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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaaacctctttctttcaagaacttatctcagtttttctatacgcctacattttggtttcttatcaaaatttctttgaatatattttagGCGTTTTTAGCTTATGGGATTCCACAGAACAATGTGAAGAGAGTCTTACTTCTACTCAAG

Basic information

species Arabidopsis thaliana
transcript AT5G66600.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G66600.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA01G38680.1 (Glycine max), 3'ss of exon 9
---gtaaaacctctttctttcaagaacttatctcagttt--ttctatacgcctacattttggtttctta--tcaaaatttctttgaatatattt--tagGCGTTTTTAGCTTATGGGATTCCACAGAACAATGTGAAGAGAGTCTTACTTCTACTCAAG
    |  |   | || || |||||||  |   || || |  | || | |   | |  |||| ||  ||   | | ||||| ||    | | | |  ||||| ||||| ||||||||||||||||| ||||||||||| |||||||| |||||| | |||
gtaatttattattttactatcaagaatatgcttctgtataatactttcccattcccatttgattagttgggttataatttgttcttttgtttctaatagGCATTTTTGGCTTATGGGATTCCACAAAACAATGTGAAAAGAGTCTTTCTTCTATTGAAG

upper sequence: AT5G66600.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA11G06610.1 (Glycine max), 3'ss of exon 3
---gtaaaacctctttctttcaagaacttatctcagtttttctatacgcctacattttggtt--tcttatcaaaatttctttgaatatattt--tagGCGTTTTTAGCTTATGGGATTCCACAGAACAATGTGAAGAGAGTCTTACTTCTACTCAAG
    |  |   |  | || |||||||  | | ||||| |    |||    | |  |||| ||  |  | | | ||||| ||      | | |  ||||| ||| | ||||||||||||||||| ||||||||||| |||||||| |||||  | |||
gtaatttattattatactatcaagaatatgtttcagtgta---atatttttcccatttgattagttgtgttataatttgttctttcgtttctaatagGCATTTCTGGCTTATGGGATTCCACAAAACAATGTGAAAAGAGTCTTTCTTCTTTTGAAG

upper sequence: AT5G66600.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA16G25820.1 (Glycine max), 3'ss of exon 6
gtaaaacctctttctttcaa---gaacttatctcagtt---tttctatacgcctacattttggtttcttatcaaaatttctttgaatatattttagGCGTTTTTAGCTTATGGGATTCCACAGAACAATGTGAAGAGAGTCTTACTTCTACTCAAG
||||    | || || ||||    || ||  ||   ||   |||| ||    ||  |||  ||||   ||  |   | | |||   | | |  ||||| ||||| |||||||| |||||||| ||||||||||| || ||||| |||||  | |||
gtaattattattactctcaaaacaaatttccctttattagttttccatttctcttgattgaggtta--taatatgctcttttttggtttctaatagGCATTTTTGGCTTATGGAATTCCACAAAACAATGTGAAAAGGGTCTTCCTTCTGTTAAAG

upper sequence: AT5G66600.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA02G06790.1 (Glycine max), 3'ss of exon 7
gtaaaacctctttctttcaagaacttatctcagtttttctatacgcctacattttggtttc-------ttatcaaaatttctttgaatatattttagGCGTTTTTAGCTTATGGGATTCCACAGAACAATGTGAAGAGAGTCTTACTTCTACTCAAG
||||    | |  || |||| |   | | ||  ||| |   |   || |   | |   |||       |||| || || | ||||  | | |  ||||| ||||| |||||||| |||||||| ||||||||||| || || || |||||  | |||
gtaattattatcactctcaaaacaatgtttccctttcttagttttccaatgctctcacttcattgaggttat-aatatgtttttgggtttctaatagGCATTTTTGGCTTATGGAATTCCACAAAACAATGTGAAAAGGGTATTCCTTCTGTTAAAG

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|116429882|gb|EG472474.1|EG472474
EST:     AAGAGAAGCTAGCGTTTTGGATAAATGTGCACAATGCACTTGTGATGCAT                         GCGTTTTTAGCTTATGGGATTCCACAGAACAATGTGAAGAGAGTCTTACTT
genomic: AAGAGAAGCTAGCGTTTTGGATAAATGTGCACAATGCACTTGTGATGCATgtaaaacctc ... tatattttagGCGTTTTTAGCTTATGGGATTCCACAGAACAATGTGAAGAGAGTCTTACTT
EST: gi|116429885|gb|EG472477.1|EG472477
EST:     AAGAGAAGCTAGCGTTTTGGATAAATGTGCACAATGCACTTGTGATGCAT                         GCGTTTTTTAGCTTATGGGATTCCACAGAACAATGTGAAGAGAGTCTTACT
genomic: AAGAGAAGCTAGCGTTTTGGATAAATGTGCACAATGCACTTGTGATGCATgtaaaacctc ... tatattttagGCGTTTTT-AGCTTATGGGATTCCACAGAACAATGTGAAGAGAGTCTTACT
EST: gi|116429875|gb|EG472467.1|EG472467
EST:     AAGAGAAGCTAGCGTTTTGGATAAATGTGCACAATGCACTTGTGATGCAT                         GCGTTTTTAGCTTATGGGATTCCACAGAACAATGTGAAGAGAGTCTTACTT
genomic: AAGAGAAGCTAGCGTTTTGGATAAATGTGCACAATGCACTTGTGATGCATgtaaaacctc ... tatattttagGCGTTTTTAGCTTATGGGATTCCACAGAACAATGTGAAGAGAGTCTTACTT
EST: gi|116429897|gb|EG472489.1|EG472489
EST:     AAGAGAAGCTAGCGTTTTGGATAAATGTGCACAATGCACTTGTGATGCAT                         GCGTTTTTAGCTTATGGGATTCCACAGAACAATGTGAAGAGAGTCTTACTT
genomic: AAGAGAAGCTAGCGTTTTGGATAAATGTGCACAATGCACTTGTGATGCATgtaaaacctc ... tatattttagGCGTTTTTAGCTTATGGGATTCCACAGAACAATGTGAAGAGAGTCTTACTT
EST: gi|116429899|gb|EG472491.1|EG472491
EST:     AAGAGAAGCTAGCGTTTTGGATAAATGTGCACAATGCACTTGTGATGCAT                         GCGTTTTTAGCTTATGGGATTCCACAGAACAATGTGAAGAGAGTCTTACTT
genomic: AAGAGAAGCTAGCGTTTTGGATAAATGTGCACAATGCACTTGTGATGCATgtaaaacctc ... tatattttagGCGTTTTTAGCTTATGGGATTCCACAGAACAATGTGAAGAGAGTCTTACTT
EST: gi|116429876|gb|EG472468.1|EG472468
EST:     GAAGCTAGCGTTTTGGATAAATGTGCACAATGCACTTGTGATGCAT                         GCGTTTTTAGCTTATGGGATTCCACAGAACAATGTGAAGAGAGTCTTACTT
genomic: GAAGCTAGCGTTTTGGATAAATGTGCACAATGCACTTGTGATGCATgtaaaacctc ... tatattttagGCGTTTTTAGCTTATGGGATTCCACAGAACAATGTGAAGAGAGTCTTACTT
EST: gi|116429878|gb|EG472470.1|EG472470
EST:     AAGAGAAGCTAGCGTTTTGGATAAATGTGCACAATGCACTTGTGATGCAT                         GCGTTTTTAGCTTATGGGATTCCACAGAACAATGTGAAGAGAGTCTTACAT
genomic: AAGAGAAGCTAGCGTTTTGGATAAATGTGCACAATGCACTTGTGATGCATgtaaaacctc ... tatattttagGCGTTTTTAGCTTATGGGATTCCACAGAACAATGTGAAGAGAGTCTTACTT
EST: gi|116429887|gb|EG472479.1|EG472479
EST:     AAGAGAAGCTAGCGTTTTGGATAAATGTGCACAATGCACTTGTGATGCAT                         GCGTTTTTAGCTTATGGGATTCCACAGAACAATGTGAAGAGAGTCTTACTT
genomic: AAGAGAAGCTAGCGTTTTGGATAAATGTGCACAATGCACTTGTGATGCATgtaaaacctc ... tatattttagGCGTTTTTAGCTTATGGGATTCCACAGAACAATGTGAAGAGAGTCTTACTT
EST: gi|116429896|gb|EG472488.1|EG472488
EST:     AAGAGAAGCTAGCGTTTTGGATAAATGTGCACAATGCACTTGTGATGCAT                         GCGTTTTTAGCTTATGGGATTCCACAGAACAATGTGAAGAGAGTCTTACTT
genomic: AAGAGAAGCTAGCGTTTTGGATAAATGTGCACAATGCACTTGTGATGCATgtaaaacctc ... tatattttagGCGTTTTTAGCTTATGGGATTCCACAGAACAATGTGAAGAGAGTCTTACTT
EST: gi|116429893|gb|EG472485.1|EG472485
EST:     AAGAGAAGCTAGCGTTTTGGATAAATGTGCACAATGCACTTGTGATGCAT                         GCGTTTTTAGCTTATGGGATTCCACAGAACAATGTGAAGAGAGTCTTACTT
genomic: AAGAGAAGCTAGCGTTTTGGATAAATGTGCACAATGCACTTGTGATGCATgtaaaacctc ... tatattttagGCGTTTTTAGCTTATGGGATTCCACAGAACAATGTGAAGAGAGTCTTACTT
EST: gi|116429873|gb|EG472465.1|EG472465
EST:     AAGAGAAGCTAGCGTTTTGGATAAATGTGCACAATGCACTTGTGATGCAT                         GCGTTTTTAGCTTATGGGATTCCACAGAACAATGTGAAGAGAGTCTTACTT
genomic: AAGAGAAGCTAGCGTTTTGGATAAATGTGCACAATGCACTTGTGATGCATgtaaaacctc ... tatattttagGCGTTTTTAGCTTATGGGATTCCACAGAACAATGTGAAGAGAGTCTTACTT
EST: gi|116429874|gb|EG472466.1|EG472466
EST:     TAAATGTGCACAATGCACTTGTGATGCAT                         GCGTTTTTAGCTTATGGGATTCCACAGAACAATGTGAAGAGAGTCTTACTT
genomic: TAAATGTGCACAATGCACTTGTGATGCATgtaaaacctc ... tatattttagGCGTTTTTAGCTTATGGGATTCCACAGAACAATGTGAAGAGAGTCTTACTT
EST: gi|116429880|gb|EG472472.1|EG472472
EST:     AAGAGAAGCTAGCGTTTTGGATAAATGTGCACAATGCACTTGTGATGCAT                         GCGTTTTTAGCTTATGGGATTCCACAGAACAATGTGAAGAGAGTCTTACTT
genomic: AAGAGAAGCTAGCGTTTTGGATAAATGTGCACAATGCACTTGTGATGCATgtaaaacctc ... tatattttagGCGTTTTTAGCTTATGGGATTCCACAGAACAATGTGAAGAGAGTCTTACTT
EST: gi|116429891|gb|EG472483.1|EG472483
EST:     AAGAGAAGCTAGCGTTTTGGATAAATGTGCACAATGCACTTGTGATGCAT                         GCGTTTTTAGCTTATGGGATTCCACAGAACAATGTGAAGAGAGTCTTACTT
genomic: AAGAGAAGCTAGCGTTTTGGATAAATGTGCACAATGCACTTGTGATGCATgtaaaacctc ... tatattttagGCGTTTTTAGCTTATGGGATTCCACAGAACAATGTGAAGAGAGTCTTACTT
EST: gi|116429889|gb|EG472481.1|EG472481
EST:     AAGAGAAGCTAGCGTTTTGGATAAATGTGCACAATGCACTTGTGATGCAT                         GCGTTTTTAGCTTATGGGATTCCACAGAACAATGTGAAGAGAGTCTTACTT
genomic: AAGAGAAGCTAGCGTTTTGGATAAATGTGCACAATGCACTTGTGATGCATgtaaaacctc ... tatattttagGCGTTTTTAGCTTATGGGATTCCACAGAACAATGTGAAGAGAGTCTTACTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttctatacgcctacattttggtttcttatcaaaatttctttgaatatattttagGCGTTTTTAGCTTATGGGATTCCACAGAACAATGTGAAGAGAGTCTTACTTCTACTCAAG
                      tttcttatcaaaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaaacctctttctttcaagaacttatctcagtttttctatacgcctacattttggtttcttatcaaaatttctttgaatatattttagGCGTTTTTAGCTTATGGGATTCCACAGAACAATGTGAAGAGAGTCTTACTTCTACTCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA