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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACTAGAGCTAGAAGAGGAGAAGGTCCAACCTTGGTTGAATGTGAGACTTATAGATTCAGAGGACACTCCTTGGCTGATCCCGATGAGCTCCGTGATGCTGgtaaatatcgacttccttctgcttcttgatgcttgtactgattatctaagggttgaaacaaccttctctttaatttgaatttttttttgcag

Basic information

species Arabidopsis thaliana
transcript AT1G01090.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G01090.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GLYMA07G05550.1 (Glycine max), 5'ss of exon 2
ACTAGAGCTAGAAGAGGAGAAGGTCCAACCTTGGTTGAATGTGAGACTTATAGATTCAGAGGACACTCCTTGGCTGATCCCGATGAGCTCCGTGATGCTGgtaaatatcgacttccttctgcttcttgatgcttgtactgattatctaagggt---tgaaacaaccttctctttaatttgaa----tttttttttgcag-
   || |||||||||||||| || |||||  | || ||||||||||| |||||||| ||||| || || |||||||||||||||||||| |||||  ||||| |  ||| | ||   |    |  |   | | | |  |  | || |    ||   ||     |  ||   ||  ||||       | ||| | | ||| 
GAAAGGGCTAGAAGAGGAGATGGACCAACTCTAGTGGAATGTGAGACCTATAGATTTAGAGGGCATTCATTGGCTGATCCCGATGAGCTTCGTGACCCTGgtgagcatctatttagataatatattctctccctatgttcttaattttgaagtacatgtgctgatgtttctttgcatttctggtcgtatttatcttcagt

upper sequence: AT1G01090.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GLYMA19G44930.1 (Glycine max), 5'ss of exon 2
ACTAGAGCTAGAAGAGGAGAAGGTCCAACCTTGGTTGAATGTGAGACTTATAGATTCAGAGGACACTCCTTGGCTGATCCCGATGAGCTCCGTGATGCTGgtaaatatcgac------ttccttctgcttcttgatgcttgtactgattatctaagggttgaaacaaccttctctttaatttgaatttttttttgcag--
   || || ||| ||||||| || ||||| || || ||||| |||||||||||||| |||||||| || ||||||||||| |||||||| |||||  ||||| |   |  ||      ||   | | ||| |       |  | | ||  | | |   ||| |  || ||    || ||  ||    ||     |     
GAAAGGGCCAGACGAGGAGAGGGACCAACTTTAGTAGAATGCGAGACTTATAGATTTAGAGGACATTCATTGGCTGATCCTGATGAGCTTCGTGACCCTGgtgagcgtttacattatgttttctttacttataatctacttcagttatgctgttaattttggagtaaactagatttgaacctgtgcattgcacagggatc

upper sequence: AT1G01090.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GLYMA16G02090.1 (Glycine max), 5'ss of exon 2
ACTAGAGCTAGAAGAGGAGAAGGTCCAACCTTGGTTGAATGTGAGACTTATAGATTCAGAGGACACTCCTTGGCTGATCCCGATGAGCTCCGTGATGCTGgtaaatat-cgacttccttctgcttcttgatgcttgtactgattatctaagggt---tgaaacaaccttctctttaatttg----aatttttttttgcag
   || ||||||||||| || || |||||  | || ||||| ||||| |||||||| ||||| || || |||||||||||||||||||| |||||  ||||| |  || | | ||   |    |  |   | | | |  |  | || |    ||   ||     |  |||  ||  ||||       | ||  | | |||
GGAAGGGCTAGAAGAGGTGAGGGACCAACTCTAGTGGAATGCGAGACCTATAGATTTAGAGGGCATTCATTGGCTGATCCCGATGAGCTTCGTGACCCTGgtgagaattctatttagataatatcttctctccctatgttcttaattttgaagtacatgtgctgatgttcctttgcatttctggtggtattcatcttcag

