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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGAGCCTGATACCGTTCAATGGGCTGGTCGGATCCAGTTTCATCGTATCAACATTAAGCATGATTCTAGACTTGAAGGACTGATCAAGATGGCAGATCTGgtatttgttcttcgtttcttcttagtaaatcgttaatgtgaaaatgttgaatgtgaagactcagatctgattcgttatgtgaaatcgaatttcgaattgtggatgtcttgtttaattaatctgttgttgttgttttggattttgcag

Basic information

species Arabidopsis thaliana
transcript AT1G08200.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G08200.1 (Arabidopsis thaliana), 5'ss of exon 1
lower sequence: Vv06s0061g01120.t01 (Vitis vinifera), 5'ss of exon 1
TGAGCCTGATACCGTTCAATGGGCTGGTCGGATCCAGTTTCATCGTATCAACATTAAGCATGATTCTAGACTTGAAGGACTGATCAAGATGGCAGATCTGgtatttgttcttcgtttcttcttagtaaatcgttaatgtgaaaatgttgaatgtgaagactcagatct-gattcgttatgtgaaatcgaatttcgaattgtggatgtcttgtttaattaatctgttgttgttgttttggattttgcag
 |||||   |||   ||  ||| | | ||| || |||||||| || |||||||| ||||| ||||| || || |||||||| |||||||||||||||||||  || ||| |||     ||  || |   || |  ||      || ||| || |     ||  ||| | || ||  | ||||   |    ||| | | ||  |                                             
CGAGCCGTCTACGCATCCTTGGTCCGATCGCATTCAGTTTCACCGCATCAACATCAAGCACGATTCGAGGCTCGAAGGACTCATCAAGATGGCAGATCTGg--ttcgttattccccaatttctatt---tcttgcatt---ggattttgcattt-----cttggattttgaatcaatttgtggcgttttctttggtaatgcag---------------------------------------------

upper sequence: AT1G08200.1 (Arabidopsis thaliana), 5'ss of exon 1
lower sequence: Vv03s0017g00680.t01 (Vitis vinifera), 5'ss of exon 1
TGAGCCTGATACCGTTCAATGGGCTGGTCGGATCCAGTTTCATCGTATCAACATTAAGCATGATTCTAGACTTGAAGGACTGATCAAGATGGCAGATCTGgtatttg--ttcttcgtttcttcttagtaaatcgttaatgtgaaaatgttgaatgtgaagactcagatctgattcgttatgtgaaatcgaatttcgaattgtggatgtcttgtttaattaatctgttgttgttgttttggattttgcag
 ||||| | | |   ||  ||| | | ||| || |||||||| || |||||||| ||||| ||||| || || |||||||| ||||||||||||||||||||   ||  | | ||||||||  ||  |  || |  | | ||||  | ||| ||             | ||  ||  | ||||   |    ||| | | ||  |                                             
CGAGCCGGCTGCACATCCTTGGTCCGATCGCATTCAGTTTCACCGCATCAACATCAAGCACGATTCGAGGCTCGAAGGACTCATCAAGATGGCAGATCTGgttcgtgattccctcgtttctatttcttgcattgg-attttgaatttcttgtat-------------tttgtatcaatttgtggcgttttctttggtaatgcag---------------------------------------------
















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|124744244|gb|EH835406.1|EH835406
EST:     ACATTAAGCATGATTCTAGACTTGAAGGACTGATCAAGATGGCAGATCTG                         ACGATAAATCTAG
genomic: ACATTAAGCATGATTCTAGACTTGAAGGACTGATCAAGATGGCAGATCTGgtatttgttc ... gattttgcagACGATAAATCTAG
EST: gi|124937914|gb|EL014596.1|EL014596
EST:     TGAAGGACTGATCAAGATGGCAGATCTG                         ACGATAAATCTAGCTGCGATCTGTACTCCAGCAGATTACAATACGCGTCCT
genomic: TGAAGGACTGATCAAGATGGCAGATCTGgtatttgttc ... gattttgcagACGATAAATCTAGCTGCGATCTGTACTCCAGCAGATTACAATACGCGTCCT
EST: gi|116456216|gb|EG498808.1|EG498808
EST:     ACATTAAGCATGATTCTAGACTTGAAGGACTGATCAAGATGGCAGATCTG                         ACGATAAATCTAGCTGCGATCTGTACTCCAGCAGATTACAATACGCGTCCT
genomic: ACATTAAGCATGATTCTAGACTTGAAGGACTGATCAAGATGGCAGATCTGgtatttgttc ... gattttgcagACGATAAATCTAGCTGCGATCTGTACTCCAGCAGATTACAATACGCGTCCT
EST: gi|116456222|gb|EG498814.1|EG498814
EST:     ACATTAAGCATGATTCTAGACTTGAAGGACTGATCAAGATGGCAGATCTG                         ACGATAAATCTAGCTGCGATCTGTACTCCAGCAGATTACAATACGCGTCCC
genomic: ACATTAAGCATGATTCTAGACTTGAAGGACTGATCAAGATGGCAGATCTGgtatttgttc ... gattttgcagACGATAAATCTAGCTGCGATCTGTACTCCAGCAGATTACAATACGCGTCCT
EST: gi|116456221|gb|EG498813.1|EG498813
EST:     ACATTAAGCATGATTCTAGACTTGAAGGACTGATCAAGATGGCAGATCTG                         ACGATAAATCTAGCTGCGATCTGTACTCCAGCAGATTACAATACGCGTCCC
genomic: ACATTAAGCATGATTCTAGACTTGAAGGACTGATCAAGATGGCAGATCTGgtatttgttc ... gattttgcagACGATAAATCTAGCTGCGATCTGTACTCCAGCAGATTACAATACGCGTCCT
EST: gi|125222386|gb|EL236471.1|EL236471
EST:     ATTCTAGACTTGAAGGACTGATCAAGATGGCAGATCTG                         ACGATAAATCTAGCTGCGATCTGTACTCCAGCAGATTACAATACGCGTCC
genomic: ATTCTAGACTTGAAGGACTGATCAAGATGGCAGATCTGgtatttgttc ... gattttgcagACGATAAATCTAGCTGCGATCTGTACTCCAGCAGATTACAATACGCGTCC
EST: gi|116456217|gb|EG498809.1|EG498809
EST:     ACATTAAGCATGATTCTAGACTTGAAGGACTGATCAAGATGGCAGATCTG                         ACGATAAATCTAGCTGCGATCTGTACTCCAGCAGATTACAATACGCGTCCT
genomic: ACATTAAGCATGATTCTAGACTTGAAGGACTGATCAAGATGGCAGATCTGgtatttgttc ... gattttgcagACGATAAATCTAGCTGCGATCTGTACTCCAGCAGATTACAATACGCGTCCT
EST: gi|164118847|gb|ES043443.1|ES043443
EST:     GATGGCAGATCTG                         ACGATAAATCTAGCTGCGATCTGTACTCCCGCAGATTACAATACGCGTCCT
genomic: GATGGCAGATCTGgtatttgttc ... gattttgcagACGATAAATCTAGCTGCGATCTGTACTCCAGCAGATTACAATACGCGTCCT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGAGCCTGATACCGTTCAATGGGCTGGTCGGATCCAGTTTCATCGTATCAACATTAAGCATGATTCTAGACTTGAAGGACTGATCAAGATGGCAGATCTGgtatttgttcttcgtttcttcttagtaaatcgttaatgtgaaaatgttgaatgtgaagactcagatctgattcgttatgtgaaatcgaatttcgaattgtggatgtcttgtttaattaatctgttgttgttgttttggattttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT