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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgttggatgccttcaagtgacccaatttttagaacactttattgacctttttatatccagagggatagtatcttatggttttcttcatgcgttttttcagGGTAACTTTGACCTCGTGGGTAACAACATGCCTGTGTTTTTCATACGAGATGGGATGAAATTCCCTGACATGGTCCACGCTTTCAAGCCGAATCCAAAGA

Basic information

species Zea mays
transcript GRMZM2G088212_T02
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G088212_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os06g51150.1 (Oryza sativa), 3'ss of exon 3
tgttggatgccttcaagtgacccaatttttagaacactttattgacctttttatatccagagggatagtatcttatggttttcttcatgcgt-tttttcagGGTAACTTTGACCTCGTGGGTAACAACATGCCTGTGTTTTTCATACGAGATGGGATGAAATTCCCTGACATGGTCCACGCTTTCAAGCCGAATCCAAAGA
| |   |    |   |   ||  | ||| |   ||  |||||| ||   |||  || ||| |      ||| ||    ||||||   |   |  |||||||||||| ||||| || || || ||||| |||||||| ||||| || |||||||||||||||||||||||||||||||| ||||||||||| | ||||||||
tatctaaccagtgtcacctaca-actttgtcttactgtttatttactgatttgcattcagtgctgccatattttgatattttctgagtcaatgcttttcagGGTAATTTTGATCTTGTTGGGAACAATATGCCTGTCTTTTTTATCCGAGATGGGATGAAATTCCCTGACATGGTCCATGCTTTCAAGCCAAGTCCAAAGA

upper sequence: GRMZM2G088212_T02 (Zea mays), 3'ss of exon 2
lower sequence: EFJ37039 (Selaginella moellendorffii), 3'ss of exon 3
tgttggatgccttcaagtgacccaatttttagaacactttattgacctttttatatccagagggatagtatcttatggttttcttcatgcgtttttt--cagGGTAACTTTGACCTCGTGGGTAACAACATGCCTGTGTTTTTCATACGAGATGGGATGAAATTCCCTGACATGGTCCACGCTTTCAAGCCGAATCCAAAGA
                ||||   || | |  |   |  ||  | |  |    |        |  ||   |||||    |||| |   |  ||||     ||||| ||||| || || || || |||||||| || ||||| ||| |||| ||||| || || |||||||||||| |||||||| ||||||| || |||||||
----------------gtgagtaaactatctggtgatgttgctaagttggacac-------gaaattccatctttgacttttttcgctttgtttgcgagcagGGAAACTTCGATCTGGTTGGAAACAACATTCCCGTGTTCTTCGTACGTGATGGCATCAAGTTCCCTGACATGATCCACGCTCTCAAGCCAAACCCAAAGA

upper sequence: GRMZM2G088212_T02 (Zea mays), 3'ss of exon 2
lower sequence: EFJ33688 (Selaginella moellendorffii), 3'ss of exon 3
tgttggatgccttcaagtgacccaatttttagaacactttattgacctttttatatccagagggatagtatcttatggttttcttcatgcgtttttt--cagGGTAACTTTGACCTCGTGGGTAACAACATGCCTGTGTTTTTCATACGAGATGGGATGAAATTCCCTGACATGGTCCACGCTTTCAAGCCGAATCCAAAGA
                ||||   || | |  |  ||  ||  | |  |    |        |  ||   |||||    |||| |   |  ||||     ||||| ||||| || || || || |||||||| || ||||| ||| |||| ||||| || || |||||||||||| |||||||| ||||||| || |||||||
----------------gtgagtaaactatctggtcatgttgctaagttggacac-------gaaattccatctttgacttttttcgctttgtttgcgagcagGGAAACTTCGATCTGGTTGGAAACAACATTCCCGTGTTCTTCGTACGTGATGGCATCAAGTTCCCTGACATGATCCACGCTCTCAAGCCAAACCCAAAGA

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|37622130|gb|CF675183.1|CF675183
EST:     AGACCTTGAGGGATCCACGTGGTTTTGCTGTCAAGTTCTACACCAGAGAG                         GGTAACTTTGACCTCGTGGGTAACAACATGCCTGTGTTTTTCATACGAGAT
genomic: AGACCTTGAGGGATCCACGTGGTTTTGCTGTCAAGTTCTACACCAGAGAGgtactgagga ... gttttttcagGGTAACTTTGACCTCGTGGGTAACAACATGCCTGTGTTTTTCATACGAGAT
EST: gi|211375400|gb|FK987885.1|FK987885
EST:     AGACCTTGAGGGATCCACGTGGTTTTGCTGTCAAGTTCTACACCAGAGAG                         GGTAACTTTGACCTCGTGGGTAACAACATGNCTGTGTTTTTCATACGAGAT
genomic: AGACCTTGAGGGATCCACGTGGTTTTGCTGTCAAGTTCTACACCAGAGAGgtactgagga ... gttttttcagGGTAACTTTGACCTCGTGGGTAACAACATGCCTGTGTTTTTCATACGAGAT
EST: gi|211023549|gb|FK987906.1|FK987906
EST:     AGACCTTGAGGGATCCACGTGGTTTTGCTGTCAAGTTCTACACCAGAGAG                         GGTAACTTTGACCTCGTGGGTAACAACATGCCTGTGTTTTTCATACGAGAT
genomic: AGACCTTGAGGGATCCACGTGGTTTTGCTGTCAAGTTCTACACCAGAGAGgtactgagga ... gttttttcagGGTAACTTTGACCTCGTGGGTAACAACATGCCTGTGTTTTTCATACGAGAT
EST: gi|28187880|gb|CB179490.1|CB179490
EST:     GACCTTGAGGGATCCACGTGGGTTTTGCTGTCAAGTTCTACACCAGAGAG                         GGTAACTTTGACCTCGTGGGTAACAACATGCCTGTGTTTTTCATAC
genomic: GACCTTGAGGGATCCACGTGG-TTTTGCTGTCAAGTTCTACACCAGAGAGgtactgagga ... gttttttcagGGTAACTTTGACCTCGTGGGTAACAACATGCCTGTGTTTTTCATAC
EST: gi|38229627|gb|CF919940.1|CF919940
EST:     AGACCTTGAGGGATCCACGTGGTTTTGCTGTCAAGTTCTACACCAGAGAG                         GGTAACTTTGACCTCGTGGGTAACAACATGCCTGTGTTTTTCATACGAGAT
genomic: AGACCTTGAGGGATCCACGTGGTTTTGCTGTCAAGTTCTACACCAGAGAGgtactgagga ... gttttttcagGGTAACTTTGACCTCGTGGGTAACAACATGCCTGTGTTTTTCATACGAGAT
EST: gi|211375397|gb|FK987882.1|FK987882
EST:     AGACCTTGAGGGATCCACGTGGTTTTGCTGTCAAGTTCTACACCAGAGAG                         GGTAACTTTGACCTCGTGGGTAACAACATGCCTGTGTTTTTCATACGAGAT
genomic: AGACCTTGAGGGATCCACGTGGTTTTGCTGTCAAGTTCTACACCAGAGAGgtactgagga ... gttttttcagGGTAACTTTGACCTCGTGGGTAACAACATGCCTGTGTTTTTCATACGAGAT
EST: gi|211372735|gb|FK987872.1|FK987872
EST:     AGACCTTGAGGGATCCACGTGNTTTTGCTGTCAAGTTNTACACCAGAGAG                         GGTAACTTTGACCTCGTGGGTAACAACATGCCTGTGTTTTTTCATACGAGA
genomic: AGACCTTGAGGGATCCACGTGGTTTTGCTGTCAAGTTCTACACCAGAGAGgtactgagga ... gttttttcagGGTAACTTTGACCTCGTGGGTAACAACATGCCTGTGTTTTT-CATACGAGA
EST: gi|32920070|gb|CF024882.1|CF024882
EST:     AGACCTTGAGGGATCCACGTGGTTTTGCTGTCAAGTTCTACACCAGAGAG                         GGTAACTTTGACCTCGTGGGTAACAACATGCCTGTGTTTTTCATACGAGAT
genomic: AGACCTTGAGGGATCCACGTGGTTTTGCTGTCAAGTTCTACACCAGAGAGgtactgagga ... gttttttcagGGTAACTTTGACCTCGTGGGTAACAACATGCCTGTGTTTTTCATACGAGAT
EST: gi|211021129|gb|FK987901.1|FK987901
EST:     AGACCTTGAGGGATCCACGNGNNTTTGCTGTCAAGTTCTACACCAGAGAG                         GGTAACTTTGACCTCGTGGGTAACAACATGCCTGTGTTTTTCATA
genomic: AGACCTTGAGGGATCCACGTGGTTTTGCTGTCAAGTTCTACACCAGAGAGgtactgagga ... gttttttcagGGTAACTTTGACCTCGTGGGTAACAACATGCCTGTGTTTTTCATA
EST: gi|211023559|gb|FK987916.1|FK987916
EST:     AGACCTTGAGGGATCCACGTGGTTTTGCTGTCAAGTTCTACACCAGAGAG                         GGTAACTTTGACCTCGTGGGTAACAACATGCCTGTGTTTTTCATACGAGAT
genomic: AGACCTTGAGGGATCCACGTGGTTTTGCTGTCAAGTTCTACACCAGAGAGgtactgagga ... gttttttcagGGTAACTTTGACCTCGTGGGTAACAACATGCCTGTGTTTTTCATACGAGAT
EST: gi|31356065|gb|CD440422.1|CD440422
EST:     AGACCTTGAGGGATCCACGTGGTTTTGCTGTCAAGTTCTACACCAGAGAG                         GGTAACTTTGACCTCGTGGGTAACAACATGCCTGTGTTTTTCATACCAGAT
genomic: AGACCTTGAGGGATCCACGTGGTTTTGCTGTCAAGTTCTACACCAGAGAGgtactgagga ... gttttttcagGGTAACTTTGACCTCGTGGGTAACAACATGCCTGTGTTTTTCATACGAGAT
EST: gi|211375396|gb|FK987881.1|FK987881
EST:     AGACCTTGAGGGATCCACGTGGTTTTGCTGTCAAGTTCTACACCAGAGAG                         GGTAACTTTGACCTCGTGGGTAACAACATGCCTGTGTTTTTCATACGAGAT
genomic: AGACCTTGAGGGATCCACGTGGTTTTGCTGTCAAGTTCTACACCAGAGAGgtactgagga ... gttttttcagGGTAACTTTGACCTCGTGGGTAACAACATGCCTGTGTTTTTCATACGAGAT
EST: gi|211023553|gb|FK987910.1|FK987910
EST:     AGACCTTGAGGGATCCACGTGGTTTTGCTGTCAAGTTCTACACCAGAGAG                         GGTAACTTTGACCTCGTGGGTAACAACATGCCTGTGTTTTTCATACGAGAT
genomic: AGACCTTGAGGGATCCACGTGGTTTTGCTGTCAAGTTCTACACCAGAGAGgtactgagga ... gttttttcagGGTAACTTTGACCTCGTGGGTAACAACATGCCTGTGTTTTTCATACGAGAT
EST: gi|211370083|gb|FK987860.1|FK987860
EST:     AGACCTTGAGGGATCCACGTGGTTTTGCTGTCAAGTTCTACACCAGAGAG                         GGTAACTTTGACCTCGTGGGTAACAACATGCCTGTGTTTTTCATACGAGAT
genomic: AGACCTTGAGGGATCCACGTGGTTTTGCTGTCAAGTTCTACACCAGAGAGgtactgagga ... gttttttcagGGTAACTTTGACCTCGTGGGTAACAACATGCCTGTGTTTTTCATACGAGAT
EST: gi|211370080|gb|FK987857.1|FK987857
EST:     AGACCTTGAGGGATCCACGTGGTTTTGCTGTCAAGTTCTACACCAGAGAG                         GGTAACTTTGACCTCGTGGGTAACAACATGCCTGTGTTTTTCATACGAGAT
genomic: AGACCTTGAGGGATCCACGTGGTTTTGCTGTCAAGTTCTACACCAGAGAGgtactgagga ... gttttttcagGGTAACTTTGACCTCGTGGGTAACAACATGCCTGTGTTTTTCATACGAGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cctttttatatccagagggatagtatcttatggttttcttcatgcgttttttcagGGTAACTTTGACCTCGTGGGTAACAACATGCCTGTGTTTTTCATACGAGATGGGATGAAATTCCCTGACATGGTCCACGCTTTCAAGCCGAATCCAAAGA
                                            cgttttttc  CT-rich tract
                       tatcttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgttggatgccttcaagtgacccaatttttagaacactttattgacctttttatatccagagggatagtatcttatggttttcttcatgcgttttttcagGGTAACTTTGACCTCGTGGGTAACAACATGCCTGTGTTTTTCATACGAGATGGGATGAAATTCCCTGACATGGTCCACGCTTTCAAGCCGAATCCAAAGA

- -tggatgc