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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaggtaagccagcgcgccgcacgccattgccgccctcgttgtttacttcgcgtttggatctgtggctgaggagctgcgcgttggttggcctgtggccatgcagATGTCGTCCGTGGCGTCGAAGGTGGCGGTGCCGGAGTCTGTGCTCCGCAAGCGGAAGCGCGAGGAACAGTGGGCCACCGAGAAGAAGGAGAAGGCCCTAG

Basic information

species Zea mays
transcript GRMZM2G094051_T05
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G094051_T06 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os04g51630.3 (Oryza sativa), 3'ss of exon 1
gtaaggtaagccagcgcgccgcacgccattgccgccctcgttgtttac-ttcgcgtttggatctgtggctgaggagctgcgcgttggttggcctgtg-gccatgcagATGTCGTCCGTGGCGTCGAAGGTGGCGGTGCCGGAGTCTGTGCTCCGCAAGCGGAAGCGCGAGGAACAGTGGGCCACCGAGAAGAAGGAGAAGGCCCTAG
|||||   |||  |  |||||   ||||||||||||||  |  | |   |||||   | |  | ||  | ||   |   |  || ||||   ||||  ||   ||||||| |||||| |||| | ||||||| |||||||||||| |||||||||||| ||||||| |||||   ||||||  ||| ||  |||||||||||| | |
gtaag---agctcgt-cgccggtagccattgccgccctgctcctctctgttcgctcgtcgccccgtc-ccgatctgaccctggtgggtttcgctgttcgctgcgcagATGGCGTCCGAGGCGGCCAAGGTGGTGGTGCCGGAGTCCGTGCTCCGCAAGAGGAAGCGGGAGGAGGTGTGGGCGGCCGCGAGCAAGGAGAAGGCCGTCG
















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|211364904|gb|FL335329.1|FL335329
EST:     CTCCGCTCGCCGCTCTCCCCGCGTATCCCTCTCATACGCAGCTCGCCCAGGTAAG                     
genomic: CTCCGCTCGCCGCTCTCCCCGCGTATCCCTCTCATACGCAGCTCGCCC-----AGgtaaggtaag ... ggccat
EST: gi|211439886|gb|FL309186.1|FL309186
EST:     CTCCGCTCGCCGCTCTCCCCGCGTATCCCTCTCATACGCAGCTCGCCCAGGTAAG                     
genomic: CTCCGCTCGCCGCTCTCCCCGCGTATCCCTCTCATACGCAGCTCGCCC-----AGgtaaggtaag ... ggccat
EST: gi|211381235|gb|FL355200.1|FL355200
EST:     CTCCGCTCGCCGCTCTCCCCGCGTATCCCTCTCATACGCAGCTCGCCCAGGTNAG                     
genomic: CTCCGCTCGCCGCTCTCCCCGCGTATCCCTCTCATACGCAGCTCGCCC-----AGgtaaggtaag ... ggccat
EST: gi|211197410|gb|FL309893.1|FL309893
EST:     CTCCGCTCGCCGCTCTCCCCGCGTATCCCTCTCATACGCAGCTCGCCCAGGTAAG                     
genomic: CTCCGCTCGCCGCTCTCCCCGCGTATCCCTCTCATACGCAGCTCGCCC-----AGgtaaggtaag ... ggccat
EST: gi|211467480|gb|FL327940.1|FL327940
EST:     CTCCGCTCGCCGCTCTCCCCGCGTATCCCTCTCATACGCAGCTCGCCCAG                         ATGTCGTCCGTGGCGTCGAAGGTGGCGGTGCCGGAGTCTGTGCTCCGCAAG
genomic: CTCCGCTCGCCGCTCTCCCCGCGTATCCCTCTCATACGCAGCTCGCCCAGgtaaggtaag ... ggccatgcagATGTCGTCCGTGGCGTCGAAGGTGGCGGTGCCGGAGTCTGTGCTCCGCAAG
EST: gi|211099200|gb|FL356880.1|FL356880
EST:     CTCCGCTCGCCGCTCTCCCCGCGTATCCCTCTCATACGCAGCTCGCCCAG                         ATGTCGTCCGTGGCGTCGAAGGTGGCGGTG-CGGAGTCTGTGCTCCGCAAG
genomic: CTCCGCTCGCCGCTCTCCCCGCGTATCCCTCTCATACGCAGCTCGCCCAGgtaaggtaag ... ggccatgcagATGTCGTCCGTGGCGTCGAAGGTGGCGGTGCCGGAGTCTGTGCTCCGCAAG
EST: gi|211430944|gb|FL367566.1|FL367566
EST:     CTCCGCTCGCCGCTCTCCCCGCGTATCCCTCTCATACGCAGCTCGCCCAGGTAAG                     
genomic: CTCCGCTCGCCGCTCTCCCCGCGTATCCCTCTCATACGCAGCTCGCCC-----AGgtaaggtaag ... ggccat
EST: gi|211331288|gb|FL346026.1|FL346026
EST:     CTCCGCTCGCCGCTCTCCCCGCGTATCCCTCTCATACGCAGCTCGCCCAG                         ATGTCGTCCGTGGCGTCGAAGGTGGCGGTG-CGGAGTCTGTGCTCCGCAAG
genomic: CTCCGCTCGCCGCTCTCCCCGCGTATCCCTCTCATACGCAGCTCGCCCAGgtaaggtaag ... ggccatgcagATGTCGTCCGTGGCGTCGAAGGTGGCGGTGCCGGAGTCTGTGCTCCGCAAG
EST: gi|76281808|gb|DV021376.1|DV021376
EST:     CTCATACGCAGCTCGCCCAGGTAAG                     
genomic: CTCATACGCAGCTCGCCC-----AGgtaaggtaag ... ggccat
EST: gi|211467080|gb|FL315617.1|FL315617
EST:     CTCCGCTCGCCGCTCTCCCCGCGTATCCCTCTCATACGCAGCTCGCCCAGGTAAG                     
genomic: CTCCGCTCGCCGCTCTCCCCGCGTATCCCTCTCATACGCAGCTCGCCC-----AGgtaaggtaag ... ggccat
EST: gi|211369599|gb|FL314676.1|FL314676
EST:     CTCCGCTCGCCGCTCTCCCCGCGTATCCCTCTCATACGCAGCTCGCCCAGGTAAG                     
genomic: CTCCGCTCGCCGCTCTCCCCGCGTATCCCTCTCATACGCAGCTCGCCC-----AGgtaaggtaag ... ggccat
EST: gi|211425293|gb|FL350052.1|FL350052
EST:     CTCCGCTCGCCGCTCTCCCCGCGTATCCCTCTCATACGCAGCTCGCCCAGGTAAG                     
genomic: CTCCGCTCGCCGCTCTCCCCGCGTATCCCTCTCATACGCAGCTCGCCC-----AGgtaaggtaag ... ggccat
EST: gi|211419805|gb|FL340213.1|FL340213
EST:     CTCCGCTCGCCGCTCTCCCCGCGTATCCCTCTCATACGCAGCTCGCCCAGGTAAG                     
genomic: CTCCGCTCGCCGCTCTCCCCGCGTATCCCTCTCATACGCAGCTCGCCC-----AGgtaaggtaag ... ggccat
EST: gi|211489662|gb|FL352063.1|FL352063
EST:     CTCCGCTCGCCGCTCTCCCCGCGTATCCCTCTCATACGCAGCTCGCCCAG                         ATGTCGTCCGTGGCGTCGAAGGTGGCGGTGCCGGAGTCTGTGCTCCGCAAG
genomic: CTCCGCTCGCCGCTCTCCCCGCGTATCCCTCTCATACGCAGCTCGCCCAGgtaaggtaag ... ggccatgcagATGTCGTCCGTGGCGTCGAAGGTGGCGGTGCCGGAGTCTGTGCTCCGCAAG
EST: gi|211522433|gb|FL327538.1|FL327538
EST:     CTCCGCTCGCCGCTCTCCCCGCGTATCCCTCTCATACGCAGCTCGCCCAGGTNAG                     
genomic: CTCCGCTCGCCGCTCTCCCCGCGTATCCCTCTCATACGCAGCTCGCCC-----AGgtaaggtaag ... ggccat
EST: gi|211262500|gb|FL327821.1|FL327821
EST:     CTCCGCTCGCCGCTCTCCCCGCGTATCCCTCTCATACGCAGCTCGCCCAG                         ATGTCGTCCGTGGCGTCGAAGGTGGCGGTGCCGGAGTCTGTGCTCCGCAAG
genomic: CTCCGCTCGCCGCTCTCCCCGCGTATCCCTCTCATACGCAGCTCGCCCAGgtaaggtaag ... ggccatgcagATGTCGTCCGTGGCGTCGAAGGTGGCGGTGCCGGAGTCTGTGCTCCGCAAG
EST: gi|211430817|gb|FL361882.1|FL361882
EST:     CTCCGCTCGCCGCTCTCCCCGCGTATCCCTCTCATACGCAGCTCGCCCAGGTAAG                     
genomic: CTCCGCTCGCCGCTCTCCCCGCGTATCCCTCTCATACGCAGCTCGCCC-----AGgtaaggtaag ... ggccat
EST: gi|211489013|gb|FL325724.1|FL325724
EST:     CTCCGCTCGCCGCTCTCCCCGCGTATCCCTCTCATACGCAGCTCGCCCAG                         ATGTCGTCCGTGGCGTCGAAGGTGGCGGTGCCGGAGTCTGTGCTCCGCAAG
genomic: CTCCGCTCGCCGCTCTCCCCGCGTATCCCTCTCATACGCAGCTCGCCCAGgtaaggtaag ... ggccatgcagATGTCGTCCGTGGCGTCGAAGGTGGCGGTGCCGGAGTCTGTGCTCCGCAAG
EST: gi|211365538|gb|FL366724.1|FL366724
EST:     CTCCGCTCGCCGCTCTCCCCGCGTATCCCTCTCATACGCAGCTCGCCCAGGTAAG                     
genomic: CTCCGCTCGCCGCTCTCCCCGCGTATCCCTCTCATACGCAGCTCGCCC-----AGgtaaggtaag ... ggccat
EST: gi|211479805|gb|FL307417.1|FL307417
EST:     CTCCGCTCGCCGCTCTCCCCGCGTATCCCTCTCATACGCAGCTCGCCCAGGTAAG                     
genomic: CTCCGCTCGCCGCTCTCCCCGCGTATCCCTCTCATACGCAGCTCGCCC-----AGgtaaggtaag ... ggccat
EST: gi|211427800|gb|FL348316.1|FL348316
EST:     CTCCGCTCGCCGCTCTCCCCGCGTATCCCTCTCATACGCAGCTCGCCCAGGTAAG                     
genomic: CTCCGCTCGCCGCTCTCCCCGCGTATCCCTCTCATACGCAGCTCGCCC-----AGgtaaggtaag ... ggccat

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaggtaagccagcgcgccgcacgccattgccgccctcgttgtttacttcgcgtttggatctgtggctgaggagctgcgcgttggttggcctgtggccatgcagATGTCGTCCGTGGCGTCGAAGGTGGCGGTGCCGGAGTCTGTGCTCCGCAAGCGGAAGCGCGAGGAACAGTGGGCCACCGAGAAGAAGGAGAAGGCCCTAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA