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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTTGTTGAGATTATGGCACCTGTATTTTCTAGAGAAGCATGGCGATGTGTATGGCATATGATTCAGgtttttgtttaactttattcacctttttacgatcggtattcacatgacccaaatttgtggcattgatgaatctacgttggtttctgattaagctatcaaaaggagtttgtctagtcttccagaccatcacttggtagcctaaaaacaatcttgtttgtttctggtgcag

Basic information

species Arabidopsis thaliana
transcript AT1G08040.2
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G08040.2 (Arabidopsis thaliana), 5'ss of exon 11
lower sequence: LOC_Os01g68260.1 (Oryza sativa), 5'ss of exon 10
GTTTGTTGAGATTATGGCACCTGTATTTTCTAGAGAAGCATGGCGATGTGTATGGCATATGATTCAGgt----ttttgttta-act-ttattcacctttttacgatcggtattcacatgacccaaatttgtggcattgatgaatctacgttggtttctgattaagctatcaaaaggagtttgtctagtcttccagaccatcacttggtagcctaaaaacaatcttgtttgtttctggtgcag
 |||||||| ||||||||| |||| || ||||| || |||||||| |||||||||||||||||||||||    |    | |  ||| || ||  | ||  |   | | |||| |  ||| |||   ||| ||                                                                                                              
ATTTGTTGAAATTATGGCAACTGTGTTCTCTAGGGATGCATGGCGCTGTGTATGGCATATGATTCAGgtggagtggcatctgcactgttcttagctttgcttgaagctgtatgcttatg-cccggctttttgcag-----------------------------------------------------------------------------------------------------------

upper sequence: AT1G08040.2 (Arabidopsis thaliana), 5'ss of exon 11
lower sequence: LOC_Os05g01760.1 (Oryza sativa), 5'ss of exon 11
GTTTGTTGAGATTATGGCACCTGTATTTTCTAGAGAAGCATGGCGATGTGTATGGCATATGATTCAGgtttttgtttaactttattcacctttttacgatcggtattcacatgacccaaatttgtg--gcattgatgaatctacgttggtttctgattaagctatcaaaaggagtttgtctagtcttccagaccatcacttggtagcctaaaaacaatcttgtttgtttctggtgcag
 |||||||| || ||||| || || || |||||||| |||||| ||||||||||||||||||||||||||| | ||| |   ||    |    |||  |||    |||     |  ||  ||| |    |||| ||     |  |||  ||||   |  ||                                                                             
CTTTGTTGAAATAATGGCTCCAGTCTTCTCTAGAGATGCATGGAGATGTGTATGGCATATGATTCAGgtttgtatttcatagtaa--gctcaattagtatc----ttcgggccattcattttttttcttcatttatttgattgtgttaatttcctctgcag-----------------------------------------------------------------------------

upper sequence: AT1G08040.2 (Arabidopsis thaliana), 5'ss of exon 11
lower sequence: LOC_Os01g73970.1 (Oryza sativa), 5'ss of exon 11
GTTTGTTGAGATTATGGCACCTGTATTTTCTAGAGAAGCATGGCGATGTGTATGGCATATGATTCAGgtttttgtttaactttattcacctttttacgatcggtattcac-atgacccaaatttgtggcattgatgaatctacgttggtttctgattaagctatcaaaaggagtttgtctagtcttccagaccatcacttggtagcctaaaaacaatcttgtttgtttctggtgcag
 |||||||| || ||||| || || || || ||||| |||||| ||||||||||||||||||||||||| |       || | |||  | |   ||| |  | | | ||  ||   || |  |  |  ||| | ||| | |       |||  ||  | | |||         |||  |  | ||                                                    
CTTTGTTGAAATAATGGCCCCGGTGTTCTCCAGAGATGCATGGAGATGTGTATGGCATATGATTCAGgtat------gacataattttcataggtacca--gatttccattatctgcccacctcttcacatggttgatttttt-----ttttagagaagggtattt-------tttacccggcctct--------------------------------------------------

upper sequence: AT1G08040.2 (Arabidopsis thaliana), 5'ss of exon 11
lower sequence: LOC_Os02g19510.1 (Oryza sativa), 5'ss of exon 11
GTTTGTTGAGATTATGGCACCTGTATTTTCTAGAGAAGCATGGCGATGTGTATGGCATATGATTCAGgtttttgtttaactttattcacctttttacgatcggtattcacatgacccaaatttgtggcattgatgaatctacgttggtttctgattaagctatcaaaaggagtttgtctagtcttccagaccatcacttggtagcctaaaaacaatcttgtttgtttctggtgcag
 |||||||| || |||||| | || || ||||| || |||||||| ||||| |||||||||||||||||    |  |  |  ||           | | ||    || ||||     | |   |||| |||  |      ||  ||  |||||                                                                                   
ATTTGTTGAAATCATGGCAACCGTGTTCTCTAGGGATGCATGGCGCTGTGTCTGGCATATGATTCAGgtg---gagtggcactac----------atgttcaactttaacattgtttataacagtggtattctta----cacactgtcttctgcag--------------------------------------------------------------------------------

upper sequence: AT1G08040.2 (Arabidopsis thaliana), 5'ss of exon 11
lower sequence: GRMZM5G801369_T03 (Zea mays), 5'ss of exon 11
GTTTGTTGAGATTATGGCACCTGTATTTTCTAGAGAAGCATGGCGATGTGTATGGCATATGATTCAGgtttttgtttaactttattcacctttttacgatcggtattcacatgacccaaatttgtggcattgatgaatctacgttggtttctgattaagctatcaaaaggagtttgtctagtcttccagaccatcacttggtagcctaaaaacaatcttgtttgtttctggtgcag
||||||||| ||||||||| ||||||| || || || |||||||| |||||||||||||||||||||||    |   |    |||      |  |||      | ||| | | ||   | ||||  || |  ||   |  |  ||| ||||||                                                                                   
GTTTGTTGAAATTATGGCAACTGTATTCTCAAGGGATGCATGGCGCTGTGTATGGCATATGATTCAGgt----ggggagtggtatc-----tcctac------tgttctcttaacttca-tttgaagcctgtattcttacatattgttttctgcag--------------------------------------------------------------------------------

upper sequence: AT1G08040.2 (Arabidopsis thaliana), 5'ss of exon 11
lower sequence: GRMZM2G119725_T03 (Zea mays), 5'ss of exon 10
GTTTGTTGAGATTATGGCACCTGTATTTTCTAGAGAAGCATGGCGATGTGTATGGCATATGATTCAGgtttttgtttaactttattcacctttttacgatcggtattcacatgacccaaatttgtggcattgatgaatctacgttggtttctgattaagctatcaaaaggagtttgtctagtcttccagaccatcacttggtagcctaaaaacaatcttgtttgtttctggtgcag
 |||||||||||||||||| | || || || ||| | |||||||| |||||||||||||||||||||||       |||| |      |   |      |  ||  | |  ||    |   || || || |  |  ||  |                                                                                               
ATTTGTTGAGATTATGGCAACAGTGTTCTCCAGAAATGCATGGCGCTGTGTATGGCATATGATTCAGgtg---aggtaacatggcatgcaagtcattagtttgt-ctgaagtggagtatgcttatg-cacttctatatgcag----------------------------------------------------------------------------------------------

upper sequence: AT1G08040.2 (Arabidopsis thaliana), 5'ss of exon 11
lower sequence: GRMZM2G006507_T03 (Zea mays), 5'ss of exon 11
GTTTGTTGAGATTATGGCACCTGTATTTTCTAGAGAAGCATGGCGATGTGTATGGCATATGATTCAGgtttttgtt-taactttattcacc--tttttacgatcggtattcacatgacccaaatttgtggcattgatgaatctacgttggtttctgattaagctatcaaaaggagtttgtctagtcttccagaccatcacttggtagcctaaaaacaatcttgtttgtttctggtgcag
 |||||||| ||||||||| | || || |||||| | |||||||| |||||||||||||||||||||||    |   ||   | || ||    ||| |   |   ||| |    | |||||    ||   |||  |                                                                                                       
ATTTGTTGAAATTATGGCAACGGTGTTCTCTAGAAATGCATGGCGCTGTGTATGGCATATGATTCAGgtgaacgcaatatgctaatgcattagtttgtctaaagtgtagtatgcttaccca---ctgcttcatgcag------------------------------------------------------------------------------------------------------

upper sequence: AT1G08040.2 (Arabidopsis thaliana), 5'ss of exon 11
lower sequence: GRMZM5G846339_T01 (Zea mays), 5'ss of exon 11
GTTTGTTGAGATTATGGCACCTGTATTTTCTAGAGAAGCATGGCGATGTGTATGGCATATGATTCAGgtt--tttgtttaactttattcacctttttacgatcggtattca---catgacccaaatttgtggcattgatgaatctacgttggtttctgattaagctatcaaaaggagtttgtctagtcttccagaccatcacttggtagcctaaaaacaatcttgtttgtttctggtgcag
 |||||||| || ||||| || || || || ||||| |||||| ||||||| ||||||||||||||||||  | ||| |  | |  ||| |||| |  |  ||  | |||    | | ||  || | |  ||||||| |   |  |||  |                                                                                          
TTTTGTTGAAATAATGGCTCCAGTCTTCTCAAGAGATGCATGGAGATGTGTGTGGCATATGATTCAGgttcgtctgtctgtcatacttctccttgtgtctgtctatcttcggtcctttacataattgttcggcattgctt--tggacgcag------------------------------------------------------------------------------------------

upper sequence: AT1G08040.2 (Arabidopsis thaliana), 5'ss of exon 11
lower sequence: GLYMA12G29800.1 (Glycine max), 5'ss of exon 11
GTTTGTTGAGATTATGGCACCTGTATTTTCTAGAGAAGCATGGCGATGTGTATGGCATATGATTCAGgtttttgtttaactttattcacctttttacgatcggtattcacatgacccaaatttgtggcattgatgaatcta-cgttggtttctgattaagctatcaaaaggagtttgtctagtcttccagaccatcacttggtagcctaaaaacaatcttgtttgtttctggtgcag
 ||||| || |||||||||||||| |||||| | ||||| ||||| ||||| ||||| ||||||||||| |       | ||||||  |||| |  |    | |    | |  |    | |   ||  |  | ||||| |  |  |    |   ||  |    | | ||  |   ||   |   ||||| |  |||  || ||||                                
ATTTGTGGAAATTATGGCACCTGTCTTTTCTCGTGAAGCTTGGCGTTGTGTGTGGCACATGATTCAGgtat-------attttattttccttgtcgcatatgatggctatagtaatgtagtggatga-acaggtgaatttttctcttacatgatatataatcttaataattatactgatgaactttccaaat-atctatttgtag--------------------------------

upper sequence: AT1G08040.2 (Arabidopsis thaliana), 5'ss of exon 11
lower sequence: GLYMA13G39990.1 (Glycine max), 5'ss of exon 11
GTTTGTTGAGATTATGGCACCTGTATTTTCTAGAGAAGCATGGCGATGTGTATGGCATATGATTCAGgtttttgtttaactttattcacctttttacgatcggtattcacatgacccaaatttgtggcattgatgaatcta-cgttggtttctgattaagctatcaaaaggagtttgtctagtcttccagaccatcacttggtagcctaaaaacaatcttgtttgtttctggtgcag
 ||||| || |||||||||||||| |||||| | || || ||||| ||||| ||||| ||||||||||| |       | ||||||  |||| || |    | |    |    | |  | | | ||  |  | ||||| |  |  |    |   ||  |    |   ||  |   ||   |   ||||| |  |||   | ||||                                
ATTTGTGGAAATTATGGCACCTGTCTTTTCTCGTGAGGCTTGGCGTTGTGTGTGGCACATGATTCAGgtat-------attttattttccttgttgcatatgatggctatggtaacatagtctatga-acaggtgaatttttctcttacatgctatataatcttagtaattatactgatgaactttccaaat-atcttcttgtag--------------------------------

upper sequence: AT1G08040.2 (Arabidopsis thaliana), 5'ss of exon 11
lower sequence: Vv06s0004g02700.t01 (Vitis vinifera), 5'ss of exon 11
GTTTGTTGAGATTATGGCACCTGTATTTTCTAGAGAAGCATGGCGATGTGTATGGCATATGATTCAGgtttttgtttaactttattcacctttttacgatcggtattcacatgacccaaatttgtggcattgatgaatctacgttggtttctgattaagctatcaaaaggagtttgtctagtcttccagaccatcacttggtagcctaaaaacaatcttgtttgtttctggtgcag
 ||||| || |||||||| ||||| || ||| | ||||| ||||| ||||| ||||||||||||||||| |   |||| ||||    |   | || |  ||    | |||||| | ||  ||    ||||      ||||       |||||  | ||| |||          || | |  |||   ||                                               
ATTTGTGGAAATTATGGCCCCTGTCTTCTCTCGGGAAGCTTGGCGTTGTGTGTGGCATATGATTCAGgtatcc-tttatcttttaggattatattgctttc----tacacatggcacatgttacaagcat--gcacatct-------tttctcttcaagttatt--------cttctgttatctcatag-----------------------------------------------

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|86085178|gb|DR380937.1|DR380937
EST:     CACCTGTATTTTCTAGAGAAGCATGGCGATGTGTATGGCATATGATTCAG                         AATGATCTTGTTCATGGATGGGGTCTCGATTTTGCTCTCAGACGATGCGTT
genomic: CACCTGTATTTTCTAGAGAAGCATGGCGATGTGTATGGCATATGATTCAGgtttttgttt ... tctggtgcagAATGATCTTGTTCATGGATGGGGTCTCGATTTTGCTCTCAGACGATGCGTT
EST: gi|125181984|gb|EL197797.1|EL197797
EST:     TATTTTCTAGAGAAGCATGGCGATGTGTATGGCATATGATTCAG                         AATGATCTTGTTCATGGATGGGGTCTCGATTTTGCT
genomic: TATTTTCTAGAGAAGCATGGCGATGTGTATGGCATATGATTCAGgtttttgttt ... tctggtgcagAATGATCTTGTTCATGGATGGGGTCTCGATTTTGCT
EST: gi|125296189|gb|EL310274.1|EL310274
EST:     CACCTGTATTTTCTAGAGAAGCATGGCGATGTGTATGGCATATGATTCAG                         AATGATCTTGTTCATGGATGGGGT
genomic: CACCTGTATTTTCTAGAGAAGCATGGCGATGTGTATGGCATATGATTCAGgtttttgttt ... tctggtgcagAATGATCTTGTTCATGGATGGGGT
EST: gi|164232774|gb|ES119532.1|ES119532
EST:     CACCTGTATTTTCTAGAGAAGCATGGCGATGTGTATGGCATATGATTCAG                         AATGATCTTGTTCATGGATGGGGTC
genomic: CACCTGTATTTTCTAGAGAAGCATGGCGATGTGTATGGCATATGATTCAGgtttttgttt ... tctggtgcagAATGATCTTGTTCATGGATGGGGTC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTTGTTGAGATTATGGCACCTGTATTTTCTAGAGAAGCATGGCGATGTGTATGGCATATGATTCAGgtttttgtttaactttattcacctttttacgatcggtattcacatgacccaaatttgtggcattgatgaatctacgttggtttctgattaagctatcaaaaggagtttgtctagtcttccagaccatcacttggtagcctaaaaacaatcttgtttgtttctggtgcag

- - - - - - - - - - - - - - - -  AGAAGC