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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taaatttgagattgttagaatctgccccgaaaacgacattatatgacagatgtatttataatttacgaattgaaatgttaatattaattgggttatgcagGAGAATAAGCCACCGGACACACCACCAGAACCATGGCCATGTTGAAAACGACGAGTCATGGGTTCCG

Basic information

species Arabidopsis thaliana
transcript AT2G29980.2
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G29980.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA11G27190.1 (Glycine max), 3'ss of exon 2
--------------taaatttgagattgttagaatctgccccgaaaacgacattatatgacagatgtattta---taatttacgaa--ttgaaatgttaatattaat---tgggttatgcagGAGAATAAGCCACCGGACACACCACCAGAACCATGGCCATGTTGAAAACGACGAGTCATGGGTTCCG
              | || ||   || |||    |   ||   || |     || | | | | |    |||    | ||||   ||  |    || ||| || | ||   |   || ||||||||||| |||||| |||| ||||| |||||||||||||||||||| || || || ||||||||||||
gtcgattccttttatcaacttttcat-gttcactttgtccttaaatatttttttttgttaaaaaatcttttggtctgatttgtcaacctcaccattttactactcatggatatcttttgcagGAGAATTAGCCACAGGACTCACCATCAGAACCATGGCCATGTTGAGAAGGATGAATCATGGGTTCCG

upper sequence: AT2G29980.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA18G06950.1 (Glycine max), 3'ss of exon 2
--------taaatttgagattgttagaatctgccccg----aaaacgacattatatgac-----agatgtattta---taatttacgaattgaaatgttaatattaattggg----ttatgcagGAGAATAAGCCACCGGACACACCACCAGAACCATGGCCATGTTGAAAACGACGAGTCATGGGTTCCG
            || |  | | ||    |   |   |     |||     || ||||       | |  | |||    | |||||  ||   ||   ||  ||  | |   |    || ||||||||||| |||||| |||| ||||| |||||||||||||||||||| || || || ||||||||||| 
ggtcggttccttttagcaacttttcatgttcactttgtccttaaatttttttttatgtttgttaaaaaatctttggtctgatttaacaacctaaccatttttacaactcatggattttttgcaGGAGAATTAGCCACAGGACTCACCATCAGAACCATGGCCATGTTGAGAAGGATGAATCATGGGTTCC-

upper sequence: AT2G29980.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv06s0004g06720.t01 (Vitis vinifera), 3'ss of exon 3
-taaatttgagattgttagaatctgccccgaaaacgacattatatgacagatgtatttataatttacgaattgaaatgttaatattaattgggttatgcagGAGAATAAGCCACCGGACACACCACCAGAACCATGGCCATGTTGAAAACGACGAGTCATGGGTTCCG
 ||  |    ||       ||  ||   |     | | |  |     ||||||    | | || || |   | || | | |||   |||  | | || ||||||||| |||||| | || ||||| |||||||| || ||||||||||| || || ||||||||||| 
gtaggtcactgacaaactcaaattgtttcattttcaagacgacc---cagatg----tttgatgtatgt-ctcaattatcaatg--aat--gatgatacagGAGAATCAGCCACAGAACTCACCATCAGAACCAAGGTCATGTTGAAAATGATGAATCATGGGTTCCA

upper sequence: AT2G29980.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv06s0004g06730.t01 (Vitis vinifera), 3'ss of exon 3
-taaatttgagattgttagaatctgccccgaaaacgacattatatgacagatgtatttataatttacgaattgaaatgttaatattaattgggttatgcagGAGAATAAGCCACCGGACACACCACCAGAACCATGGCCATGTTGAAAACGACGAGTCATGGGTTCCG
 ||       |||  | |   | |  |   ||  |      |   |        || | | |||||  |  | |  |   | ||  ||| |  | ||  |||||||| |||||| | || ||||| || |||||||| ||||||||||| || || |||||||| |||
gtaggccct-gatactcaatttttttctttaattcttaggaactagtatcccacatgtttgatttataa--tcattttccattaccaat-gaataatatagGAGAATCAGCCACAGAACTCACCATCAAAACCATGGTCATGTTGAAAATGATGAATCATGGGTCCCG

upper sequence: AT2G29980.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: PP1S98_209V6.1 (Physcomitrella patens), 3'ss of exon 2
taaatttgagattgttagaatctgccccgaaaacgacattatatgacagatgtat-ttataatttacgaattgaaatgttaata-----ttaattgggtt--atgcagGAGAATAAGCCACCGGACACACCACCAGAACCATGGCCATGTTGAAAACGACGAGTCATGGGTTCCG
    |  ||   | ||    |   |  |   | ||   | |  | |  || |||  || || |   |     ||  ||| | ||     ||   ||||||  | ||||| | || |||||| |||| |||||||||||||| || || || || |||||||||||||||  ||| 
---gtgagaagct-ttcacgtgcccttcttcatcgtgctgaagttaatgacgtacattgtattcagctggcagagttgtgagtaaagtttttgatgggttggacgcagGCGCATTAGCCACAGGACTCACCACCAGAACCACGGGCACGTGGAGAACGACGAGTCATGGCATCCT

upper sequence: AT2G29980.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: PP1S69_223V6.1 (Physcomitrella patens), 3'ss of exon 2
------------taaatttgagattgttagaatctgccccgaaaacgacattatatgacagatgtatttata---atttacgaattgaaatgttaatattaattgggtta-tgcagGAGAATAAGCCACCGGACACACCACCAGAACCATGGCCATGTTGAAAACGACGAGTCATGGGTTCCG
            ||  | |       || || | || |    ||    |  | |     |   ||  || ||   ||  | | |    |||  | || || ||| ||||  | |||| |||| || ||| |||| |||||||| |||||||||||||| || |||||||||||||||   || 
gtgaggcaagcctatctcttcttacatttgagtttggcgttgaatgatccatttcctgtaatcgtgcttgtagcaatggaagtacccgaat-ctgatgttgatttggttggtacagGCGAATCAGTCACAGGACCCACCACCAAAACCATGGCCATGTGGAGAACGACGAGTCATGGCACCCT

upper sequence: AT2G29980.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: PP1S65_6V6.1 (Physcomitrella patens), 3'ss of exon 2
-------taaatttgagattgttagaatctgccccgaaaacgacattatatgacagatgt-atttataatttacgaattgaaatgttaatattaattgggttatgcagGAGAATAAGCCACCGGACACACCACCAGAACCATGGCCATGTTGAAAACGACGAGTCATGGGTTCCG
       |   | | | | |||     |  | |  | |   ||   | | | ||| |||  |||  ||   |    | |||| |||    ||    |||||   ||||| | || |||||| | || ||||||||||||||||| ||||| || ||||||||||| |||  ||||
gtgagaatctttctcataatgtcctccttcgtcttggagtagatgctgtttcacacatgccattggtagagttgtgactgaattgt-gtgatggggtgggt---gcagGCGGATTAGCCACAGAACTCACCACCAGAACCATGGGCATGTGGAGAACGACGAGTCGTGGCATCCG

upper sequence: AT2G29980.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: EFJ23113 (Selaginella moellendorffii), 3'ss of exon 2
taaatttgagattgttagaatctgccccgaaaacgacattatatgacagatgtatttataatttacg---aattgaaatgttaatattaattgggttatgcagGAGAATAAGCCACCGGACACACCACCAGAACCATGGCCATGTTGAAAACGACGAGTCATGGGTTCCG
                                             ||  |||  |||  | ||   |      | | |  ||||  ||  |  ||  || |||||| |||||||||||||| || |||||||| || |||||||| || ||||||||||| |||  ||| 
-------------------------------------------gtacgtatgcttttccatttcttgtttggcttagagcttaaactttgt--ggaaatccagGAGGATAAGCCACCGGACGCATCACCAGAATCACGGCCATGTCGAGAACGACGAGTCCTGGCATCCA

upper sequence: AT2G29980.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: EFJ20170 (Selaginella moellendorffii), 3'ss of exon 2
taaatttgagattgttagaatctgccccgaaaacgacattatatgacagatgtatttataatttacgaattgaaatgttaatattaattgggttatgcagGAGAATAAGCCACCGGACACACCACCAGAACCATGGCCATGTTGAAAACGACGAGTCATGGGTTCCG
                                     |   |||| |   |  |||| |  |||  |  ||  | | | ||  ||     ||  || |||||| |||||||||||||| || |||||||| || |||||||| || ||||||||||| |||  ||| 
-----------------------------------gtac-gtatg-cttttccatttcttgttt--ggcttagagtttaaactttgt---ggaaatccagGAGGATAAGCCACCGGACGCATCACCAGAATCACGGCCATGTCGAGAACGACGAGTCCTGGCATCCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acagatgtatttataatttacgaattgaaatgttaatattaattgggttatgcagGAGAATAAGCCACCGGACACACCACCAGAACCATGGCCATGTTGAAAACGACGAGTCATGGGTTCCG
                                    tattaat  putative branch site (score: 2)
     tgtatttataatttac  TA-rich tract