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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgtgctcttcagaaaattaaatctctcttgtgttaattgtttcctatgtttccaaattcattgatagaatgtggattgaaaattgcagATCTTGTTTGTGATATCAAAACCTGATGTGTTCAAGAGTCCAGCTTCAGATACATATGTGATCTTTGGTGAGGCCAAGATAGAGGATTTGAGCTCGCAGC

Basic information

species Arabidopsis thaliana
transcript AT5G13850.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G13850.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os01g71230.2 (Oryza sativa), 3'ss of exon 3
-------gtttgtgctct-tcagaaaattaaatctctcttgtgttaattgt-ttcctatgtttccaaattcattgatagaatgtggattgaaaattgcagATCTTGTTTGTGATATCAAAACCTGATGTGTTCAAGAGTCCAGCTTCAGATACATATGTGATCTTTGGTGAGGCCAAGATAGAGGATTTGAGCTCGCAGC
       | ||   | || | |    |||   | |||  |  | | |  |  ||  ||| |  |        ||| |  | | |    || |  |  |||||  |||| || || || ||||| ||||| |||||||| |||   ||||| || || || ||||| |||||||| ||||| |||||| ||||||||||||
gtgagctgcttaatcactgttatgccattg--tttcttgtaggctcacagaattgttatataccattgcattttgcttaacttttccctgcac-taccagATTCTGTTCGTCATCTCTAAACCAGATGTCTTCAAGAGCCCAAACTCAGACACCTACGTCATCTTCGGTGAGGCGAAGATCGAGGATCTGAGCTCGCAGC

upper sequence: AT5G13850.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv13s0067g00710.t01 (Vitis vinifera), 3'ss of exon 3
------------------------------------gtttgtgctcttcagaa---aattaaatctctcttgtgttaattgtttcctatgtttccaaattcattgatagaatgtggattgaaaattgc----agATCTTGTTTGTGATATCAAAACCTGATGTGTTCAAGAGTCCAGCTTCAGATACATATGTGATCTTTGGTGAGGCCAAGATAGAGGATTTGAGCTCGCAGC
                                      |  |||||  ||      |  |   |    ||| |||      |||    |   |   || |   || |  ||| | | ||   | ||||    ||||||||||||| ||||||||||| ||||| |||||||| ||| | |||||||||||||| || ||||| ||||| ||||| || || |||||||| ||||
gttagtttccctctcttttctttgtgtgtatattcccctcttgctccccatgccccatctgcttaatccttttgtcctccttttgtcctccctttgaactt-ctgttgtaatctcggttattacttgctatcagATCTTGTTTGTCATATCAAAACCAGATGTCTTCAAGAGCCCAACATCAGATACATATGTCATTTTTGGCGAGGCAAAGATTGAAGACTTGAGCTCACAGC

upper sequence: AT5G13850.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv08s0040g00600.t01 (Vitis vinifera), 3'ss of exon 3
-----------------------------------gtttgtgctcttcagaaaattaa-atctctcttgtgttaattgtttcctatgtttccaaattcattgatagaa------tgtggattgaaaattgcagATCTTGTTTGTGATATCAAAACCTGATGTGTTCAAGAGTCCAGCTTCAGATACATATGTGATCTTTGGTGAGGCCAAGATAGAGGATTTGAGCTCGCAGC
                                    ||| |  | ||  |   |||   | |||| |  | | |  | ||   | | |||   |||  ||||| || |      | ||| ||  |   | |||||  | ||||| || || || || |||||||||||||| ||| ||||||| || ||||| || ||||| ||||| ||||| ||||||||||| || || |
gtcagtttctctttgcccactgttgattactttttatttttcatgttgggcctattgtcacctctttaatatcaggt-ttctttctattttacaatctattgaaagcagtttactatggtttttattattcagATTCTCTTTGTCATCTCGAAGCCAGATGTGTTCAAGAGCCCAACTTCAGACACTTATGTAATATTTGGCGAGGCAAAGATTGAGGATTTGAGTTCACAAC

upper sequence: AT5G13850.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: PP1S539_1V6.1 (Physcomitrella patens), 3'ss of exon 3
-----gtttgtgctcttcagaaaatt--aaatctctcttgtgttaattgtttcctatgtttccaaattcattgatagaatgtggat--tgaaaattgcagATCTTGTTTGTGATATCAAAACCTGATGTGTTCAAGAGTCCAGCTTCAGATACATATGTGATCTTTGGTGAGGCCAAGATAGAGGATTTGAGCTCGCAGC
      ||    || |   | | |||  | || |   ||  | |  |||     |  |  |   |||   |||  || |  |  ||  || || ||||||||| | |||||||| || || ||||||||||||||||| || || ||||| || || || ||||| || ||||| ||||| ||||||||||| || ||  
tataccttcaatctttatcgcagattctacatattctttcagatccttgagatgtcagaatttcaatagcttgcaagtaacttcatcgtgcaacttgcagATCCTCTTTGTGATCTCGAAGCCTGATGTGTTCAAGAGCCCTGCATCAGACACTTACGTAATCTTCGGCGAGGCAAAGATTGAGGATTTGAGTTCTCAAT

upper sequence: AT5G13850.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: PP1S156_120V6.1 (Physcomitrella patens), 3'ss of exon 2
--------------gtttgtgctcttcagaaa--attaaatctctcttgtgtta-attgtttcctatgtttccaaattcattgatagaatgtggattgaaaattgcagATCTTGTTTGTGATATCAAAACCTGATGTGTTCAAGAGTCCAGCTTCAGATACATATGTGATCTTTGGTGAGGCCAAGATAGAGGATTTGAGCTCGCAGC
              | |||   | | ||  ||   ||  |  | ||  |   || ||| |  ||| ||  |     ||  ||         ||  ||| || | ||||||  | |||||||| || || || ||||| |||||||| || || || || ||  || | |||||||| ||||||||||| ||||||||||| |||||||
ttaacttcaattctgcttgaattgtgcaataatagtttgagttatccagcaatagattttcacctgtggcttatgctttcttt--------tgttttggaattcgcagATTCTTTTTGTGATCTCTAAGCCCGATGTATTCAAGAGCCCTGCCTCTGACACCCATATCATCTTTGGAGAGGCCAAGATCGAGGATTTGAGTTCGCAGC

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|164191811|gb|ES069080.1|ES069080
EST:     TGAAACCAATCACTGGTGTTAGCCGTGTCACCGTCAAAA-GAGCAAGAAT                         ATCTTGTTTGTGATATCAAAACCTGATGTG
genomic: TGAAACCAATCACTGGTGTTAGCCGTGTCACCGTCAAAAAGAGCAAGAATgtttgtgctc ... aaaattgcagATCTTGTTTGTGATATCAAAACCTGATGTG
EST: gi|164143802|gb|ES055077.1|ES055077
EST:     TGAAACCAATCACTGGTGTTAGCCGTGTCACCGTCAAAAAGAGCAAGAAT                         ATCTTGTTTGTGATATCAAAACCTGATGTG
genomic: TGAAACCAATCACTGGTGTTAGCCGTGTCACCGTCAAAAAGAGCAAGAATgtttgtgctc ... aaaattgcagATCTTGTTTGTGATATCAAAACCTGATGTG
EST: gi|125267302|gb|EL281387.1|EL281387
EST:     ATCACTGGTGTTAGCCGTGTCACCGTCAAAAAGAGCAAGAAT                         ATCTTGTTTGTGATATCAAAACCTGATGTG
genomic: ATCACTGGTGTTAGCCGTGTCACCGTCAAAAAGAGCAAGAATgtttgtgctc ... aaaattgcagATCTTGTTTGTGATATCAAAACCTGATGTG
EST: gi|125240695|gb|EL254780.1|EL254780
EST:     TCACCGTCAAAAAGAGCAAGAAT                         ATCTTGTTTGTGATATCAAAACCTGATGTGTTCAAGAGTCCAGCTTCAGAT
genomic: TCACCGTCAAAAAGAGCAAGAATgtttgtgctc ... aaaattgcagATCTTGTTTGTGATATCAAAACCTGATGTGTTCAAGAGTCCAGCTTCAGAT
EST: gi|163970268|gb|EL983547.1|EL983547
EST:     GTCACCGTCAAAAAGAGCAAGAAT                         ATCTTGTTTGTGATATCAAAACCTGATGTGTTCAAGAGTCCAGCTTCAGAT
genomic: GTCACCGTCAAAAAGAGCAAGAATgtttgtgctc ... aaaattgcagATCTTGTTTGTGATATCAAAACCTGATGTGTTCAAGAGTCCAGCTTCAGAT
EST: gi|164089148|gb|ES136083.1|ES136083
EST:     CACTGGTGTTAGCCGTGTCACCGTCAAAAAAGAGCAAGAAT                         ATCTTGTTTGTGATATCAAAACCTGATGTGTTCAAGAGTCCAGCTTCAGAT
genomic: CACTGGTGTTAGCCGTGTCACCGTC-AAAAAGAGCAAGAATgtttgtgctc ... aaaattgcagATCTTGTTTGTGATATCAAAACCTGATGTGTTCAAGAGTCCAGCTTCAGAT
EST: gi|164067138|gb|ES148883.1|ES148883
EST:     GAAACCAATCACTGGTGTTAGCCGTGTCTACCGTCAAAAAGAGCAAGAAT                         ATCTTGTTTGTGATATCAAAACCTGATGTGTTCAAGAGTCCAGCTTCAGA
genomic: GAAACCAATCACTGGTGTTAGCCGTGTC-ACCGTCAAAAAGAGCAAGAATgtttgtgctc ... aaaattgcagATCTTGTTTGTGATATCAAAACCTGATGTGTTCAAGAGTCCAGCTTCAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taattgtttcctatgtttccaaattcattgatagaatgtggattgaaaattgcagATCTTGTTTGTGATATCAAAACCTGATGTGTTCAAGAGTCCAGCTTCAGATACATATGTGATCTTTGGTGAGGCCAAGATAGAGGATTTGAGCTCGCAGC
                                         attgaaaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgtgctcttcagaaaattaaatctctcttgtgttaattgtttcctatgtttccaaattcattgatagaatgtggattgaaaattgcagATCTTGTTTGTGATATCAAAACCTGATGTGTTCAAGAGTCCAGCTTCAGATACATATGTGATCTTTGGTGAGGCCAAGATAGAGGATTTGAGCTCGCAGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT