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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TACCAAAGTAGCATCAGATCCTGGTGCTGGTGACATCTTAATGGGTTTTCTTGGCTCTGTCATTCTCTCTTTCGCTTTCTCCATGTTCAAACAAAGAAAGgtaaaacaaacaacaaacttgttctgttttgctttagaaaactggtaacaatcgctttggtttgcctctgtcttcttcag

Basic information

species Arabidopsis thaliana
transcript AT1G32080.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G32080.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GRMZM2G478212_T01 (Zea mays), 5'ss of exon 5
TACCAAAGTAGCATCAGATCCTGGTGCTGGTGACATCTTAATGGGTTTTCTTGGCTCTGTCATTCTCTCTTTCGCTTTCTCCATGTTCAAACAAAGAAAGgtaaaa---caaacaacaaacttgt---tctgttttgctttagaa--aactggtaacaatcgctttggtttgcctctgtcttcttcag-------------------------
 || || |   | ||  ||||||| ||||||||| |  |||||||||| ||||| ||||| ||  | || || || ||||| ||||||||||| |||||||||  |   || |     | |||||       ||| | || ||         |   |||  || ||   |    ||||||  |||                            
CACAAAGGCGCCCTCTAATCCTGGAGCTGGTGACGTACTAATGGGTTTCCTTGGGTCTGTGATCATATCATTTGCATTCTCAATGTTCAAACAGAGAAAGgtactactgcacatggttatcttgtgacatcatttcggttaagctctgctccgctgcaagtgccttttatgtgatctgtcaacttgtccatgctcttgaacccctgatttcag

upper sequence: AT1G32080.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GLYMA09G34440.1 (Glycine max), 5'ss of exon 4
TACCAAAGTAGCATCAGATCCTGGTGCTGGTGACATCTTAATGGGTTTTCTTGGCTCTGTCATTCTCTCTTTCGCTTTCTCCATGTTCAAACAAAGAAAGgtaaa-acaaaca---acaa-----actt-----gttctgttttgctttagaaaactggtaacaa-tcgctttggtttgcctctgtc-ttcttcag----
||| ||   | |||| |||||||| |||||||||||  ||||||| ||| | || ||||| |||||||| || || ||||| ||||||||||||||||||||||  |   |||     ||     ||||      | || |  |||   | ||||     | ||| |        | |       |   | | |||    
TACTAACTCATCATCTGATCCTGGAGCTGGTGACATTCTAATGGGATTTTTGGGATCTGTTATTCTCTCATTTGCCTTCTCTATGTTCAAACAAAGAAAGgtaaccatctacatttgtaattgttacttcatgaatcctatactgcagcaaaaaaagtaaagcaaataaaagcaatatattctcattactttgcagactg

upper sequence: AT1G32080.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GLYMA01G01340.1 (Glycine max), 5'ss of exon 4
TACCAAAGTAGCATCAGATCCTGGTGCTGGTGACATCTTAATGGGTTTTCTTGGCTCTGTCATTCTCTCTTTCGCTTTCTCCATGTTCAAACAAAGAAAGgtaa-------aacaaacaacaa--actt-----gttctgttttgctttagaaaactggtaacaatcgctttggtttgcctctgtcttcttcag------
||| ||   | |||| |||||||| || ||||||||  ||||||| ||| | || ||||| |||||||| || || ||||| ||||||||||||||||||||||        |     ||     ||||      | || |  |||   | ||||     | |||          |    ||| || ||    |      
TACAAACTCATCATCTGATCCTGGAGCCGGTGACATTCTAATGGGATTTTTGGGATCTGTTATTCTCTCATTTGCCTTCTCTATGTTCAAACAAAGAAAGgtaaccatctagatttgtaatcgttacttcatgaatcctatactgcagcaaaaaaagtaaagcaaataaaagcaatattttctttcgtcacaggctgttt

upper sequence: AT1G32080.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GLYMA16G15800.1 (Glycine max), 5'ss of exon 5
TACCAAAGTAGCATCAGATCCTGGTGCTGGTGACATCTTAATGGGTTTTCTTGGCTCTGTCATTCTCTCTTTCGCTTTCTCCATGTTCAAACAAAGAAAGgtaaaaca---aa------caacaaacttgttctgttttgctttagaaaactggtaacaatcgctttggtttgcctctgtcttcttcag-----------
||| || | | ||||| ||||||| ||||||||||| |||||||| ||| | || ||||| |||||||| ||  | ||||| ||||| || |||||||||||||| ||   ||      ||  |||    | || |  |||| || |||| |    |  |      |   ||  |  ||   ||    |           
TACAAAGGCATCATCAAATCCTGGAGCTGGTGACATTTTAATGGGATTTTTAGGATCTGTTATTCTCTCATTTTCCTTCTCTATGTTTAAGCAAAGAAAGgtaaaccatctaagtttctcagtaaataaatcctatactgctataaaaaaataaagatgaataaagtatgttctcattgctgtcaattgcttttgatatt

upper sequence: AT1G32080.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: Vv08s0056g01690.t01 (Vitis vinifera), 5'ss of exon 5
TACCAAAGTAGCATCAGATCCTGGTGCTGGTGACATCTTAATGGGTTTTCTTGGCTCTGTCATTCTCTCTTTCGCTTTCTCCATGTTCAAACAAAGAAAGgtaaaacaaacaacaaacttgttctgttttgctttagaaaactggtaacaatcgctttggtttgcctctg-tcttcttcag---------------------
||| || | | | ||  ||||||| |||||||||||  ||||||| ||| | || ||||| |||||||| || |||||||||||||||||||| ||||||||||   |         |    ||||   ||   | ||  | |  | |   | |||    ||     ||  |  ||  |||                     
TACGAAGGCATCTTCTAATCCTGGAGCTGGTGACATTCTAATGGGATTTTTAGGATCTGTTATTCTCTCATTTGCTTTCTCCATGTTCAAACAGAGAAAGgtaagtgaccactttttcaaactctgacatgaaattgaccatt--ttatggttgctaaaattatttactaattctcagcaggtttaaagtagaatttagtcc

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|125214754|gb|EL229062.1|EL229062
EST:     CGCTTTCTCCATGTTCAAACAAAGAAAG                         CTCGTGAAGAGGCACGCAGCTGAGATCTTCACATCTGTGATAGTTTCAACG
genomic: CGCTTTCTCCATGTTCAAACAAAGAAAGgtaaaacaaa ... tcttcttcagCTCGTGAAGAGGCACGCAGCTGAGATCTTCACATCTGTGATAGTTTCAACG
EST: gi|125282554|gb|EL296639.1|EL296639
EST:     TCTGTCATTCTCTCTTTCGCTTTCTCCATGTTCAAACAGAGAAAG                         CTCGTGAAGAGGCACGCAGCTGAGATCTTCACATCTGTGATAG
genomic: TCTGTCATTCTCTCTTTCGCTTTCTCCATGTTCAAACAAAGAAAGgtaaaacaaa ... tcttcttcagCTCGTGAAGAGGCACGCAGCTGAGATCTTCACATCTGTGATAG
EST: gi|125192503|gb|EL207457.1|EL207457
EST:     TTGGCTCTGTCATTCTCTCTTTCGCTTTCTCCATGTTCAAACAAAGAAAG                         CTCGTGAAGAGGCACGCAGCTGAGATCTT
genomic: TTGGCTCTGTCATTCTCTCTTTCGCTTTCTCCATGTTCAAACAAAGAAAGgtaaaacaaa ... tcttcttcagCTCGTGAAGAGGCACGCAGCTGAGATCTT
EST: gi|47830990|gb|CK120674.1|CK120674
EST:     CTTTCTCCATGTTCAAACAAAGAAAG                         CTCGTGAAGAGGCACGCAGCTGAGATCTTCACATCTGTGATAGTTTCAACG
genomic: CTTTCTCCATGTTCAAACAAAGAAAGgtaaaacaaa ... tcttcttcagCTCGTGAAGAGGCACGCAGCTGAGATCTTCACATCTGTGATAGTTTCAACG
EST: gi|124955714|gb|EL030704.1|EL030704
EST:     TTGGCTCTGTCATTCTCTCTTTCGCTTTCTCCATGTTCAAACAAAGAAAG                         CTCGTGAAGAGGCACGCAGCTGAG
genomic: TTGGCTCTGTCATTCTCTCTTTCGCTTTCTCCATGTTCAAACAAAGAAAGgtaaaacaaa ... tcttcttcagCTCGTGAAGAGGCACGCAGCTGAG
EST: gi|124991035|gb|EL063304.1|EL063304
EST:     TGGCTCTGTCATTCTCTCTTTCGCTTTCTCCATAGTTCAAACAAAGAAAG                         CTCGTGAAGAGGCACGCAGCTGAGATCTTCACAT
genomic: TGGCTCTGTCATTCTCTCTTTCGCTTTCTCCAT-GTTCAAACAAAGAAAGgtaaaacaaa ... tcttcttcagCTCGTGAAGAGGCACGCAGCTGAGATCTTCACAT
EST: gi|125021035|gb|EL093304.1|EL093304
EST:     TTCTCTCTTTCGCTTTCTCCATGTTCAAACAAAGAAAG                         CTCGTGAAGAGGCACGCAGTCTGAGATCTTCACATCTGTGATAGTTTCAAC
genomic: TTCTCTCTTTCGCTTTCTCCATGTTCAAACAAAGAAAGgtaaaacaaa ... tcttcttcagCTCGTGAAGAGGCACGCAG-CTGAGATCTTCACATCTGTGATAGTTTCAAC
EST: gi|125083006|gb|EL143723.1|EL143723
EST:     TTGGCTCTGTCATTCTCTCTTTCGCTTTCTCCATGTTCAAACAAAGAAAG                         CTCGTGAAGAGGCACGCAGCTGA
genomic: TTGGCTCTGTCATTCTCTCTTTCGCTTTCTCCATGTTCAAACAAAGAAAGgtaaaacaaa ... tcttcttcagCTCGTGAAGAGGCACGCAGCTGA
EST: gi|124993217|gb|EL065486.1|EL065486
EST:     TTGGCTCTGTCATTCTCTCTTTCGCTTTCTCCATGTTCAAACAAAGAAAG                         CTCGTGAAGAGGCACGCAG
genomic: TTGGCTCTGTCATTCTCTCTTTCGCTTTCTCCATGTTCAAACAAAGAAAGgtaaaacaaa ... tcttcttcagCTCGTGAAGAGGCACGCAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TACCAAAGTAGCATCAGATCCTGGTGCTGGTGACATCTTAATGGGTTTTCTTGGCTCTGTCATTCTCTCTTTCGCTTTCTCCATGTTCAAACAAAGAAAGgtaaaacaaacaacaaacttgttctgttttgctttagaaaactggtaacaatcgctttggtttgcctctgtcttcttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA