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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgctattaaatagaagatagtagtttaaaccattgttgtctgtttttgtaacgttttatttctctcgttagGATTTTGATTTCGAAGAGATTAATGAAGTTTTGAAACATTACCCACAATGTTATCACGGTGTTGACAAAGAAGGTAGACCTATTTACATTGAAAGGCTAG

Basic information

species Arabidopsis thaliana
transcript AT2G21520.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G21520.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os02g04020.1 (Oryza sativa), 3'ss of exon 4
------------gtatgctattaaatagaagatagtagtttaaaccattgttgtctgtttttgtaacgttttatttctctcgttagGATTTTGATTTCGAAGAGATTAATGAAGTTTTGAAACATTACCCACAATGTTATCACGGTGTTGACAAAGAAGGTAGACCTATTTACATTGAAAGGCTAG
            |  ||    || | |  |  | | | |||       | |      |   ||||||    ||  | ||||  ||||||||||||| | | ||| |  | |  ||| || || |||| || ||  ||||||| || ||||||||||| || |||||| |||| ||||||||||| |
gttagtgttcttgcttgtgcctataaaacaatttggattttgtttggctataaataatgcctgtaac----tacatttctctgtagGATTTTGATTACAATGAGTTAGACGCTGTTCTGCAATATTATCCTCACGGTTATCATGGAGTTGACAAAGACGGGAGACCTGTTTATATTGAAAGGCTTG

upper sequence: AT2G21520.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G073571_T03 (Zea mays), 3'ss of exon 3
--------------gtatgctattaaatagaagatagtagtttaaaccattgttgtct-------gtttttgtaac-gttttatttctctcgttagGATTTTGATTTCGAAGAGATTAATGAAGTTTTGAAACATTACCCACAATGTTATCACGGTGTTGACAAAGAAGGTAGACCTATTTACATTGAAAGGCTAG
               ||| |  ||    |     |  |  |||| |    |  |||||        |    | ||   |||||| | |  | | |||| || || | |   ||| | |     |||||| || |||| || ||  ||||||| || ||||||||||| || |||||| |||||||||||||||| |
gttattggctgagcttattcagtttttcactttgtt-tgatttatatggctcctgtcttaaaacaatgaccggaattattttatgtgttccat-agGACTTCGAATACACTGAGTTGAGCACCGTTTTGCAATATTATCCTCATGGTTATCATGGAGTTGACAAAGAGGGGAGACCTGTTTACATTGAAAGGCTTG
















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|124732641|gb|EH824043.1|EH824043
EST:     TGATATGATTCAATGGAGGAAAGAGTTTGGTACTGACACTATTAATTCAG                         GATTTTGATTTCGAAGAGATTAAT
genomic: TGATATGATTCAATGGAGGAAAGAGTTTGGTACTGACACTATTA-TTCAGgtatgctatt ... ctctcgttagGATTTTGATTTCGAAGAGATTAAT
EST: gi|124726173|gb|EH817575.1|EH817575
EST:     AATGGAGGAAAGAGTTTGGTACTGACACTATTATTCAG                         GATTTTGATTTCGAAGAGATTAATGAAGTTTTGAAACATTACCCACAATGT
genomic: AATGGAGGAAAGAGTTTGGTACTGACACTATTATTCAGgtatgctatt ... ctctcgttagGATTTTGATTTCGAAGAGATTAATGAAGTTTTGAAACATTACCCACAATGT
EST: gi|125132548|gb|EL174570.1|EL174570
EST:     CTGATATGATTCAATGGAGGAAAGAGTTTGGTACTGACACTATTATTCAG                         GATTTTGATTTCGAAGAGATTAATGAAGTTTTGAAACATTACCCACAA
genomic: CTGATATGATTCAATGGAGGAAAGAGTTTGGTACTGACACTATTATTCAGgtatgctatt ... ctctcgttagGATTTTGATTTCGAAGAGATTAATGAAGTTTTGAAACATTACCCACAA
EST: gi|124710536|gb|EH801938.1|EH801938
EST:     TCAATGGAGGAAAGAGTTTGGTACTGACACTATTATTCAG                         GATTTTGATTTCGAAGAGATTAATGAAGTTTTGAAACATTACCCACAATGT
genomic: TCAATGGAGGAAAGAGTTTGGTACTGACACTATTATTCAGgtatgctatt ... ctctcgttagGATTTTGATTTCGAAGAGATTAATGAAGTTTTGAAACATTACCCACAATGT
EST: gi|124892031|gb|EH970933.1|EH970933
EST:     CTGATATGATTCAATGGAGGAAAGAGTTTGGTACTGACACTATTATTCAG                         GATTTTAGAATTTCGAAGAGATTAATGAAGTTTTGAAACATTA
genomic: CTGATATGATTCAATGGAGGAAAGAGTTTGGTACTGACACTATTATTCAGgtatgctatt ... ctctcgttagGATTTT-GA-TTTCGAAGAGATTAATGAAGTTTTGAAACATTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atagtagtttaaaccattgttgtctgtttttgtaacgttttatttctctcgttagGATTTTGATTTCGAAGAGATTAATGAAGTTTTGAAACATTACCCACAATGTTATCACGGTGTTGACAAAGAAGGTAGACCTATTTACATTGAAAGGCTAG
                             ttgtaac  putative branch site (score: 2)
                                     ttttatttctctcgtt  CT-rich tract
                                     ttttatttct  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgctattaaatagaagatagtagtttaaaccattgttgtctgtttttgtaacgttttatttctctcgttagGATTTTGATTTCGAAGAGATTAATGAAGTTTTGAAACATTACCCACAATGTTATCACGGTGTTGACAAAGAAGGTAGACCTATTTACATTGAAAGGCTAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG