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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATTGAAGCTTGATTTGTCTTTGATGGAGCATTATGAACGTCACTGTCCTCCTCCTGAAAGGAGGTTTAATTGCTTGATTCCTCCTCCTCCAGGGTATAAGgtgtgttatttctctagctttgttgatatgatcagtgtcttgacatattttgaagtttttttctatgtgaatgtgtctag

Basic information

species Arabidopsis thaliana
transcript AT3G23300.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G23300.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GRMZM2G067764_T02 (Zea mays), 5'ss of exon 3
ATTGAAGCTTGATTTGTCTTTGATGGAGCATTATGAACGTCACTGTCCTCCTCCTGAAAGGAGGTTTAATTGCTTGATTCCTCCTCCTCCAGGGTATAAGgt------------gtgttatttctcta---gctttgttgatatgatcagtgtcttgacatattttgaagtttttttctatg---tgaatgtgtctag--
  ||||||| |||||     |||||||||| |||||  | || || ||||| ||||||||| | |||||||||||||||||||| || |  || ||||||||               |  | |||| |   | | | ||  |   || ||  | |  || | ||||||  |  |   ||  |   || |  ||| | |  
GCTGAAGCTGGATTTAAACCTGATGGAGCACTATGAGAGGCATTGCCCTCCACCTGAAAGGCGTTTTAATTGCTTGATTCCTCCACCACATGGCTATAAGgtcactactgatttaaatcttctctcaaagtgttcttttattccaattaggttttgtacttgttttgagttcatggactgagcattgcacctgttttgag

upper sequence: AT3G23300.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GRMZM2G107629_T03 (Zea mays), 5'ss of exon 4
ATTGAAGCTTGATTTGTCTTTGATGGAGCATTATGAACGTCACTGTCCTCCTCCTGAAAGGAGGTTTAATTGCTTGATTCCTCCTCCTCCAGGGTATAAGgtgtgttatttctctagctttgttgatatgatcagtgtcttgacatattttgaagtttttttctatgtgaatgtgtctag----------------------
  ||||||| |||||     |||||||||| |||||  | || || ||||| ||||||||| | |||||||||||||||||||| || |  || ||||||||    || |  |||| || |  |   |   |   | | ||     | || ||  ||   |   || |   |  |  |                        
GCTGAAGCTGGATTTAAACCTGATGGAGCACTATGAGAGGCATTGCCCTCCACCTGAAAGGCGTTTTAATTGCTTGATTCCTCCACCACATGGCTATAAGgt-cactactgatctaactcttctctcaaagt-gttcttttattccaattagatcttgcatgagatatatcttcgcttgacttgagttcatagactgactat

upper sequence: AT3G23300.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA19G34890.2 (Glycine max), 5'ss of exon 3
ATTGAAGCTTGATTTGTCTTTGATGGAGCATTATGAACGTCACTGTCCTCCTCCTGAAAGGAGGTTTAATTGCTTGATTCCTCCTCCTCCAGGGTATAAGgtg---tgttatt-tctctagctttgttgatatgatcagt--gtcttgacatattttgaagtttttttctatgtgaatgtgtctag-----------------------------------
||||||||||||||| |||||||||||||| |||||  | ||||| ||  | ||||| ||||| |  ||||| || |||||||||||||||||||| ||||||   | | ||| ||   || ||  ||||||| || ||   |   | | | | ||   ||| | ||   || |   | ||  ||                                    
ATTGAAGCTTGATTTATCTTTGATGGAGCACTATGAGAGACACTGCCCAACACCTGATAGGAGATACAATTGTTTAATTCCTCCTCCTCCAGGGTACAAGgtgacatttcattctccagagattgcttgatattattagatggaactaagacaattcatagtgtattgaaattttcttttgcttaagcatttaatttgttgtgttgttcttgataacatag

upper sequence: AT3G23300.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA03G32130.2 (Glycine max), 5'ss of exon 2
ATTGAAGCTTGATTTGTCTTTGATGGAGCATTATGAACGTCACTGTCCTCCTCCTGAAAGGAGGTTTAATTGCTTGATTCCTCCTCCTCCAGGGTATAAGgtg---tgttatttctctagctttgtt--------gatatgatcagtgtc-ttgacatattttgaagtttttttctatgtgaatgtgtctag---------------------------
||||||||||||||| |||||||||||||| |||||  | ||||| ||  | ||||| ||||| || || || || |||||||||||||||||||| ||||||   | | | |   |  |  ||| |        |||   |  |   |  || | |   | || |   ||||  | ||   | || | |||                           
ATTGAAGCTTGATTTATCTTTGATGGAGCACTATGAGAGACACTGCCCAACACCTGATAGGAGATTCAACTGTTTAATTCCTCCTCCTCCAGGGTACAAGgtgaaatttcactctccagggattgcttagtattagatggaactaagatagttcatagtgtatggaaaattttcttttgcttaagtatttagtttgttgtgttgttcttgataatatag

upper sequence: AT3G23300.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA02G00550.1 (Glycine max), 5'ss of exon 2
ATTGAAGCTTGATTTGTCTTTGATGGAGCATTATGAACGTCACTGTCCTCCTCCTGAAAGGAGGTTTAATTGCTTGATTCCTCCTCCTCCAGGGTATAAGgtgtgttatttctctagctttgttgatatgatcagtgtcttgacatattttgaagtttttttctatgtgaatgtgtctag---------------------------------
| ||||||| ||| | ||||||||||| || |||||  | || ||||||||| | |||||||| |||||||| ||||||||||||||  |||| || |||||     || |  | ||  | | ||  ||  |||   ||   ||||||  | |    |   | | | | | | |||| |                                  
ACTGAAGCTGGATCTTTCTTTGATGGAACACTATGAGAGACATTGTCCTCCTTCAGAAAGGAGATTTAATTGTTTGATTCCTCCTCCGGCAGGATACAAGgtaaagaatatgccgagactcgatgtgatcttcaacttc--aacatatcctcattaatacatttgtataattttgtcaatgctaaaacaattgttgtttctatggtgtttcag

upper sequence: AT3G23300.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA20G35120.4 (Glycine max), 5'ss of exon 3
ATTGAAGCTTGATTTGTCTTTGATGGAGCATTATGAACGTCACTGTCCTCCTCCTGAAAGGAGGTTTAATTGCTTGATTCCTCCTCCTCCAGGGTATAAGgtgtgttatttctctagctttgttgatatgatcagtgtcttgacatattttga---agtttttttctatgtgaatgtgtctag
  ||||||| ||  ||||| |||||||||| |||||| | || ||||||||| | |||||| |||  ||||||||||||||||||||  |||| || ||||||    ||||    ||  |   ||  ||  ||| | |  |  |  ||  |||   | || || | ||| | ||||| |  ||
GATGAAGCTGGACCTGTCTGTGATGGAGCACTATGAAAGACATTGTCCTCCTGCGGAAAGGCGGTACAATTGCTTGATTCCTCCTCCATCAGGATACAAGgtgaaa-atttgctaagagtatatgtgatcttcaatatactctctgatactgatgtaattgttgtttatat-aatgt-tgcag

upper sequence: AT3G23300.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA10G32470.1 (Glycine max), 5'ss of exon 3
ATTGAAGCTTGATTTGTCTTTGATGGAGCATTATGAACGTCACTGTCCTCCTCCTGAAAGGAGGTTTAATTGCTTGATTCCTCCTCCTCCAGGGTATAAGgtgtgttatttctctagctttgttgatatgatcagtgtcttgacatattttgaagtttttttctatgtgaatgtgtctag-----------------
  ||||||| ||  ||||| |||||||||| |||||  | || ||||||||| | |||||| |||  ||||||||||||||||||||  | || || ||||||    ||||    ||  |   ||  ||  |||         |  ||    | || || || ||    ||  | | | |                 
GATGAAGCTGGACCTGTCTGTGATGGAGCACTATGAGAGACATTGTCCTCCTGCAGAAAGGCGGTACAATTGCTTGATTCCTCCTCCATCTGGATACAAGgtgaaa-atttgctaagagtatatgtgatcttcaacacaccctctgatacatatgtattattttagtccaacatttgttgtttctataatgttgcag

upper sequence: AT3G23300.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA10G04370.1 (Glycine max), 5'ss of exon 2
ATTGAAGCTTGATTTGTCTTTGATGGAGCATTATGAACGTCACTGTCCTCCTCCTGAAAGGAGGTTTAATTGCTTGATTCCTCCTCCTCCAGGGTATAAGgtgtgtt--atttctctag-----------ctttgttgatatgatcagtgtcttgacatattttgaagtttttt---tctatg----tgaatgtgtctag---------------------------
||||||||||||| || |||| |||||||| || ||||| ||||| ||    |||||  || | | |||||| |||||||| |||||||||||||| ||||||| |    |||||||||           ||| | ||  |  || |  || |  | | |||| |||||||| |     ||      ||| ||| |   |                           
ATTGAAGCTTGATCTGACTTTAATGGAGCACTACGAACGGCACTGCCCAATGCCTGAGCGGCGCTATAATTGTTTGATTCCCCCTCCTCCAGGGTACAAGgtgtctctcttttctctaggcattgcttctcttagatggaactatgaaagt-taaataaatttggaagttttctgtgcttacagctttgagtgtcttatgctgttcttgatgataaattgattatag

upper sequence: AT3G23300.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA13G18630.1 (Glycine max), 5'ss of exon 2
ATTGAAGCTTGATTTGTCTTTGATGGAGCATTATGAACGTCACTGTCCTCCTCCTGAAAGGAGGTTTAATTGCTTGATTCCTCCTCCTCCAGGGTATAAGgtgtgttatttctct---agctttgttgatat--gatcagtgtcttgacatattttgaagtttttttctatgtgaatgtgtctag--------------------------------------------
||||||||||||| || | ||||||||||| ||||| || || || ||    ||||| ||| | | |||||| |||||||| |||||||||||||| ||||||  |   || |||    || ||| |  | |  ||| |  ||| ||| |   | ||||  ||   |  || ||    | | | |                                            
ATTGAAGCTTGATCTGACGTTGATGGAGCACTATGAGCGACATTGCCCGATGCCTGAGAGGCGCTATAATTGTTTGATTCCCCCTCCTCCAGGGTACAAGgtggctctcttttcttcaggcgttgcttctcttagatgaaagtcatgaaac--tgtgaaagttaaataaatttggtaattttttgtgcttacagctttgagtgtcttatgctgttcttgatgataatag

upper sequence: AT3G23300.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: Vv07s0005g03630.t01 (Vitis vinifera), 5'ss of exon 2
ATTGAAGCTTGATTTGTCTTTGATGGAGCATTATGAACGTCACTGTCCTCCTCCTGAAAGGAGGTTTAATTGCTTGATTCCTCCTCCTCCAGGGTATAAGgtgtgttatttctctagctttgttgatatgatcagtgtcttgacatattttgaagtttttttctatgtgaatgtgtctag-------------------------------
 |||||| | |||||||||||||||||||| |||||  | || || || || ||||||||| | | |||||||||||||||||||||  ||||||| |||||| ||   | ||  || ||| |||| || ||  |   |  |  |  || |   |||||  | |||    ||||  |||                                
GTTGAAGTTGGATTTGTCTTTGATGGAGCACTATGAGAGACATTGCCCACCACCTGAAAGGCGCTATAATTGCTTGATTCCTCCTCCAGCAGGGTACAAGgtgagtctgtgcttaagtttt-ttgaaat-attgggaccaaggaagtttatattgttttcat-tatccacatgtacctaagatgattctcttctgctgtgggcggtaacag

upper sequence: AT3G23300.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: Vv05s0049g01180.t01 (Vitis vinifera), 5'ss of exon 3
ATTGAAGCTTGATTTGTCTTTGATGGAGCATTATGAACGTCACTGTCCTCCTCCTGAAAGGAGGTTTAATTGCTTGATTCCTCCTCCTCCAGGGTATAAGgtgtgttatttctctagctttgttgatatgatcagtgtcttgacatattttgaagtttttttctatgtgaatgtgtctag
||||||||| ||| | |||||||||||||| |||||| | || || |||| |||||| ||| |||  ||||||||||||||||| ||  ||||||| |||||| |    | |   |||||  | |   | |  || || ||||  | || | |  ||| | | | | |       |  ||
ATTGAAGCTGGATCTTTCTTTGATGGAGCACTATGAAAGACATTGCCCTCTTCCTGAGAGGCGGTACAATTGCTTGATTCCTCCACCAGCAGGGTACAAGgtgagaatgtgcgtaagcttaatag---taacaagggtgttgaagttttcttatttttgtgtgtgtctcttcccttgcag

upper sequence: AT3G23300.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: PP1S322_38V6.1 (Physcomitrella patens), 5'ss of exon 2
ATTGAAGCTTGATTTGTCTTTGATGGAGCATTATGAACGTCACTGTCCTCCTCCTGAAAGGAGGTTTAATTGCTTGATTCCTCCTCCTCCAGGGTATAAGgtg-tgtta-------tttctctagctttgt----tgatatgatcagtgtcttgacatattttgaagtttttttctatgtgaatgtgtctag-------------------------------------------------------------------
| |||||||  ||||||| |||||||||||||||||||| || ||||| ||   | |     |  | |||||  | || || || ||||||   || |||||  ||| |        ||||  | ||||||    | || || |  || |   |  |  |   || |   |    ||| | |||  ||| |                                                                    
ACTGAAGCTGAATTTGTCGTTGATGGAGCATTATGAACGGCATTGTCCGCCGAATCATCTCCGCCTGAATTGTCTCATCCCACCCCCTCCAAATTACAAGgtactgtgaacatccccttctaaaactttgtccatttatgtgcttggt-ttacgggaagtcaagacgaaataaggtat-tcaatcagtccacaatgggcacccaaccagcagctgtcatctcactcttgaattgatctattgtacaccattgagggaag

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|125071109|gb|EL136278.1|EL136278
EST:     CCTCCTCCAGGGTATAAG                         ATTCCAATCAAGTGGCCGAAAAGCAGAGACGAAGTTTGGAAAGTGAACATT
genomic: CCTCCTCCAGGGTATAAGgtgtgttatt ... atgtgtctagATTCCAATCAAGTGGCCGAAAAGCAGAGACGAAGTTTGGAAAGTGAACATT




















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATTGAAGCTTGATTTGTCTTTGATGGAGCATTATGAACGTCACTGTCCTCCTCCTGAAAGGAGGTTTAATTGCTTGATTCCTCCTCCTCCAGGGTATAAGgtgtgttatttctctagctttgttgatatgatcagtgtcttgacatattttgaagtttttttctatgtgaatgtgtctag

- - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTCCTC