Skip to another splice site:
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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttagacaataaacaaatcctctgttccatgatttaagagtgaaatatgttttacttattatgatttgaatatgtttcagGCACTTCCACTTGTGAGTACATTTTGGGGGATATTGTTGTTTGGAGAATATAGAAGATCATCAAGAAAAACATATACACTTCTCATCAGTATGCTTCTTA

Basic information

species Arabidopsis thaliana
transcript AT2G03590.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G03590.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA02G12980.1 (Glycine max), 3'ss of exon 6
------------------gtttagacaataaacaaatcctctgttccatgatttaagagtgaaatatgttttacttattatgatttgaatatgttt---cagGCACTTCCACTTGTGAGTACATTTTGGGGGATATTGTTGTTTGGAGAATATAGAAGATCATCAAGAAAAACATATACACTTCTCATCAGTATGCTTCTTA
                   |||  ||| |  ||   |  | ||||||   |  ||  | |   | || |  |  | |       |    | |||||   |||||||||||||| |||||||| |||||||| ||  | ||||||||||| ||  | | ||||||||||| |||||||   || ||    || ||| | ||||
gcttaccgaaaaacactcattttaacatttgacttgtgat-tgttcctcaaactaccaatttca-atttcatggtaacagaagatgtgttttgtttgtacagGCACTTCCACTAGTGAGTACCTTTTGGGGCATTGTTTTGTTTGGAGAGTACCGCAAATCATCAAGAAGAACATATGTGCTACTTGGGAGCATGTTGCTTA

upper sequence: AT2G03590.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv01s0011g00530.t01 (Vitis vinifera), 3'ss of exon 6
-----------------------------------------gtttagacaat----aaacaaatcctctgt-tccatgatttaagagtgaaat----atgttttacttattatgatttgaatatgtt----tcagGCACTTCCACTTGTGAGTACATTTTGGGGGATATTGTTGTTTGGAGAATATAGAAGATCATCAAGAAAAACATATACACTTCTCATCAGTATGCTTCTTA
                                          |  || ||||    || |      | ||| |   |  |     | |  |||    ||||  |  | ||| |||  |    ||| |    ||||||||| ||||||||||| || || ||||| ||| |  |||||||||||||  ||| ||| ||||||| |||||||| | | ||    || |||||  | |
gtgagtttaagcacagcatacatattgacaaacacatacacatagaggcaatcataaatcggggtgtttgtgtgtgttttcctgcaatccaatcagaatgtgctgatcatt-tgaacttttcatggtaacatcagGCACTCCCACTTGTGAGCACTTTCTGGGGAATAGTTCTGTTTGGAGAATACCGAAAATCGTCAAGAAGAACATATATATTGCTTGGGAGCATGCTGTTCA
















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|116439994|gb|EG482586.1|EG482586
EST:     AGTTCATGGGTGGTCAAGCCGCAGGCTATGCAGCTGCAGACGCTGTTCAG                         GCACTTCCACTTGTGAGTACATTTTGGGGGATATTGTTGTTTGGAGAATAT
genomic: AGTTCATGGGTGGTCAAGCCGCAGGCTATGCAGCTGCAGACGCTGTTCAGgtttagacaa ... tatgtttcagGCACTTCCACTTGTGAGTACATTTTGGGGGATATTGTTGTTTGGAGAATAT
EST: gi|19743503|gb|AU228856.1|AU228856
EST:     AGTTCATGGGTGGTCAAGCCGCAGGCTATGCAGCTCCAAACCCTGTTCAG                         GCACTTCCACTTGTGAGTACATTTTGGGGGATATTGTTGTTTGGAGAATAT
genomic: AGTTCATGGGTGGTCAAGCCGCAGGCTATGCAGCTGCAGACGCTGTTCAGgtttagacaa ... tatgtttcagGCACTTCCACTTGTGAGTACATTTTGGGGGATATTGTTGTTTGGAGAATAT
EST: gi|116439996|gb|EG482588.1|EG482588
EST:     AGTTCATGGGTGGTCAAGCCGCAGGCTATGCAGCTGCAGACGCTGTTCAG                         GCACTTCCACTTGTGAGTACATTTTGGGGGATATTGTTGTTTGGAGAATAT
genomic: AGTTCATGGGTGGTCAAGCCGCAGGCTATGCAGCTGCAGACGCTGTTCAGgtttagacaa ... tatgtttcagGCACTTCCACTTGTGAGTACATTTTGGGGGATATTGTTGTTTGGAGAATAT
EST: gi|116439987|gb|EG482579.1|EG482579
EST:     AGTTCATGGGTGGTCAAGCCGCAGGCTATGCAGCTGCAGACGCTGTTCAG                         GCACTTCCACTTGTGAGTACATTTTGGGGGATATTGTTGTTTGGAGAATAT
genomic: AGTTCATGGGTGGTCAAGCCGCAGGCTATGCAGCTGCAGACGCTGTTCAGgtttagacaa ... tatgtttcagGCACTTCCACTTGTGAGTACATTTTGGGGGATATTGTTGTTTGGAGAATAT
EST: gi|116439991|gb|EG482583.1|EG482583
EST:     AGTTCATGGGTGGTCAAGCCGCAGGCTATGCAGCTGCAGACGCTGTTCAG                         GCACTTCCACTTGTGAGTACATTTTGGGGGATATTGTTGTTTGGAGAATAT
genomic: AGTTCATGGGTGGTCAAGCCGCAGGCTATGCAGCTGCAGACGCTGTTCAGgtttagacaa ... tatgtttcagGCACTTCCACTTGTGAGTACATTTTGGGGGATATTGTTGTTTGGAGAATAT
EST: gi|116439995|gb|EG482587.1|EG482587
EST:     AGTTCATGGGTGGTCAAGCCGCAGGCTATGCAGCTGCAGACGCTGTTCAG                         GCACTTCCACTTGTGAGTACATTTTGGGGGATATTGTTGTTTGGAGAATAT
genomic: AGTTCATGGGTGGTCAAGCCGCAGGCTATGCAGCTGCAGACGCTGTTCAGgtttagacaa ... tatgtttcagGCACTTCCACTTGTGAGTACATTTTGGGGGATATTGTTGTTTGGAGAATAT
EST: gi|116439988|gb|EG482580.1|EG482580
EST:     AGTTCATGGGTGGTCAAGCCGCAGGCTATGCAGCTGCAGACGCTGTTCAG                         GCACTTCCACTTGTGAGTACATTTTGGGGGATATTGTTGTTTGGAGAATAT
genomic: AGTTCATGGGTGGTCAAGCCGCAGGCTATGCAGCTGCAGACGCTGTTCAGgtttagacaa ... tatgtttcagGCACTTCCACTTGTGAGTACATTTTGGGGGATATTGTTGTTTGGAGAATAT
EST: gi|116425505|gb|EG468097.1|EG468097
EST:     GGTGTTCAAGCCGCAGGCTATGCAGCTGCAGACGCTGTTCAG                         GCACTTCCACTTGTGAGTACATTTTGGGGGATATTGTTGTTTGGAGAATAT
genomic: GGTGGTCAAGCCGCAGGCTATGCAGCTGCAGACGCTGTTCAGgtttagacaa ... tatgtttcagGCACTTCCACTTGTGAGTACATTTTGGGGGATATTGTTGTTTGGAGAATAT
EST: gi|116439992|gb|EG482584.1|EG482584
EST:     AGTTCATGGGTGGTCAAGCCGCAGGCTATGCAGCTGCAGACGCTGTTCAG                         GCACTTCCACTTGTGAGTACATTTTGGGGGATATTGTTGTTTGGAGAATAT
genomic: AGTTCATGGGTGGTCAAGCCGCAGGCTATGCAGCTGCAGACGCTGTTCAGgtttagacaa ... tatgtttcagGCACTTCCACTTGTGAGTACATTTTGGGGGATATTGTTGTTTGGAGAATAT
EST: gi|116425506|gb|EG468098.1|EG468098
EST:     GGTGTTCAAGCCGCAGGCTATGCAGCTGCAGACGCTGTTCAG                         GCACTTCCACTTGTGAGTACATTTTGGGGGATATTGTTGTTTGGAGAATAT
genomic: GGTGGTCAAGCCGCAGGCTATGCAGCTGCAGACGCTGTTCAGgtttagacaa ... tatgtttcagGCACTTCCACTTGTGAGTACATTTTGGGGGATATTGTTGTTTGGAGAATAT
EST: gi|116439990|gb|EG482582.1|EG482582
EST:     AGTTCATGGGTGGTCAAGCCGCAGGCTATGCAGCTGCAGACGCTGTTCAG                         GCACTTCCACTTGTGAGTACATTTTGGGGGATATTGTTGTTTGGAGAATAT
genomic: AGTTCATGGGTGGTCAAGCCGCAGGCTATGCAGCTGCAGACGCTGTTCAGgtttagacaa ... tatgtttcagGCACTTCCACTTGTGAGTACATTTTGGGGGATATTGTTGTTTGGAGAATAT
EST: gi|116439989|gb|EG482581.1|EG482581
EST:     AGTTCATGGGTGGTCAAGCCGCAGGCTATGCAGCTGCAGACGCTGTTCAG                         GCACTTCCACTTGTGAGTACATTTTGGGGGATATTGTTGTTTGGAGAATAT
genomic: AGTTCATGGGTGGTCAAGCCGCAGGCTATGCAGCTGCAGACGCTGTTCAGgtttagacaa ... tatgtttcagGCACTTCCACTTGTGAGTACATTTTGGGGGATATTGTTGTTTGGAGAATAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tccatgatttaagagtgaaatatgttttacttattatgatttgaatatgtttcagGCACTTCCACTTGTGAGTACATTTTGGGGGATATTGTTGTTTGGAGAATATAGAAGATCATCAAGAAAAACATATACACTTCTCATCAGTATGCTTCTTA
                 aaatatgttttactta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttagacaataaacaaatcctctgttccatgatttaagagtgaaatatgttttacttattatgatttgaatatgtttcagGCACTTCCACTTGTGAGTACATTTTGGGGGATATTGTTGTTTGGAGAATATAGAAGATCATCAAGAAAAACATATACACTTCTCATCAGTATGCTTCTTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA