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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaggcttcttagttctcatatttcccgtcagctgatagcatcaaaagtatgtattaacttttattcttacaatcgactattgtggctcactgaaattccagTGTGATTCAATTCTGCGCCACTGCATTTGGATATTATGCTCAAGCCACCGCCGCTCAGGAGATATTTGGCCACACTTTGCAGTCCCTTCGCGGTATTAAG

Basic information

species Arabidopsis thaliana
transcript AT5G01460.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G01460.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: LOC_Os06g03760.2 (Oryza sativa), 3'ss of exon 11
gtaggcttcttagttctcatatttcccgtcagctgatagcatcaaaagtatgtattaact-tttattcttacaatcgactattgtggctcactgaaattc----cagTGTGATTCAATTCTGCGCCACTGCATTTGGATATTATGCTCAAGCCACCGCCGCTCAGGAGATATTTGGCCACACTTTGCAGTCCCTTCGCGGTATTAAG
      || || |||     |       |      ||| ||| |    ||  |  | | | | | ||  |    || ||||  | |||   || ||||      |||||||||||| ||||| ||||| || ||||  |||||||| ||||| || || ||||||||||| |||||||||||  |||| || || || || ||||||
-----tttgttggtttcatcaaccttgcttcctccataacat-atgcatacctgctgattatctgttaattttctccactaa-gaggccatctaaaatcttttgcagTGTGATTCAGTTCTGTGCCACAGCTTTTGCTTATTATGCGCAAGCAACTGCAGCTCAGGAGATCTTTGGCCACACACTGCAATCTCTCCGTGGAATTAAG

upper sequence: AT5G01460.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GRMZM2G012284_T01 (Zea mays), 3'ss of exon 9
-gtaggcttcttagttctcatatttcccgtcagctgatagcatcaaaagtatgtattaacttttattcttacaatcgactattgtggctcactgaaattccagTGTGATTCAATTCTGCGCCACTGCATTTGGATATTATGCTCAAGCCACCGCCGCTCAGGAGATATTTGGCCACACTTTGCAGTCCCTTCGCGGTATTAAG
  |  |  | | | | |  || |||  || |  |  ||  ||| | |    | |||   || ||| ||| |  |||   | ||   ||| | |  |  | |||||||||||| ||||| ||||| || ||||  || || || ||||| || || ||||| ||||||||||||||||||||||| |||||||| || ||||||
catgagtat-tgactgcctatttttgtcgacttcacatttcatgatagtcctctatcc-ctcttaatctaattatcatatttttctgct-attctatgtgcagTGTGATTCAGTTCTGTGCCACGGCTTTTGCCTACTACGCACAAGCAACTGCAGCTCAAGAGATATTTGGCCACACTTTGCAATCCCTTCGTGGAATTAAG

upper sequence: AT5G01460.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GRMZM5G871262_T02 (Zea mays), 3'ss of exon 11
----gtaggcttcttag--ttctcatatttcccgtcagctgatagcatcaaaagtatgtattaacttttattcttacaatcg-actattgtggctcactgaaattccagTGTGATTCAATTCTGCGCCACTGCATTTGGATATTATGCTCAAGCCACCGCCGCTCAGGAGATATTTGGCCACACTTTGCAGTCCCTTCGCGGTATTAAG
     | || || || |  | || |  |||  | ||   |      ||| |||      || |  | ||| ||| || | |  ||| ||   ||    ||    | |||||||||||| ||||| ||||| || ||||  |||||||| ||||| || || ||||| ||||| ||||||||||| ||||| |||||||| || ||||||
tttgattggtttatttggctgctgagctttgtcttcgtatttcgtgatcgaaaa-----atca--tcttaatctaactaccatacttttcctgccatatgtg--tgcagTGTGATTCAGTTCTGTGCCACGGCTTTTGCCTATTATGCACAAGCAACTGCTGCTCAAGAGATCTTTGGCCACACATTGCAATCCCTTCGTGGAATTAAG

upper sequence: AT5G01460.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA16G19230.1 (Glycine max), 3'ss of exon 10
gtaggcttcttagttctcatatttcccgtcagctgatagcatcaaaagtatgtattaacttttattcttacaatcgactattgtggctcactgaaattccagTGTGATTCAATTCTGCGCCACTGCATTTGGATATTATGCTCAAGCCACCGCCGCTCAGGAGATATTTGGCCACACTTTGCAGTCCCTTCGCGGTATTAAG
 ||     | ||||  || |||||   |      |      | |        |  |||  |       ||||    |   || |       |    || ||||||||| || |||||| |||| |||||||  || ||||||||||| || || || ||||| |||||||||||||||||| |||| ||||| || ||||| 
-tatagcgcatagtgttc-tatttaaagcataaggcacttgttatgttgtcatgataatgtgatgctgtacagctcaaagttctattgttttaccttttcagTGTGATCCAGTTCTGCTCCACAGCATTTGCCTACTATGCTCAAGCAACTGCAGCCCAGGAAATATTTGGCCACACTTTGGAGTCTCTTCGAGGAATTAAA

upper sequence: AT5G01460.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA18G43020.1 (Glycine max), 3'ss of exon 11
--gtaggcttcttagttctcatatttcccgtcagctgatagcatcaaaagtatgtattaacttttattcttacaatcgactattgtggctcactgaaattccagTGTGATTCAATTCTGCGCCACTGCATTTGGATATTATGCTCAAGCCACCGCCGCTCAGGAGATATTTGGCCACACTTTGCAGTCCCTTCGCGGTATTAAG
   |  |  |  ||  |      |    |    | | ||    |||  |  |||   |    |  |  ||| |       | |  ||  | ||     || ||||||||| || |||||| |||| |||||||  || ||||||||||| || || || ||||| |||||||| ||||||||| |||| ||||| || ||||| 
cacttagtgttctatataaagcgtaaggcacttgtt-atgttgtcatgataatggggtgctgtacaaccttgctgaaagttctattgttttacct---tttcagTGTGATCCAGTTCTGCTCCACAGCATTTGCCTACTATGCTCAAGCAACTGCAGCCCAGGAAATATTTGGTCACACTTTGGAGTCTCTTCGAGGAATTAAA

upper sequence: AT5G01460.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA03G07890.1 (Glycine max), 3'ss of exon 11
gtaggcttcttagttctcatatttcccgtcagctgatagcatcaaaagtatg-tattaacttttattcttacaatcgactattgtggctcactgaaattccagTGTGATTCAATTCTGCGCCACTGCATTTGGATATTATGCTCAAGCCACCGCCGCTCAGGAGATATTTGGCCACACTTTGCAGTCCCTTCGCGGTATTAAG
     |   | |  |   |||  |   |  |  |  | |       |  ||  | | |   | |  |   |     ||   ||   | |   |    || ||||||||| || |||||| |||| |||||||  || ||||||||||| || || || ||||| |||||||||||||| ||| |||| ||||| || ||||| 
--taccaagtcatgttctatacatagtgaaaaattgtggtgctttcatgataatgtcatggtgtgataacatcgatgaaagtt-cagttttttaccttttcagTGTGATCCAGTTCTGCTCCACAGCATTTGCCTACTATGCTCAAGCAACTGCAGCACAGGAAATATTTGGCCACACCTTGGAGTCTCTTCGTGGAATTAAA

upper sequence: AT5G01460.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA01G30400.1 (Glycine max), 3'ss of exon 11
gtaggcttcttagt-tctcatatttcccgtcagctgatagcatcaaaagtatg-tattaacttttattcttacaatcgactattgtggctcactgaaattccagTGTGATTCAATTCTGCGCCACTGCATTTGGATATTATGCTCAAGCCACCGCCGCTCAGGAGATATTTGGCCACACTTTGCAGTCCCTTCGCGGTATTAAG
     ||   | || |   |||  |   |  |  | || |       |  ||  | | |   | |  |   |     ||   ||  |      |    || ||||||||| || |||||| |||| |||||||  || ||||||||||| || || || ||||| |||||||||||||| ||| | || ||||| || ||||| 
----actaagttgtgttctatacatagtgaaaaattatggtgctgtcatgataatgtcatgctgtgataacattgctgaaagttcggttgttttaccttttcagTGTGATCCAGTTCTGCTCCACAGCATTTGCCTACTATGCTCAAGCAACTGCAGCACAGGAAATATTTGGCCACACCTTGGAATCTCTTCGTGGAATTAAA

upper sequence: AT5G01460.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: Vv08s0007g02270.t01 (Vitis vinifera), 3'ss of exon 11
----------------------------------------------------------------gtaggcttcttagttctcatatttcccgtcagctgatagcatcaaaagtatgtattaacttttattcttacaatcgactattgtggctcactgaaattccagTGTGATTCAATTCTGCGCCACTGCATTTGGATATTATGCTCAAGCCACCGCCGCTCAGGAGATATTTGGCCACACTTTGCAGTCCCTTCGCGGTATTAAG
                                                                |  ||  |||||   ||  |||||   || ||   |||    || |  |  |||   |  |||||   || |||| | | |||| |    ||  |||| |||||||||||||||||||||||| |||||||| || ||||||||||| || || || ||||| ||||||||||||||  || | || ||    || ||||| 
gtttgcatgtttagtcctctaaattcattaacagatataattgggttgggaccagcaccacaaggggggactctta---ctgttattttatgt-agaatatatttccagaccttggta--gatgtttatc--tataatc-attgttgttggctcctccaatttcagTGTGATTCAATTCTGCGCCACAGCATTTGGTTACTATGCTCAAGCAACTGCTGCACAGGAAATATTTGGCCACACACTGGAATCTCTCAAAGGAATTAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtatgtattaacttttattcttacaatcgactattgtggctcactgaaattccagTGTGATTCAATTCTGCGCCACTGCATTTGGATATTATGCTCAAGCCACCGCCGCTCAGGAGATATTTGGCCACACTTTGCAGTCCCTTCGCGGTATTAAG
     tattaacttttattct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaggcttcttagttctcatatttcccgtcagctgatagcatcaaaagtatgtattaacttttattcttacaatcgactattgtggctcactgaaattccagTGTGATTCAATTCTGCGCCACTGCATTTGGATATTATGCTCAAGCCACCGCCGCTCAGGAGATATTTGGCCACACTTTGCAGTCCCTTCGCGGTATTAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT