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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AACGGTACTGGCGAGGACGTGAAGAAGATCGTCACCGTGCTCAACCAAGCCGAGGTGCCCTCTGAAGACGTCGTCGgtgagtcgtctcacttctcatggcatcatctctccccgcgtttgcagttgcgggcctgtgtcggttgtggtttggtttttgactagaccgatctatgtgctgatctcttggttggctggaactcggggaggtgagcag

Basic information

species Zea mays
transcript GRMZM2G146206_T03
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G146206_T03 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os01g62420.4 (Oryza sativa), 5'ss of exon 1
------------------------AACGGTACTGGCGAGGACGTGAAGAAGATCGTCACCGTGCTCAACCAAGCCGAGGTGCCCTCTGAAGACGTCGTCGgtgagtcgtc--tcacttctcatggcatcatctctccccgcgtttgcagttgcgggcctgtgtcggttgtggtttggtttttgactagaccgatctatgtgctgatctcttggttggctggaactcggggaggtgagcag
                        || || || || |||||||||||||||||||||||||| |||||| | |||||||||||||| || ||||||||||||||| ||||   | || |  | ||| |  | |      |  |   |  ||     | ||  ||| |   |   || | | ||  |      || ||| |  | || | ||  |||| || |                  
GCGCTGCGCTGTTGCTGCGTGCAGAATGGGACAGGGGAGGACGTGAAGAAGATCGTCACCGTCCTCAACGAGGCCGAGGTGCCCTCCGAGGACGTCGTCGgtgagccgtcgtcccctcccgagggcgttgtttggagttggat---cgatt-----catgaatcgatctggtgctgatctgtgggtttgtttatttattt--taatttttt--ttgggtgcag-----------------

upper sequence: GRMZM2G146206_T03 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os01g62420.2 (Oryza sativa), 5'ss of exon 2
AACGGTACTGGCGAGGACGTGAAGAAGATCGTCACCGTGCTCAACCAAGCCGAGGTGCCCTCTGAAGACGTCGTCGgtgagtcgtc--tcacttctcatggcatcatctctccccgcgtttgcagttgcgggcctgtgtcggttgtggtttggtttttgactagaccgatctatgtgctgatctcttggttggctggaactcggggaggtgagcag
|| || || || |||||||||||||||||||||||||| |||||| | |||||||||||||| || ||||||||||||||| ||||   | || |  | ||| |  | |      |  |   |  ||     | ||  ||| |   |   || | | ||  |      || ||| |  | || | ||  |||| || |                  
AATGGGACAGGGGAGGACGTGAAGAAGATCGTCACCGTCCTCAACGAGGCCGAGGTGCCCTCCGAGGACGTCGTCGgtgagccgtcgtcccctcccgagggcgttgtttggagttggat---cgatt-----catgaatcgatctggtgctgatctgtgggtttgtttatttattt--taatttttt--ttgggtgcag-----------------
















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|211368671|gb|FL393821.1|FL393821
EST:     ATCGTCACCGTGCTCAACCAAGCCGANGGTGCCCTCTGAAGAMGTCGTCG                         AAGTGGTGGTGAGTCCGCCGTTCGTTTTTCTGCAGCAGGTCAAGGGGCTGC
genomic: ATCGTCACCGTGCTCAACCAAGCCGA-GGTGCCCTCTGAAGACGTCGTCGgtgagtcgtc ... aggtgagcagAGGTGGTGGTGAGTCCGCCTTTCGTTTTTCTGCAGCAGGTCAAGGGGCTGC
EST: gi|28187879|gb|CB179489.1|CB179489
EST:     GATCGTCACCGTGCTCAACGAAGCCGAGGTGCCCTCTGAAGACGTCGTCG                         AGGTGGTGGTGAGTCCGCCGTTCGTTTTTCTGCAGCAGGTCAAGGGGCTGC
genomic: GATCGTCACCGTGCTCAACCAAGCCGAGGTGCCCTCTGAAGACGTCGTCGgtgagtcgtc ... aggtgagcagAGGTGGTGGTGAGTCCGCCTTTCGTTTTTCTGCAGCAGGTCAAGGGGCTGC
EST: gi|38229506|gb|CF919819.1|CF919819
EST:     GATCGTCACCGTGCTCAACGAAGCCGAGGTGCCCTCTGAAGACGTCGTCG                         AGGTGGTGGTGAGTCCGCCGTTCGTTTTTCTGCAGCAGGTCAAGGGGCTGC
genomic: GATCGTCACCGTGCTCAACCAAGCCGAGGTGCCCTCTGAAGACGTCGTCGgtgagtcgtc ... aggtgagcagAGGTGGTGGTGAGTCCGCCTTTCGTTTTTCTGCAGCAGGTCAAGGGGCTGC
EST: gi|101388917|gb|EB816440.1|EB816440
EST:     GATCGTCACCGTGCTCAACCAAGCCGAGGTGCCCTCTGAAGACGTCGTCG                         AGGTGGTGGTGAGTCCGCCTTTCGTTTTTCTGCAGCAGGTCAAGGGGCTGC
genomic: GATCGTCACCGTGCTCAACCAAGCCGAGGTGCCCTCTGAAGACGTCGTCGgtgagtcgtc ... aggtgagcagAGGTGGTGGTGAGTCCGCCTTTCGTTTTTCTGCAGCAGGTCAAGGGGCTGC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AACGGTACTGGCGAGGACGTGAAGAAGATCGTCACCGTGCTCAACCAAGCCGAGGTGCCCTCTGAAGACGTCGTCGgtgagtcgtctcacttctcatggcatcatctctccccgcgtttgcagttgcgggcctgtgtcggttgtggtttggtttttgactagaccgatctatgtgctgatctcttggttggctggaactcggggaggtgagcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA