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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattttatcattacttacgaaaattcttgttactctcacaatggtgactttgtagtttgttaatacacaagttttcaattgtagGTATGTAGTGGAGAGGATGGATGGTGATCTGTGGGATAAGGTTCTCGATGAAAACAATGATTATAGAAGACAGCTTATTGACCAAGTTGTGTCTACTGCT

Basic information

species Arabidopsis thaliana
transcript AT3G08530.1
intron # 23
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G08530.1 (Arabidopsis thaliana), 3'ss of exon 23
lower sequence: LOC_Os12g01390.1 (Oryza sativa), 3'ss of exon 23
-----------gtattttatcattacttacgaaaattcttgttactctcacaat---ggtgactttgtagtttgttaatacacaagt---tttcaattgt-agGTATGTAGTGGAGAGGATGGATGGTGATCTGTGGGATAAGGTTCTCGATGAAAACAATGATTATAGAAGACAGCTTATTGACCAAGTTGTGTCTACTGCT
           || |||  || | |        |||| |  ||  ||| |   |     |   | | | | ||| | | | | || |   ||| |||||  |||||||| || || || ||||||||||||||||||||||| |||||  |     | ||||| |||||||| || || ||||||||||| || ||||| |||
gtatgcaaattgtttttattcttcataccttttaattttatttcttctgaatctttaaatccatctattgattgcttacatagaaatcgatttgaattgccagGTATGTGGTTGAAAGAATGGATGGTGATCTGTGGGATAAAGTTCTACAGCCTGAAAATGAATATAGAAGGCAACTCATTGACCAAGTGGTTTCTACGGCT

upper sequence: AT3G08530.1 (Arabidopsis thaliana), 3'ss of exon 23
lower sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 23
---------gtattttatcattacttacgaaaattcttgttactctcacaatggtgactttgtagtttg----ttaatacacaagt---tttcaattgt-agGTATGTAGTGGAGAGGATGGATGGTGATCTGTGGGATAAGGTTCTCGATGAAAACAATGATTATAGAAGACAGCTTATTGACCAAGTTGTGTCTACTGCT
          | ||||     | | |||    | | || || ||     |    | | |   | | |||     | | | | || |   ||| |||||  |||||||| || || || ||||||||||||||||||||||| |||||  |     | ||||| |||||||| || || ||||||||||| || ||||| |||
gtatgcaaattgtttttattcttcatacttttaattttatttcttctgaatctttaaatccatcgattgattgcttacatagaaatcgatttgaattgccagGTATGTGGTTGAAAGAATGGATGGTGATCTGTGGGATAAAGTTCTACAGCCTGAAAATGAATATAGAAGGCAACTCATTGACCAAGTGGTTTCTACGGCT

upper sequence: AT3G08530.1 (Arabidopsis thaliana), 3'ss of exon 23
lower sequence: GRMZM2G325285_T01 (Zea mays), 3'ss of exon 12
------------gtattttatcattacttacgaaaattctt----gttactctca-caatgg--tgac--tttgtagtttgttaatacacaagttttcaattgtagGTATGTAGTGGAGAGGATGGATGGTGATCTGTGGGATAAGGTTCTCGATGAAAACAATGATTATAGAAGACAGCTTATTGACCAAGTTGTGTCTACTGCT
             | | || |  | ||||  || |  | ||    | |   | || |||| |  ||||   ||  |  ||  || | ||    |||  |||   |||||||| || ||||| ||||||||||||||||||||||| |||||  |     | ||||| |||||||| || || ||||||||||| || || ||||| 
gtatgtaataatttttattgttgtgacttgtgacacctgtttcaagatgtccacatcaattgtctgacgacttacatgttcatattgcatttatttaaaatgacagGTATGTGGTTGAGAGAATGGATGGTGATCTGTGGGATAAAGTTCTTCAGCCCGAGAATGAATATAGAAGGCAACTCATTGACCAAGTGGTTTCGACTGCA

upper sequence: AT3G08530.1 (Arabidopsis thaliana), 3'ss of exon 23
lower sequence: GRMZM2G057576_T02 (Zea mays), 3'ss of exon 21
------------------gtattttatc-attacttacgaaaattcttgttactctcacaatggtgactttgtagtttgttaat---acacaagttttcaattgtagGTATGTAGTGGAGAGGATGGATGGTGATCTGTGGGATAAGGTTCTCGATGAAAACAATGATTATAGAAGACAGCTTATTGACCAAGTTGTGTCTACTGCT
                     | |||   ||  |||  |    |||  ||       | | ||   | |   | | ||| | ||   ||| || |||  ||||  || ||||| || ||||| ||||||||||||||||||||||| |||||  |     | ||||| |||||||| || || ||||||||||| || || || || 
gtatataattatttttgttcctgttactgatgccttttgtttgttccagtcctctatatattgagcaatggctcgcttggtcatgtcacataaatttaaaatttcagATATGTGGTTGAGAGAATGGATGGTGATCTGTGGGATAAAGTTCTTCAGCCTGAGAATGAATATAGAAGGCAACTCATTGACCAAGTGGTTTCGACCGCA

upper sequence: AT3G08530.1 (Arabidopsis thaliana), 3'ss of exon 23
lower sequence: GRMZM2G111355_T01 (Zea mays), 3'ss of exon 3
------------gtattttatcattacttacgaaaattctt----gttactctca-caatgg--tgac--tttgtagtttgttaatacacaagttttcaattgtagGTATGTAGTGGAGAGGATGGATGGTGATCTGTGGGATAAGGTTCTCGATGAAAACAATGATTATAGAAGACAGCTTATTGACCAAGTTGTGTCTACTGCT
             | | || |  | ||||  || |  | ||    | |   | || |||| |  ||||   ||  |  ||  || | ||    |||  |||   |||||||| || ||||| |||||||||||||| |||||||| |||||  |     | ||||| |||||||| || || ||||||||||| || || ||||| 
gtatgtaataatttttattgttgtgacttgtgacacctgtttcaagatgtccacatcaattgtctgacgacttacatgttcatattgcatttatttaaaatgacagGTATGTGGTTGAGAGAATGGATGGTGATCTATGGGATAAAGTTCTTCAGCCCGAGAATGAATATAGAAGGCAACTCATTGACCAAGTGGTTTCGACTGCA

upper sequence: AT3G08530.1 (Arabidopsis thaliana), 3'ss of exon 23
lower sequence: GLYMA14G06340.1 (Glycine max), 3'ss of exon 23
gtattttatcattacttacgaaaa----ttcttgttactct-----cacaatggtgacttt-----gtagtttgttaatacacaagtttt-caattgtagGTATGTAGTGGAGAGGATGGATGGTGATCTGTGGGATAAGGTTCTCGATGAAAACAATGATTATAGAAGACAGCTTATTGACCAAGTTGTGTCTACTGCT
 |       | | ||||  ||  |    |  |||| |  ||     ||| |     | |||      ||   |||| | |  |   | ||   ||   || ||||| || ||||| |||||||||||| |||||| ||| ||||| |||    | ||||| |||||||| || |||||||| || ||||| |||||||||
ctgcacctccgtcactttagaggagctatatttgtgatccttaatacaccaaatcaattttctttaatacaatgttcacatgcttatattgtgatgacagATATGTTGTTGAGAGAATGGATGGTGATTTGTGGGCTAAAGTTCTTGATCCTGATAATGAATATAGAAGGCAACTTATTGATCAGGTTGTATCTACTGCT

upper sequence: AT3G08530.1 (Arabidopsis thaliana), 3'ss of exon 23
lower sequence: GLYMA02G42560.1 (Glycine max), 3'ss of exon 23
---gtattttatcattacttacgaa---aattcttgttactc---tcacaatggtgactttgt--agtttg---ttaatacacaagt-tttcaattgtagGTATGTAGTGGAGAGGATGGATGGTGATCTGTGGGATAAGGTTCTCGATGAAAACAATGATTATAGAAGACAGCTTATTGACCAAGTTGTGTCTACTGCT
     | |   ||| |    | ||     |||  || | ||     ||| |     | ||| |  | ||     || | | ||   | |||  ||   || ||||| || ||||| |||||||||||| |||||| ||| ||||| |||    | ||||| |||||||| || |||||||| || ||||| |||||||||
agtacactccgtcactttagaggagctctatttgtggtccttaatccaccaaatcaattttctttaattcaacattcacatacttatattttgatgacagATATGTTGTTGAGAGAATGGATGGTGATTTGTGGGCTAAAGTTCTTGATCCTGATAATGAATATAGAAGGCAACTTATTGATCAGGTTGTATCTACTGCT

upper sequence: AT3G08530.1 (Arabidopsis thaliana), 3'ss of exon 23
lower sequence: Vv13s0067g01290.t01 (Vitis vinifera), 3'ss of exon 23
----gtattttatcattacttacgaaaattcttgttactctcacaatggtgactttgtagtttgttaatac--acaagt-tttcaattgtagGTATGTAGTGGAGAGGATGGATGGTGATCTGTGGGATAAGGTTCTCGATGAAAACAATGATTATAGAAGACAGCTTATTGACCAAGTTGTGTCTACTGCT
    ||   || |  |||||| |  | ||  || | |    ||      | | || |||  | |    |||  |||  |  ||| |||  || |||||||| || |||||||||  |||||| ||||| || ||||| ||     | |||||||||||||||||||| ||||| ||||| || |||||||||
gtttgtgacttgt--ttacttcccgatata-ttatcatatgcatgg-attcatttggtacatggacgctacttacacatacttccatttcagATATGTAGTTGAAAGGATGGATTCTGATCTCTGGGAGAAAGTTCTTGACCCTGATAATGATTATAGAAGACAGCTCATTGATCAAGTAGTATCTACTGCT

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|116430174|gb|EG472766.1|EG472766
EST:     GAACTCATCAATGTCACTAACAAAAACTCTTTGTTTAAGTTACAAGCCAG                         GTATGTAGTGGAGAGGATGGATGGTGATCTGTGGGATAAGGTTCTCGATGA
genomic: GAACTCATCAATGTCACTAACAAAAACTCTTTGTTTAAGTTACAAGCCAGgtattttatc ... tcaattgtagGTATGTAGTGGAGAGGATGGATGGTGATCTGTGGGATAAGGTTCTCGATGA
EST: gi|116430171|gb|EG472763.1|EG472763
EST:     GAACTCATCAATGTCACTAACAAAAACTCTTTGTTTAAGTTACAAGCCAG                         GTATGTAGTGGAGAGGATGGATGGTGATCTGTGGGATAAGGTTCTCGATGA
genomic: GAACTCATCAATGTCACTAACAAAAACTCTTTGTTTAAGTTACAAGCCAGgtattttatc ... tcaattgtagGTATGTAGTGGAGAGGATGGATGGTGATCTGTGGGATAAGGTTCTCGATGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttactctcacaatggtgactttgtagtttgttaatacacaagttttcaattgtagGTATGTAGTGGAGAGGATGGATGGTGATCTGTGGGATAAGGTTCTCGATGAAAACAATGATTATAGAAGACAGCTTATTGACCAAGTTGTGTCTACTGCT
                            tgttaat  putative branch site (score: 3)
                                          ttttc  putative PPT
                          tttgttaata  TA-rich tract