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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gattatttttcttctgggtacccaaaaggttgaaactataataactttctcaaaacttaaagaggctaacaaggttttatatatatgttctgtttggcagCTCTGGGACATCTGGTGGGGAGAGGAAGCTAATGCCAACAATCGAAGAGGAGCTAGACAGGAGATCACTCCTCTACAGTCTCTTGATGCCTGTGATGAGC

Basic information

species Arabidopsis thaliana
transcript AT4G27260.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G27260.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G061515_T01 (Zea mays), 3'ss of exon 1
---gattatttttcttctgggtac--ccaaaaggttgaaactataataactttc---tcaaaacttaaagaggctaacaaggt-------tttatatat----atgttc-tgtttgg--cagCTCTGGGACATCTGGTGGGGAGAGGAAGCTAATGCCAACAATCGAAGAGGAGCTAGACAGGAGATCACTCCTCTACAGTCTCTTGATGCCTGTGATGAGC
   |  ||||  ||      ||||   || || | ||  |         || |    |||||| |||| |    |   ||  |       ||||||  |    |||||  ||| ||   ||||||||| ||||| || |||||||||||||| ||||| || ||||  || ||||| |||||||| ||  | || || || ||   |||||| |||||||||
gtagtatattcatccctcacgtacgatcacaacgctgtgatgcatgcggctgtggaatcaaaatttaacggacatgggaacatgtactgatttataactgaggatgtttgtgtgtgaaccagCTCTGGAACATCCGGAGGGGAGAGGAAGCTGATGCCGACCATCGCCGACGAGCTGGACAGGAGGTCGTTGCTGTATAGCCTGCAGATGCCGGTGATGAGC

upper sequence: AT4G27260.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA12G11200.1 (Glycine max), 3'ss of exon 2
gattatttttcttctgggtacccaaaaggttgaaactataataactttctcaaaacttaaagaggctaacaaggttttatatatatgttctgtttg-gcagCTCTGGGACATCTGGTGGGGAGAGGAAGCTAATGCCAACAATCGAAGAGGAGCTAGACAGGAGATCACTCCTCTACAGTCTCTTGATGCCTGTGATGAGC
 |  |         || | |    ||      ||| ||| | ||   |        | |||   |  |  ||  |   ||   | ||||   ||     |||||||| ||||||||||||||||| || || |||||||| || ||||||||||||||  | |||||| | |||||||| ||| ||||||| ||||||   
-agaaacaagagaatgtgaattataataaagaaaattatgaaaaaagtgcatgttgtaaaaagagtgagtaaaataacattattctgttgatttaatatagCTCTGGAACATCTGGTGGGGAGAGAAAACTGATGCCAACCATAGAAGAGGAGCTAGAGCGAAGATCATTACTCTACAGCCTCCTGATGCCAGTGATGGAG

upper sequence: AT4G27260.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA13G38000.1 (Glycine max), 3'ss of exon 1
gattatttttcttctgggtacccaaaaggttgaaactataataactttctcaaaacttaaa--gaggctaac-aaggttttatatatatgttctgtttggcagCTCTGGGACATCTGGTGGGGAGAGGAAGCTAATGCCAACAATCGAAGAGGAGCTAGACAGGAGATCACTCCTCTACAGTCTCTTGATGCCTGTGATGAGC
  ||   |    ||| |  | | |     || | || ||  |  | ||||      |||||   ||  || |  |  ||  |||||| | ||   |     ||||||||||| |||||||||||||| ||  | |||||||| || |||||||||||||| ||||||||| | || || || ||||||||||| ||||||   
--tttgctaaaatcttgacatcaattttcttcatacaatt-tgtccttcttcctttttaaattaagtatagctgaaattagatatatttattgaatgaaatagCTCTGGGACTTCTGGTGGGGAGAGAAAATTGATGCCAACCATAGAAGAGGAGCTAGAGAGGAGATCAATGCTTTATAGCCTCTTGATGCCAGTGATGGAT

upper sequence: AT4G27260.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA12G32410.1 (Glycine max), 3'ss of exon 1
gattatttttcttctgggtacccaaaaggttgaaactataataactttctcaaaacttaaagaggctaacaaggttttatatatatgttctgtttgg--cagCTCTGGGACATCTGGTGGGGAGAGGAAGCTAATGCCAACAATCGAAGAGGAGCTAGACAGGAGATCACTCCTCTACAGTCTCTTGATGCCTGTGATGAGC
   ||||     |     | |   | |        |  |  |   ||||  | ||  |  |   |  |  ||  |   |||||| | |  ||  ||    ||||||||||| |||||||||||||| ||  | |||||||| || |||||||||||||| ||||||||| | || || || ||||||||||| ||||||   
--atattgacaataaattttcttcatataacttgtccttcttccttttcaaataaagtgcaactgaaattaatctgagatatatgtttcttgaatgaattagCTCTGGGACTTCTGGTGGGGAGAGAAAATTGATGCCAACCATAGAAGAGGAGCTAGAGAGGAGATCAATGCTTTATAGCCTCTTGATGCCGGTGATGGAT

upper sequence: AT4G27260.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA06G45640.1 (Glycine max), 3'ss of exon 1
-----gattatttttcttctgggtacccaaaaggttgaaactataataactttctcaaaacttaaagaggctaacaaggttttatatatatgttctgtttggcagCTCTGGGACATCTGGTGGGGAGAGGAAGCTAATGCCAACAATCGAAGAGGAGCTAGACAGGAGATCACTCCTCTACAGTCTCTTGATGCCTGTGATGAGC
     ||  |         || | |    |||     ||| ||| | ||  |  |  |||   |  ||    || ||  || | | | |   ||   | |   |||||||| |||||||| |||||||| || || |||||||| || ||||| ||||||||  | |||||| | |||||||| ||||||||||| ||||||  |
aagaagagaaacaagaggatgtgaattataaaaag-aaaattatgaaaaagtgttgtaaagagagtgaatgaaataacattat-tctgttgatttaatct---agCTCTGGAACATCTGGAGGGGAGAGAAAACTGATGCCAACCATAGAAGACGAGCTAGAGCGAAGATCATTGCTCTACAGCCTCTTGATGCCAGTGATGGAC

upper sequence: AT4G27260.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA06G40860.1 (Glycine max), 3'ss of exon 1
gattatttttcttctgggtacccaaaaggttgaaactataataactttctcaaaacttaaagaggctaacaaggt-tttatatatatgttc---tgtttggcagCTCTGGGACATCTGGTGGGGAGAGGAAGCTAATGCCAACAATCGAAGAGGAGCTAGACAGGAGATCACTCCTCTACAGTCTCTTGATGCCTGTGATGAGC
|||   | | | ||    |  |   |    |  | | || | | |   || | || ||       ||||  | || || |||| | | ||    ||| |||||| ||||||||||| || || ||||||||||| ||||||||||| ||||| |||||||  || ||     | || || || ||  ||||||| |||||||||
gatc--tctccatccttttttcttgatcccttcacccatcaaaccaaccttataatttttgtt--ctaatcatgtgttcatatttttttttttgtgtgtggcagTTCTGGGACATCAGGAGGTGAGAGGAAGCTGATGCCAACAATTGAAGAAGAGCTAGGTAGAAGGAGTTTGCTGTATAGCCTTCTGATGCCAGTGATGAGC

upper sequence: AT4G27260.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA12G17510.1 (Glycine max), 3'ss of exon 1
--------gattatttttcttctgggtacccaaaaggttgaaactataataactttctcaaaacttaaagaggctaacaaggttttatatatatgttctgtttggcagCTCTGGGACATCTGGTGGGGAGAGGAAGCTAATGCCAACAATCGAAGAGGAGCTAGACAGGAGATCACTCCTCTACAGTCTCTTGATGCCTGTGATGAGC
         ||  ||||| ||      |   |  |  |  |   ||||||  | || |       |||   ||    ||    ||| | | | |||   | |    || ||||||||||| || || ||||||||||| ||||||||||| ||||| |||||||  || ||     | |||||||| ||||||||||| ||||||  |
aatctcccaatcttttttttttctttcaattatcaaatcaatgttataatcccattttttttttctaatttggtgttca----tttttgtgtgtgtggggct----agTTCTGGGACATCAGGAGGTGAGAGGAAGCTGATGCCAACAATTGAAGAAGAGCTAGGGAGAAGGAGTTTGCTCTACAGCCTCTTGATGCCAGTGATGTCC

upper sequence: AT4G27260.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA13G36030.1 (Glycine max), 3'ss of exon 1
gattatttttcttctgggtacccaaaaggttgaaactataataactttctcaaaacttaaagaggctaacaag---gttttatatatat--gttctg--tttggcagCTCTGGGACATCTGGTGGGGAGAGGAAGCTAATGCCAACAATCGAAGAGGAGCTAGACAGGAGATCACTCCTCTACAGTCTCTTGATGCCTGTGATGAGC
       |||  | | ||||         || |     |  |  | ||     |   |||  |  ||||   |   ||||| | ||| |  ||| ||  ||| | |||||||| ||||| || || ||||| ||| | ||||||||||| |||||||||||||  ||||| |   |  | ||||| |||||||||||  | ||||  
-------tttggttttggtattttttttcttcagttagttttttcatttggtcaggctaattaaactaatgggcatgttttgtttatttctgttttggattttgaagCTCTGGCACATCAGGGGGTGAGAGAAAGTTGATGCCAACAATTGAAGAGGAGCTAGGAAGGAGGTGTATGTTGTACAGCCTCTTGATGCCAATAATGAAT

upper sequence: AT4G27260.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv19s0014g04690.t01 (Vitis vinifera), 3'ss of exon 1
gattatttttc-ttctgggtacccaaaaggttgaaactataataactt-tctcaaaacttaaagaggct-aacaaggtt-ttatatatatgttctgtttggcagCTCTGGGACATCTGGTGGGGAGAGGAAGCTAATGCCAACAATCGAAGAGGAGCTAGACAGGAGATCACTCCTCTACAGTCTCTTGATGCCTGTGATGAGC
   |||| ||| || | ||||        |       | | | ||  | |    |||   |  ||  || ||   ||||  | | ||| || | || || ||||||| ||||| ||||| |||||||||||||| |||||||| || ||||| ||||| || ||||| ||| | || || |||||  | ||||| |||||||||
--gtattgttcgttgttggtaattggggtgagaggcttttcagaatgtgtactcaaatggattgaaactgaatgcggttgctttttatttgctttgctttgcagCTCGGGGACTTCTGGCGGGGAGAGGAAGCTGATGCCAACCATAGAAGAAGAGCTGGAGAGGAGGTCATTGCTTTATAGTCTGCTCATGCCGGTGATGAGC

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|116444574|gb|EG487166.1|EG487166
EST:     GATAAATCACCTATCCTCTCTTCCAAACCCATCTCTGAGTTCCTCACAAG                         CTCTGGGACATCTGGTGGGGAGAGGAAGCTAATGCCAACAATCGAAGAGGA
genomic: GATAAATCACCTATCCTCTCTTCCAAACCCATCTCTGAGTTCCTCACAAGgtaaacattc ... tgtttggcagCTCTGGGACATCTGGTGGGGAGAGGAAGCTAATGCCAACAATCGAAGAGGA
EST: gi|116443601|gb|EG486193.1|EG486193
EST:     GATAAATCACCTATCCTCTCTTCCAAACCCATCTCTGAGTTCCTCACAAG                         CTCTGGGACATCTGGTGGGGAGAGGAAGCTAATGCCAACAATCGAAGAGGA
genomic: GATAAATCACCTATCCTCTCTTCCAAACCCATCTCTGAGTTCCTCACAAGgtaaacattc ... tgtttggcagCTCTGGGACATCTGGTGGGGAGAGGAAGCTAATGCCAACAATCGAAGAGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttctcaaaacttaaagaggctaacaaggttttatatatatgttctgtttggcagCTCTGGGACATCTGGTGGGGAGAGGAAGCTAATGCCAACAATCGAAGAGGAGCTAGACAGGAGATCACTCCTCTACAGTCTCTTGATGCCTGTGATGAGC
                  ggctaac  putative branch site (score: 2)
                                          ttctgttt  putative PPT
                             ttttatatatatgttc  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gattatttttcttctgggtacccaaaaggttgaaactataataactttctcaaaacttaaagaggctaacaaggttttatatatatgttctgtttggcagCTCTGGGACATCTGGTGGGGAGAGGAAGCTAATGCCAACAATCGAAGAGGAGCTAGACAGGAGATCACTCCTCTACAGTCTCTTGATGCCTGTGATGAGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTCCTC
- - - - - - - - - -acccaaa
- - - - - - - - - - - - - - - -gaaacta
- - - - - - - - - - - - - - - - - - - - - - - - - - - acttaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctaacaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ggtttta