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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatgtttctttcttcacattataagtgttcttaaacccatttttgtcaagatcaagtttagaagaaatgctgaaatatgtgattttgtttctagGTTTTCGATTTGTTTGATACAAAGCACAATGGAATACTGGGGTTTGAGGAATTTGCTCGTGCTCTCTCCGTCTTTCACCCAAATGCGCCTATAGATGACA

Basic information

species Arabidopsis thaliana
transcript AT5G55990.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G55990.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os12g40510.1 (Oryza sativa), 3'ss of exon 4
gtaatgtttctttct----tcacattataagtgttcttaaacccatttttgtcaagatcaagtt--tagaagaaatgctgaaatatgtgattttgtttctagGTTTTCGATTTGTTTGATACAAAGCACAATGGAATACTGGGGTTTGAGGAATTTGCTCGTGCTCTCTCCGTCTTTCACCCAAATGCGCCTATAGATGACA
  |||  ||  |       |  |  ||| |  | | | |   |   ||||| |   |||    |  |     |  | || ||   | |   |    ||  |||| || ||||||||||| ||||| |||||||||||  | || ||||| |||||||||||||| ||||| || ||||| |||| ||| ||  | ||||| |
--aattctttgtagaaaaatagctgtatgatagatgtcagtgcagattttgcctttatctccgtgctgcctcatgttcttaatattctccctgctcttacagGTATTTGATTTGTTTGACACAAAACACAATGGAATTTTAGGATTTGATGAATTTGCTCGTGCACTCTCAGTATTTCATCCAAGTGCTCCACTTGATGAGA

upper sequence: AT5G55990.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G007555_T01 (Zea mays), 3'ss of exon 4
-gtaatgtttctttcttcacatta--taagtgttcttaaacccatttttgtcaagatcaagtttagaagaaatgctga----aatatgtgattttgtttctagGTTTTCGATTTGTTTGATACAAAGCACAATGGAATACTGGGGTTTGAGGAATTTGCTCGTGCTCTCTCCGTCTTTCACCCAAATGCGCCTATAGATGACA
 |||       |  || |||   |  |  | || | | | |    |||||   |   |   | || ||| |||  ||     |||||    | |   ||  |||| || ||||||||||| |||||||||||||||||  | || ||||| |||||||||||||||||||| || ||||| || ||||| ||  | ||||| |
tgtagaaaaattagctgcacgaaaattgtgggtccctgatcttgcttttggtta---ctgatataaaagtaatcatgtccctaatattccttgtcccttgcagGTATTTGATTTGTTTGACACAAAGCACAATGGAATTTTAGGATTTGAAGAATTTGCTCGTGCTCTCTCAGTATTTCATCCTAATGCTCCCCTTGATGAGA

upper sequence: AT5G55990.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G173424_T02 (Zea mays), 3'ss of exon 4
-gtaatgtttctttcttcacattataagtgttcttaaacccatttttgtcaa--gat-caagtttagaagaaatgctgaaatatgtgattttgtttctagGTTTTCGATTTGTTTGATACAAAGCACAATGGAATACTGGGGTTTGAGGAATTTGCTCGTGCTCTCTCCGTCTTTCACCCAAATGCGCCTATAGATGACA
   ||   ||   |   || |   |  |  | ||| | |    |||||   |  |||  ||   || |  |  | |  ||   | |  | |   || ||||| || ||||| ||||| |||||||||| ||||||  |||| ||||| |||||||||||||||||||| || ||||| || ||||| ||  | ||||| |
tagaaaaattagctgcacaaaaattgtggatccttgatcttgcttttggttactgatataaaagtatatcatgtccctaatattttcttgtccattgtagGTATTTGATTTATTTGACACAAAGCACAGTGGAATTTTGGGATTTGAAGAATTTGCTCGTGCTCTCTCAGTATTTCATCCTAATGCTCCCCTTGATGAGA

upper sequence: AT5G55990.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G112672_T01 (Zea mays), 3'ss of exon 3
-------gtaatgtttctttcttcacattataagtgttcttaaacccatttttgtcaagatcaagtttagaagaaatgctgaaata--tgtgattttgtttctagGTTTTCGATTTGTTTGATACAAAGCACAATGGAATACTGGGGTTTGAGGAATTTGCTCGTGCTCTCTCCGTCTTTCACCCAAATGCGCCTATAGATGACA
         ||   |  |    | | ||  |  |  | ||||    | ||   || |  || |  ||     | | ||||  ||    ||| ||| |  ||  |||| || || || ||||||||||| |||||||| || || || ||||| ||||||||||| || ||||| || ||||| || ||||| ||  | ||||| |
tgtccaatgaaaaatagtcaagtgagatcctgtggatgcttactttctttccagttagtatgacatt-----gtattgctataaccattgtcattgttcttgcagGTATTTGACTTATTTGATACAAAACACAATGGGATTCTTGGATTTGAAGAATTTGCTCGGGCGCTCTCAGTATTTCATCCCAATGCTCCCTTGGATGAGA

upper sequence: AT5G55990.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA18G08230.1 (Glycine max), 3'ss of exon 5
--gtaatgtttctttcttcacattataagt-gttcttaaacccatttttg-tcaagatcaagtttagaagaaatgctgaaatatgtgattttgtttctagGTTTTCGATTTGTTTGATACAAAGCACAATGGAATACTGGGGTTTGAGGAATTTGCTCGTGCTCTCTCCGTCTTTCACCCAAATGCGCCTATAGATGACA-
   | | || |  || |  ||||||||  | ||||  |||   |||     |  |  |   | || |||   |   |||| |      |     |  ||||| || ||||| ||||| |||||||||||||| ||||| || ||||| || |||||||||||||||||||| ||||| |||||||| ||||| ||||| | 
tgtttacgtattatt-tcaacattatattttgttcaaaaattgattcacaattcaacttgtgattggaatctaatatgaacttctctctaactctattaggTATTTGATTTATTTGACACAAAGCACAATGGGATACTAGGTTTTGAAGAGTTTGCTCGTGCTCTCTCCGTTTTTCATCCAAATGCCCCTATTGATGATAA

upper sequence: AT5G55990.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA08G44580.1 (Glycine max), 3'ss of exon 4
-------gtaatgtttctttcttcacattataagt-gttcttaaacccatttttgtcaagatcaagtttagaagaaatgctgaaatatgtgattttgtttctagGTTTTCGATTTGTTTGATACAAAGCACAATGGAATACTGGGGTTTGAGGAATTTGCTCGTGCTCTCTCCGTCTTTCACCCAAATGCGCCTATAGATGACA
       ||  |   | ||| |  | ||||||  | ||||  |||   |||    | |        | | |  |  ||     |  |  |  | |      ||||| || ||||| ||||| ||||| |||||||| |||||||| ||||| || |||||||||||||||||||| || || || ||||| || || ||||| |
tatatctgtt-tacgtatttttcaatattatattttgttcaaaaattgattcacattactcct---tgtggttggtatctcatatgaacttctctctaacttagGTATTTGATTTATTTGACACAAAACACAATGGGATACTGGGTTTTGAAGAGTTTGCTCGTGCTCTCTCCGTTTTCCATCCTAATGCCCCCATTGATGATA

upper sequence: AT5G55990.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA07G39940.1 (Glycine max), 3'ss of exon 4
gtaatgtttctttcttcacattataagtgttcttaaacccatttttgt-caagatcaagtttagaagaaatgctgaa---atatgtgattttg-----tttctagGTTTTCGATTTGTTTGATACAAAGCACAATGGAATACTGGGGTTTGAGGAATTTGCTCGTGCTCTCTCCGTCTTTCACCCAAATGCGCCTATAGATGACA
      | | | |  ||  |||| ||||    |  |  || | |   |    | | ||  ||||||    |  |       |   ||||||||     | | ||||| || || ||||||||||||||||||||||| ||||| |  ||||| || ||||| ||||||||||| |||||||| || ||||| || || ||||| |
-----atatttatgatctgattacaagttagttgcataccgtatacatatggggttaaccttagaatttgtatttgtcctgttcatgattttgtactgtctgtagGTGTTTGACTTGTTTGATACAAAGCACAATGGGATACTTGATTTTGAAGAGTTTGCACGTGCTCTCTCTGTCTTTCATCCCAATGCACCAATTGATGATA

upper sequence: AT5G55990.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA17G00830.1 (Glycine max), 3'ss of exon 4
gtaatgtttctttcttcacattataagtgt-tcttaaacccatttt-tgtcaagatcaagtttagaagaaatgctg--aaatatgtgattttgtttctagGTTTTCGATTTGTTTGATACAAAGCACAATGGAATACTGGGGTTTGAGGAATTTGCTCGTGCTCTCTCCGTCTTTCACCCAAATGCGCCTATAGATGACA
 ||   | |  ||  | |     ||  ||| |   | |  ||| |  ||| ||  | |   ||   |    | |||   |  || |  |  ||||| ||||| || || |||||||||||||||||||| || ||||| |  ||||| || ||||| || |||||||| |||||||| || ||||| || || ||||| |
ttatgatctgattacttaagagttagttgtatgccatatacatatgatgtgaaccttagaatttttatttgtcctgttcatgattttgtactgtttgtagGTGTTTGACTTGTTTGATACAAAGCACAACGGGATACTTGATTTTGAAGAGTTTGCACGAGCTCTCTCTGTCTTTCATCCCAATGCACCAATTGATGATA

upper sequence: AT5G55990.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv00s1569g00020.t01 (Vitis vinifera), 3'ss of exon 3
gtaatgtttctttcttcacattataagtgttcttaaacccatttttgtcaagatcaagtttagaagaaatg---ctgaaatatgtgattttgtt-------tctagGTTTTCGATTTGTTTGATACAAAGCACAATGGAATACTGGGGTTTGAGGAATTTGCTCGTGCTCTCTCCGTCTTTCACCCAAATGCGCCTATAGATGACA
   ||||| ||| | | |  |     ||  ||||     || |||| |||| ||  |||  | |  || |    ||  ||| | ||  | | ||       | ||||| || || |||||||| |||||||||||||||||||| |  ||||| || ||||| ||||| ||||| |||||||| || ||||| || || || ||||
---atgttcctt-cattagttggcttgtagtcttct-ttcagttttttcaaaat-gagtccaaataaattattcctacaatttatgcctctattcaaatcttgtagGTATTTGACTTGTTTGACACAAAGCACAATGGAATACTAGATTTTGAAGAGTTTGCGCGTGCCCTCTCTGTCTTTCATCCCAATGCACCCATTGAAGACA

upper sequence: AT5G55990.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv19s0015g01070.t01 (Vitis vinifera), 3'ss of exon 3
gtaatgtttctttcttcacattataagtgttcttaaacccatttttgtcaagatcaagtttagaagaaatgctg--aaatatgtgattttgtt----tctagGTTTTCGATTTGTTTGATACAAAGCACAATGGAATACTGGGGTTTGAGGAATTTGCTCGTGCTCTCTCCGTCTTTCACCCAAATGCGCCTATAGATGACA
  ||   ||   || |   |||   ||| |  ||  |    |||     |    |||     |   |  |||      |||||| ||  |  |    | ||||| || || |||||||| |||||||| || |||||||| || |||||||| |||||||||||||| || || |||||||| || || ||||| || ||||
--aactcttgcatcattgaattggtagtttcattggatatttttggaagagttccaaaagacgctcatttgccattgtatatgtaatgctaatcaattgtagGTATTTGACTTGTTTGACACAAAGCATAACGGAATACTTGGCTTTGAGGAGTTTGCTCGTGCTCTATCTGTTTTTCACCCCAACGCACCTATCGACGACA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttttgtcaagatcaagtttagaagaaatgctgaaatatgtgattttgtttctagGTTTTCGATTTGTTTGATACAAAGCACAATGGAATACTGGGGTTTGAGGAATTTGCTCGTGCTCTCTCCGTCTTTCACCCAAATGCGCCTATAGATGACA
                                           ttttgtttct  CT-rich tract
                                 aaatatgtgatttt  TA-rich tract