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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TACTAAACCAATCACCAAACTCGAAGATTGTGAAAGCTTCTTCAACTTCTTTAGTCCTCCAGAAGTTCCGGATGAAGATGAAGATATCGACGAGGAAAGAgtaagataacgattgttagaaaaacctgtcatcatttagttaatgtatttagtaactctttctcgttctttgatgcag

Basic information

species Arabidopsis thaliana
transcript AT4G26110.2
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G26110.2 (Arabidopsis thaliana), 5'ss of exon 8
lower sequence: GRMZM2G121186_T01 (Zea mays), 5'ss of exon 8
TACTAAACCAATCACCAAACTCGAAGATTGTGAAAGCTTCTTCAACTTCTTTAGTCCTCCAGAAGTTCCGGATGAAGATGAAGATATCGACGAGGAAAGAgtaagataacgattgttagaaaaacctgtcatcatttagttaatgtatttagtaactctttctcgttctttgatgcag------------
 || ||||| ||||| |||  |||||||||||| ||||||||||||||||| ||||| ||  |||| || ||||| || || || || || ||||| | |||||| |      |  |  |    | | | ||  || |       ||       |   ||   | |   |||||                
CACGAAACCTATCACAAAAACCGAAGATTGTGAGAGCTTCTTCAACTTCTTCAGTCCACCTCAAGTCCCTGATGACGACGAGGAAATTGATGAGGACACAgtaagtttttagcttatgtacctgctt-ttatggttaaacatgcatacacgaacataattgaacatgacttgatattcacttttcaatag

upper sequence: AT4G26110.2 (Arabidopsis thaliana), 5'ss of exon 8
lower sequence: GRMZM2G176707_T01 (Zea mays), 5'ss of exon 8
TACTAAACCAATCACCAAACTCGAAGATTGTGAAAGCTTCTTCAACTTCTTTAGTCCTCCAGAAGTTCCGGATGAAGATGAAGATATCGACGAGGAAAGAgtaagataacgattgttagaaaaacctgtcatcatttagttaatgtatttagtaactctttctcgttctttgatgcag------------
 |||||||| ||||| |||   ||||||||||| ||||||||||||||||| ||||| ||  |||| || ||||| ||||| || || || ||||| | |||||| | |   || |  | |    || | ||  || |       ||       |   ||   | |  |||| |                
CACTAAACCTATCACAAAAACTGAAGATTGTGAGAGCTTCTTCAACTTCTTCAGTCCACCTCAAGTCCCTGATGATGATGAGGAAATTGATGAGGATATAgtaagtttatc-ttatatgtacctgcttttatggttaaacatgcatacacgaacatcattgaacttgatttggttttcccttttcaatag

upper sequence: AT4G26110.2 (Arabidopsis thaliana), 5'ss of exon 8
lower sequence: GLYMA17G06170.4 (Glycine max), 5'ss of exon 8
TACTAAACCAATCACCAAACTCGAAGATTGTGAAAGCTTCTTCAACTTCTTTAGTCCTCCAGAAGTTCCGGATGAAGATGAAGATATCGACGAGGAAAGAgtaa-gataacgattgttagaaaaacctgtcatcatttagttaatgtatttagtaactctt-tctcgttctttgatgcag--------------------------------------
| |||||||||| ||||||   ||| ||||||||||||||||||| ||||| |  || ||  ||||||| || || |||||||| ||||| || ||    |||  ||||  |||| ||||| ||    ||    ||  |  ||| ||| || || | | || |   ||| ||   |||||                                      
TGCTAAACCAATTACCAAAACTGAAAATTGTGAAAGCTTCTTCAATTTCTTCAACCCCCCGCAAGTTCCTGAAGATGATGAAGACATCGATGAAGATGTGgtattgatattgatt-ttagataacagagtagaaataaaaataa-gtaatttgtgatttttatactgttgttatttgcagaactacttttttttagctttgattaatttttttaacag

upper sequence: AT4G26110.2 (Arabidopsis thaliana), 5'ss of exon 8
lower sequence: GLYMA13G16500.2 (Glycine max), 5'ss of exon 8
TACTAAACCAATCACCAAACTCGAAGATTGTGAAAGCTTCTTCAACTTCTTTAGTCCTCCAGAAGTTCCGGATGAAGATGAAGATATCGACGAGGAAAGAgtaa-gataacgattgttagaaaaacctgtcatcatttag--ttaatgtatttagtaactctttctcgttctttgatgcag--------------------------------------------
| |||||||||| ||||||   ||| ||||||||||||||||||| ||||| |  || ||  ||||||| || || |||||||| || || || ||    |||  ||||  |||| |     ||||   | |  | | |   | | |  ||||      | | |   | |  |   |||||                                            
TGCTAAACCAATTACCAAAACTGAAAATTGTGAAAGCTTCTTCAATTTCTTCAACCCACCGCAAGTTCCTGAAGATGATGAAGACATTGATGAAGATGCGgtattgatattgattttagattaaacagattagaaataaaaatcagtaaattttaattttttatactgctgctatttgcagaactttttttttttctgctttgattgattcatttttttaaacag

upper sequence: AT4G26110.2 (Arabidopsis thaliana), 5'ss of exon 8
lower sequence: Vv11s0016g02050.t01 (Vitis vinifera), 5'ss of exon 9
TACTAAACCAATCACCAAACTCGAAGATTGTGAAAGCTTCTTCAACTTCTTTAGTCCTCCAGAAGTTCCGGATGAAGATGAAGATATCGACGAGGAAAGAgtaaga----taacgat-tgttagaaaaacctgtcatcatttagttaatg---tatttagtaactctttctcgttctttgatgcag----
| | || |||||||| |||   |||  ||||||||| || ||||| ||||||||||| ||| ||||||| || || ||||||||||| || || || |  ||||||    | ||  |   ||   | ||    | |     ||  | ||    ||||  |||  | ||||   ||   || |        
TGCCAAGCCAATCACAAAAACAGAAAGTTGTGAAAGTTTTTTCAATTTCTTTAGTCCACCACAAGTTCCTGAGGATGATGAAGATATTGATGAAGACACTgtaagaacagtgacagtgcattccgataaatgattaaatgctaactgattatttattctgtatttatttcattttacatgttttgaacag

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|164190917|gb|ES069066.1|ES069066
EST:     TAGTCCTCCAGAAGTTCCGGATGAAGATAGAAGATATCGACGAGGAAAGA                         GCTGAGGATCTTCAAAACCTGATGGAACAAGATTATGACAT
genomic: TAGTCCTCCAGAAGTTCCGGATGAAGAT-GAAGATATCGACGAGGAAAGAgtaagataac ... tttgatgcagGCTGAGGATCTTCAAAACCTGATGGAACAAGATTATGACAT
EST: gi|124972455|gb|EL046148.1|EL046148
EST:     AAGTTCCGGATGAAGATGAAGATATCGACGAGGAAAGA                         GCTGAGGATCTTCAAAACCTGATGGAACAAAGATTATGACATCGGATCTAC
genomic: AAGTTCCGGATGAAGATGAAGATATCGACGAGGAAAGAgtaagataac ... tttgatgcagGCTGAGGATCTTCAAAACCTGATGGAACAA-GATTATGACATCGGATCTAC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TACTAAACCAATCACCAAACTCGAAGATTGTGAAAGCTTCTTCAACTTCTTTAGTCCTCCAGAAGTTCCGGATGAAGATGAAGATATCGACGAGGAAAGAgtaagataacgattgttagaaaaacctgtcatcatttagttaatgtatttagtaactctttctcgttctttgatgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA