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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactcctttgtttgcatgagttttgcattttggttggataacatgtcttgggatttagtttaagtagtatttggaatttacttatggatagGTATGGTTTAGCAATGTTCCTCATACTCGGCTTGTTGAAGACAAAGGAGGTCAGAACTGGATTTCACGAGACAAGAACAAGTTCAAGTTTCCTGGAGGTG

Basic information

species Arabidopsis thaliana
transcript AT2G39750.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G39750.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: LOC_Os01g62800.1 (Oryza sativa), 3'ss of exon 1
gtactcctttgtttgcatgagttttgcattttggttggat---aacatgtcttgggatttagtttaagtagtatttggaatttactt--atggat---agGTATGGTTTAGCAATGTTCCTCATACTCGGCTTGTTGAAGACAAAGGAGGTCAGAACTGGATTTCACGAGACAAGAACAAGTTCAAGTTTCCTGGAGGTG
 |        |   | || |       |||| | ||   |    | |   ||  || || || | ||| ||| | |  ||   ||||  ||| ||   ||||||||||||||||||| ||||| || ||| | ||||| ||||||||||| ||||| ||||||     ||  ||| | || || |  ||||||||||| |
atgaaatggagggagtataaccaactgatttggtttaatttttcaaagacctctgggttcaggtaaaggagtttctataacacactttgatgaattgcagGTATGGTTTAGCAATGTACCTCACACGCGGTTGGTTGATGACAAAGGAGGGCAGAATTGGATTAGTAAAGCTAAGGATAAATTTAGATTTCCTGGAGGAG

upper sequence: AT2G39750.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA18G03890.2 (Glycine max), 3'ss of exon 1
--gtactcctttgtttgcatgagttttgc--attttggttggataacatgtc----ttgggatttagtttaagtagtatttggaatttacttat-ggatagGTATGGTTTAGCAATGTTCCTCATACTCGGCTTGTTGAAGACAAAGGAGGTCAGAACTGGATTTCACGAGACAAGAACAAGTTCAAGTTTCCTGGAGGTG
  | |   | | || || ||   | | ||  | ||  || ||| || |  |     |||  ||||  |     |    ||||   |||  || | |  ||||||||||  |  |||||||||||||| || ||||||||||| |||||||| || |||||||||||  |||||||| | ||||| || || || |||||||
ctgaatgacgtggtgtg-atctatatagccgacttcagtgggacaagactttgttgttgttatttcataagcatgaggtttgttttttgtttcttgtgtagGTATGGTACAATAATGTTCCTCATACACGTCTTGTTGAAGATAAAGGAGGCCAAAACTGGATTTCTAGAGACAAGGATAAGTTTAAATTCCCGGGAGGTG

upper sequence: AT2G39750.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA14G07190.1 (Glycine max), 3'ss of exon 1
-------gtactcctttgtttgcatgagttttgcattttggttggataacatgtcttgggatttagttt--aagtagtatttggaatttacttatggatagGTATGGTTTAGCAATGTTCCTCATACTCGGCTTGTTGAAGACAAAGGAGGTCAGAACTGGATTTCACGAGACAAGAACAAGTTCAAGTTTCCTGGAGGTG
         |||  |    ||   |   ||||   ||||||| || |       || |    || ||||   | |   || |    |||   ||| | ||||| ||||  |  ||||||||||| ||||| ||||||||||| ||||| ||||| ||||||||| |  ||| |||| | ||||||| ||||||||| ||||
ttatgactaacttttagaatttactcgattttctgttttggtggggtggggatgctagtaccttggtttcttaatgtaatgttatgttttgctattg-tagGTCTGGTACAATAATGTTCCTCACACTCGTCTTGTTGAAGATAAAGGGGGTCAAAACTGGATTACCAGAGGCAAGGATAAGTTCAGGTTTCCTGGGGGTG

upper sequence: AT2G39750.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA11G34430.1 (Glycine max), 3'ss of exon 1
--gtactcctttgtttgcatgagttttgc--attttggttggataacatgtc----ttgggatttagtttaagtagtatttggaatttacttatggatagGTATGGTTTAGCAATGTTCCTCATACTCGGCTTGTTGAAGACAAAGGAGGTCAGAACTGGATTTCACGAGACAAGAACAAGTTCAAGTTTCCTGGAGGTG
    | |    || |   ||   | | ||  | |||||| ||| || |  |     |||  ||||  |      |   |||    ||   |  ||  ||||||||||  |  |||||||||||||| || ||||||||||| || ||||| || |||||||||||  |||||||| | ||||| || || || |||||||
acccaatgacctggtgtgatctatatagctgactttggtgggacaagactttgttgttgttatttcataagcacaaggtttatttttgtttcttgtgtagGTATGGTACAATAATGTTCCTCATACACGTCTTGTTGAAGATAAGGGAGGCCAAAACTGGATTTCTAGAGACAAGGATAAGTTTAAATTCCCGGGAGGTG

upper sequence: AT2G39750.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA02G41770.1 (Glycine max), 3'ss of exon 1
gtactcctttgtttgcatgagttttgcattttggttggataacatgtcttgggatttagttt----aagtagtatttggaat-ttacttatgg-----atagGTATGGTTTAGCAATGTTCCTCATACTCGGCTTGTTGAAGACAAAGGAGGTCAGAACTGGATTTCACGAGACAAGAACAAGTTCAAGTTTCCTGGAGGTG
  | |      ||| |  || ||||   ||||||| || |       || |    || ||||    | ||| | ||   | | |||  | | |      ||||| ||||  |  |||||||||||  |||| ||||||||||| ||||| ||||| ||||||||| |  ||| |||| | ||||| | ||||||||| ||||
-aattttagaatttactcga-ttttctgttttggtggggtggggatgctagtacattggtttctcaatgtaatgttattattgttatgttttgctcttgtagGTTTGGTACAATAATGTTCCTCACCCTCGTCTTGTTGAAGATAAAGGGGGTCAAAACTGGATTACCAGAGGCAAGGATAAGTTTAGGTTTCCTGGGGGTG

upper sequence: AT2G39750.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv13s0019g02250.t01 (Vitis vinifera), 3'ss of exon 1
-----------gtactcctttgtttgcatgagttttgcattttggttggataacatgtcttgggattta--gt--ttaagtagtatttggaatttacttatggatagGTATGGTTTAGCAATGTTCCTCATACTCGGCTTGTTGAAGACAAAGGAGGTCAGAACTGGATTTCACGAGACAAGAACAAGTTCAAGTTTCCTGGAGGTG
           | ||   |||  | |||  | | ||| ||| || | |         |      ||| |  ||  ||  |||||   ||  | ||| ||      |||| ||||||||||||||||| |||||   ||| || ||||| |||||||||||||| |||||||||  ||| ||||| |||||||||||||| |||||||
ttgaatttttggaaccaatttaatggca--actattgtattctgatagctcgtttctttaacatattcatggtcgttgggtagtcactgtcacttattt-----cagGTGTGGTTTAGCAATGTTCCACATACAAAGCTAGTGGAAGATAAAGGAGGTCAGAATTGGATTTCAGTAGATAAGAATAAGTTCAAGTTTCCAGGAGGTG

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|164010336|gb|ES139812.1|ES139812
EST:     CTCCTAAAGGTTACCGTCAGCCGATTCCATGGCCTAAAAGCCGTGACGAG                         GTATGGTTTAGCAATGTTCCTCATACTCGGCTTGTTGAAGAC
genomic: CTCCTAAAGGTTACCGTCAGCCGATTCCATGGCCTAAAAGCCGTGACGAGgtactccttt ... ttatggatagGTATGGTTTAGCAATGTTCCTCATACTCGGCTTGTTGAAGAC
EST: gi|125298452|gb|EL312537.1|EL312537
EST:     CCTAAAAGCCGTGACGAG                         GTATGGTTTAGCAATGTTCCTCATACTCGGCTTGTTGAAGACAAAGGAGGT
genomic: CCTAAAAGCCGTGACGAGgtactccttt ... ttatggatagGTATGGTTTAGCAATGTTCCTCATACTCGGCTTGTTGAAGACAAAGGAGGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gataacatgtcttgggatttagtttaagtagtatttggaatttacttatggatagGTATGGTTTAGCAATGTTCCTCATACTCGGCTTGTTGAAGACAAAGGAGGTCAGAACTGGATTTCACGAGACAAGAACAAGTTCAAGTTTCCTGGAGGTG
 ggataac  putative branch site (score: 3)
                                        tttactt  putative PPT
                atttagtttaagta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtactcctttgtttgcatgagttttgcattttggttggataacatgtcttgggatttagtttaagtagtatttggaatttacttatggatagGTATGGTTTAGCAATGTTCCTCATACTCGGCTTGTTGAAGACAAAGGAGGTCAGAACTGGATTTCACGAGACAAGAACAAGTTCAAGTTTCCTGGAGGTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG