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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCAAAACTGGATGGTTGTCAAAGGAGATAAGATTAATTTCCCTGGTGGAGGCACACATTTTCATTATGGTGCTGATAAGTATATTGCATCGATGGCAAATgtaaggaagttacacttggtgtttgtacaagagaacgtatattattctttcatttgctaattgtattcttggaaatttttcag

Basic information

species Arabidopsis thaliana
transcript AT4G14360.2
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G14360.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA13G18630.1 (Glycine max), 5'ss of exon 3
CCAAAACTGGATGGTTGTCAAAGGAGATAAGATTAATTTCCCTGGTGGAGGCACACATTTTCATTATGGTGCTGATAAGTATATTGCATCGATGGCAAATgtaaggaagttacacttgg-tgtttgtacaagagaacgtatattattctttcatttgctaattgtattcttggaaatttttcag----------------------------------
||| |  ||||||||||| ||||| || |||||   ||| ||||||||||| || || || |||||||||||||| || ||||||||||| || || ||||||||  |||||| | |   |  ||   ||  | ||     || |      |||       || |||   ||||||   ||                                     
CCAGAGATGGATGGTTGTAAAAGGTGAAAAGATAGTTTTTCCTGGTGGAGGAACCCACTTCCATTATGGTGCTGACAAATATATTGCATCAATTGCCAATgtaagctagttactcctatctagtttggcactaaaata---atcaccaaaacataaaactcttatatgactggaaaaagttgtaactttattgtttatattcatgattggtattacag

upper sequence: AT4G14360.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA02G00550.1 (Glycine max), 5'ss of exon 3
CCAAAACTGGATGGTTGTCAAAGGAGATAAGATTAATTTCCCTGGTGGAGGCACACATTTTCATTATGGTGCTGATAAGTATATTGCATCGATGGCAAATgtaaggaagttacacttggtgtttgtacaagagaacg------tatat-tattct-ttcatttgctaattgtattcttggaaatttttcag-----------
||| ||||||||| |||| ||||| || |||||    || ||||| ||||| ||||||||||| || || ||||| ||||| |||||||| || ||||||||||||   ||||   |  | | | || |  | || |      |||||  ||||| ||  |   || || | ||  |||||  || | |             
CCAGAACTGGATGATTGTAAAAGGTGAAAAGATAGTGTTTCCTGGAGGAGGGACACATTTTCACTACGGAGCTGACAAGTACATTGCATCTATTGCAAATgtaaggt--ttactggttatctctataaagcataatgaaatgctatatgcattctgtttttcaactgatagaatcattggactttatccgtgttatgaagta

upper sequence: AT4G14360.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA10G04370.1 (Glycine max), 5'ss of exon 3
CCAAAACTGGATGGTTGTCAAAGGAGATAAGATTAATTTCCCTGGTGGAGGCACACATTTTCATTATGGTGCTGATAAGTATATTGCATCGATGGCAAATgtaaggaagttacacttggtgtttgtacaagagaacgtatattattctttcatttgctaattgtattcttggaaat--ttttcag--------------------------------
||| |  ||||||||||| ||||| || |||||   ||| ||||||||||| || || || |||||||| ||||  |||||||||||||| || || ||||||||  |||||| | |       |||    |  |     || |      |||       || |||   ||||||   || | ||                                
CCAGAGATGGATGGTTGTAAAAGGTGAAAAGATAGGTTTTCCTGGTGGAGGAACCCACTTCCATTATGGCGCTGGCAAGTATATTGCATCAATTGCCAATgtaagctagttactcctatc--cggtatggcactaaaataatcaccaaaacatgaaactcttatatgactggaaaaagttataagtttgtagtttatattcatgattggtatttcag

upper sequence: AT4G14360.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA10G32470.1 (Glycine max), 5'ss of exon 4
CCAAAACTGGATGGTTGTCAAAGGAGATAAGATTAATTTCCCTGGTGGAGGCACACATTTTCATTATGGTGCTGATAAGTATATTGCATCGATGGCAAATgtaag---gaagttacacttggtgttt----gtacaagagaacgta--tattattctttcatttgctaattgt--attcttggaaatttttcag------
||| || ||||||||||| ||||| || || ||    || ||||| || || || ||||| |||||||| ||||||||||| |||||||| || |||||||| ||   | |  ||   ||  || ||     || || | || | |   |||  | |||  |||   |||||    ||||  || |||||  |       
CCAGAATTGGATGGTTGTAAAAGGTGAAAAAATAGTATTTCCTGGAGGTGGGACTCATTTCCATTATGGAGCTGATAAGTACATTGCATCAATTGCAAATgtgagtctgcatctaactttactggttttggatataaaaaaatgaaaccatttatattttgtttttgaattggtagttctatgagattttatattatgca

upper sequence: AT4G14360.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA10G00880.2 (Glycine max), 5'ss of exon 4
CCAAAACTGGATGGTTGTCAAAGGAGATAAGATTAATTTCCCTGGTGGAGGCACACATTTTCATTATGGTGCTGATAAGTATATTGCATCGATGGCAAATgtaaggaagttacacttggtgtttgtacaagagaacg------tatat-tattctttcatttg-ctaattgtattcttggaaatttttcag---------
||| ||||||||| |||| ||||| || |||||    || ||||| ||||| |||||||||||  | || ||||| ||||| |||||||| || |||||||||||    ||||   |    | | || |  | || |      |||||  ||||| |  ||    |  | | ||  |||||  |  |             
CCAGAACTGGATGATTGTAAAAGGTGAAAAGATAGTGTTTCCTGGAGGAGGGACACATTTTCACAAAGGAGCTGACAAGTACATTGCATCAATTGCAAATgtaagaggcttactggttacctctataaagcataatgaaatgatatatgcattctgtttttcaattggtagcatcattggacttcatgtgtgttatgcag

upper sequence: AT4G14360.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: Vv05s0049g01180.t01 (Vitis vinifera), 5'ss of exon 4
CCAAAACTGGATGGTTGTCAAAGGAGATAAGATTAATTTCCCTGGTGGAGGCACACATTTTCATTATGGTGCTGATAAGTATATTGCATCGATGGCAAATgtaaggaagttacacttggtgtttgtacaagagaacgt--------atattattctttcatttgctaattgtattcttggaaatttttcag-----------
||| || ||||||||||| ||||| || |||||    || ||||| ||||||||||||||||||||||| |||||||| |||||||| ||  | |||||||||||   | | | ||       | |  || |||| |         |     ||| || |||||   |||   |||||| || | |||| |           
CCAGAATTGGATGGTTGTAAAAGGTGAAAAGATAGTATTTCCTGGGGGAGGCACACATTTTCATTATGGAGCTGATAAATATATTGCTTCACTTGCAAATgtaagattgatgccctgttacactattaaaaagaatgggaaaggaaacgcatttcctttatttgg-gattcctttcttg-aattatttctgtgttcaatgtt

upper sequence: AT4G14360.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: Vv07s0005g03630.t01 (Vitis vinifera), 5'ss of exon 3
CCAAAACTGGATGGTTGTCAAAGGAGATAAGATTAATTTCCCTGGTGGAGGCACACATTTTCATTATGGTGCTGATAAGTATATTGCATCGATGGCAAATgtaaggaagttacacttggtgtttgtacaagagaa-cgtatatt----attctttcatttgctaattgtattcttggaaatttttcag------------------------------------
||| |||||||||||||||||||| || ||||||   || |||||||| || || |||||||||||||| ||||| ||||||||||| || || |||||||||||   |||        |||    |   || ||  | | |      | |  |  ||    ||||  | | ||||     |  | |                                     
CCAGAACTGGATGGTTGTCAAAGGTGAAAAGATTGCATTTCCTGGTGGTGGAACTCATTTTCATTATGGAGCTGACAAGTATATTGCCTCAATTGCAAATgtaagttggttctttacaatgtccaaaagggaaaaatggaaagccaagacttgtaaatacattaatcttgtgcttgtgttctgctgaataagtgatgatcatttttaatggattggactggcag

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|86064589|gb|DR360346.1|DR360346
EST:     CATTATGGTGCTGATAAGTATATTGCATCGATGGCAAAT                         ATGCTTAACTATCCTAACAACGTGCTGAACAACGGTGGAAGGCTAAGGACG
genomic: CATTATGGTGCTGATAAGTATATTGCATCGATGGCAAATgtaaggaagt ... aatttttcagATGCTTAACTATCCTAACAACGTGCTGAACAACGGTGGAAGGCTAAGGACG




















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCAAAACTGGATGGTTGTCAAAGGAGATAAGATTAATTTCCCTGGTGGAGGCACACATTTTCATTATGGTGCTGATAAGTATATTGCATCGATGGCAAATgtaaggaagttacacttggtgtttgtacaagagaacgtatattattctttcatttgctaattgtattcttggaaatttttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT