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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATGTTGAAGCATGCAAAAGGAACAACCACTCTCGCTTTTATCTTCAAAGGTGGTGTTATGGTCGCTGCTGATTCTCGGGCTAGCATGGGAGGATATATCTgtatgttctcttttatcactttacttttagttttgtttgcagactttgacgatgtttagctgtgagctctcttaagaattcctccaaaaatatgcatcct...

Basic information

species Arabidopsis thaliana
transcript AT1G13060.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G13060.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA04G37030.3 (Glycine max), 5'ss of exon 3
ATGTTGAAGCATGCAAAAGGAACAACCACTCTCGCTTTTATCTTCAAAGGTGGTGTTATGGTCGCTGCTGATTCTCGGGCTAGCATGGGAGGATATATCTgtatgttctcttt----tatcactttactttt-agttttgtttgcagactttgacgatgtttagctgtgagctctcttaagaattcctcca----aaaat-atgcatcct---------------------------------------------------
||| ||||||  || || || || || ||||| |||||||| || ||||  ||||||||||| |||||||||||||| |||||||||||||||||||| |||  ||  |  ||    | | | || | |||| | | || ||||     || |  || |   || | |  | | |  |   |||| || ||    ||||| |||  |  |                                                   
ATGGTGAAGCCCGCGAAGGGTACTACAACTCTTGCTTTTATATTTAAAGAGGGTGTTATGGTAGCTGCTGATTCTCGAGCTAGCATGGGAGGATATATATgtgagtatttgttagattttaatttcatttttcactgttctttgttcctttggctgaggcagagttttttgtttttgtgctaattgctgcaaattaaaatgatgggttttatctatttgcattgtgtttgatcttgaattctgactgttggctgtctccag

upper sequence: AT1G13060.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA06G17960.1 (Glycine max), 5'ss of exon 3
ATGTTGAAGCATGCAAAAGGAACAACCACTCTCGCTTTTATCTTCAAAGGTGGTGTTATGGTCGCTGCTGATTCTCGGGCTAGCATGGGAGGATATATCTgtatgttctcttttatc---actttacttttagttttgtttgcagactttgacgatgtttagctgtgagctctcttaagaattcc-tccaaaaatatgcatcct---------------------------------
||| ||||||  || || || || || ||||| |||||||| || || |  ||||||||||| |||||||||||||| |||||||||||||||||||| |||  ||  |  || ||    |||||| ||| | | || ||||     || |   ||| | || | | |  |  |||   | ||   || |    |     || |                                 
ATGGTGAAGCCCGCGAAGGGTACTACGACTCTTGCTTTTATATTTAAGGAGGGTGTTATGGTAGCTGCTGATTCTCGAGCTAGCATGGGAGGATATATATgtgagtgtttgttaattttaactttaatttcactattctttgttcctttggtgaatgctgagtttttatgttacttgttacttttatctatttgtggttgtctttgttcttgaattttgagtgttggctgtctccag

upper sequence: AT1G13060.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: Vv01s0010g02900.t01 (Vitis vinifera), 5'ss of exon 3
ATGTTGAAGCATGCAAAAGGAACAACCACTCTCGCTTTTATCTTCAAAGGTGGTGTTATGGTCGCTGCTGATTCTCGGGCTAGCATGGGAGGATATATCTgtatgttctcttttatcactttacttttagttttgtttgcag-actttgacgatgtttagctgtgagctctcttaagaattcctccaaaaatatgcatcct
||| ||||||  ||||| |||||||| ||||| || || || || || |  ||||| ||||| |||||||||||||| ||||||||||||||||||||||||| ||| | |||| |   |      ||  |||||        |  || |   ||||||| | |        |||      | |  |||  | | |||   
ATGGTGAAGCCAGCAAAGGGAACAACAACTCTTGCCTTCATTTTTAAGGAGGGTGTAATGGTTGCTGCTGATTCTCGTGCTAGCATGGGAGGATATATCTgtaagtttttttttgttcttacttggttcattttgaggaagatatatttatactgtttagat-tagttaggattagtggaccatataaacctgttcatgaa

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|124913898|gb|EH987772.1|EH987772
EST:     TGGTGTTATGGTCGCTGCTGATTCTCGGGCTAGCATGGGAGGATATATCT                         CCTCACAATCTGTGAAGAAGA
genomic: TGGTGTTATGGTCGCTGCTGATTCTCGGGCTAGCATGGGAGGATATATCTgtatgttctc ... ccacattcagCCTCACAATCTGTGAAGAAGA
EST: gi|116463327|gb|EG505919.1|EG505919
EST:     GCTGATTTCTCGGGCTAGCATGAGAAGGATATATCT                         CCTCACAATCTGTGAAGAAGATTATTGAAATCAATCCTTATATGCTCGGTA
genomic: GCTGA-TTCTCGGGCTAGCATG-GGAGGATATATCTgtatgttctc ... ccacattcagCCTCACAATCTGTGAAGAAGATTATTGAAATCAATCCTTATATGCTCGGTA
EST: gi|116444339|gb|EG486931.1|EG486931
EST:     TGGTGTTATGGTCGCTGCTGATTCTCGGGCTAGCATGGGAGGATATATCT                         CCTCACAATCTGTGAAGAAGATTATTGAAATCAATCCTTATATGCTCGGTA
genomic: TGGTGTTATGGTCGCTGCTGATTCTCGGGCTAGCATGGGAGGATATATCTgtatgttctc ... ccacattcagCCTCACAATCTGTGAAGAAGATTATTGAAATCAATCCTTATATGCTCGGTA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATGTTGAAGCATGCAAAAGGAACAACCACTCTCGCTTTTATCTTCAAAGGTGGTGTTATGGTCGCTGCTGATTCTCGGGCTAGCATGGGAGGATATATCTgtatgttctcttttatcactttacttttagttttgtttgcagactttgacgatgtttagctgtgagctctcttaagaattcctccaaaaatatgcatcct

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tctctttt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - agctctct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaaata