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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgcaccgctcttgagatagattggttgggtgaaacatccaagttcgtatgcaaacactcctcttctgtagtaactcttcttttgttgttatgttcttcagGATGTTGAAATCGACGAGGAGGTTGATGTTATAATTTCAGAGTGGATGGGTTACATGCTCTTGTATGAG

Basic information

species Arabidopsis thaliana
transcript AT3G20020.2
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G20020.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os04g58060.2 (Oryza sativa), 3'ss of exon 5
tgcaccgctcttgagatagattggttgggtgaaacatccaagttcgtatgcaaacactcct--cttctgtagtaactcttcttttgtt---gttatgtt----cttcagGATGTTGAAATCGACGAGGAGGTTGATGTTATAATTTCAGAGTGGATGGGTTACATGCTCTTGTATGAG
           ||||  |   | ||| |   | | ||  |  || ||||    |||    |   || | ||    |  || |||   |     |   ||     | |||||||||||| | || ||  |||||||||| ||||| ||||||||||||||||| |||||  | ||||||
---------tctgagtcattattgtttgaaaatatatttacattagtatttttacatctttactttttttatctgcatttttttaacttacactgaattgacagtgcagGATGTTGAAGTTGAGGATAAGGTTGATGTGATAATATCAGAGTGGATGGGTTATATGCTTCTCTATGAG

upper sequence: AT3G20020.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA20G23410.1 (Glycine max), 3'ss of exon 5
---tgcaccgctcttgagatagattggttgggtgaaacatccaagttcgtatgcaaacactcctcttctgtagtaactcttcttttgttgttatgttcttcagGATGTTGAAATCGACGAGGAGGTTGATGTTATAATTTCAGAGTGGATGGGTTACATGCTCTTGTATGAG
   ||  |   |  |    |    || |    |   | ||   |  |  |   |   | ||  | ||||  |   |   ||  || ||| |  ||  || ||||||||||||||||  ||  |||||||||||||||||||||| |||||||| || |||||  | | ||||
ttttgttcaatttatattgttttctgatcaatttgtatatttgatattattaactggctcttttgttcttcac--atatttacttagttatggtgc-ctgcagGATGTTGAAATCGGTGAAAAGGTTGATGTTATAATTTCAGAATGGATGGGCTATATGCTTCTATGTGAG

upper sequence: AT3G20020.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA0048S00320.1 (Glycine max), 3'ss of exon 5
tgcaccgctcttgagatagattggttgggtgaaacatccaagttcgtatgcaaacactcctcttctgtagtaactcttcttttgttgttatgttctt----cagGATGTTGAAATCGACGAGGAGGTTGATGTTATAATTTCAGAGTGGATGGGTTACATGCTCTTGTATGAG
  |   |   ||   |||| ||       |  ||| |  | ||||||    ||  ||   |  | |    ||| | |||   |   |||||| | ||    |||||||||||||| || || ||||| ||||||||||||||||| |||||||| || |||||  | ||||||
--ctttgaaatttttatagtttttcctttttcaac-tttatgttcgttactaagaacaagttgtatagtttaa-tattcacctcaggttatgctttttgtgcagGATGTTGAAATTGATGAAGAGGTGGATGTTATAATTTCAGAATGGATGGGCTATATGCTTCTATATGAG

upper sequence: AT3G20020.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA15G10450.1 (Glycine max), 3'ss of exon 5
-----tgcaccgctcttgagatagattggttgggtgaaacatccaagttcgtatgcaaacactcctcttctgtagtaactcttcttttgttgttatgttcttcagGATGTTGAAATCGACGAGGAGGTTGATGTTATAATTTCAGAGTGGATGGGTTACATGCTCTTGTATGAG
     || ||    ||      |   |  ||          | |   |   | || |   | |     |   || |  |   | ||||||| |  ||| || ||||||||||||||| | ||  | |||||||||||||||||||| |||||||| || |||||  |  || ||
agccttggacaatcctcacttcattgtatttatactttgttttctgatcaatttgta--tatttgctgttaataat--cggctgttttgttatggtgt-ctgcagGATGTTGAAATCAAGGAACAAGTTGATGTTATAATTTCAGAATGGATGGGCTATATGCTTCTACATAAG

upper sequence: AT3G20020.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv10s0071g00750.t01 (Vitis vinifera), 3'ss of exon 5
tgcaccgctcttgagatagattggttgggtgaaacatccaagttcgtatgcaaacactcctcttc-tgtagta-actcttcttttgttgttatgttcttcagGATGTTGAAATCGACGAGGAGGTTGATGTTATAATTTCAGAGTGGATGGGTTACATGCTCTTGTATGAG
|| |      |     |  |   | |   |    ||        | ||  ||  || |  | | | |||   | |||  ||||   || || |   || |||||||||||||| || || | |||||||||||||||||||||||||||||||||||||||  ||||||||
tgtattttgttcccattgcaccagcttactctttcacttggaagc-tagccatgcattgatgtgcatgttaaacactaatcttgaattcttgtaa-ctgcagGATGTTGAAATTGATGAAGGGGTTGATGTTATAATTTCAGAGTGGATGGGTTACATGCTGCTGTATGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtatgcaaacactcctcttctgtagtaactcttcttttgttgttatgttcttcagGATGTTGAAATCGACGAGGAGGTTGATGTTATAATTTCAGAGTGGATGGGTTACATGCTCTTGTATGAG
                      tagtaac  putative branch site (score: 1)
                                             tgttcttc  putative PPT
                               ttctttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgcaccgctcttgagatagattggttgggtgaaacatccaagttcgtatgcaaacactcctcttctgtagtaactcttcttttgttgttatgttcttcagGATGTTGAAATCGACGAGGAGGTTGATGTTATAATTTCAGAGTGGATGGGTTACATGCTCTTGTATGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA