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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgtgtaatgctgattagcctatgaccagaacacaaacatttttgctagtactacttatattgggtattatgactgacatatgatggtggggttgtttcagATTGGGAACAGGATCATAAGGAAGAGGATTCATGTTCGTGTGGAGCATGTGCAGCAGTCAAGATGTGCCGAGGAGTTCAAGCTGAGGAAGAAGAAAAACG

Basic information

species Arabidopsis thaliana
transcript AT1G09590.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G09590.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: LOC_Os10g32820.1 (Oryza sativa), 3'ss of exon 1
--tgtgtaatgctgattagcctatgaccagaacacaaacatttttgctagtactacttatattgggtattatgactgacatatgatggtggggttgttt-cagATTGGGAACAGGATCATAAGGAAGAGGATTCATGTTCGTGTGGAGCATGTGCAGCAGTCAAGATGTGCCGAGGAGTTCAAGCTGAGGAAGAAGAAAAACG
  ||||||||| | | |  | | ||   |         |    ||  |   | |  | | ||   ||||      |      || | ||     | ||   || |||||||| | || || ||||||||||| ||||| |||||||||||||||||||  || || ||  | |||||||||   ||||||||||  || ||||
catgtgtaatgttcagt--catgtggatatgtagtcttcgggattattta-atttttgaaatcatgtatctgttttactgattgtttgttaatctcttggtagGTTGGGAACCGCATTATCAGGAAGAGGATCCATGTCCGTGTGGAGCATGTGCAGCCATCCAGGTGCACTGAGGAGTTCCGCCTGAGGAAGATCAAGAACG

upper sequence: AT1G09590.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: LOC_Os03g04750.1 (Oryza sativa), 3'ss of exon 1
--tgtgtaatgctg-attagcctatgaccagaacacaaacatttttgctagtactacttatattgggtattatgactgacatatgatggtggggttgtt-tcagATTGGGAACAGGATCATAAGGAAGAGGATTCATGTTCGTGTGGAGCATGTGCAGCAGTCAAGATGTGCCGAGGAGTTCAAGCTGAGGAAGAAGAAAAACG
  | |  ||||    || |     |||  |    |||   | |   ||| |  ||||||    |||  | |     |   | |   || |     |||  |||| | || ||| | ||||| ||||||||||| ||||| |||||||||||||| ||||  || || ||  |||||||| ||   |||||||| |  || ||||
attttagaatggaacatcaaatattgagtattgaacatcaaatagggctcg--ctacttgatgtggcaacttcacattgaagactctgtttt--ctgtcatcagGTCGGTAACCGCATCATCAGGAAGAGGATCCATGTCCGTGTGGAGCATGTCCAGCCATCCAGGTGCACCGAGGAGCTCCGCCTGAGGAAAATCAAGAACG

upper sequence: AT1G09590.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA03G36560.1 (Glycine max), 3'ss of exon 1
tgtgtaatgctgattagcctatgaccagaacacaaacatttttgctagtac--tacttatattgggtat--tatgactgacatatgatggtggggttgt-ttcagATTGGGAACAGGATCATAAGGAAGAGGATTCATGTTCGTGTGGAGCATGTGCAGCAGTCAAGATGTGCCGAGGAGTTCAAGCTGAGGAAGAAGAAAAACG
    |  |||   |  |   ||    ||     |    ||| ||    | |     | || ||||| ||  | | | ||| ||    |  ||  |||   ||||| | || ||||| |||||||||||||||||||| || ||||||||||||||   ||  ||||| ||  | |||||||||   || |||||||  || || |
----ttctgcccgtgtgttaatt-ttagtttctagggttttatgtgtatgcctcgttgattttgggaatggttttattgaaattactttttgatgtttcattcagGTCGGCAACAGAATCATAAGGAAGAGGATTCACGTGCGTGTGGAGCATGTTATGCCATCAAGGTGCACTGAGGAGTTCCGCCTTAGGAAGATCAAGAATG

upper sequence: AT1G09590.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA06G22900.1 (Glycine max), 3'ss of exon 2
-------tgtgtaatgctgattagcctatgaccagaacacaaacatttttgctagtactacttatattgggtattatgactgacatatgatggtggggttgtttcagATTGGGAACAGGATCATAAGGAAGAGGATTCATGTTCGTGTGGAGCATGTGCAGCAGTCAAGATGTGCCGAGGAGTTCAAGCTGAGGAAGAAGAAAAACG
       ||||| |   | | |  |    |          |  | |  ||| |      | ||    ||  ||||   | |  | | ||||| |     |  ||||| | || ||||| |||||||||||||||||||| || ||||||||||||||   ||  || || ||  | |||||||||   || ||||| |  || || |
ctgcccgtgtgttaattttagtttctagggttttatgtgtatgcctcattgatttggggatttgg--tgtttattgaaattaccttttgatgtt-----tcattcagGTCGGCAACAGAATCATAAGGAAGAGGATTCACGTGCGTGTGGAGCATGTTATGCCATCGAGGTGCACTGAGGAGTTCCGCCTTAGGAAAATCAAGAATG

upper sequence: AT1G09590.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA19G39240.1 (Glycine max), 3'ss of exon 1
tgtgtaatgctgattagcctatgaccagaacacaaacatttttgctagtactacttatattgggtattatg----actgacat-atgatg-gtggggttgtttcagATTGGGAACAGGATCATAAGGAAGAGGATTCATGTTCGTGTGGAGCATGTGCAGCAGTCAAGATGTGCCGAGGAGTTCAAGCTGAGGAAGAAGAAAAACG
  | || |    |   |  | |      ||| |     | | ||| |    || | || ||||| ||||||      ||| || |   || |||  |||  ||||| |||| ||||| || |||||||||||||||||||| || || ||||||||   ||  ||||| ||  | |||||||||   || |||||||  || || |
--tttagtttctag-ggtttttatgtcaaactct--tgtgtatgccaaccttattgat-ttggggattatgttttgttgaaattactttgtgtgatgttcattcagGTTGGCAACAGAATTATAAGGAAGAGGATTCATGTGCGGGTAGAGCATGTTATGCCTTCAAGGTGCACTGAGGAGTTCCGCCTCAGGAAGATTAAGAATG

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|152033789|gb|BP816092.2|BP816092
EST:     GTATCTGGAACGTCACCAAGCGCGCCGTCGGTGTTGAAGTCAACAAACAG                         ATTGGGAACAGGATCATAAGGAAGAGGATTCATGTTCGTGTGGAGNATGTG
genomic: GTATCTGGAACGTCACCAAGCGCGCCGTCGGTGTTGAAGTCAACAAACAGgtctgatgat ... gttgtttcagATTGGGAACAGGATCATAAGGAAGAGGATTCATGTTCGTGTGGAGCATGTG
EST: gi|116411851|gb|EG454443.1|EG454443
EST:     GTATCTGGAACGTCACTAAACGCGCCGTCGGTGTTGAAGTCAACAAACAG                         ATTGGCAACAGGATCATAAGGAAGAGGATTCATGTTCGTGTGGAGCATGTG
genomic: GTATCTGGAACGTCACCAAGCGCGCCGTCGGTGTTGAAGTCAACAAACAGgtctgatgat ... gttgtttcagATTGGGAACAGGATCATAAGGAAGAGGATTCATGTTCGTGTGGAGCATGTG
EST: gi|116432980|gb|EG475572.1|EG475572
EST:     GTATCTGGAACGTCACCAAGCGCGCCGTCGGTGTTGAAGTCAACAAACAG                         ATTGGGAACAGGATCATAAGGAAGAGGATTCATGTTCGTGTGGAGCATGTG
genomic: GTATCTGGAACGTCACCAAGCGCGCCGTCGGTGTTGAAGTCAACAAACAGgtctgatgat ... gttgtttcagATTGGGAACAGGATCATAAGGAAGAGGATTCATGTTCGTGTGGAGCATGTG
EST: gi|47830708|gb|CK120392.1|CK120392
EST:     GTATCTGGAACGTCACCAAGCGCGCCGTCGGTGTTGAAGTCAACAAACAG                         ATTGGGAACAGGATCATAAGGAAGAGGATTCATGTTCGTGTGGAGCATGTG
genomic: GTATCTGGAACGTCACCAAGCGCGCCGTCGGTGTTGAAGTCAACAAACAGgtctgatgat ... gttgtttcagATTGGGAACAGGATCATAAGGAAGAGGATTCATGTTCGTGTGGAGCATGTG
EST: gi|47828314|gb|CK117998.1|CK117998
EST:     GTATCTGGAACGTCACCAAGCGCGCCGTCGGTGTTGAAGTCAACAAACAG                         ATTGGGAACAGGATCATAAGGAAGAGGATTCATGTTCGTGTGGAGCATGTG
genomic: GTATCTGGAACGTCACCAAGCGCGCCGTCGGTGTTGAAGTCAACAAACAGgtctgatgat ... gttgtttcagATTGGGAACAGGATCATAAGGAAGAGGATTCATGTTCGTGTGGAGCATGTG
EST: gi|47830270|gb|CK119954.1|CK119954
EST:     GTATCTGGAACGTCACCAAGCGCGCCGTCGGTGTTGAAGTCAACAAACAG                         ATTGGGAACAGGATCATAAGGAAGAGGATTCATGTTCGTGTGGAGCATGTG
genomic: GTATCTGGAACGTCACCAAGCGCGCCGTCGGTGTTGAAGTCAACAAACAGgtctgatgat ... gttgtttcagATTGGGAACAGGATCATAAGGAAGAGGATTCATGTTCGTGTGGAGCATGTG
EST: gi|125046487|gb|EL118756.1|EL118756
EST:     GTATCTGGAACGTCACCAGGCGCGCCGTCGGTGTTGAAGTCAACAAACAG                         ATTGGGAACAGGATCATAAGGAAGAGGATTCATGTTCGTGTGGAGCATG
genomic: GTATCTGGAACGTCACCAAGCGCGCCGTCGGTGTTGAAGTCAACAAACAGgtctgatgat ... gttgtttcagATTGGGAACAGGATCATAAGGAAGAGGATTCATGTTCGTGTGGAGCATG
EST: gi|47828948|gb|CK118632.1|CK118632
EST:     GTATCTGGAACGTCACCAAGCGCGCCGTCGGTGTTGAAGTCAACAAACAG                         ATTGGGAACAGGATCATAAGGAAGAGGATTCATGTTCGTGTGGAGCATGTG
genomic: GTATCTGGAACGTCACCAAGCGCGCCGTCGGTGTTGAAGTCAACAAACAGgtctgatgat ... gttgtttcagATTGGGAACAGGATCATAAGGAAGAGGATTCATGTTCGTGTGGAGCATGTG
EST: gi|164128498|gb|ES025390.1|ES025390
EST:     GTATCTGGAACGTCACCAAGCGCGCCGTCGGTGTTGAAGTCAACAAACAG                         ATTGGGAACAGGATCATAAGGAAGAGGAT
genomic: GTATCTGGAACGTCACCAAGCGCGCCGTCGGTGTTGAAGTCAACAAACAGgtctgatgat ... gttgtttcagATTGGGAACAGGATCATAAGGAAGAGGAT
EST: gi|116411846|gb|EG454438.1|EG454438
EST:     GTATCTGGAACGTCACCAAGCGCGCCGTCGGTGTTGAAGTCAACAAACAG                         ATTGGGAACAGGATCATAAGGAAGAGGATTCATGTTCGTGTGGAGCATGTG
genomic: GTATCTGGAACGTCACCAAGCGCGCCGTCGGTGTTGAAGTCAACAAACAGgtctgatgat ... gttgtttcagATTGGGAACAGGATCATAAGGAAGAGGATTCATGTTCGTGTGGAGCATGTG
EST: gi|86085947|gb|DR381706.1|DR381706
EST:     GTATCTGGAACGTCACCAAGCGCNCCGTCGGTGTTGAAGTCAACAAACAG                         ATTGGGAACAGGATCATAAGGAAGAGGATTCATGTTCGTGTGGAGCATGTG
genomic: GTATCTGGAACGTCACCAAGCGCGCCGTCGGTGTTGAAGTCAACAAACAGgtctgatgat ... gttgtttcagATTGGGAACAGGATCATAAGGAAGAGGATTCATGTTCGTGTGGAGCATGTG
EST: gi|164197736|gb|ES061380.1|ES061380
EST:     GTATCTGGAACGTCACCAAGCGCGCCGTCGGTGTTGAAGTCAACAAACAG                         ATTGGGAACAGGATCATAAGGAAGAGGATTCATGTTCGTGTGG
genomic: GTATCTGGAACGTCACCAAGCGCGCCGTCGGTGTTGAAGTCAACAAACAGgtctgatgat ... gttgtttcagATTGGGAACAGGATCATAAGGAAGAGGATTCATGTTCGTGTGG
EST: gi|47828177|gb|CK117861.1|CK117861
EST:     GTATCTGGAACGTCACCAAGCGCGCCGTCGGTGTTGAAGTCAACAAACAG                         ATTGGGAACAGGATCATAAGGAAGAGGATTCATGTTCGTGTGGAGCATGTG
genomic: GTATCTGGAACGTCACCAAGCGCGCCGTCGGTGTTGAAGTCAACAAACAGgtctgatgat ... gttgtttcagATTGGGAACAGGATCATAAGGAAGAGGATTCATGTTCGTGTGGAGCATGTG
EST: gi|124815280|gb|EH900146.1|EH900146
EST:     AAGTCAACAAACAG                         ATTGGGAACAGGATCATAAGGAAGAGGATTCATGTTCGTGTGGAGCATGTG
genomic: AAGTCAACAAACAGgtctgatgat ... gttgtttcagATTGGGAACAGGATCATAAGGAAGAGGATTCATGTTCGTGTGGAGCATGTG
EST: gi|116411853|gb|EG454445.1|EG454445
EST:     GTATCTGGAACGTCACTAAACGCGCCGTCGGTGTTGAAGTCAACAAACAG                         ATTGGCAACAGGATCATAAGGAAGAGGATTCATGTTCGTGTGGAGCATGTG
genomic: GTATCTGGAACGTCACCAAGCGCGCCGTCGGTGTTGAAGTCAACAAACAGgtctgatgat ... gttgtttcagATTGGGAACAGGATCATAAGGAAGAGGATTCATGTTCGTGTGGAGCATGTG
EST: gi|47831769|gb|CK121453.1|CK121453
EST:     GTATCTGGAACGTCACCAAGCGCGCCGTCGGTGTTGAAGTCAACAAACAG                         ATTGGGAACAGGATCATAAGGAAGAGGATTCATGTTCGTGTGGAGCATGTG
genomic: GTATCTGGAACGTCACCAAGCGCGCCGTCGGTGTTGAAGTCAACAAACAGgtctgatgat ... gttgtttcagATTGGGAACAGGATCATAAGGAAGAGGATTCATGTTCGTGTGGAGCATGTG
EST: gi|116466688|gb|EG509280.1|EG509280
EST:     GTATCTGGAACGTCACCAAGCGCGCCGTCGGTGTTGAAGTCAACAAACAG                         ATTGGGAACAGGATCATAAGGAAGAGGATTCATGTTCGTGTGGAGCATGTG
genomic: GTATCTGGAACGTCACCAAGCGCGCCGTCGGTGTTGAAGTCAACAAACAGgtctgatgat ... gttgtttcagATTGGGAACAGGATCATAAGGAAGAGGATTCATGTTCGTGTGGAGCATGTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tagtactacttatattgggtattatgactgacatatgatggtggggttgtttcagATTGGGAACAGGATCATAAGGAAGAGGATTCATGTTCGTGTGGAGCATGTGCAGCAGTCAAGATGTGCCGAGGAGTTCAAGCTGAGGAAGAAGAAAAACG
                         gactgac  putative branch site (score: 2)
                                              ttgtttc  putative PPT
      tacttatatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgtgtaatgctgattagcctatgaccagaacacaaacatttttgctagtactacttatattgggtattatgactgacatatgatggtggggttgtttcagATTGGGAACAGGATCATAAGGAAGAGGATTCATGTTCGTGTGGAGCATGTGCAGCAGTCAAGATGTGCCGAGGAGTTCAAGCTGAGGAAGAAGAAAAACG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - -accagaa
- - - - - - - - - - - - - - - cacaaac