattgatttactcaaaacagGAACTTCTGACAAGGCATAAAGCTACCGTGGCAGAATTTCTGTCAAAGAATTATGACTGG
















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|37401622|gb|CF638179.1|CF638179
EST:     TCCAGTTTCCAAATTTTGACATAGCTTTTGATGCTTCGGCTACCTTTAAG                         GAACTGTTGACAAGGCATAAAGCAACCGTGGCTGAATTTCTCTCCAACAAT
genomic: TACAGCTTCCAAATTTTGACATAGCTTCTGATGCTTCGGCTACCTTTAAGgcaagttgct ... ctataagcagGAACTGTTGACAAGGCATAAAGCAACCGTGGCTGAATTTCTCTCCAACAAT
EST: gi|18660671|gb|BM500986.1|BM500986
EST:     TACAGCTTCCAAATTTTGACATAGCTTCTGATGCTTCGGCTACCTTTAAG                         GAACTGTTGACAAGGCATAAAGCAACCGTGGCTGAATTTCTCTCCAACAAT
genomic: TACAGCTTCCAAATTTTGACATAGCTTCTGATGCTTCGGCTACCTTTAAGgcaagttgct ... ctataagcagGAACTGTTGACAAGGCATAAAGCAACCGTGGCTGAATTTCTCTCCAACAAT
EST: gi|148999213|gb|EE036132.2|EE036132
EST:     TACAGCTTCCAAATTTTGACATAGCTTCTGATGCTTCGGCTACCTTTAAG                         GAACTGTTGACAAGGCATAAAGCAACCGTGGCTGAATTTCTCTCCAACAAT
genomic: TACAGCTTCCAAATTTTGACATAGCTTCTGATGCTTCGGCTACCTTTAAGgcaagttgct ... ctataagcagGAACTGTTGACAAGGCATAAAGCAACCGTGGCTGAATTTCTCTCCAACAAT
EST: gi|149082295|gb|EE171480.2|EE171480
EST:     AGCTTCCAAATTTTGACATAGCTTCTGATGCTTCGGCTACCTTTAAG                         GAACTGTTGACAAGGCATAAAGCAACCGTGGCTGAATTTCTCTCCAACAAT
genomic: AGCTTCCAAATTTTGACATAGCTTCTGATGCTTCGGCTACCTTTAAGgcaagttgct ... ctataagcagGAACTGTTGACAAGGCATAAAGCAACCGTGGCTGAATTTCTCTCCAACAAT
EST: gi|7844268|gb|AW787490.1|AW787490
EST:     TACAGCTTCCAAATTTTGACATAGCTTCTGATGCTTCGGCTACCTTTAAG                         GAACTGTTGACAAGGCATAAAGCAACCGTGGCTGAATTTCTCTCCAACAAT
genomic: TACAGCTTCCAAATTTTGACATAGCTTCTGATGCTTCGGCTACCTTTAAGgcaagttgct ... ctataagcagGAACTGTTGACAAGGCATAAAGCAACCGTGGCTGAATTTCTCTCCAACAAT
EST: gi|6194845|gb|AW146949.1|AW146949
EST:     TACAGCTTCCAAATTTTGACATAGCTTCTGATGCTTCGGCTACCTTTAAG                         GAACTGTTGACAAGGCATAAAGCAACCGNGGCTGAATTTCTATCCAACAAT
genomic: TACAGCTTCCAAATTTTGACATAGCTTCTGATGCTTCGGCTACCTTTAAGgcaagttgct ... ctataagcagGAACTGTTGACAAGGCATAAAGCAACCGTGGCTGAATTTCTCTCCAACAAT
EST: gi|111192096|gb|EE290232.1|EE290232
EST:     TACAGCTTCCAAATTTTGACATAGCTTCTGATGCTTCGGCTACCTTTAAG                         GAACTGTTGACAAGGCATAAAGCAACCGTGGCTGAATTTCTCTCCAACAAT
genomic: TACAGCTTCCAAATTTTGACATAGCTTCTGATGCTTCGGCTACCTTTAAGgcaagttgct ... ctataagcagGAACTGTTGACAAGGCATAAAGCAACCGTGGCTGAATTTCTCTCCAACAAT
EST: gi|71328881|gb|DR801123.1|DR801123
EST:     TACAGCTTCCAAATTTTGACATAGCTTCTGATGCTTCGGCTACCTTTAAG                         GAACTGTTGACAAGGCATAAAGCAACCGTGGC
genomic: TACAGCTTCCAAATTTTGACATAGCTTCTGATGCTTCGGCTACCTTTAAGgcaagttgct ... ctataagcagGAACTGTTGACAAGGCATAAAGCAACCGTGGC
EST: gi|31354689|gb|CD439046.1|CD439046
EST:     TACAGCTTCCAAATTTTGACATAGCTTCTGATGCTTCGGCTACCTTTAAG                         GAACTGTTGGACA-GGCATAAAGCA
genomic: TACAGCTTCCAAATTTTGACATAGCTTCTGATGCTTCGGCTACCTTTAAGgcaagttgct ... ctataagcagGAACTGTTG-ACAAGGCATAAAGCA
EST: gi|149041351|gb|EE046989.2|EE046989
EST:     TACAGCTTCCAAATTTTGACATAGCTTCTGATGCTTCGGCTACCTTTAAG                         GAACTGTTGACAAGGCATAAAGCAACCGTGGCTGAATTTCTCTCCAACAAT
genomic: TACAGCTTCCAAATTTTGACATAGCTTCTGATGCTTCGGCTACCTTTAAGgcaagttgct ... ctataagcagGAACTGTTGACAAGGCATAAAGCAACCGTGGCTGAATTTCTCTCCAACAAT
EST: gi|78107218|gb|DV525636.1|DV525636
EST:     TACAGCTTCCAAATTTTGACATAGCTTCTGATGCTTCGGCTACCTTTAAG                         GAACTGTTGACAAGGCATAAAGCAACCGTGGCTGAATTTCTCTCCAACAAT
genomic: TACAGCTTCCAAATTTTGACATAGCTTCTGATGCTTCGGCTACCTTTAAGgcaagttgct ... ctataagcagGAACTGTTGACAAGGCATAAAGCAACCGTGGCTGAATTTCTCTCCAACAAT
EST: gi|33467028|gb|CF244077.1|CF244077
EST:     GATGCTTCGGCTCCCTTTAAG                         GAACTGTTGACAAGGCATAAAGCAACCGTGGCTGAATTTCTCTCCAACAAT
genomic: GATGCTTCGGCTACCTTTAAGgcaagttgct ... ctataagcagGAACTGTTGACAAGGCATAAAGCAACCGTGGCTGAATTTCTCTCCAACAAT
EST: gi|32856027|gb|CD995708.1|CD995708
EST:     TACAGCTTCCAAATTTTGACATAGCTTCTGATGCTTCGGCTACCTTTAAG                         GAACTGTTGACAAGGCATAAAGCA
genomic: TACAGCTTCCAAATTTTGACATAGCTTCTGATGCTTCGGCTACCTTTAAGgcaagttgct ... ctataagcagGAACTGTTGACAAGGCATAAAGCA
EST: gi|60354560|gb|DN221533.1|DN221533
EST:     TACAGCTTCCAAATTTTGACATAGCTTCTGATGCTTCGGCTACCTTTAAG                         GAACTGTTGACAAGGCATAAAGCAACCGTGGCTGAATTTCTCTCCAACAAT
genomic: TACAGCTTCCAAATTTTGACATAGCTTCTGATGCTTCGGCTACCTTTAAGgcaagttgct ... ctataagcagGAACTGTTGACAAGGCATAAAGCAACCGTGGCTGAATTTCTCTCCAACAAT
EST: gi|5895944|gb|AW037190.1|AW037190
EST:     TACAGCTTCCAAATTTTGACATAGCTTCTGATGCTTCGGCTACCTTTAAG                         GAACTGTTGACAAGGCATAAAGCAACCGTGGCTGAATTTCTCTCCAACAAT
genomic: TACAGCTTCCAAATTTTGACATAGCTTCTGATGCTTCGGCTACCTTTAAGgcaagttgct ... ctataagcagGAACTGTTGACAAGGCATAAAGCAACCGTGGCTGAATTTCTCTCCAACAAT
EST: gi|6022524|gb|AW067557.1|AW067557
EST:     TACAGCTTCCAAATTTTGACATAGCTTCTGATGCTTCGGCTACCTTTAAG                         GAACTGTTGACAAGGCATAAAGCA
genomic: TACAGCTTCCAAATTTTGACATAGCTTCTGATGCTTCGGCTACCTTTAAGgcaagttgct ... ctataagcagGAACTGTTGACAAGGCATAAAGCA
EST: gi|6445388|gb|AW179351.1|AW179351
EST:     TACAGCTTCCAAATTTTGACATAGCTTCTGATGCTTCGGCTACCTTTAAG                         GAACTGTTGACAAGGCATAAAGCAACCGTGGCTGAATTTCTCTCCAACAAT
genomic: TACAGCTTCCAAATTTTGACATAGCTTCTGATGCTTCGGCTACCTTTAAGgcaagttgct ... ctataagcagGAACTGTTGACAAGGCATAAAGCAACCGTGGCTGAATTTCTCTCCAACAAT
EST: gi|6056599|gb|AW091004.1|AW091004
EST:     TACAGCTTCCAAATTTTGACATAGCTTCTGATGCTTCGGCTACCTTTAAG                         GAACTGTTGACAAGGCATAAAGCAACCGTGGCTGAATTTCTCTCCAACAAT
genomic: TACAGCTTCCAAATTTTGACATAGCTTCTGATGCTTCGGCTACCTTTAAGgcaagttgct ... ctataagcagGAACTGTTGACAAGGCATAAAGCAACCGTGGCTGAATTTCTCTCCAACAAT
EST: gi|5525422|gb|AI861315.1|AI861315
EST:     GATGCTTCGGCTACCTTTAAG                         GAACTGTTG-CAAGGCATAAAGCAACCGTGGCTGAATTTCTCTCCAACAAT
genomic: GATGCTTCGGCTACCTTTAAGgcaagttgct ... ctataagcagGAACTGTTGACAAGGCATAAAGCAACCGTGGCTGAATTTCTCTCCAACAAT
EST: gi|60350125|gb|DN217098.1|DN217098
EST:     TACAGCTTCCAAATTTTGACATAGCTTCTGATGCTTCGGCTACCTTTAAG                         GAACTGTTGACAAGGCATAAAGCAACCGTGGCTGAATTTCTCTCCAACAAT
genomic: TACAGCTTCCAAATTTTGACATAGCTTCTGATGCTTCGGCTACCTTTAAGgcaagttgct ... ctataagcagGAACTGTTGACAAGGCATAAAGCAACCGTGGCTGAATTTCTCTCCAACAAT
EST: gi|211020659|gb|FL429513.1|FL429513
EST:     TACAGCTTCCAAATTTTGACATAGCTTCTGATGCTTCGGCTACCTTTAAG                         GAACTGTTGACAAGGCATAAAGCAACCGTGGCTGAATTTCTCTCCAACAAT
genomic: TACAGCTTCCAAATTTTGACATAGCTTCTGATGCTTCGGCTACCTTTAAGgcaagttgct ... ctataagcagGAACTGTTGACAAGGCATAAAGCAACCGTGGCTGAATTTCTCTCCAACAAT
EST: gi|71328879|gb|DR801122.1|DR801122
EST:     TACAGCTTCCAAATTTTGACATAGCTTCTGATGCTTCGGCTACCTTTAAG                         GAACTGTTGACAAGGCATAAAGCAACCGTGGCTGAATTTCTCTCCAACAAT
genomic: TACAGCTTCCAAATTTTGACATAGCTTCTGATGCTTCGGCTACCTTTAAGgcaagttgct ... ctataagcagGAACTGTTGACAAGGCATAAAGCAACCGTGGCTGAATTTCTCTCCAACAAT

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: 48 (upstream exon), 49 (downstream exon)
Score: 199

GTATGTTTTAGAGTCTGAACACATGAAGAAGTTCTTTGACTATATACAGCTTCCAAATTTTGACATAGCTTCTGATGCTTCGGCTACCTTTAAGgcaagttgct ... ctataagcagGAACTGTTGACAAGGCATAAAGCAACCGTGGCTGAATTTCTCTCCAACAATTATGATTGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 227

GTATGTTTTAGAGTCTGAACACATGAAGAAGTTCTTTGACTATATACAGCTTCCAAATTTTGACATAGCTTCTGATGCTTCGGCTACCTTTAAGgcaagttgct ... ctataagcagGAACTGTTGACAAGGCATAAAGCAACCGTGGCTGAATTTCTCTCCAACAATTATGATTGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 200

GTATGTTTTAGAGTCTGAACACATGAAGAAGTTCTTTGACTATATACAGCTTCCAAATTTTGACATAGCTTCTGATGCTTCGGCTACCTTTAAGgcaagttgct ... ctataagcagGAACTGTTGACAAGGCATAAAGCAACCGTGGCTGAATTTCTCTCCAACAATTATGATTGG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 210

GTATGTTTTAGAGTCTGAACACATGAAGAAGTTCTTTGACTATATACAGCTTCCAAATTTTGACATAGCTTCTGATGCTTCGGCTACCTTTAAGgcaagttgct ... ctataagcagGAACTGTTGACAAGGCATAAAGCAACCGTGGCTGAATTTCTCTCCAACAATTATGATTGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aagtacttttcatatattgtggtctagtctggtcatattatgctactataagcagGAACTGTTGACAAGGCATAAAGCAACCGTGGCTGAATTTCTCTCCAACAATTATGATTGG
      ttttcatatattgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcaagttgcttcattttttaactcataagtacttttcatatattgtggtctagtctggtcatattatgctactataagcagGAACTGTTGACAAGGCATAAAGCAACCGTGGCTGAATTTCTCTCCAACAATTATGATTGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA