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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatattatattgattcaagaacctcatgtacttctccggccgtcgattctatgaatgatcttatctatttatcttttacgtatgtacctcaatatctttggatgtgtgtatgtatgtatagGTGCAGCACATGATAGAGAAATGTTTGATCTTCCATATGAGCAAAGAAGAGTGTGTGGAAGCTCTCTCTAAGCATGCAAACATCACTCCTGTCATCACCT

Basic information

species Arabidopsis thaliana
transcript AT3G55240.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G55240.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA20G38420.1 (Glycine max), 3'ss of exon 1
gtaatattatattgattcaagaacctcatgtacttctccggccgtcgattctatgaatgatcttatctatttatcttttacgtatgtacctcaatatctttggatgtgtgtatgtatgtatagGTGCAGCACATGATAGAGAAATGTTTGATCTTCCATATGAGCAAAGAAGAGTGTGTGGAAGCTCTCTCTAAGCATGCAAACATCACTCCTGTCATCACCT
                             ||| |  |   ||  |  ||| | |      | ||||      ||| |||       |   |  | |  |||   |  |  |   |   |||||||||||||  |||| ||||| ||||||||||| || |||| ||| ||||| ||  |||||||||||||||| |||||||| || | |||| | || || |
-----------------------------gtaatattatagctttaaattatttct----tattataagaccatcgttt-------tgttttgacaagttttc-tacgaattaattgatatagGTGCAGCATCTGATCGAGAAGTGTTTGATCTTTCACATGACCAAGGAAGAATGCATGGAAGCTCTCTCTAAACATGCAAATATTAATCCTATTATAACAT

upper sequence: AT3G55240.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA02G10620.1 (Glycine max), 3'ss of exon 1
gtaatattatattgattcaagaacctcatgtacttctccggccgtcgattctatgaatgatcttatctatttatcttttacgtatgtacctcaatatctttg-gatgtgtgtatgtatgtatagGTGCAGCACATGATAGAGAAATGTTTGATCTTCCATATGAGCAAAGAAGAGTGTGTGGAAGCTCTCTCTAAGCATGCAAACATCACTCCTGTCATCACCT
                  ||||     |  |||  || | ||  || ||  |     |  | || | |  ||   |  ||  ||      |||  ||| ||| ||  ||  |   ||    ||||||||||||||||| ||||| ||||||||||| || |||   || ||||| ||  ||||||||||||| ||||||||||| || |  |||||||| || |
----------------gtaagagggctagctacaacttctgc--tctatctttctttttttttttttttgtttgatcatatatacccctttcatgatcgttgtgacatgcttggataaaattagGTGCAGCACATGATTGAGAAGTGTTTGATCTTTCACATGTCAAAGGAAGAATGCATGGAAGCTCTCTCCAAGCATGCAAATATTAAGCCTGTCATAACAT

upper sequence: AT3G55240.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA10G43720.1 (Glycine max), 3'ss of exon 1
gtaatattatattgattcaagaacctcatgtacttctccggccgtcgattctatgaatgatcttatctatttatcttttacgtatgtacctcaatatctttggatgtgtgtatgtatgtatagGTGCAGCACATGATAGAGAAATGTTTGATCTTCCATATGAGCAAAGAAGAGTGTGTGGAAGCTCTCTCTAAGCATGCAAACATCACTCCTGTCATCACCT
                            | ||  | |   ||  |  ||||| ||  |  | ||||  |   ||| |   ||| | |   |  | |  |||   |  |  |   |   |||||||||||||  |||| ||||| ||||||||||| || |||| ||| ||||| ||  ||||||| |||||||| |||||||| || | |||| | || || |
---------------------------gtatatatatatagctttaaattctttgt-tattgttataaag--atcat---cgtgt-tgttttgacaagttttc-tacgaattaattaatatagGTGCAGCATCTGATCGAGAAGTGTTTGATCTTTCACATGACCAAGGAAGAATGCATGGAAGCGCTCTCTAAACATGCAAATATTAATCCTATTATAACAT

upper sequence: AT3G55240.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA18G52240.1 (Glycine max), 3'ss of exon 1
gtaatattatattgattcaagaacctcatgtacttctccggccgtcgattctatgaatgatcttatctatttatcttttacgtatgtacc---tcaatatctttg-gatgtgtgtatgtatgtatagGTGCAGCACATGATAGAGAAATGTTTGATCTTCCATATGAGCAAAGAAGAGTGTGTGGAAGCTCTCTCTAAGCATGCAAACATCACTCCTGTCATCACCT
                  ||||          ||||  |  | |       |||     || ||   | ||| | ||   | ||||||||   |||  ||| ||| ||| ||| |   ||    |||||||| ||| |||| ||||| ||||||| ||| || |||   || ||||||||  ||||||||||||| ||||||||||| || |  |||||||| || |
----------------gtaagagagcagctagcttcaacttcagctttaattatcttcaatttttattttttgtgttgatcatatgtaccctttcatgatcgttgtgatatgtttggatacaattagGTGCACCACCTGATTGAGAAGTGTTTGACCTTTCACATGTCAAAGGAAGAGTGCATGGAAGCTCTCTCCAAGCATGCAAATATTAAGCCTGTCATAACAT

upper sequence: AT3G55240.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv14s0036g00440.t01 (Vitis vinifera), 3'ss of exon 1
gtaatattatattgattcaagaacctcatgtacttctccggccgtcgattctatgaatgatcttatctatttatcttttacgtatgtacctcaatatctt-tggatgt-gtgtatgtatgtatagGTGCAGCACATGATAGAGAAATGTTTGATCTTCCATATGAGCAAAGAAGAGTGTGTGGAAGCTCTCTCTAAGCATGCAAACATCACTCCTGTCATCACCT
            |   | ||  |   ||| |||| |||     |  |||||||    |||| || | | ||           ||| | | | | | | || | ||||| |||     |  | |||||||| ||| |||| |||||||||||||||||||| |||| ||||||| ||||  ||||||| || || || |||||  |||||   || |||||||| |
-----------gtagctgaattataacat-tactcctcacatgg--gattctactg-tgattttgttt-ttagcaaaccttctatct-ctttattgttttgttgatgttgtggcctgacttttagGTGCAACACCTGATCGAGAAATGTTTGATCTTCCACATGACCAAAGAACAGTGCATGGAAGCCCTTTCCAAACATGCTGACATCCAACCAGTCATCACGT

upper sequence: AT3G55240.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv00s0317g00030.t01 (Vitis vinifera), 3'ss of exon 1
gtaatattatattgattcaagaacctcatgtacttctccggccgtcgattctatgaatgatcttatctatttatcttttacgtatgtacctcaatatctttggatgtgtgtatgtatgtatagGTGCAGCACATGATAGAGAAATGTTTGATCTTCCATATGAGCAAAGAAGAGTGTGTGGAAGCTCTCTCTAAGCATGCAAACATCACTCCTGTCATCACCT
            ||| ||||     |||| |    |  |     ||    | |     | |||    |||||    ||   || | | |    |||| | | | || ||   || || |  |||| || ||| | |||||||| |||||||||||||| ||||| |||||||||||  ||||||| ||||| || ||||||||||||   || ||||||||||
-----------gtgactcaaa----tcatatgtaacatcatttttcatgccca-----ggtctcccatatttgatctt---gtttttgct--gatatgtattggtgggt---tgaat-tgcagGTACAACACCTAATAGAGAATTGTTTGATCTTCCACATGAGTAAAGAAGAGTGCATGGAAGCCCTCTCCAAACATGCAAACATCGAACCCGTCATCACCT

upper sequence: AT3G55240.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv00s0317g00020.t01 (Vitis vinifera), 3'ss of exon 1
gtaatattatattgattcaagaacctcatgtacttctccggccgtcgattct-atgaatgatcttatctatttatcttttacgtatgtacctcaatatctttggatgtgtgtatgtatgtatagGTGCAGCACATGATAGAGAAATGTTTGATCTTCCATATGAGCAAAGAAGAGTGTGTGGAAGCTCTCTCTAAGCATGCAAACATCACTCCTGTCATCACCT
                          |   |  ||||||     | |||| |  |   |  | || | | ||| || |||||   |||   | |  ||||| || ||  ||     || | |||||||| ||| |||||||||| || ||||||||||| ||||| |||||||||||  ||||||| ||||| || |||||| ||||||  |  ||||||||||
----------------------gttcctaattattctcctatatttgatttttgtttctttttttctttctttttcgtttactactgttttttatgatctt-gggtggttg-----atttgtagGTGCAACACCTGATAGAGAAGTGCTTGATCTTCCACATGAGTAAAGAAGAGTGCATGGAAGCCCTCTCCAAACATGCAGACATCAACCAAGTCATCACCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttatcttttacgtatgtacctcaatatctttggatgtgtgtatgtatgtatagGTGCAGCACATGATAGAGAAATGTTTGATCTTCCATATGAGCAAAGAAGAGTGTGTGGAAGCTCTCTCTAAGCATGCAAACATCACTCCTGTCATCACCT
                        aatatcttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatattatattgattcaagaacctcatgtacttctccggccgtcgattctatgaatgatcttatctatttatcttttacgtatgtacctcaatatctttggatgtgtgtatgtatgtatagGTGCAGCACATGATAGAGAAATGTTTGATCTTCCATATGAGCAAAGAAGAGTGTGTGGAAGCTCTCTCTAAGCATGCAAACATCACTCCTGTCATCACCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG