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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcctctaggaaatgcagtttactatggtggacagtctgcatacctttctgcctttttcctgaaactcccaactaatatatccgggtgttaataataccagGTTAAGCATGCTATTAAGGTCCTTCGTGATTCCGGACCATACAAGGAAGACATACTGAAAGAGTTCGCTGCTCAACAAGACGACGACCTGTAGAATACAG

Basic information

species Zea mays
transcript GRMZM2G158097_T02
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G158097_T03 (Zea mays), 3'ss of exon 11
lower sequence: LOC_Os04g36062.2 (Oryza sativa), 3'ss of exon 11
tcctctaggaaatgcagtttactatggtgga-cagtc--tgcatacctttctgcctttttcctgaaac-tcccaactaa-tatatccgggtgttaataataccagGTTAAGCATGCTATTAAGGTCCTTCGTGATTCCGGACCATACAAGGAAGACATACTGAAAGAGTTCGCTGCTCA-ACAAGACGACGACCTGTAGAATACAG
       |     ||| | |||||||  | | ||     |||||   | ||   | ||  ||| || | |   | |||| |||   |   || |   |||  |||||||| |||| |||||||||||| | ||||||||| |||||||||||||| |||||||| || ||   |||| | |||||  || |   ||||||| |   
-----ccgtgttcgcattgtactatgaagaaacaactaatgcatcattgtccttcattagccttaatcgttggagctaaatattctcttttggtgtaaatgtcagGTTAAACATGTTATTAAGGTCCTGCATGATTCCGGCCCATACAAGGAAGATATACTGAACGAATTT-TTGCTTACACAAGGGGATGGAGTGTAGAACATCA
















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|78124181|gb|DV542565.1|DV542565
EST:     CTGGTTTTGCGGCAGCTATTGGAAATTATCTTACTCATGAGACGGCTCAG                         GTTAAGCATGCTATTAAGGTCCTTCGTGATTCCGGACCATACAAGGAAGAC
genomic: CTGGTTTTGCGGCAGCTATTGGAAATTATCTTACTCATGAGACGGCTCAGgtatttccat ... ataataccagGTTAAGCATGCTATTAAGGTCCTTCGTGATTCCGGACCATACAAGGAAGAC
EST: gi|71766886|gb|DR964823.1|DR964823
EST:     CTGGTTTTGCGGCAGCTATTGGAAATTATCTTACTCATGAGACGGCTCAG                         GTTAAGCATGCTATTAAGGTCCTTCGTGATTCCGGACCATACAAGGAAGAC
genomic: CTGGTTTTGCGGCAGCTATTGGAAATTATCTTACTCATGAGACGGCTCAGgtatttccat ... ataataccagGTTAAGCATGCTATTAAGGTCCTTCGTGATTCCGGACCATACAAGGAAGAC
EST: gi|32841037|gb|CD980718.1|CD980718
EST:     CTGGTTTTGCGGCAGCTATTGGAAATTATCTTACTCATGAGACGGCTCAG                         GTTAAGCATGCTATTAAGGTCCTTCGTGATTCCGGACCATACAAGGAAGAC
genomic: CTGGTTTTGCGGCAGCTATTGGAAATTATCTTACTCATGAGACGGCTCAGgtatttccat ... ataataccagGTTAAGCATGCTATTAAGGTCCTTCGTGATTCCGGACCATACAAGGAAGAC
EST: gi|32841492|gb|CD981173.1|CD981173
EST:     CTGGTTTTGCGGCAGCTATTGGAAATTATCTTACTCATGAGACGGCTCAG                         GTTAAGCATGCTATTAAGGTCCTTCGTGATTCCGGACCATACAAGGAAGAC
genomic: CTGGTTTTGCGGCAGCTATTGGAAATTATCTTACTCATGAGACGGCTCAGgtatttccat ... ataataccagGTTAAGCATGCTATTAAGGTCCTTCGTGATTCCGGACCATACAAGGAAGAC
EST: gi|71766748|gb|DR964685.1|DR964685
EST:     CTGGTTTTGCGGCAGCTATTGGAAATTATTTTACTCATGAGACGGCTCAG                         GTTAAGCATGCTATTAAGGTCCTTCGTGATTCCGGCCCATACAAGGAAGAC
genomic: CTGGTTTTGCGGCAGCTATTGGAAATTATCTTACTCATGAGACGGCTCAGgtatttccat ... ataataccagGTTAAGCATGCTATTAAGGTCCTTCGTGATTCCGGACCATACAAGGAAGAC
EST: gi|32841296|gb|CD980977.1|CD980977
EST:     CTGGTTTTGCGGCAGCTATTGGAAATTATCTTACTCATGAGACGGCTCAG                         GTTAAGCATGCTATTAAGGTCCTTCGTGATTCCGGACCATACAAGGAAGAC
genomic: CTGGTTTTGCGGCAGCTATTGGAAATTATCTTACTCATGAGACGGCTCAGgtatttccat ... ataataccagGTTAAGCATGCTATTAAGGTCCTTCGTGATTCCGGACCATACAAGGAAGAC
EST: gi|50325271|gb|CO520397.1|CO520397
EST:     CTGGTTTTGCGGCAGCTATTGGAAATTATCTTACTCATGAGACGGCTCAG                         GTTAAGCATGCTATTAAGGTCCTTCGTGATTCCGGCCCATCCAAGGAAGAC
genomic: CTGGTTTTGCGGCAGCTATTGGAAATTATCTTACTCATGAGACGGCTCAGgtatttccat ... ataataccagGTTAAGCATGCTATTAAGGTCCTTCGTGATTCCGGACCATACAAGGAAGAC
EST: gi|89249944|gb|DY621730.1|DY621730
EST:     CTGGTTTTGCGGCAGCTATTGGAAATTATTTTACTCATGAGACGGCTCAG                         GTTAAGCATGCTATTAAGGTCCTTCGTGATTCCGGACCATACAAGGAAGAC
genomic: CTGGTTTTGCGGCAGCTATTGGAAATTATCTTACTCATGAGACGGCTCAGgtatttccat ... ataataccagGTTAAGCATGCTATTAAGGTCCTTCGTGATTCCGGACCATACAAGGAAGAC
EST: gi|32841681|gb|CD981362.1|CD981362
EST:     CTGGTTTTGCGGCAGCTATTGGAAATTATCTTACTCATGAGACGGCTCAG                         GTTAAGCATGCTATTAAGGTCCTTCGTGATTCCGGACCATACAAGGAAGAC
genomic: CTGGTTTTGCGGCAGCTATTGGAAATTATCTTACTCATGAGACGGCTCAGgtatttccat ... ataataccagGTTAAGCATGCTATTAAGGTCCTTCGTGATTCCGGACCATACAAGGAAGAC
EST: gi|32841005|gb|CD980686.1|CD980686
EST:     CTGGTTTTGCGGCAGCTATTGGAAATTATCTTACTCATGAGACGGCTCAG                         GTTAAGCATGCTATTAAGGTCCTTCGTGATTCCGGACCATACAAGGAAGAC
genomic: CTGGTTTTGCGGCAGCTATTGGAAATTATCTTACTCATGAGACGGCTCAGgtatttccat ... ataataccagGTTAAGCATGCTATTAAGGTCCTTCGTGATTCCGGACCATACAAGGAAGAC
EST: gi|32840850|gb|CD980531.1|CD980531
EST:     CTGGTTTTGCGGCAGCTATTGGAAATTATCTTACTCATGAGACGGCTCAG                         GTTAAGCATGCTATTAAGGTCCTTCGTGATTCCGGACCATACAAGGAAGAC
genomic: CTGGTTTTGCGGCAGCTATTGGAAATTATCTTACTCATGAGACGGCTCAGgtatttccat ... ataataccagGTTAAGCATGCTATTAAGGTCCTTCGTGATTCCGGACCATACAAGGAAGAC
EST: gi|71766749|gb|DR964686.1|DR964686
EST:     CTGGTTTTGCGGCAGCTATTGGAAATTATCTTACTCATGAGACGGCTCAG                         GTTAAGCATGCTATTAAGGTCCTTCGTGATTCCGGACCATACAAGGAAGAC
genomic: CTGGTTTTGCGGCAGCTATTGGAAATTATCTTACTCATGAGACGGCTCAGgtatttccat ... ataataccagGTTAAGCATGCTATTAAGGTCCTTCGTGATTCCGGACCATACAAGGAAGAC
EST: gi|32841261|gb|CD980942.1|CD980942
EST:     CTGGTTTTGCGGCAGCTATTGGAAATTATCTTACTCATGAGACGGCTCAG                         GTTAAGCATGCTATTAAGGTCCTTCGTGATTCCGGACCATACAAGGAAGAC
genomic: CTGGTTTTGCGGCAGCTATTGGAAATTATCTTACTCATGAGACGGCTCAGgtatttccat ... ataataccagGTTAAGCATGCTATTAAGGTCCTTCGTGATTCCGGACCATACAAGGAAGAC
EST: gi|16379420|gb|BI992935.1|BI992935
EST:     CTGGTTTTGCGGCAGCTATTGGAAATTATCTTACTCATGAGACGGCTCAG                         GTTAAGCATGCTATTAAGGTCCTTCGTGATTCCGGACCATACAAGGAAGAC
genomic: CTGGTTTTGCGGCAGCTATTGGAAATTATCTTACTCATGAGACGGCTCAGgtatttccat ... ataataccagGTTAAGCATGCTATTAAGGTCCTTCGTGATTCCGGACCATACAAGGAAGAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttctgcctttttcctgaaactcccaactaatatatccgggtgttaataataccagGTTAAGCATGCTATTAAGGTCCTTCGTGATTCCGGACCATACAAGGAAGACATACTGAAAGAGTTCGCTGCTCAACAAGACGACGACCTGTAGAATACAG
                        aactaatatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcctctaggaaatgcagtttactatggtggacagtctgcatacctttctgcctttttcctgaaactcccaactaatatatccgggtgttaataataccagGTTAAGCATGCTATTAAGGTCCTTCGTGATTCCGGACCATACAAGGAAGACATACTGAAAGAGTTCGCTGCTCAACAAGACGACGACCTGTAGAATACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT