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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggcttgatcatggattttgtactatctgaatttgttaaacaagcctagagaaaacattttagaggctaatcacttatgatttcgcttgttgaattcgcagGGGCCTGAGATTCGTACTGGTTTCTTGAAAGATGGGAACCCTATACAACTGAAGGAAGGTCAAGAGATTACTATAACCACTGATTATGACATTCAAGGAG

Basic information

species Arabidopsis thaliana
transcript AT5G08570.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G08570.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA19G00870.1 (Glycine max), 3'ss of exon 2
ggcttgatcatggattttgtactatctgaatttgttaaacaagcctagagaaaacattttagaggctaatcacttatgatttcgcttgttgaattcgcagGGGCCTGAGATTCGTACTGGTTTCTTGAAAGATGGGAACCCTATACAACTGAAGGAAGGTCAAGAGATTACTATAACCACTGATTATGACATTCAAGGAG
          | | ||||   ||  ||||||   |||   | |   |  |   |    | |  |  |  | | | || |   |   ||||   |  |||||| ||||||||||| ||||||||  |||||||||| || ||||| ||||| |||||||| ||||| || || ||||| ||||||||||||||| | || |
---------gtaggtttt---ctcactgaatgccttatgtatggtgaatggtgaatggtgatcgatttcttattcattaacgcttctgttttgt--gcagGGACCTGAGATTCGGACTGGTTTTCTGAAAGATGGAAAACCTATTCAACTTAAGGAAGGACAAGAAATCACCATAACTACTGATTATGACATTAAGGGGG

upper sequence: AT5G08570.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA05G09310.1 (Glycine max), 3'ss of exon 1
-------ggcttgatcatggattttgtactatctgaatttgttaaacaagcctagagaaaacattttagaggctaatcacttatgatttcgcttgttgaattcgcagGGGCCTGAGATTCGTACTGGTTTCTTGAAAGATGGGAACCCTATACAACTGAAGGAAGGTCAAGAGATTACTATAACCACTGATTATGACATTCAAGGAG
         |||| | | |    | |  |   |||  | | ||  |      |  |      |||  |     | | |  || ||  | |   || |   |  |||||| ||||||||||| ||||||||  |||||||||| || ||||| ||||| || ||||| |||||  | || ||||| ||||||||||||||| | || |
cgtaaatatcttgttgaggaggatggctcgtcctgtttctcttgtatggttgtcaatttcttattcca-----ttaacgtttctgtctacatctgctttgt--gcagGGACCTGAGATTCGGACTGGTTTTCTGAAAGATGGAAAACCTATTCAACTTAAAGAAGGGCAAGAAGTCACCATAACTACTGATTATGACATTAAGGGGG

upper sequence: AT5G08570.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv10s0071g01060.t01 (Vitis vinifera), 3'ss of exon 1
ggcttgatcatggattttgtactatctgaat-ttgttaaacaagccta---gagaaaacattttagaggctaatc-acttatgatttcgcttgttgaattcgcagGGGCCTGAGATTCGTACTGGTTTCTTGAAAGATGGGAACCCTATACAACTGAAGGAAGGTCAAGAGATTACTATAACCACTGATTATGACATTCAAGGAG
  |  | |||  |||    || ||   |||| || || ||| ||  |    ||  | |  |   ||  | |  || |   ||  ||   | | ||    |  ||||||||||| ||||| ||||||||| | || ||||| || ||||| ||||| ||||||||  | || || || || || ||||| ||   |||  | || |
--cacgctcaaagat---atattaatggaatcttcttgaactagttttactgattacaagtaacagcagttgttccatgcatttttaatcctctttttctttcagGGGCCTGAAATTCGAACTGGTTTCCTAAAGGATGGAAAACCTATTCAACTTAAGGAAGGCGAGGAAATCACCATTACTACTGACTACAGCATCAAGGGGG

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|125162091|gb|EL188932.1|EL188932
EST:     CTATGCATAATACCGGCATTCTCGCTGCTGTCATGCTTGATACTAAG                         GGGCCTGAGATTCGTACTGGTTTCTTGAAAGATGGGAACCCTATACAACT
genomic: CTATGCATAATACCGGCATTCTCGCTGCTGTCATGCTTGATACTAAGgttaaacctc ... gaattcgcagGGGCCTGAGATTCGTACTGGTTTCTTGAAAGATGGGAACCCTATACAACT
EST: gi|86064591|gb|DR360348.1|DR360348
EST:     CTGCTATGCATAATACCGGCATTCTCGCTGCTGTCATGCTTGATACTAAG                         GGGCCTGAGATTCGTACTGGTTTCTTGAAAGATGGGAACC-TATACAACTG
genomic: CTGCTATGCATAATACCGGCATTCTCGCTGCTGTCATGCTTGATACTAAGgttaaacctc ... gaattcgcagGGGCCTGAGATTCGTACTGGTTTCTTGAAAGATGGGAACCCTATACAACTG
EST: gi|86064590|gb|DR360347.1|DR360347
EST:     CTGCTATGCATAATACCGGCATTCTCGCTGCTGTCATGCTTGATACTAAG                         GGGCCTGAGATTCGTACTGGTTTCTTGAAAGATGGGAACCCTATACAACTG
genomic: CTGCTATGCATAATACCGGCATTCTCGCTGCTGTCATGCTTGATACTAAGgttaaacctc ... gaattcgcagGGGCCTGAGATTCGTACTGGTTTCTTGAAAGATGGGAACCCTATACAACTG
EST: gi|125246003|gb|EL260088.1|EL260088
EST:     CTATGCATAATACCGGCATTCTCGCTGCTGTCATGCTTGATACTAAG                         GGGCCTGAGATTCGTACTGGTTTCTTGAAAGATGGGAACCCTATACAA
genomic: CTATGCATAATACCGGCATTCTCGCTGCTGTCATGCTTGATACTAAGgttaaacctc ... gaattcgcagGGGCCTGAGATTCGTACTGGTTTCTTGAAAGATGGGAACCCTATACAA
EST: gi|124804949|gb|EH892440.1|EH892440
EST:     TTGATACTAAG                         GGGCCTGAGATTCGTACTGGTTTTCTTGAAAGATGGGAACCCTATACAACT
genomic: TTGATACTAAGgttaaacctc ... gaattcgcagGGGCCTGAGATTCGTACTGG-TTTCTTGAAAGATGGGAACCCTATACAACT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tagagaaaacattttagaggctaatcacttatgatttcgcttgttgaattcgcagGGGCCTGAGATTCGTACTGGTTTCTTGAAAGATGGGAACCCTATACAACTGAAGGAAGGTCAAGAGATTACTATAACCACTGATTATGACATTCAAGGAG
                  ggctaat  putative branch site (score: 3)
     aaaacatttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggcttgatcatggattttgtactatctgaatttgttaaacaagcctagagaaaacattttagaggctaatcacttatgatttcgcttgttgaattcgcagGGGCCTGAGATTCGTACTGGTTTCTTGAAAGATGGGAACCCTATACAACTGAAGGAAGGTCAAGAGATTACTATAACCACTGATTATGACATTCAAGGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - gattttg
- - - - - - - - - - -ctatctg
- - - - - - - - - - - - - - - - - -taaacaa
- - - - - - - - - - - - - - - - - - - - - - - - -gaaaaca