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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagtttctggttgtactgtgttgttttcagtttatcttaaatctttccaaataggtgctttacagttttacacggaactcataatagaaaatgtctttttgttaatcagCCCGGGATTACTCTCAAGCATGCCAAAGAAGGAACAGAGAGCTCAACCTTTTGGTTTGCACTTGGGGGAAAACAGAATTTCACCAGCAAGAAGGCTTCCT

Basic information

species Arabidopsis thaliana
transcript AT2G41740.1
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G41740.1 (Arabidopsis thaliana), 3'ss of exon 15
lower sequence: LOC_Os03g24220.2 (Oryza sativa), 3'ss of exon 15
gttagtttctggttgtactgtgttgttttcagtttatcttaaatctttccaa-----ataggtgctttacagttttacacggaactcataatagaaaatgtctttttgttaatcagCCCGGGATTACTCTCAAGCATGCCAAAGAAGGAACAGAGAGCTCAACCTTTTGGTTTGCACTTGGGGGAAAACAGAATTTCACCAGCAAGAAGGCTTCCT
                | ||| ||||| | | |  | |  ||   |||   |      |   | | |  |  |||  |||  ||  |  | ||    |||| |      |   ||||| ||  || || |||| |||  ||| || ||||| ||||||||  ||||||||||||| ||||| ||||| ||||||| ||| ||||  || ||  |  
--------------agaatgttttgttctgaataaaccgaaagcatttgatattttcttgaattcctagctatttctcactcaatacg-attatctgatgtttccaaacttg-cagCCTGGTGTTGCTGTCAAACATTGCAAGGAGGGAACTGAGAGCTCTGCCTTTTGGTTTGCTCTTGGTGGAAAGCAGAATTACACAAGCAGAAATGCCACAC

upper sequence: AT2G41740.1 (Arabidopsis thaliana), 3'ss of exon 15
lower sequence: GLYMA19G32010.1 (Glycine max), 3'ss of exon 15
gttagtttctggttgtactgtgttgttttcagtttatcttaaatctttccaa-ataggtgctttacagttttacacggaactcataatagaaaatgtctttttgttaatcagCCCGGGATTACTCTCAAGCATGCCAAAGAAGGAACAGAGAGCTCAACCTTTTGGTTTGCACTTGGGGGAAAACAGAATTTCACCAGCAAGAAGGCTTCCT
               || |   || |   |||| ||      || |||  || ||    | |      |  ||     |    ||  ||  | ||  |   |   |   ||||| ||  || || | |||| ||| |||||||||||||| | |||||| || |||||||||||||| |||||||| | || ||||||||| || |   |  
------------acctatttctttttcaccagtatactaatgatttttttaacatttaggttaattcatactagttaaattatatgttaacatattacacatctatgtccagCCAGGAGTTTCTTTAAAGCTTGCTAAAGAAGGAACAGAAACCTCAACTTTCTGGTTTGCACTTGGAGGAAAACAAAGTTACACCAGCAAAAATGTCACTA

upper sequence: AT2G41740.1 (Arabidopsis thaliana), 3'ss of exon 15
lower sequence: GLYMA10G21350.2 (Glycine max), 3'ss of exon 14
gttagtttctggttgtactgtgttgttttcagtttatcttaaatctttccaaataggtgctttacagttttacacggaactca-taatagaaaatgtctttttgttaatcagCCCGGGATTACTCTCAAGCATGCCAAAGAAGGAACAGAGAGCTCAACCTTTTGGTTTGCACTTGGGGGAAAACAGAATTTCACCAGCAAGAAGGCTTCCT
      |  |   |  |           | | |||| | | ||  |     |||||  | ||| |   | || ||   | |   | ||   | |  | |   ||||   ||||| ||   |||| | |||||||| |||||||||||||| |||||| | || |||| |||||| || |||||||| | || |||||||||||| | |    
------tcttacctccatccaaacaaagtgattttagcatgaagttaaaataatagtagttttgc---tctatacattatttgcttatgagatacatgtccatgtt---cagCCAGGAGCTACTTTAAAGCATGCTAAAGAAGGAACAGAAAGCTCAGCTTTCTGGTCTGCACTAGGAGGAAAACAAAGTTACACCAGCAAGAAAGTTGTTA

upper sequence: AT2G41740.1 (Arabidopsis thaliana), 3'ss of exon 15
lower sequence: GLYMA02G32100.1 (Glycine max), 3'ss of exon 13
gttagtttctggttgtactgtgttgttttcagtttatcttaaatctttccaaataggtgctttacagttttacacggaactca-taatagaaaatgtctttttgttaatcagCCCGGGATTACTCTCAAGCATGCCAAAGAAGGAACAGAGAGCTCAACCTTTTGGTTTGCACTTGGGGGAAAACAGAATTTCACCAGCAAGAAGGCTTCCT
  |    ||       ||   ||  |||| | |  |  |||||  ||      |||  | ||| |   | ||  |   | |   | ||   | |  | |   ||||   ||||| ||   |||| | |||||||| |||||||||||||| |||||| | || |||| |||||| || |||||||| | || |||||||||||| | |    
-cttacctccatccaaacaaagtgattttaactcgaagttaaaaatt-----gtagtagttttgc---tctatgcattatttgcttatgagatacatgtccatgtt---cagCCAGGAGCTACTTTAAAGCATGCTAAAGAAGGAACAGAAAGCTCAGCTTTCTGGTCTGCACTAGGAGGAAAACAAAGTTACACCAGCAAGAAAGTTGTTA

upper sequence: AT2G41740.1 (Arabidopsis thaliana), 3'ss of exon 15
lower sequence: GLYMA03G29280.1 (Glycine max), 3'ss of exon 14
gttagtttctggttgtactgtgttgttttcagtttatcttaaatctttccaaataggtgctttacagttttacacggaactcataatagaaaatgtctttttgttaatcagCCCGGGATTACTCTCAAGCATGCCAAAGAAGGAACAGAGAGCTCAACCTTTTGGTTTGCACTTGGGGGAAAACAGAATTTCACCAGCAAGAAGGCTTCCT
     |  ||     || |   || |   |||| ||   |   |  |||   || | || ||||||   ||| |||  |   ||  ||  | ||  |   |   |   ||||| ||  || || | |||| ||| |||||||||||||| | |||||| || |||||||||||||| || ||||| | || || || ||| || |   |  
--ctatgcctccacctatttctttttcaccagtatactatggttaattc---attgttg-tttaca---ttatacgttat--atgttaacatattacacatccatgtccagCCAGGAGTTGCTTTAAAGCTTGCTAAAGAAGGAACAGAAACCTCAACTTTCTGGTTTGCACTTGGAGGGAAACAAAGTTACAACAACAAAAAAGTCACTA

upper sequence: AT2G41740.1 (Arabidopsis thaliana), 3'ss of exon 15
lower sequence: Vv08s0007g08690.t01 (Vitis vinifera), 3'ss of exon 14
gttagtttctggttgtactgtgttgttt-tcagtttatcttaaatctttcca-aataggtgctttacagttttacacggaactcataatagaaaatgtctt-tttgttaatcagCCCGGGATTACTCTCAAGCATGCCAAAGAAGGAACAGAGAGCTCAACCTTTTGGTTTGCACTTGGGGGAAAACAGAATTTCACCAGCAAGAAGGCTTCCT
          | |   |     |||    ||  | | |  || ||  ||  |  ||      | || |    ||    |   |  |||| || |    ||| ||| | | |||||| ||  | ||||| || ||||| ||||||||||| ||||||||  ||||||||||||| ||||| ||||||||||||| ||| ||||| || || ||| 
----------gataacatgcccttgggcatctttctgtaatagattgtttgacgatcaagattgtata----tattgtggtttattaattgagatccacttgtttataattcagCCAGGAGTAACTCTGAAACATGCTAAAGAAGGAACTGAGAGCTCGGCCTTTTGGTTTGCGCTTGGAGGAAAACAGAATTACACAAGCAAAAAAGCGTCCC

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|124883406|gb|EH962308.1|EH962308
EST:     CTAGAACTGGCCACTAAAGTTGCTGAATTCTTGAAG                         CCCGGGATTACTCTCAAGCATGCCAAAGAAGGAACAGAGAGCTCAACCTTT
genomic: CTAGAACTGGCCACTAAAGTTGCTGAATTCTTGAAGgttagtttct ... tgttaatcagCCCGGGATTACTCTCAAGCATGCCAAAGAAGGAACAGAGAGCTCAACCTTT
EST: gi|86064606|gb|DR360363.1|DR360363
EST:     GTACGCATGAACAGCTAGAACTGGCCACTAAAGTTGCTGAATTCTTGAAG                         CCCGGGATTACTCTCAAGCATGCCAAAGAAGGAACAGAGAGCTCAACCTTT
genomic: GTACGCATGAACAGCTAGAACTGGCCACTAAAGTTGCTGAATTCTTGAAGgttagtttct ... tgttaatcagCCCGGGATTACTCTCAAGCATGCCAAAGAAGGAACAGAGAGCTCAACCTTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgctttacagttttacacggaactcataatagaaaatgtctttttgttaatcagCCCGGGATTACTCTCAAGCATGCCAAAGAAGGAACAGAGAGCTCAACCTTTTGGTTTGCACTTGGGGGAAAACAGAATTTCACCAGCAAGAAGGCTTCCT
                                       tctttttgtt  CT-rich tract
                        tcataatagaaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagtttctggttgtactgtgttgttttcagtttatcttaaatctttccaaataggtgctttacagttttacacggaactcataatagaaaatgtctttttgttaatcagCCCGGGATTACTCTCAAGCATGCCAAAGAAGGAACAGAGAGCTCAACCTTTTGGTTTGCACTTGGGGGAAAACAGAATTTCACCAGCAAGAAGGCTTCCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG