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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcaacatttctcttttaccaatgacgaatgaatgatttacttttggaactctgaatcgaataactaaaaggactggctttatatatgaatgcagAAATATGACAAACTGTTTGAGAATAATGCGAAAGCAGGGAGCTTTTACCTTCAATCTAAAGTTCATCGAGCCAAAGAATGTCTAGAAGTTGTGTACAGAA

Basic information

species Arabidopsis thaliana
transcript AT3G59280.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G59280.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA02G08820.1 (Glycine max), 3'ss of exon 2
--gtcaacatttctcttttaccaatgacgaatgaatgatttacttttggaactctgaatcgaataactaa-aaggactggctttatatatga--atgcagAAATATGACAAACTGTTTGAGAATAATGCGAAAGCAGGGAGCTTTTACCTTCAATCTAAAGTTCATCGAGCCAAAGAATGTCTAGAAGTTGTGTACAGAA
  || |  | ||  |  ||          | |  |   || || |        || |||        ||| ||   ||     ||| | |    |||||||||||||||||  |||||||||||||||| |||   ||||| || ||||| || || ||||||||||| ||||| ||||||||||| |  ||  |   | 
tggttataactttgcacttgttttgctgaagtatacccttcacatcataggagctaaattattcttttaataattgcttaaaatatttcttgccatgcagAAATATGACAATTTGTTTGAGAATAATGCCAAAAATGGGAGTTTCTACCTCCAGTCCAAAGTTCATCGGGCCAAGGAATGTCTAGAGGCAGTTCAACAAG

upper sequence: AT3G59280.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA16G27940.2 (Glycine max), 3'ss of exon 3
-gtcaacatttctcttttaccaatgacgaatgaatgatttacttttggaactctgaatcgaataactaaaaggac--tggctttatatatgaa--tgcagAAATATGACAAACTGTTTGAGAATAATGCGAAAGCAGGGAGCTTTTACCTTCAATCTAAAGTTCATCGAGCCAAAGAATGTCTAGAAGTTGTGTACAGAA
 |      ||| | ||||     ||| | ||      || ||||  |     || ||         ||| ||     |     ||| | |     ||||||||||||||||  | |||||||||||||| ||    ||||| || ||||| || || ||||||||||| ||||| ||||||||||| |  ||  |   | 
tgcacttttttttttttttttgctgaagtataccattttcacttcagaggagctaaaattttcttgtaatagtttcttaaaaatatttcttgccttgcagAAATATGACAATTTATTTGAGAATAATGCTAAGAATGGGAGTTTCTACCTCCAGTCCAAAGTTCATCGGGCCAAGGAATGTCTAGAGGCAGTTCAACAAG

upper sequence: AT3G59280.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA06G20480.1 (Glycine max), 3'ss of exon 1
--gtcaacatttctcttttaccaatgacgaatgaatgatttacttttggaactctgaatcgaataactaaaaggactggctttatatatg-----aatgcagAAATATGACAAACTGTTTGAGAATAATGCGAAAGCAGGGAGCTTTTACCTTCAATCTAAAGTTCATCGAGCCAAAGAATGTCTAGAAGTTGTGTACAGAA
   | |  | ||| | |||| |  |    |  | ||  ||| |||| |      | |||    |   || ||    ||  |  | || |        ||||||||||||  |   | |||||||| ||| | ||    ||||| |||||||| ||||| ||||||||||| ||||| |||||||| || | |||  |   | 
acattataacttcacgtttatctttttaaagcgcatcctttgctttggaggagttaaattt--ttgttataatagttgtttaaacatttttcttccgtgcagAAATATGGTAGTTTATTTGAGAACAATACCAAGAATGGGAGTTTTTACCTCCAATCCAAAGTTCATCGGGCCAAGGAATGTCTGGAGGCTGTCCATCAAG

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|86063868|gb|DR359625.1|DR359625
EST:     GGCAGATTCTTGGTGTAAC-GAGAAGACCTCTTGGGAAGAGATATTACAG                         AAATATGACAAACTGTTTGAGAATAATGCGAAA
genomic: GGCAGATTCTTGGTGTAACCGAGAAGACCTCTTGGGAAGAGATATTACAGgtcaacattt ... atgaatgcagAAATATGACAAACTGTTTGAGAATAATGCGAAA
EST: gi|152038381|gb|AV821341.2|AV821341
EST:     GGCAGATTCTTGGTGTAACCGAGAAGACCTCTTGGGAAGAGATATTACAG                         AAATATGACAAACTGTTTGAGAATAATGCGAAAGCAGGGAGCTTTTACCTT
genomic: GGCAGATTCTTGGTGTAACCGAGAAGACCTCTTGGGAAGAGATATTACAGgtcaacattt ... atgaatgcagAAATATGACAAACTGTTTGAGAATAATGCGAAAGCAGGGAGCTTTTACCTT
EST: gi|86082243|gb|DR378002.1|DR378002
EST:     GGCAGATTCTTGGTGTAACCGAGAAGACCTCTTGGGAAGAGATATTACAG                         AAATATGACAAACTGTTTGAGAATAATGCGAAAGCAGGGAGCTTTTACCTT
genomic: GGCAGATTCTTGGTGTAACCGAGAAGACCTCTTGGGAAGAGATATTACAGgtcaacattt ... atgaatgcagAAATATGACAAACTGTTTGAGAATAATGCGAAAGCAGGGAGCTTTTACCTT
EST: gi|86084307|gb|DR380066.1|DR380066
EST:     GGCAGATTCTTGGTGTAACCGAGAAGACCTCTTGGGAAGAGATATTACAG                         AAATATGACAAACTGTTTGAGAATAATGCGAAAGCAGGGAGCTTTTACCTT
genomic: GGCAGATTCTTGGTGTAACCGAGAAGACCTCTTGGGAAGAGATATTACAGgtcaacattt ... atgaatgcagAAATATGACAAACTGTTTGAGAATAATGCGAAAGCAGGGAGCTTTTACCTT
EST: gi|116454644|gb|EG497236.1|EG497236
EST:     GGCAGATTCTTGGTGTAACCGAGAAGACCTCTTGGGAAGAGATATTACAG                         AAATATGACAAACTGTTTGAGAATAATGCGAAAGCAGGGAGCTTTTACCTT
genomic: GGCAGATTCTTGGTGTAACCGAGAAGACCTCTTGGGAAGAGATATTACAGgtcaacattt ... atgaatgcagAAATATGACAAACTGTTTGAGAATAATGCGAAAGCAGGGAGCTTTTACCTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttttggaactctgaatcgaataactaaaaggactggctttatatatgaatgcagAAATATGACAAACTGTTTGAGAATAATGCGAAAGCAGGGAGCTTTTACCTTCAATCTAAAGTTCATCGAGCCAAAGAATGTCTAGAAGTTGTGTACAGAA
                      aactaaa  putative branch site (score: 2)
                                      tttatatatgaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcaacatttctcttttaccaatgacgaatgaatgatttacttttggaactctgaatcgaataactaaaaggactggctttatatatgaatgcagAAATATGACAAACTGTTTGAGAATAATGCGAAAGCAGGGAGCTTTTACCTTCAATCTAAAGTTCATCGAGCCAAAGAATGTCTAGAAGTTGTGTACAGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT