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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAGAATCGCTAGATTCCTCAAATCCGGTAAATACGCCGAGCGTGTCGGTGCCGGAGCTCCGGTCTATCTCTCCGCTGTTCTCGAGTACCTCGCCGCCGAGgtaatttatttttcttgtcttccaatttggttttcaatttcgatttggtcacatctgaattggatcttgtactgatttgattttgatttggtttgggttgatag

Basic information

species Arabidopsis thaliana
transcript AT1G08880.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G08880.1 (Arabidopsis thaliana), 5'ss of exon 1
lower sequence: GRMZM2G111028_T01 (Zea mays), 5'ss of exon 2
-AAGAATCGCTAGATTCCTCAAATCCGGTAAATACGCCGAGCGTGTCGGTGCCGGAGCTCCGGTCTATCTCTCCGCTGTTCTCGAGTACCTCGCCGCCGAGgtaatttatt--tttcttgtcttccaatt-tggttttcaatttcgatttggtcacatctgaattggatctt-gtactgatttgattttgatttggtttgggttgatag
   | ||||   | | ||||||| |||| ||||| || ||||| ||||| || || || || || || |||||||| ||||||||||| |||||||||||||||||          ||  || ||   |  || ||  ||  |    | | |||  ||||   ||| |||   ||  ||| ||||||    |||  || |  |    ||
GTCGCATCGTGCGGTGCCTCAAAGCCGGCAAATATGCAGAGCGCGTCGGCGCTGG-GCCCCCGTGTACCTCTCCGCCGTTCTCGAGTATCTCGCCGCCGAGgtaatcccccgacccctcttcctctcttcatgtttaccagatctactcttgtctgatctcgtttgaatcccagttgtgaattgatt---gtttccttcgtatccgcag

upper sequence: AT1G08880.1 (Arabidopsis thaliana), 5'ss of exon 1
lower sequence: GRMZM2G163956_T01 (Zea mays), 5'ss of exon 1
-AAGAATCGCTAGATTCCTCAAATCCGGTAAATACGCCGAGCGTGTCGGTGCCGGAGCTCCGGTCTATCTCTCCGCTGTTCTCGAGTACCTCGCCGCCGAGgtaatt--tatttttcttgtcttccaatt-tggttttcaatttcgatttggtcacatctgaattggatctt-gtactgatttgattttgatttggtttgggttgatag
   | ||||   | | ||||||| |||| ||||| || ||||| ||||| || || || || || || |||||| | ||||||||||| |||||||||||||||||    |     ||  || ||   |  || ||  ||  |  | | | |||  ||||   ||| |||   ||  ||| | ||||    ||| ||| |  |    ||
GTCGCATCGTGCGGTGCCTCAAAGCCGGCAAATATGCAGAGCGCGTCGGCGCTGG-GCCCCCGTGTACCTCTCCACCGTTCTCGAGTATCTCGCCGCCGAGgtaatccccagacccctcttcctctcttcatgtttaccagatctgctcttgtccgatctcgtttgaatcccagttgtgaatcgatt---gtttcgttcgtctccgcag

upper sequence: AT1G08880.1 (Arabidopsis thaliana), 5'ss of exon 1
lower sequence: EFJ38642 (Selaginella moellendorffii), 5'ss of exon 1
AAGAATCGCTAGATTCCTCAAATCCGGTAAATACGCCGAGCGTGTCGGTGCCGGAGCTCCGGTCTATCTCTCCGCTGTTCTCGAGTACCTCGCCGCCGAGgta-atttatttttcttgtcttccaattt--ggttttcaatttcgatttggtcacatctgaattggatcttgtactgatttgattt--tgatttggtttgggttgatag
||| |||||| ||||||||||  | || || || ||||||||||| ||||||||||||||||||||  |  |||| || |||||||| || ||||||||||||  | |  | |||  |        |||  |||| |     |    || ||  ||     || | |    |||  |||||  | |  |||| |     |         
AAGGATCGCTCGATTCCTCAAGGCGGGCAAGTATGCCGAGCGTGTTGGTGCCGGAGCTCCGGTCTACATGGCCGCCGTGCTCGAGTATCTAGCCGCCGAGgtatgtgtgatcttcgcgctcatgggtttagggttcttgggcttttctttgtggca----gatcgaaga--gtaacgattttgtgtgatgatctacccag---------

upper sequence: AT1G08880.1 (Arabidopsis thaliana), 5'ss of exon 1
lower sequence: EFJ31506 (Selaginella moellendorffii), 5'ss of exon 1
AAGAATCGCTAGATTCCTCAAATCCGGTAAATACGCCGAGCGTGTCGGTGCCGGAGCTCCGGTCTATCTCTCCGCTGTTCTCGAGTACCTCGCCGCCGAGgta-atttatttttcttgtcttccaatttgg---ttttcaatttcgatttggtcacatctgaattggatcttgtactgatttgattttgatttggtttgggttgatag
||| |||||| ||||||||||  | || || || ||||||||||| ||||||||||||||||||||  |  |||| || |||||||| || ||||| ||||||  | |  | |||  |   |    ||| |   | ||    ||   ||| | || || ||||  |  |   |   |  | ||||  | || |     |         
AAGGATCGCTCGATTCCTCAAGGCGGGCAAGTATGCCGAGCGTGTTGGTGCCGGAGCTCCGGTCTACATGGCCGCCGTGCTCGAGTATCTAGCCGCGGAGgtatgtgtgatcttcgcgctcttgggtttagggttcttgggcttttcttttggcagat-tgaa--gagtaacgattttgtgtgatgatcatctacccag---------

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|164187467|gb|ES073922.1|ES073922
EST:     GTACCTCGCCGCCGAG                         GTGTTGGAGCTGGCGGGAAACGCAGCAAGGGATAACAAGAAGACACGTATA
genomic: GTACCTCGCCGCCGAGgtaatttatt ... gggttgatagGTGTTGGAGCTGGCGGGAAACGCAGCAAGGGATAACAAGAAGACACGTATA
EST: gi|116476818|gb|EG519410.1|EG519410
EST:     CCGGAGCTCCGGTCTATCTCTCCGCTGTTCTCGAGTACCTCGCCGCCGAG                         GTGTTGGAGCTGGCGGTAAACGCAGCAAGGGATAACAAGAAGACACGTATA
genomic: CCGGAGCTCCGGTCTATCTCTCCGCTGTTCTCGAGTACCTCGCCGCCGAGgtaatttatt ... gggttgatagGTGTTGGAGCTGGCGGGAAACGCAGCAAGGGATAACAAGAAGACACGTATA
EST: gi|116471932|gb|EG514524.1|EG514524
EST:     CCGGAGCTCCGGTCTATCTCTCCGCTGTTCTCGAGTACCTCGCCGCCGAG                         GTGTTGGAGCTGGCGGGAAA
genomic: CCGGAGCTCCGGTCTATCTCTCCGCTGTTCTCGAGTACCTCGCCGCCGAGgtaatttatt ... gggttgatagGTGTTGGAGCTGGCGGGAAA
EST: gi|124840931|gb|EH925370.1|EH925370
EST:     CCGGAGCTCCGGTCTATCTCTCCGCTGTTCTCGAGTACCTCGCCGCCGAG                         GTGTTGGAGCTGGACGGG
genomic: CCGGAGCTCCGGTCTATCTCTCCGCTGTTCTCGAGTACCTCGCCGCCGAGgtaatttatt ... gggttgatagGTGTTGGAGCTGG-CGGG
EST: gi|86080739|gb|DR376496.1|DR376496
EST:     CCGGAGCTCCGGTCTATCTCTCCGCTGTTCTCGAGTACCTCGCCGCCGAG                         GTGTTGGAGCTGGCGGGAAACGCAGCAAGGGATAACAAGAAGACACGTATA
genomic: CCGGAGCTCCGGTCTATCTCTCCGCTGTTCTCGAGTACCTCGCCGCCGAGgtaatttatt ... gggttgatagGTGTTGGAGCTGGCGGGAAACGCAGCAAGGGATAACAAGAAGACACGTATA
EST: gi|124706711|gb|EH798113.1|EH798113
EST:     CCGGAGCTCCGGTCTATCTCTCCGCTGTTCTCGAGTACCTCGCCGCCGAG                         GTGTTGGAGCTGGCGG
genomic: CCGGAGCTCCGGTCTATCTCTCCGCTGTTCTCGAGTACCTCGCCGCCGAGgtaatttatt ... gggttgatagGTGTTGGAGCTGGCGG
EST: gi|125225040|gb|EL239125.1|EL239125
EST:     CCGGAGCTCCGGTCTATCTCTCCGCTGTTCTCGAGTACCTCGCCGCCGAG                         GTGTTGGAGCTGGCGGGAAACGCAGCAAGGGATAACAAGAAGACACGTATA
genomic: CCGGAGCTCCGGTCTATCTCTCCGCTGTTCTCGAGTACCTCGCCGCCGAGgtaatttatt ... gggttgatagGTGTTGGAGCTGGCGGGAAACGCAGCAAGGGATAACAAGAAGACACGTATA
EST: gi|125283621|gb|EL297706.1|EL297706
EST:     CCGGAGCTCCGGTCTATCTCTCCGCTGTTCTCGAGTACCTCGCCGCCGAG                         GTGTTGGAGCTGGCGGG
genomic: CCGGAGCTCCGGTCTATCTCTCCGCTGTTCTCGAGTACCTCGCCGCCGAGgtaatttatt ... gggttgatagGTGTTGGAGCTGGCGGG
EST: gi|164094390|gb|ES079338.1|ES079338
EST:     CCGGAGCTCCGGTCTATCTCTCCGCTGTTCTCGAGTACCTCGCCGCCGAG                         GTGTTGGAGCTGGCGGG
genomic: CCGGAGCTCCGGTCTATCTCTCCGCTGTTCTCGAGTACCTCGCCGCCGAGgtaatttatt ... gggttgatagGTGTTGGAGCTGGCGGG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAGAATCGCTAGATTCCTCAAATCCGGTAAATACGCCGAGCGTGTCGGTGCCGGAGCTCCGGTCTATCTCTCCGCTGTTCTCGAGTACCTCGCCGCCGAGgtaatttatttttcttgtcttccaatttggttttcaatttcgatttggtcacatctgaattggatcttgtactgatttgattttgatttggtttgggttgatag

- - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT