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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttttctacttctgttaaatttgggtgtgaaattgtgttggtgtagacttgatactgatgttactaatgcaattcatactatttataaagGTCGCAAGAGATGATGACATCACTGAGCAAATTGGAAAGAATATATATTTTGATCTTGTTGATCATGAAAAAGTGAGGAGTTTTCGAATCCAGAAACAGA

Basic information

species Arabidopsis thaliana
transcript AT3G11910.1
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G11910.2 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: LOC_Os01g56490.1 (Oryza sativa), 3'ss of exon 14
gttttctacttctgttaaatttgggtgtgaaattgtgttggtgtagacttgatactgatgttactaatgcaattcatactatttataaagGTCGCAAGAGATGATGACATCACTGAGCAAATTGGAAAGAATATATATTTTGATCTTGTTGATCATGAAAAAGTGAGGAGTTTTCGAATCCAGAAACAGA
    | ||| ||| |  | ||     || | ||| | |     |    |   |   | || | || |   | | | |   |||| |  |||| ||  |||||  |||  |  | ||||||||||||||  ||||||||||||||||||| ||| |||| ||  |    ||  ||||    |  |||||  
---gtttacctcttt--atttgatacgttacattatctgaaaatgctatcattctagttgctcctcacttagtgctt--cattt-tctagGTTGCCCGAGATTCTGATTTTGCAGAGCAAATTGGAAAACATATATATTTTGATCTTGTGGATTATGACAACATCCAAAGCCTTCGGGCACCTAAACATT

upper sequence: AT3G11910.2 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: LOC_Os11g36470.1 (Oryza sativa), 3'ss of exon 10
----gttttctacttctgttaaatttgggtgtgaaattgtgttggtgtagact---tgatactgatgttactaatgca--attcatacta-tttataaagGTCGCAAGAGATGATGACATCACTGAGCAAATTGGAAAGAATATATATTTTGATCTTGTTGATCATGAAAAAGTGAGGAGTTTTCGAATCCAGAAACAGA
    |  |   ||| || |||  ||      |  |  |  ||  |      ||   |||  ||| |  |  || |||    ||   || | | |||  |||| ||  |||||||  |  | |  ||||||||||| ||| ||||||||||||| || || || |||||||||||  | || || ||||| ||||| ||| 
gtcagcatctgactactattatgttcatcacttcatctcagtctggaacctctctgtgaatctgtttctcatagtgctctgtttggacaaatatatctagGTGGCTCGAGATGAGAATTTGAAGGAGCAAATTGGCAAGGATATATATTTTGACCTGGTGGACCATGAAAAAGTTCGTAGCTTCCGAATTCAGAAGCAGT

upper sequence: AT3G11910.2 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: LOC_Os12g30540.1 (Oryza sativa), 3'ss of exon 14
gttttctacttctgttaaatttgggtgtgaaattgtgttggtgtagacttgatactgatgttactaatgcaatt----catactatttataaagGTCGCAAGAGATGATGACATCACTGAGCAAATTGGAAAGAATATATATTTTGATCTTGTTGATCATGAAAAAGTGAGGAGTTTTCGAATCCAGAAACAGA
          |   | | |    | | |  | || |  |||| || |  | ||  |||  ||  |  |  |||       | | || |    |||| ||  ||||||| ||  | |  || || ||||| |||||||||||||||||||| || || |||||||| ||  | || || || || ||||| ||  
-------gtctggataagaacctgtttt--agttttaatggtttaaatctcattgtgaacttttttttataatggctatgtgcaatgtccctagGTTGCCCGAGATGAGGATTTGAAGGAACAGATTGGTAAGAATATATATTTTGATCTGGTGGACCATGAAAAGGTTCGCAGCTTCCGCATACAGAAGCAAC

upper sequence: AT3G11910.2 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: GRMZM2G303655_T01 (Zea mays), 3'ss of exon 4
---gttttctacttctgttaaatttgggtgtgaaattgtgttggtgtagacttgat-actgatgttactaatgcaattcatac---tatttataaagGTCGCAAGAGATGATGACATCACTGAGCAAATTGGAAAGAATATATATTTTGATCTTGTTGATCATGAAAAAGTGAGGAGTTTTCGAATCCAGAAACAGA
      |  |  ||| || | |   |    | |   ||  |  ||     |||| | |||  | ||  ||   |  ||  |      ||  | | || ||||  |||| || ||| | |  |||||||| || |||||||||||||||||||| || || |||||||||||    ||||| || || ||||| ||| 
gtctgatcttgtttcagtcataccagcagctaag--tgcctaagttctctcttggtgactcctcttgatagaactttttgtgtaaaaatgaaaatagATCGCTCGAGACGAGGACTTAAAGGAGCAAATCGGTAAGAATATATATTTTGATCTGGTGGACCATGAAAAAGTTCACAGTTTCCGCATTCAGAAGCAGT

upper sequence: AT3G11910.2 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: GRMZM2G014805_T01 (Zea mays), 3'ss of exon 14
gttttctacttctgttaaatttgggtgtgaaattgtgttggtgtagacttgatactgatgttactaatgcaattcatactatttataaagGTCGCAAGAGATGATGACATCACTGAGCAAATTGGAAAGAATATATATTTTGATCTTGTTGATCATGAAAAAGTGAGGAGTTTTCGAATCCAGAAACAGA
    |||  |  ||||  | |       | |  |   |   |       |  |  ||||   |||  |    |  | |  ||  | | || | ||  ||||  | ||  | |  ||||||||||| || |||||||||||||| || || || |||||||||||  | || || || || ||||| ||| 
---gtctggtcttgtttcagtcataccagcagctaactctcttggtgactcctcttgatagaact--ttatttgtaaaaaatgaaaatagATTGCTCGAGACAAGGATTTAAAGGAGCAAATTGGTAAAAATATATATTTTGACCTGGTGGACCATGAAAAAGTTTGCAGCTTCCGCATTCAGAAGCAGT

upper sequence: AT3G11910.2 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: Vv08s0032g00600.t01 (Vitis vinifera), 3'ss of exon 14
---------gttttctacttctgttaaatttgggtgtgaaattgtgttggtgtag-----acttgatactgatg---------ttactaatgcaattcatactatttataaagGTCGCAAGAGATGATGACATCACTGAGCAAATTGGAAAGAATATATATTTTGATCTTGTTGATCATGAAAAAGTGAGGAGTTTTCGAATCCAGAAACAGA
         ||||  | |||    | | |||  |||  ||   || | |   |       || || | || |||         | |||||   |||  || | ||  ||  |||| ||| | ||||| ||| |  | ||||||||||||||| ||||||||||||||||||| |||||||| |||||  | |||||||| || ||||||||| 
gtaagtcgtgtttctttcttgccctcattttttgtggtaataggtctagaaatgactggaacctgttgctcatggggatcttttaactaaaataatcaat-cgatgcatctagGTTGCACGGGATGAAGACCTTGCAGAGCAAATTGGAAAGGATATATATTTTGATCTTGTGGATCATGACAAAGTCCGCAGTTTTCGCATTCAGAAACAGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgttggtgtagacttgatactgatgttactaatgcaattcatactatttataaagGTCGCAAGAGATGATGACATCACTGAGCAAATTGGAAAGAATATATATTTTGATCTTGTTGATCATGAAAAAGTGAGGAGTTTTCGAATCCAGAAACAGA
                          tactaat  putative branch site (score: 1)
                                   aattcatactatttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttttctacttctgttaaatttgggtgtgaaattgtgttggtgtagacttgatactgatgttactaatgcaattcatactatttataaagGTCGCAAGAGATGATGACATCACTGAGCAAATTGGAAAGAATATATATTTTGATCTTGTTGATCATGAAAAAGTGAGGAGTTTTCGAATCCAGAAACAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG