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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgattggcagagctcctgccttttcgttaaaaaaaatacatgacaatttattgtgacaacagagggtaacatctacaaggaacaaggtgaggataactgACAGGATGTGGGCGAGGCTGCTGTCTTCAACCAACCAACCGAGTTTCCTGAGCCAGAAGGACATCGACGCGGCCAGAGAAGCCGACAAGGCGGCCAACCG

Basic information

species Zea mays
transcript GRMZM5G879882_T02
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G879882_T02 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os01g53680.1 (Oryza sativa), 3'ss of exon 13
-----------------------------------------------------------------ttgattggcagagctcctgccttttcgttaaaaaaaatacatgaca---attt----attgtgacaa-cagagggtaacatctacaaggaacaaggtgaggataactgACAGGATGTGGGCGAGGCTGCTGTCTTCAACCAACCAACCGAGTTTCCTGAGCCAGAAGGACATCGACGCGGCCAGAGAAGCCGACAAGGCGGCCAACCG
                                                                    |||  ||    |      ||  | || || |     |||||||   ||||     || |||||| |||||||||||||| ||||| |||||||| | |||||| |||||||||||||| |||||| |||| || |||||||| || || |||||||||||||||||||                                     
gtgagtacaaatttttgtattaccttaattttctccggttcccagattcaaacatattaccctcaacaattatcatgaattaaatattaccctttaacagttcgcatgacatcaatttttgtgttctgacaaacagAGGGTAACATCAACAAGAAACAAGGTTAAGATAACCGACAGGATGTGGGCAAGGCTGTTGTCCTCGACCAACCAGCCCAGCTTCCTGAGCCAGAAGGACA-------------------------------------

upper sequence: GRMZM5G879882_T02 (Zea mays), 3'ss of exon 10
lower sequence: AT4G29220.1 (Arabidopsis thaliana), 3'ss of exon 12
----------------------ttgattggcagagctcctgccttttcgttaaaaaaaata-catgacaatttattgtgacaac-----agagggtaacatctacaaggaacaaggtgaggataactgACAGGATGTGGGCGAGGCTGCTGTCTTCAACCAACCAACCGAGTTTCCTGAGCCAGAAGGACATCGACGCGGCCAGAGAAGCCGACAAGGCGGCCAACCG
                         |   |   | ||| | | |||   | ||       | | | | ||  |  | |||  |      ||||| | ||    | |  ||||||||||  ||| |||||||| ||||||||||||||  ||||||| || ||||||||||||||| |||  ||    ||||                                     
gtgagtctcaggaccaaatactcatacctgagcatctcttacatttatatcaatttgggaatcctaataacatggtttgaatattgtgtagAGGATCACGGAGAAACAGAACAAGGTGGTGATCACTGACAGAATGTGGGCGAGGCTTTTGTCTTCGACGAACCAACCGAGTTTCATGAAGCAAGCTGACA-------------------------------------
















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|14208413|gb|BG842091.1|BG842091
EST:     GATTTATTGCCATGTATGCTACTCTTGCAA                         ACAGGATGTGGGCGAGGCTGCTGTCTTCAACCAACCAACCGAGTTTCCTGA
genomic: GATTTATTGCCATGTATGCTACTCTTGCAAgcagagatgt ... aggataactgACAGGATGTGGGCGAGGCTGCTGTCTTCAACCAACCAACCGAGTTTCCTGA
EST: gi|87153557|gb|DY398346.1|DY398346
EST:     GATTTATTGCCATGTATGCTACTCTTGCAA                         GCAGAGATGTGG
genomic: GATTTATTGCCATGTATGCTACTCTTGCAAgcagagatgt ... aggataactgACAG-GATGTGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatttattgtgacaacagagggtaacatctacaaggaacaaggtgaggataactgACAGGATGTGGGCGAGGCTGCTGTCTTCAACCAACCAACCGAGTTTCCTGAGCCAGAAGGACATCGACGCGGCCAGAGAAGCCGACAAGGCGGCCAACCG
                   gggtaac  putative branch site (score: 3)
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttgattggcagagctcctgccttttcgttaaaaaaaatacatgacaatttattgtgacaacagagggtaacatctacaaggaacaaggtgaggataactgACAGGATGTGGGCGAGGCTGCTGTCTTCAACCAACCAACCGAGTTTCCTGAGCCAGAAGGACATCGACGCGGCCAGAGAAGCCGACAAGGCGGCCAACCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
ttgattg
- - - - - - gctcctg
- - - - - - - - - - - - - - -aaaaaaa
- - - - - - - - - - - - - - - - - - atacatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -caacaga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gaacaag