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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTTTGACATGTTGAAGAGGCAGTCTCTTCGTGCTGACAACATCAAGATGTTTGTTCTCGATGAAGCTGATGAAATGCTCTCCCGTGGTTTCAAGGACCAGgtatgcaaatatttctcagtgtttcaattccattctcgttatagtttaacttgaatctcactggtttctgggttttttcag

Basic information

species Arabidopsis thaliana
transcript AT3G13920.2
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G13920.2 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA13G42360.1 (Glycine max), 5'ss of exon 4
CTTTGACATGTTGAAGAGGCAGTCTCTTCGTGCTGACAACATCAAGATGTTTGTTCTCGATGAAGCTGATGAAATGCTCTCCCGTGGTTTCAAGGACCAGgtatgcaaatatttctcagt-gtttcaattccattctcgttatagtttaacttgaatc-tcactggtttctgg--gttttttcag---------------
 ||||||||| |   ||| |||||||||||| | ||  |||| |||||||||||| | ||||| |||||||||||||| || |||||||||||||||||||| ||    | || |    | |||| ||        | ||| |  |||    ||| || | ||||   |||    ||| |||||                
ATTTGACATGCTACGGAGACAGTCTCTTCGTCCAGATCACATAAAGATGTTTGTTTTGGATGAGGCTGATGAAATGCTTTCTCGTGGTTTCAAGGACCAGgtttgatggttttccatgtttgtttaaaacattgaattgtttttttttcttctgattcctgactgtcatctaaacgttctttcatgcatgttaccaatat

upper sequence: AT3G13920.2 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA08G20300.2 (Glycine max), 5'ss of exon 4
CTTTGACATGTTGAAGAGGCAGTCTCTTCGTGCTGACAACATCAAGATGTTTGTTCTCGATGAAGCTGATGAAATGCTCTCCCGTGGTTTCAAGGACCAGgtatgc------aaatatttctcagtgtttca-attccattc-tcgttatagtttaacttgaatctcactggtttctgggttttttcag-----------
 ||||||||| ||  |||||||||||||||  | ||   ||| |||||||||||| | ||||| |||||||||||||| || |||||||||||||| ||||| ||        | || ||| ||   ||||| |||   | |     | || | |   |||  | ||      || | |  | |   |            
GTTTGACATGCTGCGGAGGCAGTCTCTTCGCCCAGATTGCATAAAGATGTTTGTTTTGGATGAGGCTGATGAAATGCTTTCACGTGGTTTCAAGGATCAGgtttgttgttttgattagttcccacattttcatatttagtgcactaatttattcttggttgtctgtcctatacttgttgactatcctacttcttgtgttg

upper sequence: AT3G13920.2 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA17G06110.1 (Glycine max), 5'ss of exon 4
CTTTGACATGTTGAAGAGGCAGTCTCTTCGTGCTGACAACATCAAGATGTTTGTTCTCGATGAAGCTGATGAAATGCTCTCCCGTGGTTTCAAGGACCAGgta---------tgcaaatatttctcagtg--tttcaattccattctcgtta-tagtttaacttgaatctcactggtttctgggttttttcag-------
 ||||| ||| ||    | ||||| ||||   | ||| ||||||||||||||||  | ||||| |||||||||||||| ||||| ||||||||||| ||||||         | || |  |   | |||   ||||| ||  ||| |   || || ||||  ||     | | |  |  ||    || |  |        
GTTTGATATGCTGCGCCGACAGTCACTTCAGCCAGACCACATCAAGATGTTTGTATTGGATGAGGCTGATGAAATGCTTTCCCGAGGTTTCAAGGATCAGgtaccttttcaattcacaactcatttagtacttttcactttaattattactaatactttatgtttttgataagtaatgcctacacttgtctatggatttt

upper sequence: AT3G13920.2 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA15G03020.1 (Glycine max), 5'ss of exon 4
CTTTGACATGTTGAAGAGGCAGTCTCTTCGTGCTGACAACATCAAGATGTTTGTTCTCGATGAAGCTGATGAAATGCTCTCCCGTGGTTTCAAGGACCAGgtatgcaaatatttctcagtgtttcaattccattctcgttatagtttaacttgaatctcactggtttctggg--ttttttcag------------------------------------------------------------------------------------------------------
 ||||||||| |    || || ||||||||  | ||  |||| || ||||||||| | ||||| |||||||||||||| || |||||||||||||||||||| ||   ||  || ||  |||||    |  |   | |  || ||||  |||     | | ||   |||     || |||||                                                                                                       
GTTTGACATGCTACGAAGACAATCTCTTCGCCCAGATCACATAAAAATGTTTGTTTTGGATGAGGCTGATGAAATGCTTTCACGTGGTTTCAAGGACCAGgtttg---atggttttccatgttttgtctaaaactttga-attgtttttcttttccttgagtgtcatctaaacattctttcatgcatgttgaaataattctttatttaaaacctgtgtgctagatgaagtcatcttgtgttagatagatagctaacagtttatatttttcgtgcatgaaatgcag

upper sequence: AT3G13920.2 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA13G16570.1 (Glycine max), 5'ss of exon 4
CTTTGACATGTTGAAGAGGCAGTCTCTTCGTGCTGACAACATCAAGATGTTTGTTCTCGATGAAGCTGATGAAATGCTCTCCCGTGGTTTCAAGGACCAGgtatgcaaatatttctcagtgtttcaattccattctcgttatagtttaacttgaatct-cactggtttctgggttttttcag-------------------
 ||||| ||| ||   || ||||| ||||   | ||  ||||||||||||||||  | ||||| |||||||||||||| ||||| ||||| ||||| ||||||        |||     |   | ||||   || | ||| |  |  || |   | || |||| || |  || |||||| |                    
GTTTGATATGCTGCGCAGACAGTCACTTCTGCCAGATCACATCAAGATGTTTGTATTGGATGAGGCTGATGAAATGCTTTCCCGAGGTTTTAAGGATCAGgtacttttcactttaattattactaaatttttttgttgttttt-tacaagtaatacctacacttgtctacggatttttttaaattgatgtgtaaacgttcg

upper sequence: AT3G13920.2 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA07G00950.1 (Glycine max), 5'ss of exon 4
CTTTGACATGTTGAAGAGGCAGTCTCTTCGTGCTGACAACATCAAGATGTTTGTTCTCGATGAAGCTGATGAAATGCTCTCCCGTGGTTTCAAGGACCAGgtatgcaaat---atttctcagtgtttcaattccattctc-gttatagtttaacttgaatctcactggtttctgggttttttcag---------------
 ||||||||| ||  |||||||||||||||  | ||   ||| |||||||||||| | ||||| |||||||||||||| || |||||||| ||||| ||||| ||  | |   ||| |   || ||   |||   | | |   | ||   |   |||  | ||      || | |  | |   |                
GTTTGACATGCTGCGGAGGCAGTCTCTTCGCCCAGATTGCATAAAGATGTTTGTTTTGGATGAGGCTGATGAAATGCTTTCACGTGGTTTTAAGGATCAGgtttgttattttgattaccatgttttcatatttagtgcactaatttatccttggttgtctgtcctatacttgttgactatcctatctcttatgttggtaa

upper sequence: AT3G13920.2 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA15G18760.3 (Glycine max), 5'ss of exon 4
CTTTGACATGTTGAAGAGGCAGTCTCTTCGTGCTGACAACATCAAGATGTTTGTTCTCGATGAAGCTGATGAAATGCTCTCCCGTGGTTTCAAGGACCAGgta---tgcaaatatttctcagtgtttcaat---------tccattctcgttatagttta--acttg-aatctcactggtttctgggttttttcag----
 ||||| ||| ||   || ||||| |||||  | ||| ||||||||||||||||  | ||||| |||||||||||||| ||||||||||| || || |||||    |  ||||  |  ||  | | | |||            |||    || | |||||  |  || |||  | |  |||||||  |||||  |     
ATTTGATATGCTGCGCAGACAGTCACTTCGGCCAGACTACATCAAGATGTTTGTATTGGATGAGGCTGATGAAATGCTTTCCCGTGGTTTTAAAGATCAGgttctttctaaatcatattccttttgttaatgaagaattactgattggatttcttgtttatgatatgtaatgccccacgtttctgtatttttgtacattg

upper sequence: AT3G13920.2 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA09G07530.3 (Glycine max), 5'ss of exon 4
CTTTGACATGTTGAAGAGGCAGTCTCTTCGTGCTGACAACATCAAGATGTTTGTTCTCGATGAAGCTGATGAAATGCTCTCCCGTGGTTTCAAGGACCAGgt--------atgcaaatatttctc---agtgtttcaatt-----ccattctcgttatagttta-acttgaatctcactggtttctgggttttttcag--
 ||||| ||| ||   || ||||| |||||  | ||| | ||||||||||||||  | ||||| |||||||||||||| ||||||||||| || || |||||        || || ||  || |    | | ||  ||||     |    || ||| |  || | |  | |  | |||  |||||||  |||||  |   
ATTTGATATGCTGCGCAGACAGTCACTTCGGCCAGACTATATCAAGATGTTTGTATTGGATGAGGCTGATGAAATGCTTTCCCGTGGTTTTAAAGATCAGgtgctttttaattcatattctttttgttaattttataattactgactggacttgttgtttttgatatgtaatgcccacacgtttctgtatttttgtacat

upper sequence: AT3G13920.2 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA04G05580.1 (Glycine max), 5'ss of exon 4
CTTTGACATGTTGAAGAGGCAGTCTCTTCGTGCTGACAACATCAAGATGTTTGTTCTCGATGAAGCTGATGAAATGCTCTCCCGTGGTTTCAAGGACCAGgtatgcaaatatttctcagtgtttcaattccattctcgttatagtttaacttgaatctcactggtttctgggttt--tttcag-------------------
 ||||||||| ||   ||||| ||  | ||  |||| ||||||| |||||||||  | ||||| || ||||| |||||||| || ||||||||||| |||||   |  || || |   ||   ||  ||  |||  | | ||  | |   |||  |     |||  |  |  |||   || |                    
ATTTGACATGCTGCGCAGGCAATCATTGCGCTCTGATAACATCAGGATGTTTGTATTGGATGAGGCAGATGAGATGCTCTCTCGAGGTTTCAAGGATCAGgtcctctcattttcccatgttgctctcttttatttgcttcattctattgtttg--ttgtgttggaatacgattttggcttaaaaataatatttagtgttttt

upper sequence: AT3G13920.2 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA06G05580.1 (Glycine max), 5'ss of exon 4
CTTTGACATGTTGAAGAGGCAGTCTCTTCGTGCTGACAACATCAAGATGTTTGTTCTCGATGAAGCTGATGAAATGCTCTCCCGTGGTTTCAAGGACCAGgt--------------atgcaaatatttctcagtgtttcaattccattctcgttatagtttaacttgaat---ctcactggtttctgggtt---ttttcag
 ||||||||| ||   || || ||| | ||  |||| ||||||| |||||||||  | ||||| || ||||| |||||||| || ||||||||||| |||||              ||||   | | | | | ||  |  |||| ||| |   |  | |||  ||| ||    ||   | |||| |   ||   |||||| 
ATTTGACATGCTGTGCAGACAATCTTTGCGCCCTGATAACATCAGGATGTTTGTATTGGATGAGGCAGATGAGATGCTCTCTCGAGGTTTCAAGGATCAGgtcctctcattttcctatgctgctctcttttattggcttcattctattgtttgtggattttggcttaaaaatactatttagttttttatttgaattttca-

upper sequence: AT3G13920.2 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: Vv04s0008g01000.t01 (Vitis vinifera), 5'ss of exon 3
CTTTGACATGTTGAAGAGGCAGTCTCTTCGTGCTGACAACATCAAGATGTTTGTTCTCGATGAAGCTGATGAAATGCTCTCCCGTGGTTTCAAGGACCAGgtatgcaaatatttctcagtgtttcaattccattctcgttata--gtttaacttgaatctcactggtttctgg----gttttttcag----------------
 ||||||||||||   ||||| || |||||| ||||  |||| |||||||||||  | |||||||| ||||||||||| || || ||||||||||| |||||         |||  |  || |     |   || | ||| |   ||||      | ||||  |   |    |     | || ||||                
TTTTGACATGTTGCGCAGGCAATCACTTCGTCCTGATTACATTAAGATGTTTGTGTTAGATGAAGCAGATGAAATGCTTTCACGAGGTTTCAAGGATCAGgtcctt---cctttgcctttgctctgtatatctttttgttgtgctgtttgctactactctctataactgtcagtatgatgttgtcagatttttgtctggatat

upper sequence: AT3G13920.2 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: Vv11s0016g01920.t01 (Vitis vinifera), 5'ss of exon 3
CTTTGACATGTTGAAGAGGCAGTCTCTTCGTGCTGACAACATCAAGATGTTTGTTCTCGATGAAGCTGATGAAATGCTCTCCCGTGGTTTCAAGGACCAGgt-atgcaaatatttc----tcagtgtt-tcaattccattctcgttatagt-ttaacttgaatctcactggtttctgggttttttcag------------
 ||||||||| ||   || ||||| |||||| ||||  |||| || ||||||||  | |||||||| |||||||||||||| || ||||||||||| ||||| || |  | |         || | || |   || || | | ||   |   ||  | | ||   || |  | | | |    | | ||            
ATTTGACATGCTGCGAAGACAGTCCCTTCGTCCTGATTACATTAAAATGTTTGTGTTGGATGAAGCAGATGAAATGCTCTCTCGAGGTTTCAAGGATCAGgtcattcttaaaccctaaatccattcttattgttttcacttttgtggcaaaatttccatcaactgcaatattcttttgacagtatgagtatatgatgcat

upper sequence: AT3G13920.2 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: Vv09s0002g01760.t01 (Vitis vinifera), 5'ss of exon 4
CTTTGACATGTTGAAGAGGCAGTCTCTTCGTGCTGACAACATCAAGATGTTTGTTCTCGATGAAGCTGATGAAATGCTCTCCCGTGGTTTCAAGGACCAGgtatg--caaatatttctcagtgtttc----aattccattctcgtt--atagtttaacttgaatctcactggtttctgggttttttcag-----------------------------------------------------------------------------------------------------
 ||||||||||||  ||| ||||| |||||  | ||  |||| |||||||||||  | ||||| |||||||||||||| || || ||||||||||| ||||| ||  | | ||| |||| || | |     | ||  | | |  ||  ||| || |   ||||   || |  |||     || ||  |                                                                                                      
GTTTGACATGTTGCGGAGACAGTCACTTCGCCCAGATTACATTAAGATGTTTGTATTGGATGAGGCTGATGAAATGCTTTCACGAGGTTTCAAGGATCAGgtctgttctattatatctctgtttctttactagttgtaatatttttgcatacttcatggtgaagaacattattttgctaattgttagaagttcatgctcattgcttattgctggatttttcaatatgtgcaagttttgactggctttgttgtttttctgataattcattaattttttttgctgctgtcag

upper sequence: AT3G13920.2 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: Vv04s0008g00980.t01 (Vitis vinifera), 5'ss of exon 1
CTTTGACATGTTGAAGAGGCAGTCTCTTCGTGCTGACAACATCAAGATGTTTGTTCTCGATGAAGCTGATGAAATGCTCTCCCGTGGTTTCAAGGACCAGgtatgcaaatatttctca---gtgtttcaattccattctcgttatagtttaa-cttgaatctcactggtttctgggttttttcag
      || | ||| | ||   ||||| | |||||||  |||||||||||||||||| ||||| |||||||||||||||||  | || || ||||| ||||| |  |  ||  |||     ||||||  ||   | | |  || |||   || ||||  |  |     | | |   |   | |||
------CACGCTGAGGCGGGGCTCTCTCCATGCTGACTCCATCAAGATGTTTGTTCTGGATGAGGCTGATGAAATGCTCTCTAGAGGCTTTAAGGATCAGgtctttatctagctcttgtccgtgttttcataagaattt--ttgtagccaaaacttgtgttcctaaattgttttcttgcctgcag

upper sequence: AT3G13920.2 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: EFJ16567 (Selaginella moellendorffii), 5'ss of exon 3
CTTTGACATGTTGAAGAGGCAGTCTCTTCGTGCTGACAACATCAAGATGTTTGTTCTCGATGAAGCTGATGAAATGCTCTCCCGTGGTTTCAAGGACCAGgtatgcaaatatttctcagtgtttcaattccattctcgttatagtttaacttgaatctcactggtttctgggttttttcag
||  || ||| | | | | |   | || ||  | ||| |||||||||||||||| || || || || || || ||||| ||||| |||||||||||||||||| |     |         || |  ||  |   |  |      | |  ||||  | || | |                  
CTACGATATGCTCAGGCGTCGCGCGCTGCGGCCGGACTACATCAAGATGTTTGTCCTGGACGAGGCGGACGAGATGCTGTCCCGCGGTTTCAAGGACCAGgtaaggtggaaggaaagctggtctatataaccaccctgcc----tgtgccttgtgtgtcgcag------------------

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|124839545|gb|EH923984.1|EH923984
EST:     GTTCTCGATGAAGCTGATGAAATGCTCTCCCGTGGTT-CAAGGACCAG                         ATCTATGACATATTCCAG
genomic: GTTCTCGATGAAGCTGATGAAATGCTCTCCCGTGGTTTCAAGGACCAGgtatgcaaat ... gttttttcagATCTATGACATATTCCAG
EST: gi|47829698|gb|CK119382.1|CK119382
EST:     TTGTTCTCGATGAAGCTGATGAAATGCTCTCCCGTGGTTTCAAGGACCAG                         ATCTATGACATATTCCAGCTTCTTCCACCAAAGATCCAAGTTGGTGTGTTC
genomic: TTGTTCTCGATGAAGCTGATGAAATGCTCTCCCGTGGTTTCAAGGACCAGgtatgcaaat ... gttttttcagATCTATGACATATTCCAGCTTCTTCCACCAAAGATCCAAGTTGGTGTGTTC
EST: gi|164080088|gb|ES153605.1|ES153605
EST:     GTTCTCGATGGAGCTGATGAAATGCTCTCCCGTGGTTTCAAGGACCAG                         ATCTATGACATATTCCAG
genomic: GTTCTCGATGAAGCTGATGAAATGCTCTCCCGTGGTTTCAAGGACCAGgtatgcaaat ... gttttttcagATCTATGACATATTCCAG
EST: gi|47831463|gb|CK121147.1|CK121147
EST:     TTGTTCTCGATGAAGCTGATGAAATGCTCTCCCGTGGTTTCAAGGACCAG                         ATCTATGACATATTCCAGCTTCTTCCACCAAAGATCCAAGTTGGTGTGTTC
genomic: TTGTTCTCGATGAAGCTGATGAAATGCTCTCCCGTGGTTTCAAGGACCAGgtatgcaaat ... gttttttcagATCTATGACATATTCCAGCTTCTTCCACCAAAGATCCAAGTTGGTGTGTTC
EST: gi|116436248|gb|EG478840.1|EG478840
EST:     TTGTTCTCGATGAAGCTGATGAAATGCTCTCCCGTGGTTTCAAGGACCTG                         ATCTATGACATATTCCAGCTTCTTCCACCAAAGATCCAAGTTGGTGTGTTC
genomic: TTGTTCTCGATGAAGCTGATGAAATGCTCTCCCGTGGTTTCAAGGACCAGgtatgcaaat ... gttttttcagATCTATGACATATTCCAGCTTCTTCCACCAAAGATCCAAGTTGGTGTGTTC
EST: gi|86034879|gb|DR330632.1|DR330632
EST:     TTGTTCTCGATGAAGCTGATGAAATGCTCTCCCGTGGTTTCAAGGACCAG                         ATCTATGACATATTCCAGCTTCTTCCACCAAAGATCCAAGTTGGTGTGTTC
genomic: TTGTTCTCGATGAAGCTGATGAAATGCTCTCCCGTGGTTTCAAGGACCAGgtatgcaaat ... gttttttcagATCTATGACATATTCCAGCTTCTTCCACCAAAGATCCAAGTTGGTGTGTTC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTTTGACATGTTGAAGAGGCAGTCTCTTCGTGCTGACAACATCAAGATGTTTGTTCTCGATGAAGCTGATGAAATGCTCTCCCGTGGTTTCAAGGACCAGgtatgcaaatatttctcagtgtttcaattccattctcgttatagtttaacttgaatctcactggtttctgggttttttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT