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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gttcgtaatgattctctgtttccatttgatatgatgcaaaatgcctcatgagcttactactgatacccatttggtttaattggattttgttatgatatagGTGATATGTGTGGTGGTACAGGAAAATGGAAAGCTCTCAACCGAAAACGTGCGAAAGATGTATATGAGTTTACGGAATGTCCAAACTGTTACG

Basic information

species Arabidopsis thaliana
transcript AT2G34860.2
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G34860.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os08g36140.1 (Oryza sativa), 3'ss of exon 3
------gttcgtaatgattctct-gtttccatttgatatgatgcaaaatgcctcatgagcttactactgatacccatttggtttaattggattttgttatgatatagGTGATATGTGTGGTGGTACAGGAAAATGGAAAGCTCTCAACCGAAAACGTGCGAAAGATGTATATGAGTTTACGGAATGTCCAAACTGTTACG
       ||| || | | ||    | |   | | |   ||  ||| | |||  |||      ||  ||   | ||||       ||||  | |       ||||||||||| ||||| || || || ||||||||||| || |||||||||||  | || |||||||| |||   || || || || |||||||| ||||
actaacattcatagtaaatcagaagatattagtagtagtgcagcatagtgctgcatctttcaacatcttggagccat-------aattcaactccagctcgatatagGTGACATGTGCGGCGGCACTGGAAAATGGAAGGCCCTCAACCGAAAGAGAGCAAAAGATGTCTATCTATTCACAGAGTGCCCAAACTGCTACG

upper sequence: AT2G34860.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA10G44020.3 (Glycine max), 3'ss of exon 3
---gttcgtaatgattctctgtttccatttgatatgatgcaaaatgcctcatgagcttactactgatacccatttggttta-attggattttgttatgatatagGTGATATGTGTGGTGGTACAGGAAAATGGAAAGCTCTCAACCGAAAACGTGCGAAAGATGTATATGAGTTTACGGAATGTCCAAACTGTTACG
   |||  |      | | |   ||   |  |||||| |   | ||    |||    |  | || | |  | |||| |  | |     |||  || | || ||||||||||||||||||| |||||||||||||||||||| ||||| || || || |||||||| ||||| ||||| || |||||||| ||||| |
tgagttgatgccatatgttttaatcttatcaatatgaggacgagtgg---atgttactgtttcttacatac-tttgatacataccatgtttacttttcatttagGTGATATGTGTGGTGGCACAGGAAAATGGAAAGCTCTTAACCGGAAGCGAGCTAAAGATGTTTATGAATTTACTGAGTGTCCAAATTGTTATG

upper sequence: AT2G34860.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA20G38750.1 (Glycine max), 3'ss of exon 3
---gttcgtaatgattctctgtttccatttgatatgatgcaaaatgcctcatgagcttactactgatacccatttggttta-attggattttgttatgatatagGTGATATGTGTGGTGGTACAGGAAAATGGAAAGCTCTCAACCGAAAACGTGCGAAAGATGTATATGAGTTTACGGAATGTCCAAACTGTTACG
    ||||  || |||| ||| | |||| || | | |    |    |    | ||   | |     |  |  |||  |  | |     |||  || | || ||| ||||||||||||||| |||||||||||||||||||| ||| | || || || |||||||| || || ||||| || |||||||| ||||| |
ttgtttcgatattattc-ctgatgccatatgctgtaaccttat---caatgtaagaccagtggatgtttctgtttcttacataccatgtttacttttcatttagATGATATGTGTGGTGGCACAGGAAAATGGAAAGCTCTTAACAGGAAGCGAGCTAAAGATGTTTACGAATTTACTGAGTGTCCAAATTGTTATG

upper sequence: AT2G34860.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA14G27040.1 (Glycine max), 3'ss of exon 1
---gttcgtaatgattctctgtttccatttgatatgatgcaaaatgcctcatgagcttactactgatacccatttggttta-attggattttgttatgatatagGTGATATGTGTGGTGGTACAGGAAAATGGAAAGCTCTCAACCGAAAACGTGCGAAAGATGTATATGAGTTTACGGAATGTCCAAACTGTTACG
    ||||  || |||| ||| | |||| || | | |    |    |    | ||   | |     |  |  |||  |  | |     |||  || | || ||| ||||||||||||||| |||||||||||||||||||| |||   || || || |||||||| || || ||||| || |||||||| ||||| |
ttgtttcgatattattc-ctgatgccatatgctgtaaccttat---caatgtaagaccagtggatgtttctgtttcttacataccatgtttacttttcatttagATGATATGTGTGGTGGCACAGGAAAATGGAAAGCTCTTAACATGAAGCGAGCTAAAGATGTTTACGAATTTACTGAGTGTCCAAATTGTTATG

upper sequence: AT2G34860.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv06s0004g01100.t01 (Vitis vinifera), 3'ss of exon 3
-----gttcgtaatgattctctgtttccatttgatatgatgcaaaatgcctcatgagcttactactgatacccatttggtttaattggattttgttatgatatagGTGATATGTGTGGTGGTACAGGAAAATGGAAAGCTCTCAACCGAAAACGTGCGAAAGATGTATATGAGTTTACGGAATGTCCAAACTGTTACG
       | || |||    || || |    |  | |   |    ||  | |  | |||  |  ||    |   ||   |||||  | |||||  || | || |||||||||||||||||||||| ||||||||||||||||||||| ||||||| || |||||||| || |||||||| ||||| ||||| ||||| |
tacctacttgtcatggacttcggtgtttcctaaacaacctatgcaacacttt-taagc--aacacatggaataatgctgttta--ttgatttgcttttcatttagGTGATATGTGTGGTGGTACGGGAAAATGGAAAGCTCTCAACAGAAAACGGGCTAAAGATGTTTACGAGTTTACTGAATGCCCAAATTGTTATG

upper sequence: AT2G34860.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: EFJ07587 (Selaginella moellendorffii), 3'ss of exon 1
gttcgtaatgattctctgtttccatttgata-tgatgcaaaatgcctcatgagcttactactgatacccatttg--gtttaattggattttgttatgatatagGTGATATGTGTGGTGGTACAGGAAAATGGAAAGCTCTCAACCGAAAACGTGCGAAAGATGTATATGAGTTTACGGAATGTCCAAACTGTTACG
                       | |||||| |  |||        |  ||  |   | ||  || |   ||||    |  ||||||||  |   ||  | ||||||||||||||| || || ||||| ||||||||||||| | | || || || || || || || ||||| || || ||||| || || ||||
--------------------gtaagttgatagtcctgccctgctagtgttgttccagccacgcattcttctttgtgactggattggattc-gcggtgccacagGTGATATGTGTGGAGGGACTGGAAAGTGGAAAGCTCTCAGCAGGAAGCGAGCCAAGGACGTGTACGAGTTCACCGAGTGTCCCAATTGCTACG

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|86073324|gb|DR369081.1|DR369081
EST:     GAAACCAGGAGGTTCATGTCGTAACTGCCAGGGCAGTGGTGCTGTTCTTT                         GTGATATGTGTGGTGGTACAGGAAAATGGAAAGCTCTCAACCGAAAACGTG
genomic: GAAACCAGGAGGTTCATGTCGTAACTGCCAGGGCAGTGGTGCTGTTCTTTgtgagtgaca ... tatgatatagGTGATATGTGTGGTGGTACAGGAAAATGGAAAGCTCTCAACCGAAAACGTG
EST: gi|124978112|gb|EL051341.1|EL051341
EST:     GAAACCAGGAGGTTCATGTCGTAACTGCCAGGGCAGTGGNGCTGTTCTTT                         GTGATATGTGTGGTGGTACAGGAAAATGGAAAGCTCTCAAACCGAAAACGT
genomic: GAAACCAGGAGGTTCATGTCGTAACTGCCAGGGCAGTGGTGCTGTTCTTTgtgagtgaca ... tatgatatagGTGATATGTGTGGTGGTACAGGAAAATGGAAAGCTCTCAA-CCGAAAACGT
EST: gi|86073323|gb|DR369080.1|DR369080
EST:     GAAACCAGGAGGTTCATGTCGTAACTGCCAGGGCAGTGGTGCTGTTCTTT                         GTGATATGTGTGGTGGTACAGGAAAATGGAAAGCTCTCAACCGANNNCGTG
genomic: GAAACCAGGAGGTTCATGTCGTAACTGCCAGGGCAGTGGTGCTGTTCTTTgtgagtgaca ... tatgatatagGTGATATGTGTGGTGGTACAGGAAAATGGAAAGCTCTCAACCGAAAACGTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcatgagcttactactgatacccatttggtttaattggattttgttatgatatagGTGATATGTGTGGTGGTACAGGAAAATGGAAAGCTCTCAACCGAAAACGTGCGAAAGATGTATATGAGTTTACGGAATGTCCAAACTGTTACG
                                       ttttgtt  CT-rich tract
                                      attttgttatgatata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttcgtaatgattctctgtttccatttgatatgatgcaaaatgcctcatgagcttactactgatacccatttggtttaattggattttgttatgatatagGTGATATGTGTGGTGGTACAGGAAAATGGAAAGCTCTCAACCGAAAACGTGCGAAAGATGTATATGAGTTTACGGAATGTCCAAACTGTTACG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG