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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaacttggtcgttctcgctttgtttcgccagttcgtagcttggcattgtggtgtctggctggtgttgaagttttgtggaaccgtgaattcagGCTGCTCCCGTGTTCACCTTTGCCAACCAAGCCGGCCTGGACATGCTGGAGACGACGCTGATTGCGCTCCAGGACATCTCCCTTGAGAAGATCCTTGATG

Basic information

species Zea mays
transcript GRMZM2G423337_T01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G423337_T01 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os03g43930.2 (Oryza sativa), 3'ss of exon 16
-gtaacttggtcgttctcgctttgtt-tcgccagttcgtagcttggcattgtggt-gtct-ggctggtgttgaagttttg--tggaaccgtgaattcagGCTGCTCCCGTGTTCACCTTTGCCAACCAAGCCGGCCTGGACATGCTGGAGACGACGCTGATTGCGCTCCAGGACATCTCCCTTGAGAAGATCCTTGATG
   |   ||||    ||   | | || ||||   | | ||  ||  |||||  ||  ||| ||||       || || ||  |    |     |||||||||||||| ||||||||||| ||||||||||||||||| |||||||||||||||||||||||||| |||||||||||||| || ||||||||||||||||
gtcagtgtggtgcgcctttttgtattgtcgctgatacata--tttacattgccgttatctaggctaacaaacaaattctggctactgcttaccattcagGCTGCTCCTGTGTTCACCTTCGCCAACCAAGCCGGCCTCGACATGCTGGAGACGACGCTGATTGCTCTCCAGGACATCTCGCTCGAGAAGATCCTTGATG

upper sequence: GRMZM2G423337_T01 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os03g43930.1 (Oryza sativa), 3'ss of exon 16
gtaacttggtcgttctcgctttgtttcgccagttcgtagcttggcattgtggt-gtct-ggctggtgttgaagttttgtggaaccgtga--attcagGCTGCTCCCGTGTTCACCTTTGCCAACCAAGCCGGCCTGGACATGCTGGAGACGACGCTGATTGCGCTCCAGGACATCTCCCTTGAGAAGATCCTTGATG
      ||  | || | |  ||||  |||   | | ||  ||  |||||  ||  ||| ||||       || || ||   |    | |  |||||||||||||| ||||||||||| ||||||||||||||||| |||||||||||||||||||||||||| |||||||||||||| || ||||||||||||||||
-----gtgcgcctttttgtattgt--cgctgatacata--tttacattgccgttatctaggctaacaaacaaattctggctactgcttaccattcagGCTGCTCCTGTGTTCACCTTCGCCAACCAAGCCGGCCTCGACATGCTGGAGACGACGCTGATTGCTCTCCAGGACATCTCGCTCGAGAAGATCCTTGATG
















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|60347903|gb|DN214876.1|DN214876
EST:     TGAAAGCGCTGTGGCAACACTCGGACTCGATCATGTGCTGTTCCCTGAAG                         GCTGCTCCCGTGTTCACCTTTGCCAACCAAGCCGGCCTGGACATGCTGGAG
genomic: TGAAAGCGCTGTGGCAACACTCGGACTCGATCATGTGCTGTTCCCTGAAGgtaacttggt ... gtgaattcagGCTGCTCCCGTGTTCACCTTTGCCAACCAAGCCGGCCTGGACATGCTGGAG
EST: gi|76912511|gb|DV164768.1|DV164768
EST:     TGAAAGCGCTGTGGCAACACTCGGACTCGATCATGTGCTGTTCCCTGAAG                         GCTGCTCCCGTGTTCACCTTTGCCAACCAAGCCGGCCTGGACATGCTGGAG
genomic: TGAAAGCGCTGTGGCAACACTCGGACTCGATCATGTGCTGTTCCCTGAAGgtaacttggt ... gtgaattcagGCTGCTCCCGTGTTCACCTTTGCCAACCAAGCCGGCCTGGACATGCTGGAG
EST: gi|71764261|gb|DR962198.1|DR962198
EST:     TGAAAGCGCTGTGGCAACACTCGGACTCGATCATGTGCTGTTCCCTGAAG                         GCTGCTCCCGTGTTCACCTTTGCCAACCAAGCCGGCCTGGACATGCTGGAG
genomic: TGAAAGCGCTGTGGCAACACTCGGACTCGATCATGTGCTGTTCCCTGAAGgtaacttggt ... gtgaattcagGCTGCTCCCGTGTTCACCTTTGCCAACCAAGCCGGCCTGGACATGCTGGAG
EST: gi|71298034|gb|DR784986.1|DR784986
EST:     TGAAAGCGCTGTGGCAACACTCGGACTCGATCATGTGCTGTTCCCTGAAG                         GCTGCTCCCGTGTTCACCTTTGCCAACCAAGCCGGCCTGGACATGCTGGAG
genomic: TGAAAGCGCTGTGGCAACACTCGGACTCGATCATGTGCTGTTCCCTGAAGgtaacttggt ... gtgaattcagGCTGCTCCCGTGTTCACCTTTGCCAACCAAGCCGGCCTGGACATGCTGGAG
EST: gi|4966813|gb|AI691669.1|AI691669
EST:     TGAAAGCGCTGTGGCAACACTCGGACTCGATCATGTGCTGTTCCCTGAAG                         GCTGCTCCCGTGTTCACCTTTGCCAACCAAGCCGGCCTGGACATGCTGGAG
genomic: TGAAAGCGCTGTGGCAACACTCGGACTCGATCATGTGCTGTTCCCTGAAGgtaacttggt ... gtgaattcagGCTGCTCCCGTGTTCACCTTTGCCAACCAAGCCGGCCTGGACATGCTGGAG
EST: gi|88756793|gb|DY540934.1|DY540934
EST:     TGAAAGCGCTGTGGCAACACTCGGACTCGATCATGTGCTGTTCCCTGAAG                         GCTGCTCCCGTGTTCACCTTTGCCAACCAAGCCGGCCTGGACATGCTGGAG
genomic: TGAAAGCGCTGTGGCAACACTCGGACTCGATCATGTGCTGTTCCCTGAAGgtaacttggt ... gtgaattcagGCTGCTCCCGTGTTCACCTTTGCCAACCAAGCCGGCCTGGACATGCTGGAG
EST: gi|60400862|gb|DN233669.1|DN233669
EST:     TGAAAGCGCTGTGGCAACACTCGGACTCGATCATGTGCTGTTCCCTGAAG                         GCTGCTCCCGTGTTCACCTTTGCCAACCAAGCCGGCCTGGACATGCTGGAG
genomic: TGAAAGCGCTGTGGCAACACTCGGACTCGATCATGTGCTGTTCCCTGAAGgtaacttggt ... gtgaattcagGCTGCTCCCGTGTTCACCTTTGCCAACCAAGCCGGCCTGGACATGCTGGAG
EST: gi|71298032|gb|DR784985.1|DR784985
EST:     TGAAAGCGCTGTGGCAACACTCGGACTCGATCATGTGCTGTTCCCTGAAG                         GCTGCTCCCGTGTTCACCTTTGCCAACCAAGCCGGCCTGGACATGCTGGAG
genomic: TGAAAGCGCTGTGGCAACACTCGGACTCGATCATGTGCTGTTCCCTGAAGgtaacttggt ... gtgaattcagGCTGCTCCCGTGTTCACCTTTGCCAACCAAGCCGGCCTGGACATGCTGGAG
EST: gi|32847407|gb|CD987088.1|CD987088
EST:     TGAAAGCGCTGTGGCAACACTCGGACTCGATCATGTGCTGTTCCCTGAAG                         GCTGCTCCCGTGTTCACCTTTGCCAACCAAGCCGGCCTGGACATGCTGGAG
genomic: TGAAAGCGCTGTGGCAACACTCGGACTCGATCATGTGCTGTTCCCTGAAGgtaacttggt ... gtgaattcagGCTGCTCCCGTGTTCACCTTTGCCAACCAAGCCGGCCTGGACATGCTGGAG
EST: gi|60401652|gb|DN234459.1|DN234459
EST:     TGAAAGCGCTGTGGCAACACTCGGACTCGATCATGTGCTGTTCCCTGAAG                         GCTGCTCCCGTGTTCACCTTTGCCAACCAAGCCGGCCTGGACATGCTGGAG
genomic: TGAAAGCGCTGTGGCAACACTCGGACTCGATCATGTGCTGTTCCCTGAAGgtaacttggt ... gtgaattcagGCTGCTCCCGTGTTCACCTTTGCCAACCAAGCCGGCCTGGACATGCTGGAG
EST: gi|60396119|gb|DN228988.1|DN228988
EST:     TGAAAGCGCTGTGGCAACACTCGGACTCGATCATGTGCTGTTCCCTGAAG                         GCTGCTCCCGTGTTCACCTTTGCCAACCAAGCCGGCCTGGACATGCTGGAG
genomic: TGAAAGCGCTGTGGCAACACTCGGACTCGATCATGTGCTGTTCCCTGAAGgtaacttggt ... gtgaattcagGCTGCTCCCGTGTTCACCTTTGCCAACCAAGCCGGCCTGGACATGCTGGAG
EST: gi|60354408|gb|DN221381.1|DN221381
EST:     TGAAAGCGCTGTGGCAACACTCGGACTCGATCATGTGCTGTTCCCTGAAG                         GCTGCTCCCGTGTTCACCTTTGCCAACCAAGCCGGCCTGGACATGCTGGAG
genomic: TGAAAGCGCTGTGGCAACACTCGGACTCGATCATGTGCTGTTCCCTGAAGgtaacttggt ... gtgaattcagGCTGCTCCCGTGTTCACCTTTGCCAACCAAGCCGGCCTGGACATGCTGGAG
EST: gi|78116184|gb|DV534571.1|DV534571
EST:     TGAAAGCGCTGTGGCAACACTCGGACTCGATCATGTGCTGTTCCCTGAAG                         GCTGCTCCCGTGTTCACCTTTGCCAACCAAGCCGGCCTGGACATGCTGGAG
genomic: TGAAAGCGCTGTGGCAACACTCGGACTCGATCATGTGCTGTTCCCTGAAGgtaacttggt ... gtgaattcagGCTGCTCCCGTGTTCACCTTTGCCAACCAAGCCGGCCTGGACATGCTGGAG
EST: gi|4804250|gb|AI666116.1|AI666116
EST:     CGGACTCGATCATGTGCTGTTCCCTGAAG                         GCTGCTCCCGTGTTCACCTTTGCCAACCAAGCCGGCCTGGACATGCTGGAG
genomic: CGGACTCGATCATGTGCTGTTCCCTGAAGgtaacttggt ... gtgaattcagGCTGCTCCCGTGTTCACCTTTGCCAACCAAGCCGGCCTGGACATGCTGGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcttggcattgtggtgtctggctggtgttgaagttttgtggaaccgtgaattcagGCTGCTCCCGTGTTCACCTTTGCCAACCAAGCCGGCCTGGACATGCTGGAGACGACGCTGATTGCGCTCCAGGACATCTCCCTTGAGAAGATCCTTGATG
                              aagtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaacttggtcgttctcgctttgtttcgccagttcgtagcttggcattgtggtgtctggctggtgttgaagttttgtggaaccgtgaattcagGCTGCTCCCGTGTTCACCTTTGCCAACCAAGCCGGCCTGGACATGCTGGAGACGACGCTGATTGCGCTCCAGGACATCTCCCTTGAGAAGATCCTTGATG

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