upper sequence: AT1G01090.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GLYMA03G42190.1 (Glycine max), 5'ss of exon 2
ACTAGAGCTAGAAGAGGAGAAGGTCCAACCTTGGTTGAATGTGAGACTTATAGATTCAGAGGACACTCCTTGGCTGATCCCGATGAGCTCCGTGATGCTGgtaaatatcgacttc---cttctgcttcttgatgcttgtactgattatctaa---gggttgaaacaaccttctctttaatttgaatttttttttgcag--
   ||||| ||  ||||||| || || || || || ||||| ||||| |||||||| |||||||| || ||||||||||| |||||||| |||||  ||||| |   |  || |    |||    || ||   |  |       |||| |        ||| |  || ||    || ||  |     ||   | |     
GAAAGAGCCAGGCGAGGAGAGGGACCGACTTTAGTAGAATGCGAGACCTATAGATTTAGAGGACATTCATTGGCTGATCCTGATGAGCTTCGTGACCCTGgtgagcctttacattatgctttatttttttagagtctacttcagttatgttgtttattttgtagtaaactagatttgaacctctgggttgcctggggatc

upper sequence: AT1G01090.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: Vv15s0048g02580.t01 (Vitis vinifera), 5'ss of exon 2
ACTAGAGCTAGAAGAGGAGAAGGTCCAACCTTGGTTGAATGTGAGACTTATAGATTCAGAGGACACTCCTTGGCTGATCCCGATGAGCTCCGTGATGCTGgtaaatatcgacttccttctgcttcttgatgcttgtactgattatctaagggttgaaacaaccttctctttaatttgaatttttttttgcag------------
   || ||||| ||||||||||| |||||  |||| ||||||||||| ||||| || ||||||||||| ||||||||||| ||||||||||||||  |||||||  |   |        ||  |     || ||   |  |||||| |   || ||    |  |||  || | |||||   ||||| |||              
CAAAGGGCTAGGAGAGGAGAAGGACCAACTCTGGTGGAATGTGAGACATATAGGTTTAGAGGACACTCTTTGGCTGATCCTGATGAGCTCCGTGACCCTGgtaagcagttagaattaattgtcttgccttgttt---cgaattatccagttgt-gatcttagtttccattaattttgatgatttttctgcctattgatttgtga

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|124856709|gb|EH941146.1|EH941146
EST:     TAGATTCAGAGGACACTCCTTGGCTGATCCCGATGAGCTCCGTGATGCTG                         CTGAGAAAGCCAAATACGCGGCTAG
genomic: TAGATTCAGAGGACACTCCTTGGCTGATCCCGATGAGCTCCGTGATGCTGgtaaatatcg ... ttttttgcagCTGAGAAAGCCAAATACGCGGCTAG
EST: gi|86085865|gb|DR381624.1|DR381624
EST:     GAGGACACTCCTTGGCTGATCCCGATGAGCTCCGTGATGCTG                         CTGAGAAAGCCAAATACGCGGCTAGAGACCCAATCGCAGCATTGAAGAAGT
genomic: GAGGACACTCCTTGGCTGATCCCGATGAGCTCCGTGATGCTGgtaaatatcg ... ttttttgcagCTGAGAAAGCCAAATACGCGGCTAGAGACCCAATCGCAGCATTGAAGAAGT
EST: gi|116405541|gb|EG448133.1|EG448133
EST:     TAGATTCAGAGGACACTCCTTGGCTGATCCCGATGAGCTCCGTGATGCTG                         CTGAGAAAGCCAAATACGCGGCTAGAGACCCAATCGCAGCATTGAAGAAGT
genomic: TAGATTCAGAGGACACTCCTTGGCTGATCCCGATGAGCTCCGTGATGCTGgtaaatatcg ... ttttttgcagCTGAGAAAGCCAAATACGCGGCTAGAGACCCAATCGCAGCATTGAAGAAGT
EST: gi|116404555|gb|EG447147.1|EG447147
EST:     TAGATTCAGAGGACACTCCTTGGCTGATCCCGATGAGCTCCGTGATGCTG                         CTGAGAAAGCCAAATACGCGGCTAGAGACCCAATCGCAGCATTGAAGAAGT
genomic: TAGATTCAGAGGACACTCCTTGGCTGATCCCGATGAGCTCCGTGATGCTGgtaaatatcg ... ttttttgcagCTGAGAAAGCCAAATACGCGGCTAGAGACCCAATCGCAGCATTGAAGAAGT
EST: gi|86047414|gb|DR343169.1|DR343169
EST:     TAGATTTAGAGGACACTCCTTGGCTGATCCCGATGAGCTCCGTGATGCTG                         CTGAGAAAGCCAAATACGCGGCTAGAGACCCAATCGCAGCATTGAAGAAGT
genomic: TAGATTCAGAGGACACTCCTTGGCTGATCCCGATGAGCTCCGTGATGCTGgtaaatatcg ... ttttttgcagCTGAGAAAGCCAAATACGCGGCTAGAGACCCAATCGCAGCATTGAAGAAGT
EST: gi|116402840|gb|EG445432.1|EG445432
EST:     TAGATTCAGAGGACACTCCTTGGCTGATCCCGATGATCTCCGTGATGCTG                         CTGAGAAAGCCAAATACGCGGCTAGAGACCCAATCGCAGCAT
genomic: TAGATTCAGAGGACACTCCTTGGCTGATCCCGATGAGCTCCGTGATGCTGgtaaatatcg ... ttttttgcagCTGAGAAAGCCAAATACGCGGCTAGAGACCCAATCGCAGCAT
EST: gi|86084902|gb|DR380661.1|DR380661
EST:     TAGATTTAGAGGACACTCCTTGGCTGATCCCGATGAGCTCCGTGATGCTG                         CTGAGAAAGCCAAATACGCGGCTAGAGACCCAATCGCAGCATTGAAGAAGT
genomic: TAGATTCAGAGGACACTCCTTGGCTGATCCCGATGAGCTCCGTGATGCTGgtaaatatcg ... ttttttgcagCTGAGAAAGCCAAATACGCGGCTAGAGACCCAATCGCAGCATTGAAGAAGT
EST: gi|86085567|gb|DR381326.1|DR381326
EST:     TAGATTTAGAGGACACTCCTTGGCTGATCCCGATGAGCTCCGTGATGCTG                         CTGAGAAAGCCAAATACGCGGCTAGAGACCCAATCGCAGCATTGAAGAAGT
genomic: TAGATTCAGAGGACACTCCTTGGCTGATCCCGATGAGCTCCGTGATGCTGgtaaatatcg ... ttttttgcagCTGAGAAAGCCAAATACGCGGCTAGAGACCCAATCGCAGCATTGAAGAAGT
EST: gi|86087430|gb|DR383189.1|DR383189
EST:     TAGATTTAGAGGACACTCCTTGGCTGATCCCGATGAGCTCCGTGATGCTG                         CTGAGAAAGCCAAATACGCGGCTAGAGACCCAATCGCAGCATTGAAGAAGT
genomic: TAGATTCAGAGGACACTCCTTGGCTGATCCCGATGAGCTCCGTGATGCTGgtaaatatcg ... ttttttgcagCTGAGAAAGCCAAATACGCGGCTAGAGACCCAATCGCAGCATTGAAGAAGT
EST: gi|164073130|gb|ES059737.1|ES059737
EST:     TAGATTCAGAGGACACTCCTTGGCTGATCCCGATGAGCTCCGTGATGCTG                         CTGAGAAAGCCAAATACGCGGCTAGAGACCCAA
genomic: TAGATTCAGAGGACACTCCTTGGCTGATCCCGATGAGCTCCGTGATGCTGgtaaatatcg ... ttttttgcagCTGAGAAAGCCAAATACGCGGCTAGAGACCCAA
EST: gi|164195579|gb|ES094288.1|ES094288
EST:     TCCTTGGCTGATCCCGATGAGCTCCGTGATGCTG                         CTGAGAAAGCCAAATACGCGGCTAGAGACCCAATCGCA
genomic: TCCTTGGCTGATCCCGATGAGCTCCGTGATGCTGgtaaatatcg ... ttttttgcagCTGAGAAAGCCAAATACGCGGCTAGAGACCCAATCGCA
EST: gi|116402841|gb|EG445433.1|EG445433
EST:     TAGATTCAGAGGACACTCCTTGGCTGATCCCGATGAGCTCCGTGATGCTG                         CTGAGAAAGCCAAATACGCGGCTAGAGACCCAATCGCAGCATTGAAGAAGT
genomic: TAGATTCAGAGGACACTCCTTGGCTGATCCCGATGAGCTCCGTGATGCTGgtaaatatcg ... ttttttgcagCTGAGAAAGCCAAATACGCGGCTAGAGACCCAATCGCAGCATTGAAGAAGT
EST: gi|124952203|gb|EL027493.1|EL027493
EST:     CCTTGGCTGATCCCGATGAGCTCCGTGATGCTG                         CTGAGAAAGCCAAATACGCGGCTAGAGACCCAATCGCAGCATTGAAGAAGT
genomic: CCTTGGCTGATCCCGATGAGCTCCGTGATGCTGgtaaatatcg ... ttttttgcagCTGAGAAAGCCAAATACGCGGCTAGAGACCCAATCGCAGCATTGAAGAAGT
EST: gi|86080274|gb|DR376031.1|DR376031
EST:     TAGATTTAGAGGACACTCCTTGGCTGATCCCGATGAGCTCCGTGATGCTG                         CTGAGAAAGCCAAATACGCGGCTAGAGACCCAATCGCAGCATTGAAGAAGT
genomic: TAGATTCAGAGGACACTCCTTGGCTGATCCCGATGAGCTCCGTGATGCTGgtaaatatcg ... ttttttgcagCTGAGAAAGCCAAATACGCGGCTAGAGACCCAATCGCAGCATTGAAGAAGT
EST: gi|124756599|gb|EH846729.1|EH846729
EST:     ACACTCCTTGGCTGATCCCGATGAGCTCCGTGATGCTG                         CTGAGAAAGCCAAATACGCGGCTAGAAGACCCAATCGCAGCATTGAAGAAG
genomic: ACACTCCTTGGCTGATCCCGATGAGCTCCGTGATGCTGgtaaatatcg ... ttttttgcagCTGAGAAAGCCAAATACGCGGCTAGA-GACCCAATCGCAGCATTGAAGAAG
EST: gi|116375670|gb|EG418262.1|EG418262
EST:     TAGATTCAGAGGACACTCCTTGGCTGATCCCGATGATCTCCGTGATGCTG                         CTGAGAAAGCCAAATACGCGGCTAGAGACCCAATCGCAGCATCGAAGAAGT
genomic: TAGATTCAGAGGACACTCCTTGGCTGATCCCGATGAGCTCCGTGATGCTGgtaaatatcg ... ttttttgcagCTGAGAAAGCCAAATACGCGGCTAGAGACCCAATCGCAGCATTGAAGAAGT
EST: gi|86081127|gb|DR376884.1|DR376884
EST:     TAGATTTAGAGGACACTCCTTGGCTGATCCCGATGAGCTCCGTGATGCTG                         CTGAGAAAGCCAAATACGCGGCTAGAGACCCAATCGCAGCATTGAAGAAGT
genomic: TAGATTCAGAGGACACTCCTTGGCTGATCCCGATGAGCTCCGTGATGCTGgtaaatatcg ... ttttttgcagCTGAGAAAGCCAAATACGCGGCTAGAGACCCAATCGCAGCATTGAAGAAGT
EST: gi|125324624|gb|EL338704.1|EL338704
EST:     CAGAGGACACTCCTTGGCTGATCCCGATGAGCTCCGTGATGCTG                         CTGAGAAAGCCAAATACGCGGCTAGAGACCCAATCGCAGCATTG
genomic: CAGAGGACACTCCTTGGCTGATCCCGATGAGCTCCGTGATGCTGgtaaatatcg ... ttttttgcagCTGAGAAAGCCAAATACGCGGCTAGAGACCCAATCGCAGCATTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACTAGAGCTAGAAGAGGAGAAGGTCCAACCTTGGTTGAATGTGAGACTTATAGATTCAGAGGACACTCCTTGGCTGATCCCGATGAGCTCCGTGATGCTGgtaaatatcgacttccttctgcttcttgatgcttgtactgattatctaagggttgaaacaaccttctctttaatttgaatttttttttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG