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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagatactaagaaacaaatcacatgatgcaaaaagcgtagcttaaggtaataagaagaataatctaaacgttttatattctttagGTTGGAGCACAAACTGAGACAGAGCTTAAGGAGAAGAAATTAAGAGTTGAAGATGCTCTTAATGCTACAAAG

Basic information

species Arabidopsis thaliana
transcript AT5G56500.2
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G56500.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: LOC_Os06g02380.2 (Oryza sativa), 3'ss of exon 9
-----------------------------------gtgag-atactaagaaacaaatcacatgatgcaaaaagcgtagcttaaggtaataagaagaataatctaaacgtt-ttatattctttagGTTGGAGCACAAACTGAGACAGAGCTTAAGGAGAAGAAATTAAGAGTTGAAGATGCTCTTAATGCTACAAAG
                                   ||     | ||          ||      || ||| |  |     |  ||| ||  |     ||||| ||   || |||  ||   ||||| ||||||||||| ||||| || || || |||||||| || |||||||| ||||| || |||||||| |||
gtataataagaaatggacaaaatgccatgttatctgtatctgttctttttcttggttctttgtttggaaagatagatagatgtggttatgtgggtcgtaatccaagttttgttacttttgatagGTGGGAGCACAAACAGAGACCGAACTAAAAGAGAAGAAGTTGAGAGTTGAGGATGCCCTAAATGCTACCAAG

upper sequence: AT5G56500.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GRMZM2G015989_T01 (Zea mays), 3'ss of exon 9
------------------------------------gtgagatactaagaaacaaatcacatgatgcaaaaagcgtagcttaa-ggtaataagaagaataatctaaacgtt-ttatattctttagGTTGGAGCACAAACTGAGACAGAGCTTAAGGAGAAGAAATTAAGAGTTGAAGATGCTCTTAATGCTACAAAG
                                     | | |  || ||   |   |      ||  |  | || ||||  ||    || ||  |||| |   ||  | ||  | | |  | ||||| |||||||| || || || ||||| ||||| |||||||| || ||||| ||||| || ||||||||||||
gtaaaccccaatgttaaaccctagttgcctcaatttttcaaaaccttagttgcctcttggtgtatttaggatgcttagcagaataaaaaaaactagaacatgatatgccttgctttgtattgtagGTAGGAGCACAGACAGAAACTGAGCTCAAGGAAAAGAAATTGAGGGTTGAGGATGCCCTGAATGCTACAAAG

upper sequence: AT5G56500.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA08G18760.1 (Glycine max), 3'ss of exon 8
gtgagatactaagaaacaaatcacatgatgcaaaaagcgtagcttaaggtaataagaagaataatctaaacgttttatattctttagGTTGGAGCACAAACTGAGACAGAGCTTAAGGAGAAGAAATTAAGAGTTGAAGATGCTCTTAATGCTACAAAG
|| | | ||| |   | |  |   |  ||   |     |||   |         |  |   |     ||   || || ||  | |||||||| |||||||||||||||||||| ||||| |||||||| ||||||||||| ||||||||||||||||||
gtaacagactcactgaaatgtggtaatatattagtttggtactctgcaaggtatatcaacttggggcaatttttgtacata-tatagGTTGGCGCACAAACTGAGACAGAGCTCAAGGAAAAGAAATTGAGAGTTGAAGACGCTCTTAATGCTACAAAG

upper sequence: AT5G56500.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA15G40110.1 (Glycine max), 3'ss of exon 8
gtgagatact-aagaaacaaatcacatgat-gcaaaaagcgtagcttaaggtaataagaagaataatctaaacgttttatattctttagGTTGGAGCACAAACTGAGACAGAGCTTAAGGAGAAGAAATTAAGAGTTGAAGATGCTCTTAATGCTACAAAG
|| | | ||| |   ||    | | ||| | |       ||  | |     ||  ||   |   ||| |     || || ||  | |||||||| |||||||||||||| ||||| ||||| |||||||| ||||||||||||||||||||||||||||||
gtaacagactcactgaaatggtaatatgttagtttggtacgccgttgggtatatcaacttgggcaattt-----ttgtacatg-tgtagGTTGGTGCACAAACTGAGACTGAGCTCAAGGAAAAGAAATTGAGAGTTGAAGATGCTCTTAATGCTACAAAG

upper sequence: AT5G56500.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: Vv06s0004g00240.t01 (Vitis vinifera), 3'ss of exon 9
gtgagatactaagaaa-caaatcacatgatgcaaaaag---cgtagcttaaggtaataagaaga-ataatctaaacgttttatattctttagGTTGGAGCACAAACTGAGACAGAGCTTAAGGAGAAGAAATTAAGAGTTGAAGATGCTCTTAATGCTACAAAG
|| |  |  ||   |  | | | | |   |  |||      | |   |  ||||  | || |   || |  ||  | ||  |  || |  ||||||||||||||||||||||||||||||| || |||||| | ||||| ||||| ||||| ||||| || |||
gtaaattcttagttagtccagttaaaatttataaatgatttcatcattgcaggtgcttagtatctattaattattcattgaac-ttttgaagGTTGGAGCACAAACTGAGACAGAGCTTAAAGAAAAGAAACTGAGAGTAGAAGACGCTCTCAATGCAACGAAG

upper sequence: AT5G56500.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: EFJ33580 (Selaginella moellendorffii), 3'ss of exon 8
gtgagatactaagaaacaaatcacatgatgcaaaaagcgtagcttaaggtaata--agaagaataatctaaacgttt-tatattctttagGTTGGAGCACAAACTGAGACAGAGCTTAAGGAGAAGAAATTAAGAGTTGAAGATGCTCTTAATGCTACAAAG
                                  |||  ||  ||   ||| |   || || | |   | ||| | | | ||   |  ||||||| |||||||||||||||||  | || || ||||| |||||||| ||||||||| | ||||| || |||
--------------------------------gtaagtttattttgcagtatttttagcagcacatctttaacttctctgtaaattgaagGTTGGTGCACAAACTGAGACAGAATTAAAAGAAAAGAAGTTAAGAGTGGAAGATGCTTTGAATGCGACGAAG

upper sequence: AT5G56500.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: EFJ36935 (Selaginella moellendorffii), 3'ss of exon 8
gtgagatactaagaaacaaatcacatgatgcaaaaagcgtagcttaaggtaata--agaagaataatctaaacgttt-tatattctttagGTTGGAGCACAAACTGAGACAGAGCTTAAGGAGAAGAAATTAAGAGTTGAAGATGCTCTTAATGCTACAAAG
                                  |||  ||  ||   ||| |   || || | |   | ||| ||| | ||   |  ||||||| ||||||||||||||||| || || || ||||| |||||||| ||||||||| | ||||| || |||
--------------------------------gtaagtttattttgcagtatttttagcagcacatcgttaacttttctgtaaattgaagGTTGGTGCACAAACTGAGACAGAACTAAAAGAAAAGAAGTTAAGAGTGGAAGATGCTTTGAATGCAACGAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaaagcgtagcttaaggtaataagaagaataatctaaacgttttatattctttagGTTGGAGCACAAACTGAGACAGAGCTTAAGGAGAAGAAATTAAGAGTTGAAGATGCTCTTAATGCTACAAAG
                               atctaaa  putative branch site (score: 3)
                                             tattcttt  putative PPT
                           aataatctaaacgttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagatactaagaaacaaatcacatgatgcaaaaagcgtagcttaaggtaataagaagaataatctaaacgttttatattctttagGTTGGAGCACAAACTGAGACAGAGCTTAAGGAGAAGAAATTAAGAGTTGAAGATGCTCTTAATGCTACAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG