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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttacttaccgaacaccgtgagatattttactttggttaaggttttattgattatcaccttaaattttaaatgttacagAACAATGTCGAATCGGTTATGAGGAACAAAATGAATGGTATTTTTTTAGTCACAAGGACAAGAAATATCCAACGGGGACAAGAACTAATAGAGCGACCAT

Basic information

species Arabidopsis thaliana
transcript AT2G18060.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G18060.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA16G24200.1 (Glycine max), 3'ss of exon 1
---------------------gttacttaccgaacaccgtgagatattttactttggttaaggttttattgat-tatcaccttaaat--tttaaatgttacagAACAATGTCGAATCGGTTATGAGGAACAAAATGAATGGTATTTTTTTAGTCACAAGGACAAGAAATATCCAACGGGGACAAGAACTAATAGAGCGACCAT
                     | ||  |    |  |   |  | | ||||| ||   ||||   |||   |||  ||     | |||  ||| | | || ||||   ||   | || || || ||||| || || || |||||||| ||||| ||||| ||||||||||||||||| ||||||||||| || ||||| |||||
ttgttaaagaaatatggtcaagctagatcttaattagtttatggt-ttttatttcttttaaa--tttggagatgcatggttgtgaatgatttgagttttgcagAGACATACAGGATTGGGTACGAGGAGCAGAACGAGTGGTATTTCTTTAGCCACAAAGACAAGAAATATCCAACTGGGACAAGAACCAACAGAGCCACCAT

upper sequence: AT2G18060.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA11G07990.1 (Glycine max), 3'ss of exon 1
---------------------gttacttaccgaacaccgtgagatattttactttggttaaggttttattgattatcaccttaaatttta-aatgttacagAACAATGTCGAATCGGTTATGAGGAACAAAATGAATGGTATTTTTTTAGTCACAAGGACAAGAAATATCCAACGGGGACAAGAACTAATAGAGCGACCAT
                      ||| |||    |     ||  |    |   | ||  | || |||||||  || |     | |  |  |  || |  ||||   |||  | || || ||||| || || ||||| |||||||| || || ||||| || || || |||||||| |||||||||||||||||||| |||||
catatttgatctaacattataatta-ttatttgatctaatgttagcaatagatctgagttagtttttattcttttttttgctgatgtgaatgatatggcagAGAGATGCAGGATAGGGTATGAAGAGCAGAATGAGTGGTATTTCTTCAGCCACAAAGATAAAAAGTATCCAACAGGGACAAGAACTAATAGAGCTACCAT

upper sequence: AT2G18060.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA01G37310.1 (Glycine max), 3'ss of exon 2
-------------------gttacttaccgaacaccgtga-gatattttactttggttaaggttttattgattatcaccttaaatttta-aatgttacagAACAATGTCGAATCGGTTATGAGGAACAAAATGAATGGTATTTTTTTAGTCACAAGGACAAGAAATATCCAACGGGGACAAGAACTAATAGAGCGACCAT
                     | || |    | |   |      ||  ||  |  ||||   |||| || ||| |     | |  |  |  || |  ||||   |||  | || || ||||| || || ||||| |||||||| || || ||||| || || || |||||||| |||||||||||||||||||| |||||
atatttgatctgacatattaattctcatttgataaaatattagcatcatagatctgttagttttttgttcattttttttctgatgtgaatgatatggcagAGAGATGCAGGATAGGGTATGACGAGCAGAATGAGTGGTATTTCTTCAGCCACAAAGATAAAAAGTATCCAACAGGGACAAGAACTAATAGAGCCACCAT

upper sequence: AT2G18060.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA02G05620.1 (Glycine max), 3'ss of exon 1
-----gttacttaccgaacaccgt---gagatattttactttggtt-aaggtttta--ttgatt--------atcaccttaaat--tttaaatgttacagAACAATGTCGAATCGGTTATGAGGAACAAAATGAATGGTATTTTTTTAGTCACAAGGACAAGAAATATCCAACGGGGACAAGAACTAATAGAGCGACCAT
      ||  | |   || |  ||   |  |   |  |  || ||| | |||||||  || |||        ||     | |||  |||   | |  ||||   |||  | || || || ||||| || ||||| |||||||| ||||| ||||| || |||||||||||||| ||||||||||| || ||||| |||||
atcatattgttaaagaaatatggtctagcaaagctagatcttagtttatggttttaatttaattttggagagatggttgtgaatgatttgggtttggcagAGATATGCAGGATTGGGTACGAGGAGCAGAATGAGTGGTATTTCTTTAGCCACAAAGATAAGAAATATCCAACTGGGACAAGAACCAACAGAGCCACCAT

upper sequence: AT2G18060.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv04s0023g03110.t01 (Vitis vinifera), 3'ss of exon 1
-----------------gttacttaccgaacacc--gtgagatattttactttggttaaggtttt----attgattatcaccttaaattttaaatgttacagAACAATGTCGAATCGGTTATGAGGAACAAAATGAATGGTATTTTTTTAGTCACAAGGACAAGAAATATCCAACGGGGACAAGAACTAATAGAGCGACCAT
                 | ||   | || |   |   | ||  | |    | || ||    | ||        || ||     | |||| |||  |  |||||   ||| || ||||| ||||| || || ||||| |||||||| || || |||||||| |||||||||||||||||||| || || ||||||||||||||
ggctaacactttcataagctagccatcgcatttctgataagtaaatccgttgtgttttccttgttcaaagcgaataattgatctgaattataatgg--acagAGAGATGCCGGATCGGGTATGAAGAGCAGAATGAGTGGTATTTCTTCAGCCACAAGGATAAGAAATATCCAACGGGGACGAGGACCAATAGAGCGACCAT

upper sequence: AT2G18060.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: EFJ22020 (Selaginella moellendorffii), 3'ss of exon 1
---gttacttaccgaacaccgtgagatattttactttggttaaggttttattgattatcaccttaaattttaaatgttacagAACAATGTCGAATCGGTTATGAGGAACAAAATGAATGGTATTTTTTTAGTCACAAGGACAAGAAATATCCAACGGGGACAAGAACTAATAGAGCGACCAT
   ||    |  |   ||    || ||  ||         | |    |  || ||| |   |||  |||||        ||||  | |||   ||||| |  |  |||||||  |||||||| ||||| ||||||||||||||||| ||||| ||||| ||  | || || ||||| |||  
gtagtctagtctcctccatttcgatatgattgcacaccactgacacctctttcattgt--tcttcgattttgg------cagAGAAGTGTAAGATCGGATCAGCTGAACAAACCGAATGGTACTTTTTCAGTCACAAGGACAAGAAGTATCCCACGGGAACTCGCACCAACAGAGCCACCGC

upper sequence: AT2G18060.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: EFJ18283 (Selaginella moellendorffii), 3'ss of exon 1
---gttacttaccgaacaccgtgagatattttactttggttaaggttttattgattatcaccttaaattttaaatgttacagAACAATGTCGAATCGGTTATGAGGAACAAAATGAATGGTATTTTTTTAGTCACAAGGACAAGAAATATCCAACGGGGACAAGAACTAATAGAGCGACCAT
   ||    |  |   ||    || ||  ||         | |    |  || ||| |   |||  |||||        ||||  | |||   ||||| |  |  |||||||  |||||||| ||||| ||||||||||||||||| ||||| ||||| ||  | || || ||||| |||  
gtagtctagtctcctccatttcgacatgattacacaccactgacacctctttcattgt--tcttcgattttgg------cagAGAAGTGTAAGATCGGATCAGCTGAACAAACCGAATGGTACTTTTTCAGTCACAAGGACAAGAAGTATCCCACGGGAACTCGCACCAACAGAGCCACCGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attttactttggttaaggttttattgattatcaccttaaattttaaatgttacagAACAATGTCGAATCGGTTATGAGGAACAAAATGAATGGTATTTTTTTAGTCACAAGGACAAGAAATATCCAACGGGGACAAGAACTAATAGAGCGACCAT
                     tattgat  putative branch site (score: 3)
                  ttttattgattatcac  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttacttaccgaacaccgtgagatattttactttggttaaggttttattgattatcaccttaaattttaaatgttacagAACAATGTCGAATCGGTTATGAGGAACAAAATGAATGGTATTTTTTTAGTCACAAGGACAAGAAATATCCAACGGGGACAAGAACTAATAGAGCGACCAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC