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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGATGCATGGGACATGGCTGCTGAAATCTGTCTTTCTCAGCTTCCCCAACTTGTTCTGGACCCAAGCACAGAGTTCCAGgtttgttttgttttgtatagtttcctgcaattgtatacgacggcgcttgttttgcttataaaacgtgttcctatcctttttctag

Basic information

species Arabidopsis thaliana
transcript AT3G08850.1
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G08850.1 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: LOC_Os11g01872.1 (Oryza sativa), 5'ss of exon 8
GGATGCATGGGACATGGCTGCTGAAATCTGTCTTTCTCAGCTTCCCCAACTTGTTCTGGACCCAAGCACAGAGTTCCAGgtttgttttgttttgtatagtttcctgcaattgtatacgacggcgcttgttttgcttataaaacgtgttcctatcctttttctag------------------------------------------------
||||||||||||||||||||| || ||||| |||||| ||||||| ||| |  ||   || || |   ||||||| |||||    ||     | | |  |||  |  |||  | ||  ||   |    |     || |     |  ||  |||  | |||                                                    
GGATGCATGGGACATGGCTGCAGAGATCTGCCTTTCTAAGCTTCCTCAATTAATTGCTGATCCTAATGCAGAGTTTCAGgtgctattaaccgtctttgctttttttgaatgatctaatactttggacatcaacattttgttg-gcattgttatgttgtttgagaattatcacttcagtaccatcactttgttcatttccttactcaaaccag

upper sequence: AT3G08850.1 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: GRMZM2G048067_T02 (Zea mays), 5'ss of exon 9
GGATGCATGGGACATGGCTGCTGAAATCTGTCTTTCTCAGCTTCCCCAACTTGTTCTGGACCCAAGCACAGAGTTCCAGgtttgttttgttttgtatagtttc------ctgcaattgtatacgacggcgcttgttttgcttataaa---acgtgttcc--tatcctttttctag------------------
|||||||||||||||||||||||| || || |||||  ||||||| ||  |  ||   || ||||   ||||||| ||||||    || |  | ||   ||||      |  || | || |  |  ||   |  |||  | | | ||   | || || |   ||   |  | |                    
GGATGCATGGGACATGGCTGCTGAGATTTGCCTTTCCAAGCTTCCTCAGTTAATTGCTGATCCAAATGCAGAGTTTCAGgttctacttatcatttagcatttcaatgaacatcagtagtttttgctggtattgttttgacatttgaatacaagtatttcagcattgctaatttcattctctacttcaaaccag

upper sequence: AT3G08850.1 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: GLYMA09G41510.1 (Glycine max), 5'ss of exon 9
GGATGCATGGGACATGGCTGCTGAAATCTGTCTTTCTCAGCTTCCCCAACTTGTTCTGGACCCAAGCACAGAGTTCCAGgttt----gttttgttttgtatagtttcc--tgcaattgtatacgacggcgcttgttttgcttataaaacgtgttcctatcctttt--tctag-----------------------------------------------------------------------------
||||||||||||||||||||||||  |||| || ||||| |||||     | |||  ||| || |   | || || ||||| |     |||| |||||||     ||   ||||| |   | | |          ||   | ||||||  ||         || |  | | |                                                                             
GGATGCATGGGACATGGCTGCTGAGCTCTGCCTCTCTCAACTTCCGTCTTTAGTTGAGGATCCTAATGCTGAATTTCAGgtatctggatttttttttgtaataactctgatgcaagttctttctaaaattgaatattaaataataaaaattggctaaggtattctggtttggcaaggaataatagtaatacgatggactattttataagttttgagcttacctgatgaagtatgtggttgttctttcag

upper sequence: AT3G08850.1 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: GLYMA18G44210.1 (Glycine max), 5'ss of exon 9
GGATGCATGGGACATGGCTGCTGAAATCTGTCTTTCTCAGCTTCCCCAACTTGTTCTGGACCCAAGCACAGAGTTCCAGgt-------ttgttttgttttgtatagtttcctgcaa--ttgtatacgacggcgcttgttttgcttataaaacgtgttcctatcctttttctag------------------------------------------------------------------------------
||||||||||||||||||||||||  |||| || ||||| |||||     | |||  ||| || |   | || || |||||       || |||| || |    | | |  || ||  || | |  ||    |  | ||        ||||   | |    |  | |   | |                                                                              
GGATGCATGGGACATGGCTGCTGAGCTCTGCCTCTCTCAACTTCCATCTTTAGTTGAGGATCCTAATTCTGAATTTCAGgtgtctggattatttttttgtaataactctgatgtaaagttctttctgaaattgaatattaaataataaaaattggctaaggtattctggtttggcaaggaataatagtaatactaaggaatattttataagttttgagcttacctgaagaagtatgtggttgttctttcag

upper sequence: AT3G08850.1 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: Vv08s0058g00890.t01 (Vitis vinifera), 5'ss of exon 9
GGATGCATGGGACATGGCTGCTGAAATCTGTCTTTCTCAGCTTCCCCAACTTGTTCTGGACCCAAGCACAGAGTTCCAGgtttgttttgttttgtata-gtttcctgcaattgtatacgacggcgcttgt-tttgctta------taaaacgtgttcctatcctttttctag-----------------------------------------------------------------------
|||||||||||||||||||||||||||||| ||||||||||||     | | |||   || || |   ||||||| |||||     ||   ||   |  || |  | ||||| |  |   |     |||  |||||||       | ||||| |    ||   |   |  |                                                                        
GGATGCATGGGACATGGCTGCTGAAATCTGCCTTTCTCAGCTTAAGTCATTGGTTGATGATCCCAATGCAGAGTTTCAGgtgcacatttccttaagtttgtgttatacaattatgaatctcttattttgggtttgcttgggtacttgaaacgagcatttagagtacctagaagaatgttgtgctggttttatcatctcatatgcccagttacgacattgatgtctatacaatgtttttttcag

upper sequence: AT3G08850.1 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: PP1S199_73V6.1 (Physcomitrella patens), 5'ss of exon 9
GGATGCATGGGACATGGCTGCTGAAATCTGTCTTTCTCAGCTTCCCCAACTTGTTCTGGACCCAAGCACAGAGTTCCAGgtttgtt-ttgttttgtatagtttcctgcaattgtatacgacggcgcttgttttgcttataaa-acgtgttcctatcctttttctag-------------
| |||||||||| |||||||||||||| |||||||| ||| | ||   | | ||    || ||||   | ||||| ||||| | |  |||  ||| |    |  |    || |  |     ||   |      || | | || |  |||   |  |   | ||                
GCATGCATGGGATATGGCTGCTGAAATTTGTCTTTCACAGTTGCCTGCATTGGTGGATGATCCAAATGCTGAGTTTCAGgtatctgattgacttgcaatcctcacatgtatcggttgaacaggttatgaacgagcctgtgaatatatgtgtgtgccacatctcagtgtacataatttca

upper sequence: AT3G08850.1 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: PP1S124_156V6.1 (Physcomitrella patens), 5'ss of exon 9
GGATGCATGGGACATGGCTGCTGAAATCTGTCTTTCTCAGCTTCCCCAACTTGTTCTGGACCCAAGCACAGAGTTCCAGgtttgttttgttttgtatagtttcctgcaattgtatacgacggcgcttgttttgctta------------taaaacgtgttcctatcctttttctag----
| | |||||||| |||||||||||||| |||||||| ||||| ||   | |  |   ||| ||||  |  || || || || ||||     |  |  |  ||       ||   ||  |  ||   | ||||| |||            ||| ||| || |   |  |||    |     
GCACGCATGGGATATGGCTGCTGAAATTTGTCTTTCGCAGCTGCCTGCATTGCTAGAGGATCCAACTATTGAATTTCATgtatgttgaaggtcttgcaacttttacatgtttagtattattgcaaatattttgtttagcgggttgtgaataagacg-gtgcaagtgttttcatcaatatg

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|116411083|gb|EG453675.1|EG453675
EST:     GTCTTTCTCAGCTTCCCCAACTTGTTCTGGACCCAAGCACAGAGTTCCAG                         CCAAGTCCGTTTTTTACTGAGCAACTGACAGCTTTTGAGGTGTGGCTTGAT
genomic: GTCTTTCTCAGCTTCCCCAACTTGTTCTGGACCCAAGCACAGAGTTCCAGgtttgttttg ... ctttttctagCCAAGTCCGTTTTTTACTGAGCAACTGACAGCTTTTGAGGTGTGGCTTGAT
EST: gi|116411080|gb|EG453672.1|EG453672
EST:     GTCTTTCTCAGCTTCCCCAACTTGTTCTGGACCCAAGCACAGAGTTCCAG                         CCAAGTCCGTTTTTTACTGAGCAACTGACAGCTTTTGAGGTGTGGCTTGAT
genomic: GTCTTTCTCAGCTTCCCCAACTTGTTCTGGACCCAAGCACAGAGTTCCAGgtttgttttg ... ctttttctagCCAAGTCCGTTTTTTACTGAGCAACTGACAGCTTTTGAGGTGTGGCTTGAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGATGCATGGGACATGGCTGCTGAAATCTGTCTTTCTCAGCTTCCCCAACTTGTTCTGGACCCAAGCACAGAGTTCCAGgtttgttttgttttgtatagtttcctgcaattgtatacgacggcgcttgttttgcttataaaacgtgttcctatcctttttctag

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