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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTGGGAACTTGGCTGCTCCTGTGGAAGAATGGACTGTAGGTGGGACTGCTCTCACAGCCTTGATGGATGTCGAGAGGAGACACGgtacagaaatataaatcaataaagcttactaagacacattttgaaatctagatattaaaaaatcagagttgatttcaacttgcag

Basic information

species Arabidopsis thaliana
transcript AT1G12000.1
intron # 13
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G12000.1 (Arabidopsis thaliana), 5'ss of exon 13
lower sequence: LOC_Os06g13810.1 (Oryza sativa), 5'ss of exon 13
GTTGGGAACTTGGCTGCTCCTGTGGAAGAATGGACTGTAGGTGGGACTGCTCTCACAGCCTTGATGGATGTCGAGAGGAGACACGgtacagaaatataaatcaataaagcttactaagacacattttgaaatctagatattaaaaaatcagagttgatt-tcaacttgcag-----------------
||||| ||| | ||||||||||||||||||||||| || ||||| |||||  | ||| | ||||||||||| |||||||| |||||||      || |  ||  |       |||  || |   || |  | |||  | | |  ||||     ||||   |  | |   |                  
GTTGGCAACCTCGCTGCTCCTGTGGAAGAATGGACCGTTGGTGGAACTGCATTGACATCGTTGATGGATGTTGAGAGGAGGCACGgtaggtttctacagttccgttgtttgcacttggaga---ttagctagctatgtttcattaaatttcttttgaccgtttattcaaatacctactatgtgattaa

upper sequence: AT1G12000.1 (Arabidopsis thaliana), 5'ss of exon 13
lower sequence: GLYMA07G39380.2 (Glycine max), 5'ss of exon 13
GTTGGGAACTTGGCTGCTCCTGTGGAAGAATGGACTGTAGGTGGGACTGCTCTCACAGCCTTGATGGATGTCGAGAGGAGACACGgtacagaaatataaatcaataaagct--tactaagacacatt----ttgaaatctagatattaaaaaatcagagttgatttcaacttgcag----------------------------------------------------------------------
||||| || ||   ||||||||| |||||||||||||| ||||| ||||| |||||  | |||||||| || ||||||||||| |||| | |  | | |   |  | ||||  | ||  | | || |     |    |||| || || |   || | |    ||||   ||    |                                                                      
GTTGGTAATTTATGTGCTCCTGTAGAAGAATGGACTGTTGGTGGAACTGCACTCACTTCATTGATGGACGTGGAGAGGAGACATGgtatatat-tgtgatctagcagagcttttgctttgccccaatatacctattttctaaatttttattcattacatgacattttgtctccatgttgttacatttatttgaatgtgctttctctgatgttctgctgttaatgaattgtgtgattttctttttag

upper sequence: AT1G12000.1 (Arabidopsis thaliana), 5'ss of exon 13
lower sequence: GLYMA17G01360.1 (Glycine max), 5'ss of exon 11
GTTGGGAACTTGGCTGCTCCTGTGGAAGAATGGACTGTAGGTGGGACTGCTCTCACAGCCTTGATGGATGTCGAGAGGAGACACGgtacagaa---atataaatcaataaagcttactaagacacattttg-aaatctagatattaaaaaatcagagttgatttcaac-ttgcag--------------------------------------------------------------
||||| || |||  ||||||||| |||||||||||||| ||||| ||||| |||||  | |||||||| || ||||||||||| ||||    |   ||   |     |        | || ||  |||||   ||| |  || | |  | || | | ||  | || |  |||                                                                 
GTTGGTAATTTGTGTGCTCCTGTAGAAGAATGGACTGTTGGTGGAACTGCACTCACTTCATTGATGGACGTGGAGAGGAGACATGgtatgtgatctattggagcttttgctttgccccaatacctattttctgaatgtttat-tcattacatgacattttgtctctatgttgttacatttatttgaatgtgctttctctgatgttctgctattaatgaattgtgattttctttttag

upper sequence: AT1G12000.1 (Arabidopsis thaliana), 5'ss of exon 13
lower sequence: GLYMA15G11890.1 (Glycine max), 5'ss of exon 13
GTTGGGAACTTGGCTGCTCCTGTGGAAGAATGGACTGTAGGTGGGACTGCTCTCACAGCCTTGATGGATGTCGAGAGGAGACACGgtacagaaatataaatcaataaagct-tactaagacacattttgaaatctagatattaaaaaatcagagttgatttcaac--ttgcag------------
||||  || ||   |||||| || |||||||||||||| ||||| ||||| |||||  |  |||||||||| |||||||| || |||||| |  |  |  |     |   | | ||    | ||||    | | |   |||||        |   |  | |  |   |||| |            
GTTGCCAATTTATGTGCTCCGGTAGAAGAATGGACTGTTGGTGGAACTGCACTCACCTCACTGATGGATGTGGAGAGGAGGCATGgtacacactttcatctttgagaccttatgctttaccccattgactattttctttattagtgttcatgcaatactctatagtgttgctgatgtattttgat

upper sequence: AT1G12000.1 (Arabidopsis thaliana), 5'ss of exon 13
lower sequence: GLYMA09G01050.1 (Glycine max), 5'ss of exon 13
GTTGGGAACTTGGCTGCTCCTGTGGAAGAATGGACTGTAGGTGGGACTGCTCTCACAGCCTTGATGGATGTCGAGAGGAGACACGgtaca------gaaatataaatcaataaagcttactaagaca--cattttgaaatctagatattaaaaaat-cagagttgatttcaacttgcag------
|||||||| ||   |||||| ||  ||||||||||||| ||||| ||||| |||||  |  |||||||||| |||||||| || ||||||      ||  | |    |  |     ||||          |||||   |  |||   | |    || |    |||  ||    | | |       
GTTGGGAATTTATGTGCTCCAGTAAAAGAATGGACTGTTGGTGGAACTGCACTCACCTCAATGATGGATGTGGAGAGGAGGCATGgtacacactttgatctttgggaccgtgtgctttaccccagtgactattttctgaattagtgttcatgcgatactctattgtgttgctgtagtattttgat

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|86088437|gb|DR384196.1|DR384196
EST:     TGTAGGTGGGACTGCTCTCACAACCTTGATGGATGTCGAGAGGAGACACG                         GTAAGTTCAAGCCTGTGATCAAGAAAGCAATGGTGGAACTTGAAG
genomic: TGTAGGTGGGACTGCTCTCACAGCCTTGATGGATGTCGAGAGGAGACACGgtacagaaat ... caacttgcagGTAAGTTCAAGCCTGTGATCAAGAAAGCAATGGTGGAACTTGAAG
EST: gi|86060419|gb|DR356176.1|DR356176
EST:     TGTAGGTGGGACTGCTCTCACAGCCTTGATGGATGTCGAGAGGAGACACG                         GTAAGTTCAAGCCTGTGATCAAGAAAGCAATGGTGGAACTTGAAG
genomic: TGTAGGTGGGACTGCTCTCACAGCCTTGATGGATGTCGAGAGGAGACACGgtacagaaat ... caacttgcagGTAAGTTCAAGCCTGTGATCAAGAAAGCAATGGTGGAACTTGAAG
EST: gi|164191865|gb|EL977965.1|EL977965
EST:     TGTAGGTGGGACTGCTCTCACAGCCTTGATGGATGTCGAGAGGAGACACG                         GTAAGTTCAAGCCTGTGATCAAGAAAGCAATGGTGGAA
genomic: TGTAGGTGGGACTGCTCTCACAGCCTTGATGGATGTCGAGAGGAGACACGgtacagaaat ... caacttgcagGTAAGTTCAAGCCTGTGATCAAGAAAGCAATGGTGGAA
EST: gi|125282197|gb|EL296282.1|EL296282
EST:     ACTGCTCTCACAGCCTTGATGGATGTCGAGAGGAGACACG                         GTAAGTTCAAGCCTGTGATCAAGAAAGCAATGGTGGAACTTGAAGGTGCAC
genomic: ACTGCTCTCACAGCCTTGATGGATGTCGAGAGGAGACACGgtacagaaat ... caacttgcagGTAAGTTCAAGCCTGTGATCAAGAAAGCAATGGTGGAACTTGAAGGTGCAC
EST: gi|124796242|gb|EH885921.1|EH885921
EST:     CCTTGATGGATGTCGAGAGGAGACACG                         GTAAGTTCAAGCCTGTGATCAAGAAAGCAATGGTGGAACTTGAAG
genomic: CCTTGATGGATGTCGAGAGGAGACACGgtacagaaat ... caacttgcagGTAAGTTCAAGCCTGTGATCAAGAAAGCAATGGTGGAACTTGAAG
EST: gi|124811301|gb|EH896167.1|EH896167
EST:     TGTAGGTGGGACTGCTCTCACAGCCTTGATGGATGTCGAGAGGAGACACG                         GTAAGTTCAAGCCTG
genomic: TGTAGGTGGGACTGCTCTCACAGCCTTGATGGATGTCGAGAGGAGACACGgtacagaaat ... caacttgcagGTAAGTTCAAGCCTG
EST: gi|86060418|gb|DR356175.1|DR356175
EST:     TGTAGGTGGGACTGCTCTCACAGCCTTGATGGATGTCGAGAGGAGACACG                         GTAAGTTCAAGCCTGTGATCAAGAAAGCAATGGTGGAACTTGAAG
genomic: TGTAGGTGGGACTGCTCTCACAGCCTTGATGGATGTCGAGAGGAGACACGgtacagaaat ... caacttgcagGTAAGTTCAAGCCTGTGATCAAGAAAGCAATGGTGGAACTTGAAG
EST: gi|124743697|gb|EH834859.1|EH834859
EST:     TGGATGTCGAGAGGAGACACG                         GTAAGTTCAAGCCTGTGATCAAGAAAGCAATGGTGGAACTTGAAG
genomic: TGGATGTCGAGAGGAGACACGgtacagaaat ... caacttgcagGTAAGTTCAAGCCTGTGATCAAGAAAGCAATGGTGGAACTTGAAG
EST: gi|125297233|gb|EL311318.1|EL311318
EST:     CTCTCACAGCCTTGATGGATGTCGAGAGGAGACACG                         GTAAGTTCAAGCCTGTGATCAAGTAAGCAATGGTGGAACTTGAAG
genomic: CTCTCACAGCCTTGATGGATGTCGAGAGGAGACACGgtacagaaat ... caacttgcagGTAAGTTCAAGCCTGTGATCAAGAAAGCAATGGTGGAACTTGAAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTGGGAACTTGGCTGCTCCTGTGGAAGAATGGACTGTAGGTGGGACTGCTCTCACAGCCTTGATGGATGTCGAGAGGAGACACGgtacagaaatataaatcaataaagcttactaagacacattttgaaatctagatattaaaaaatcagagttgatttcaacttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA