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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtagggcatcttcattgtttattccttagaattataagtttataacagacgaataaatggaactgaagtatttttgattgattatgagcagTGATTAAGCTCTGGTCCAACGGAGGTTCTGGTGGAGCCCCATGGTGGACGTATTGGAGTGCTGGCATTACTAATACCATTGGTCCTGCTATGGGCATTGA

Basic information

species Arabidopsis thaliana
transcript AT1G14360.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G14360.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA01G05170.1 (Glycine max), 3'ss of exon 2
gtgagtagggcatcttcattgtttat-tccttagaattataagtttataacagacgaataaatggaactgaagt--atttttgattgatt---atgagcagTGATTAAGCTCTGGTCCAACGGAGGTTCTGGTGGAGCCCCATGGTGGACGTATTGGAGTGCTGGCATTACTAATACCATTGGTCCTGCTATGGGCATTGA
 |    |  |  | | || | |  || |  ||  ||||| |    | || ||    | |  ||  |  |   ||  ||||| | ||  ||    ||  ||||||| ||| | ||||| |  |||  ||||||||| || || |||||||  |||||||| ||||| ||||| || |||||||||||||||||||| |||||
-tataaaaagtctttgcactatcaatgttatttaaattagatccgtttagcattttattttatttactttttgtttattttggttttgtttatgtggacagTGATAAAGATGTGGTCTAGTGGAAATTCTGGTGGTGCTCCTTGGTGGAGTTATTGGAGCGCTGGAATTACCAACACCATTGGTCCTGCTATGGGAATTGA

upper sequence: AT1G14360.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA02G02330.1 (Glycine max), 3'ss of exon 2
-gtgagtagggcatcttcattgtttattccttagaattataagtttataacagacgaataaatggaactgaagtatttttg--attgattatg--agcagTGATTAAGCTCTGGTCCAACGGAGGTTCTGGTGGAGCCCCATGGTGGACGTATTGGAGTGCTGGCATTACTAATACCATTGGTCCTGCTATGGGCATTGA
    | ||    |   |      |  |   ||  ||||| |    | || ||    | |   |  |  |    |  |||||  |||| |||||    ||||||| ||| | ||| | |  |||  ||||||||| || || |||||||  |||||||| ||||| ||||| || |||||||||||||||||||| |||||
aaacaatataaaagtctttacactggtgattttaaattagatccatttagcattttattttgtttacttttgtttattttggtattgtttatgtggacagTGATAAAGATGTGGGCTAGTGGAAATTCTGGTGGTGCTCCTTGGTGGAGTTATTGGAGCGCTGGAATTACCAACACCATTGGTCCTGCTATGGGAATTGA

upper sequence: AT1G14360.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv01s0026g01890.t01 (Vitis vinifera), 3'ss of exon 2
gtgagtagggcatcttcattgtttattccttagaattataagtttataacagacgaataaatggaactgaagt---atttttgattgattatga-gcagTGATTAAGCTCTGGTCCAACGGAGGTTCTGGTGGAGCCCCATGGTGGACGTATTGGAGTGCTGGCATTACTAATACCATTGGTCCTGCTATGGGCATTGA
||||||      | || ||| ||  |    | | |  |   |||    | |||  |   ||| || || |  |   ||||||   || ||||    ||||||| ||||||||||||    |  ||||||| || || || |||||||  || ||||||||||||||||| ||||| ||||||||  | ||||| || ||
gtgagtcccttgtttttatttttcttctacttggacca---gtt---gagagaatagataatagagctcagttttcattttttggtgcttattccacagTGATAAAGCTCTGGTCCCGAAGCAGTTCTGGAGGTGCTCCTTGGTGGAGTTACTGGAGTGCTGGCATTACAAATACAATTGGTCCAACCATGGGGATAGA

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|86025305|gb|DR321058.1|DR321058
EST:     ATTTCTGAATTTGGCTCAGAATGTAATCTGCTTGGTTTGGTCTTATATAA                         TGATTAAGCTCTGGTCCAACGGAGGTTCTGGTGGAGCCCCATGGTGGACGT
genomic: ATTTCTGAATTTGGCTCAGAATGTAATCTGCTTGGTTTGGTCTTATATAAgtgagtaggg ... ttatgagcagTGATTAAGCTCTGGTCCAACGGAGGTTCTGGTGGAGCCCCATGGTGGACGT
EST: gi|86025311|gb|DR321064.1|DR321064
EST:     ATTTCTGAATTTGGCTCAGAATGTAATCTGCTTGGTTTGGTCTTATATAA                         TGATTAAGCTCTGGTCCAACGGAGGTTCTGGTGGAGCCCCATGGTGGACGT
genomic: ATTTCTGAATTTGGCTCAGAATGTAATCTGCTTGGTTTGGTCTTATATAAgtgagtaggg ... ttatgagcagTGATTAAGCTCTGGTCCAACGGAGGTTCTGGTGGAGCCCCATGGTGGACGT
EST: gi|86025290|gb|DR321043.1|DR321043
EST:     ATTTCTGAATTTGGCTCAGAATGTAATCTGCTTGGTTTGGTCTTATATAA                         TGATTAAGCTCTGGTCCAACGGAGGTTCTGGTGGAGCCCCATGGTGGACGT
genomic: ATTTCTGAATTTGGCTCAGAATGTAATCTGCTTGGTTTGGTCTTATATAAgtgagtaggg ... ttatgagcagTGATTAAGCTCTGGTCCAACGGAGGTTCTGGTGGAGCCCCATGGTGGACGT
EST: gi|86025296|gb|DR321049.1|DR321049
EST:     ATTTCTGAATTTGGCTCAGAATGTAATCTGCTTGGTTTGGTCTTATATAA                         TGATTAAGCTCTGGTCCAACGGAGGTTCTGGTGGAGCCCCATGGTGGACGT
genomic: ATTTCTGAATTTGGCTCAGAATGTAATCTGCTTGGTTTGGTCTTATATAAgtgagtaggg ... ttatgagcagTGATTAAGCTCTGGTCCAACGGAGGTTCTGGTGGAGCCCCATGGTGGACGT
EST: gi|116432753|gb|EG475345.1|EG475345
EST:     ATTTCTGAATTTGGCTCAGAATGTAATCTGCTTGGTTTGGTCTTATATAA                         TGATTAAGCTCTGGTCCAACGGAGGTTCTGGTGGAGCCCCATGGTGGACGT
genomic: ATTTCTGAATTTGGCTCAGAATGTAATCTGCTTGGTTTGGTCTTATATAAgtgagtaggg ... ttatgagcagTGATTAAGCTCTGGTCCAACGGAGGTTCTGGTGGAGCCCCATGGTGGACGT
EST: gi|86025306|gb|DR321059.1|DR321059
EST:     TTCTGAAATTTGGGCTCAGAATGTAATCTGCTTGGTTTGGTCTTATATAA                         TGATTAAGCTCTGGTCCAACGGAGGTTCTGGTGGAGCCCCATGGTGGACGT
genomic: TTCTG-AATTT-GGCTCAGAATGTAATCTGCTTGGTTTGGTCTTATATAAgtgagtaggg ... ttatgagcagTGATTAAGCTCTGGTCCAACGGAGGTTCTGGTGGAGCCCCATGGTGGACGT
EST: gi|86025291|gb|DR321044.1|DR321044
EST:     ATTTCTGAATTTGGCTCAGAATGTAATCTGCTTGGTTTGGTCTTATATAA                         TGATTAAGCTCTGGTCCAACGGAGGTTCTGGTGGAGCCCCATGGTGGACGT
genomic: ATTTCTGAATTTGGCTCAGAATGTAATCTGCTTGGTTTGGTCTTATATAAgtgagtaggg ... ttatgagcagTGATTAAGCTCTGGTCCAACGGAGGTTCTGGTGGAGCCCCATGGTGGACGT
EST: gi|86025309|gb|DR321062.1|DR321062
EST:     ATTTCTGAATTTGGCTCAGAATGTAATCTGCTTGGTTTGGTCTTATATAA                         TGATTAAGCTCTGGTCCAACGGAGGTTCTGGTGGAGCCCCATGGTGGACGT
genomic: ATTTCTGAATTTGGCTCAGAATGTAATCTGCTTGGTTTGGTCTTATATAAgtgagtaggg ... ttatgagcagTGATTAAGCTCTGGTCCAACGGAGGTTCTGGTGGAGCCCCATGGTGGACGT
EST: gi|86025304|gb|DR321057.1|DR321057
EST:     ATTTCTGAATTTGGCTCAGAATGTAATCTGCTTGGTTTGGTCTTATATAA                         TGATTAAGCTCTGGTCCAACGGAGGTTCTGGTGGAGCCCCATGGTGGACGT
genomic: ATTTCTGAATTTGGCTCAGAATGTAATCTGCTTGGTTTGGTCTTATATAAgtgagtaggg ... ttatgagcagTGATTAAGCTCTGGTCCAACGGAGGTTCTGGTGGAGCCCCATGGTGGACGT
EST: gi|86025302|gb|DR321055.1|DR321055
EST:     ATTTCTGAATTTGGCTCAGAATGTAATCTGCTTGGTTTGGTCTTATATAA                         TGATTAAGCTCTGGTCCAACGGAGGTTCTGGTGGAGCCCCATGGTGGACGT
genomic: ATTTCTGAATTTGGCTCAGAATGTAATCTGCTTGGTTTGGTCTTATATAAgtgagtaggg ... ttatgagcagTGATTAAGCTCTGGTCCAACGGAGGTTCTGGTGGAGCCCCATGGTGGACGT
EST: gi|86025312|gb|DR321065.1|DR321065
EST:     ATTTCTGAATTTGGCTCAGAATGTAATCTGCTTGGTTTGGTCTTATATAA                         TGATTAAGCTCTGGTCCAACGGAGGTTCTGGTGGAGCCCCATGGTGGACGT
genomic: ATTTCTGAATTTGGCTCAGAATGTAATCTGCTTGGTTTGGTCTTATATAAgtgagtaggg ... ttatgagcagTGATTAAGCTCTGGTCCAACGGAGGTTCTGGTGGAGCCCCATGGTGGACGT
EST: gi|86025295|gb|DR321048.1|DR321048
EST:     ATTTCTGAATTTGGCTCAGAATGTAATCTGCTTGGTTTGGTCTTATATAA                         TGATTAAGCTCTGGTCCAACGGAGGTTCTGGTGGAGCCCCATGGTGGACGT
genomic: ATTTCTGAATTTGGCTCAGAATGTAATCTGCTTGGTTTGGTCTTATATAAgtgagtaggg ... ttatgagcagTGATTAAGCTCTGGTCCAACGGAGGTTCTGGTGGAGCCCCATGGTGGACGT
EST: gi|86025298|gb|DR321051.1|DR321051
EST:     ATTTCTGAATTTGGCTCAGAATGTAATCTGCTTGGTTTGGTCTTATATAA                         TGATTAAGCTCTGGTCCAACGGAGGTTCTGGTGGAGCCCCATGGTGGACGT
genomic: ATTTCTGAATTTGGCTCAGAATGTAATCTGCTTGGTTTGGTCTTATATAAgtgagtaggg ... ttatgagcagTGATTAAGCTCTGGTCCAACGGAGGTTCTGGTGGAGCCCCATGGTGGACGT
EST: gi|86025300|gb|DR321053.1|DR321053
EST:     ATTTCTGAATTTGGCTCAGAATGTAATCTGCTTGGTTTGGTCTTATATAA                         TGATTAAGCTCTGGTCCAACGGAGGTTCTGGTGGAGCCCCATGGTGGACGT
genomic: ATTTCTGAATTTGGCTCAGAATGTAATCTGCTTGGTTTGGTCTTATATAAgtgagtaggg ... ttatgagcagTGATTAAGCTCTGGTCCAACGGAGGTTCTGGTGGAGCCCCATGGTGGACGT
EST: gi|86025294|gb|DR321047.1|DR321047
EST:     ATTTCTGAATTTGGCTCAGAATGTAATCTGCTTGGTTTGGTCTTATATAA                         TGATTAAGCTCTGGTCCAACGGAGGTTCTGGTGGAGCCCCATGGTGGACGT
genomic: ATTTCTGAATTTGGCTCAGAATGTAATCTGCTTGGTTTGGTCTTATATAAgtgagtaggg ... ttatgagcagTGATTAAGCTCTGGTCCAACGGAGGTTCTGGTGGAGCCCCATGGTGGACGT
EST: gi|86025303|gb|DR321056.1|DR321056
EST:     ATTTCTGAATTTGGCTCAGAATGTAATCTGCTTGGTTTGGTCTTATATAA                         TGATTAAGCTCTGGTCCAACGGAGGTTCTGGTGGAGCCCCATGGTGGACGT
genomic: ATTTCTGAATTTGGCTCAGAATGTAATCTGCTTGGTTTGGTCTTATATAAgtgagtaggg ... ttatgagcagTGATTAAGCTCTGGTCCAACGGAGGTTCTGGTGGAGCCCCATGGTGGACGT
EST: gi|86025293|gb|DR321046.1|DR321046
EST:     ATTTCTGAATTTGGCTCAGAATGTAATCTGCTTGGTTTGGTCTTATATAA                         TGATTAAGCTCTGGTCCAACGGAGGTTCTGGTGGAGCCCCATGGTGGACGT
genomic: ATTTCTGAATTTGGCTCAGAATGTAATCTGCTTGGTTTGGTCTTATATAAgtgagtaggg ... ttatgagcagTGATTAAGCTCTGGTCCAACGGAGGTTCTGGTGGAGCCCCATGGTGGACGT
EST: gi|86025307|gb|DR321060.1|DR321060
EST:     ATTTCTGAATTTGGCTCAGAATGTAATCTGCTTGGTTTGGTCTTATATAA                         TGATTAAGCTCTGGTCCAACGGAGGTTCTGGTGGAGCCCCATGGTGGACGT
genomic: ATTTCTGAATTTGGCTCAGAATGTAATCTGCTTGGTTTGGTCTTATATAAgtgagtaggg ... ttatgagcagTGATTAAGCTCTGGTCCAACGGAGGTTCTGGTGGAGCCCCATGGTGGACGT
EST: gi|86025299|gb|DR321052.1|DR321052
EST:     ATTTCTGAATTTGGCTCAGAATGTAATCTGCTTGGTTTGGTCTTATATAA                         TGATTAAGCTCTGGTCCAACGGAGGTTCTGGTGGAGCCCCATGGTGGACGT
genomic: ATTTCTGAATTTGGCTCAGAATGTAATCTGCTTGGTTTGGTCTTATATAAgtgagtaggg ... ttatgagcagTGATTAAGCTCTGGTCCAACGGAGGTTCTGGTGGAGCCCCATGGTGGACGT
EST: gi|86025310|gb|DR321063.1|DR321063
EST:     ATTTCTGAATTTGGCTCAGAATGTAATCTGCTTGGTTTGGTCTTATATAA                         TGATTAAGCTCTGGTCCAACGGAGGTTCTGGTGGAGCCCCATGGTGGACGT
genomic: ATTTCTGAATTTGGCTCAGAATGTAATCTGCTTGGTTTGGTCTTATATAAgtgagtaggg ... ttatgagcagTGATTAAGCTCTGGTCCAACGGAGGTTCTGGTGGAGCCCCATGGTGGACGT
EST: gi|86025292|gb|DR321045.1|DR321045
EST:     ATTTCTGAATTTGGCTCAGAATGTAATCTGCTTGGTTTGGTCTTATATAA                         TGATTAAGCTCTGGTCCAACGGAGGTTCTGGTGGAGCCCCATGGTGGACGT
genomic: ATTTCTGAATTTGGCTCAGAATGTAATCTGCTTGGTTTGGTCTTATATAAgtgagtaggg ... ttatgagcagTGATTAAGCTCTGGTCCAACGGAGGTTCTGGTGGAGCCCCATGGTGGACGT
EST: gi|86025308|gb|DR321061.1|DR321061
EST:     ATTTCTGAATTTGGCTCAGAATGTAATCTGCTTGGTTTGGTCTTATATAA                         TGATTAAGCTCTGGTCCAACGGAGGYTCTGGTGGAGCCCCATGGTGGACGT
genomic: ATTTCTGAATTTGGCTCAGAATGTAATCTGCTTGGTTTGGTCTTATATAAgtgagtaggg ... ttatgagcagTGATTAAGCTCTGGTCCAACGGAGGTTCTGGTGGAGCCCCATGGTGGACGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtttataacagacgaataaatggaactgaagtatttttgattgattatgagcagTGATTAAGCTCTGGTCCAACGGAGGTTCTGGTGGAGCCCCATGGTGGACGTATTGGAGTGCTGGCATTACTAATACCATTGGTCCTGCTATGGGCATTGA
                                tatttttgattgatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtagggcatcttcattgtttattccttagaattataagtttataacagacgaataaatggaactgaagtatttttgattgattatgagcagTGATTAAGCTCTGGTCCAACGGAGGTTCTGGTGGAGCCCCATGGTGGACGTATTGGAGTGCTGGCATTACTAATACCATTGGTCCTGCTATGGGCATTGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG