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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgatacgatctgtttgctttttaagttaaatgaagccactgcatccaatcttctctgttcattggagtgtaacagatgctttgtgttctctattgggttctagtttacgactctcttgctcacacattcgctctcgttttgtcttttttttttcagGTTCTTGTTGTGGCCAACCCGGCAAACACCAACGCATTGATCCTCAAGGAATTTGCACCATCAATCCCTGAAAAGAACATCTCTTGTTTGACAAGGCTTG

Basic information

species Arabidopsis thaliana
transcript AT1G04410.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G04410.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA02G00810.2 (Glycine max), 3'ss of exon 3
gtgatacgatctgtttgctttttaagttaaatgaagccactgcatccaatcttctctgttcattggagtgtaacagatgctttgtgttctctattgggttctagtttacgactctcttgctcacacattcgctctcgttttgtcttttttttttcagGTTCTTGTTGTGGCCAACCCGGCAAACACCAACGCATTGATCCTCAAGGAATTTGCACCATCAATCCCTGAAAAGAACATCTCTTGTTTGACAAGGCTTG
                                      |  | ||| ||     |   ||| ||      |  ||||     ||| ||         ||| ||   |  |  | | |||     | |||   |     ||||  || | |||  |||||||||||||| || ||||| ||||||||||| ||||||||| | ||||||||||| ||||| || || || |||||||| ||||||||||| ||  | |
-------------------------------------gatggaatctaactgagttcattctttt-----ttgcagaaatcatgtatttc------agtttta---tgtggttgttttg---gaatattta-tgagactttgcattatcttt--cagGTTCTTGTTGTTGCTAACCCAGCAAACACCAATGCATTGATCTTGAAGGAATTTGCTCCATCTATTCCCGAGAAGAACATTTCTTGTTTGACTAGATTGG

upper sequence: AT1G04410.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA10G00920.1 (Glycine max), 3'ss of exon 3
gtgatacgatctgtttgctttttaagttaaatgaagccactgcatccaatcttctctgttca-ttggagtgtaacagatgctttgtgttctctattgggttctagtttacgactctcttgctcacacattcgctctcgttttgtcttttttttttcagGTTCTTGTTGTGGCCAACCCGGCAAACACCAACGCATTGATCCTCAAGGAATTTGCACCATCAATCCCTGAAAAGAACATCTCTTGTTTGACAAGGCTTG
                                      | | |||  |||||   |||||   ||   ||  || | ||| ||| || | || ||  ||||   ||||  || | | ||    ||   || ||              || | || |||||||||||||| || ||||| ||||||||||| ||||||||| | || |||||||| ||||| || || || || ||||| ||||||||||| ||  | |
--------------------------------------aattcatgaaatctgtactgttttctttttgttgaaaacatgttttttggtttc-atgtggtt---gttttagaatattttaaagac---tttgca-------------ttatcttgcagGTTCTTGTTGTTGCTAACCCAGCAAACACCAATGCATTGATCTTGAAAGAATTTGCTCCATCTATTCCCGAGAAAAACATTTCTTGTTTGACTAGATTGG

upper sequence: AT1G04410.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv07s0005g03360.t01 (Vitis vinifera), 3'ss of exon 3
---------gtgatacgatctgtttgctttttaagttaaatgaagccact-------gcatccaatcttctc--tgttcattggagtgta-----acagatgctttgtgttctctattgggttctagtttacgactctctt-----gctcacacattcgctctcgttttgtcttt---------tttttttcagGTTCTTGTTGTGGCCAACCCGGCAAACACCAACGCATTGATCCTCAAGGAATTTGCACCATCAATCCCTGAAAAGAACATCTCTTGTTTGACAAGGCTTG
          |  ||   | |||||   ||    | ||||   | |||||        |||  || |  ||   || | |  || |  ||     ||| |   ||    | |  || | ||     | ||    || |  |     | |    || ||  | |  |||  | ||          ||| ||||||||| | ||||| || ||||| ||||| || || || |||||||| |||||||||||||||||||| ||||| || |||||   |||||||||||| || |
gtgctcacgattgtatattttgtttcaattccttgataaaatcatccacttgattgaacattgaaccaccttaatggttaccggggaatacttttacatagaattaacctgcattacttggccaatgcttctttcttttcttttgtgtttttccaatcaattttatttattattcattcattcatttatttcagGTTTTGGTTGTTGCTAACCCAGCAAATACAAATGCCTTGATCCTGAAGGAATTTGCACCATCAATTCCTGAGAAAAACATTAGTTGTTTGACAAGACTGG

upper sequence: AT1G04410.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv07s0005g03350.t01 (Vitis vinifera), 3'ss of exon 4
------------------------------------gtgatacgatctgtttgctt---tttaagttaaatgaagccactgcatccaatcttctctgttcattggagtgtaacagatgctttgtgttctctattgggttctagtttacgactctcttgctcacacattcgctc-tcgttttgtcttt--tttttttcagGTTCTTGTTGTGGCCAACCCGGCAAACACCAACGCATTGATCCTCAAGGAATTTGCACCATCAATCCCTGAAAAGAACATCTCTTGTTTGACAAGGCTTG
                                     |||||  |||  |   |||   |  |  || ||  |    | |   | | |     |   || | | |   || ||  |  ||   ||  |  |  |   ||||  | | |     | || |   ||  ||   |  |  ||   || ||  ||| ||||||||| | ||||| || ||||| ||||| || || || |||||||| |||||||||||||||||||| ||||| || |||||   |||||||||||| || |
gtgctgaagattatatcatgtttcgaattttctttcttgataaaatc-atgcacttgagtgaagattgaaccaccttaatagttaccagggaatacttttacttggaagtgacccacactccttggccaatgcttctttcttttcttctgtgtttttccaatcaattttatttattattcattcattcatttatttcagGTTTTGGTTGTTGCTAACCCAGCAAATACAAATGCCTTGATCCTGAAGGAATTTGCACCATCAATTCCTGAGAAAAACATTAGTTGTTTGACAAGACTAG

upper sequence: AT1G04410.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: EFJ10745 (Selaginella moellendorffii), 3'ss of exon 3
gtgatacgatctgtttgctttttaagttaaatgaagccactgcatccaatcttctctgttcattggagtgtaacagatgctttgtgttctctattgggttctagtttacgactctcttgctcacacattcgctctcgttttgtcttttttttttcagGTTCTTGTTGTGGCCAACCCGGCAAACACCAACGCATTGATCCTCAAGGAATTTGCACCATCAATCCCTGAAAAGAACATCTCTTGTTTGACAAGGCTTG
                                                                                                     ||   ||  | |      |  |  ||   ||||  |  |     |     |  |||||||| || || || || || || || || || ||  ||||||||||||| ||||| || || || ||||| ||||||||| |||| ||||| ||||| |
----------------------------------------------------------------------------------------------------gtaacgtagaaatacaaaacgtat-cagaagctcatgact----gtgggcgtgacagGTTCTGGTGGTTGCTAATCCTGCCAATACTAATGCGCTGATCCTCAAGGAGTTTGCTCCTTCCATTCCTGACAAGAACATCACTTGCTTGACGAGGCTGG

upper sequence: AT1G04410.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: EFJ17451 (Selaginella moellendorffii), 3'ss of exon 4
gtgatacgatctgtttgctttttaagttaaatgaagccactgcatccaatcttctctgttcattggagtgtaacagatgctttgtgttctctattgggttctagtttacgactctcttgctcacacattcgctctcgttttgtcttttttttttcagGTTCTTGTTGTGGCCAACCCGGCAAACACCAACGCATTGATCCTCAAGGAATTTGCACCATCAATCCCTGAAAAGAACATCTCTTGTTTGACAAGGCTTG
                                                                                                         | ||   | |      |  |    |  |     || |    | |     |||||||| || || |||||||| || || || || || |||||||||||| | ||||| || || || ||||| ||||||||| |||| ||||||| ||| |
--------------------------------------------------------------------------------------------------------gtaacatatatacgaaacgtatgagcatttaaaattggaagctgt---gacagGTTCTGGTGGTTGCCAACCCTGCCAAAACTAATGCGTTGATCCTCAAGAATTTTGCCCCTTCCATTCCTGACAAGAACATCACTTGCTTGACAAAGCTGG

upper sequence: AT1G04410.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: EFJ07542 (Selaginella moellendorffii), 3'ss of exon 3
gtgatacgatctgtttgctttttaagttaaatgaagccactgcatccaatcttctctgttcattggagtgtaacagatgctttgtgttctctattgggttctagtttacgactctcttgctcacacattcgctctcgttttgtcttttttttttcagGTTCTTGTTGTGGCCAACCCGGCAAACACCAACGCATTGATCCTCAAGGAATTTGCACCATCAATCCCTGAAAAGAACATCTCTTGTTTGACAAGGCTTG
                                                                                                         | || |      | |  |     |||    |   |     |     |  |||||||| || || || || || || || || || ||  ||||||||||||| ||||| || || || ||||| ||||||||| |||| ||||| ||||| |
--------------------------------------------------------------------------------------------------------gtaaccatagaaatacaaaacgtatcggaagctcatgactgtgggcgtgacagGTTCTGGTGGTTGCTAATCCAGCCAATACAAATGCGCTGATCCTCAAGGAGTTTGCTCCTTCCATTCCTGACAAGAACATCACTTGCTTGACGAGGCTGG

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|124765673|gb|EH855803.1|EH855803
EST:     ACAAGTCTCAGGCTGCTGCCTTGGAGAAGCATGCCGCTCCTAACTGCAAG                         GTTCTTGTTGTGGCCAACCCGGCAAAACACCAACGCATTGA
genomic: ACAAGTCTCAGGCTGCTGCCTTGGAGAAGCATGCCGCTCCTAACTGCAAGgtgatacgat ... tttttttcagGTTCTTGTTGTGGCCAACCCGGCAAA-CACCAACGCATTGA
EST: gi|124733580|gb|EH824982.1|EH824982
EST:     ACAAGTCTCAGGCTGCTGCCTTGGAGAAGCATGCCGCTCCTAACTGCAAG                         GTTCTTGTTGTGGCCAACCCGGCAAACACCAACGCATTGATCCTCAAGG
genomic: ACAAGTCTCAGGCTGCTGCCTTGGAGAAGCATGCCGCTCCTAACTGCAAGgtgatacgat ... tttttttcagGTTCTTGTTGTGGCCAACCCGGCAAACACCAACGCATTGATCCTCAAGG
EST: gi|47829836|gb|CK119520.1|CK119520
EST:     ACAAGTCTCAGGCTGCTGCCTTGGAGAAGCATGCCGCTCCTAACTGCAAG                         GTTCTTGTTGTGGCCAACCCGGCAAACACCAACGCATTGATCCTCAAGGAA
genomic: ACAAGTCTCAGGCTGCTGCCTTGGAGAAGCATGCCGCTCCTAACTGCAAGgtgatacgat ... tttttttcagGTTCTTGTTGTGGCCAACCCGGCAAACACCAACGCATTGATCCTCAAGGAA
EST: gi|47830669|gb|CK120353.1|CK120353
EST:     ACAAGTCTCAGGCTGCTGCCTTGGAGAAGCATGCCGCTCCTAACTGCAAG                         GTTCTTGTTGTGGCCAACCCGGCAAACACCAACGCATTGATCCTCAAGGAA
genomic: ACAAGTCTCAGGCTGCTGCCTTGGAGAAGCATGCCGCTCCTAACTGCAAGgtgatacgat ... tttttttcagGTTCTTGTTGTGGCCAACCCGGCAAACACCAACGCATTGATCCTCAAGGAA
EST: gi|47828241|gb|CK117925.1|CK117925
EST:     ACAAGTCTCAGGCTGCTGCCTTGGAGAAGCATGCCGCTCCTAACTGCAAG                         GTTCTTGTTGTGGCCAACCCGGCAAACACCAACGCATTGATCCTCAAGGAA
genomic: ACAAGTCTCAGGCTGCTGCCTTGGAGAAGCATGCCGCTCCTAACTGCAAGgtgatacgat ... tttttttcagGTTCTTGTTGTGGCCAACCCGGCAAACACCAACGCATTGATCCTCAAGGAA
EST: gi|301503095|gb|HO208635.1|HO208635
EST:     ACAAGTCTCAGGCTGCTGCCTTGGAGAAGCATGCCGCTCCTAACTGCAAG                         GTTCTTGTTGTGGCCAACCCGGCAAACACCAACGCATTGATCCTCAAGGAA
genomic: ACAAGTCTCAGGCTGCTGCCTTGGAGAAGCATGCCGCTCCTAACTGCAAGgtgatacgat ... tttttttcagGTTCTTGTTGTGGCCAACCCGGCAAACACCAACGCATTGATCCTCAAGGAA
EST: gi|47829133|gb|CK118817.1|CK118817
EST:     ACAAGTCTCAGGCTGCTGCCTTGGAGAAGCATGCCGCTCCTAACTGCAAG                         GTTCTTGTTGTGGCCAACCCGGCAAACACCAACGCATTGATCCTCAAGGAA
genomic: ACAAGTCTCAGGCTGCTGCCTTGGAGAAGCATGCCGCTCCTAACTGCAAGgtgatacgat ... tttttttcagGTTCTTGTTGTGGCCAACCCGGCAAACACCAACGCATTGATCCTCAAGGAA
EST: gi|47829241|gb|CK118925.1|CK118925
EST:     ACAAGTCTCAGGCTGCTGCCTTGGAGAAGCATGCCGCTCCTAACTGCAAG                         GTTCTTGTTGTGGCCAACCCGGCAAACACCAACGCATTGATCCTCANGGAA
genomic: ACAAGTCTCAGGCTGCTGCCTTGGAGAAGCATGCCGCTCCTAACTGCAAGgtgatacgat ... tttttttcagGTTCTTGTTGTGGCCAACCCGGCAAACACCAACGCATTGATCCTCAAGGAA
EST: gi|125191671|gb|EL206625.1|EL206625
EST:     ACAAGTCTCAGGCTGCTGCCTTGGAGAAGCATGCCGCTCCTAACTGCAAG                         GTTCTTGTTGTGGCCAACCCGGCAAACACCAACG
genomic: ACAAGTCTCAGGCTGCTGCCTTGGAGAAGCATGCCGCTCCTAACTGCAAGgtgatacgat ... tttttttcagGTTCTTGTTGTGGCCAACCCGGCAAACACCAACG
EST: gi|125232877|gb|EL246962.1|EL246962
EST:     CTCCTAACTGCAAG                         GTTCTTGTTGTGGCCAACCCGGCAAACACCAACGCATTGATCCTACAAGGA
genomic: CTCCTAACTGCAAGgtgatacgat ... tttttttcagGTTCTTGTTGTGGCCAACCCGGCAAACACCAACGCATTGATCCT-CAAGGA
EST: gi|47828264|gb|CK117948.1|CK117948
EST:     ACAAGTCTCAGGCTGCTGCCTTGGAGAAGCATGCCGCTCCTAACTGCAAG                         GTTCTTGTTGTGGCCAACCCGGCAAACACCAACGCATTGATCCTCAAGGAA
genomic: ACAAGTCTCAGGCTGCTGCCTTGGAGAAGCATGCCGCTCCTAACTGCAAGgtgatacgat ... tttttttcagGTTCTTGTTGTGGCCAACCCGGCAAACACCAACGCATTGATCCTCAAGGAA
EST: gi|47832292|gb|CK121976.1|CK121976
EST:     ACAAGTCTCAGGCTGCTGCCTTGGAGAAGCATGCCGCTCCTAACTGCAAG                         GTTCTTGTTGTGGCCAACCCGGCAAACACCAACGCATTGATCCTCAAGGAA
genomic: ACAAGTCTCAGGCTGCTGCCTTGGAGAAGCATGCCGCTCCTAACTGCAAGgtgatacgat ... tttttttcagGTTCTTGTTGTGGCCAACCCGGCAAACACCAACGCATTGATCCTCAAGGAA
EST: gi|125223552|gb|EL237637.1|EL237637
EST:     CTCCTAACTGCAAG                         GTTCTTGTTGTGGCCAACCCGGCAAACACCAACGCATTGATCCTCAAGGAA
genomic: CTCCTAACTGCAAGgtgatacgat ... tttttttcagGTTCTTGTTGTGGCCAACCCGGCAAACACCAACGCATTGATCCTCAAGGAA
EST: gi|301501445|gb|HO206985.1|HO206985
EST:     ACAAGTCTCAGGCTGCTGCCTTGGAGAAGCATGCCGCTCCTAACTGCAAG                         GATCTTGTTGTGGCCAACCCGGCAAACACCAACGCATTGATCCTCAAGGAA
genomic: ACAAGTCTCAGGCTGCTGCCTTGGAGAAGCATGCCGCTCCTAACTGCAAGgtgatacgat ... tttttttcagGTTCTTGTTGTGGCCAACCCGGCAAACACCAACGCATTGATCCTCAAGGAA
EST: gi|124891668|gb|EH970570.1|EH970570
EST:     CAAGTCTCAGGCTGCTGCCTTGGAGAAGCATGCCGCTCCTAACTGCAAG                         GTTCTTGTTGTGGCCAACCCGGCAAACACCAACGCATTGATCCTCAAGG
genomic: CAAGTCTCAGGCTGCTGCCTTGGAGAAGCATGCCGCTCCTAACTGCAAGgtgatacgat ... tttttttcagGTTCTTGTTGTGGCCAACCCGGCAAACACCAACGCATTGATCCTCAAGG
EST: gi|116378554|gb|EG421146.1|EG421146
EST:     ACAAGTCTCAGGCTGCTGCCTTGGAGAAGCATGCCGCTCCTAACTGCAAG                         GTTCTTGTTGTGGCCAACCCGGCAAACACCAACGCATTGATCCTCAAGGAA
genomic: ACAAGTCTCAGGCTGCTGCCTTGGAGAAGCATGCCGCTCCTAACTGCAAGgtgatacgat ... tttttttcagGTTCTTGTTGTGGCCAACCCGGCAAACACCAACGCATTGATCCTCAAGGAA
EST: gi|125312257|gb|EL326342.1|EL326342
EST:     AGAAGCATGCCGCTCCTAACTGCAAG                         GTTCTTGTTGTGGCCAACCCGGCAAACACCAACGCATTGATCCTCAAGGAA
genomic: AGAAGCATGCCGCTCCTAACTGCAAGgtgatacgat ... tttttttcagGTTCTTGTTGTGGCCAACCCGGCAAACACCAACGCATTGATCCTCAAGGAA
EST: gi|47828810|gb|CK118494.1|CK118494
EST:     ACAAGTCTCAGGCTGCTGCCTTGGAGAAGCATGCCGCTCCTAACTGCAAG                         GTTCTTGGTGTGGCCAACCCGGCAAACACCAACGCATTGATCCTCAAGGAA
genomic: ACAAGTCTCAGGCTGCTGCCTTGGAGAAGCATGCCGCTCCTAACTGCAAGgtgatacgat ... tttttttcagGTTCTTGTTGTGGCCAACCCGGCAAACACCAACGCATTGATCCTCAAGGAA
EST: gi|116378552|gb|EG421144.1|EG421144
EST:     ACAAGTCTCAGGCTGCTGCCTTGGAGAAGCATGCCGCTCCTAACTGCAAG                         GTTCTTGTTGTGGCCAACCCGGCAAACACCAACGCATTGATCCTCAAGGAA
genomic: ACAAGTCTCAGGCTGCTGCCTTGGAGAAGCATGCCGCTCCTAACTGCAAGgtgatacgat ... tttttttcagGTTCTTGTTGTGGCCAACCCGGCAAACACCAACGCATTGATCCTCAAGGAA
EST: gi|47831346|gb|CK121030.1|CK121030
EST:     ACAAGTCTCAGGCTGCTGCCTTGGAGAAGCATGCCGCTCCTAACTGCAAG                         GTTCTTGTTGTGGCCAACCCGGCAAACACCAACGCATTGATCCTCAAGGAA
genomic: ACAAGTCTCAGGCTGCTGCCTTGGAGAAGCATGCCGCTCCTAACTGCAAGgtgatacgat ... tttttttcagGTTCTTGTTGTGGCCAACCCGGCAAACACCAACGCATTGATCCTCAAGGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtttacgactctcttgctcacacattcgctctcgttttgtcttttttttttcagGTTCTTGTTGTGGCCAACCCGGCAAACACCAACGCATTGATCCTCAAGGAATTTGCACCATCAATCCCTGAAAAGAACATCTCTTGTTTGACAAGGCTTG
               tgctcac  putative branch site (score: 2)
                       cattcgctctcgtttt  CT-rich tract
                                   ttttgtcttttttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgatacgatctgtttgctttttaagttaaatgaagccactgcatccaatcttctctgttcattggagtgtaacagatgctttgtgttctctattgggttctagtttacgactctcttgctcacacattcgctctcgttttgtcttttttttttcagGTTCTTGTTGTGGCCAACCCGGCAAACACCAACGCATTGATCCTCAAGGAATTTGCACCATCAATCCCTGAAAAGAACATCTCTTGTTTGACAAGGCTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC