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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttggattctgatttatcgtactgtgttgtggtattgatgtgtgactactgatctttaagtttttttatgtatagGCTCGGTTCTTCTTTCAGCAGCTTATATCTGGAGTTAGCTATTGTCATGCAATG

Basic information

species Arabidopsis thaliana
transcript AT3G50500.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G50500.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os12g39630.1 (Oryza sativa), 3'ss of exon 3
-------------------------------------gtttggattctgatttatcgtactgtgt---tgtggtattgatgtgtgactactgatctttaagtttt--tttatgtatagGCTCGGTTCTTCTTTCAGCAGCTTATATCTGGAGTTAGCTATTGTCATGCAATG
                                      |||   |    | | || ||   || |   | | ||| || ||| |     || |   | || ||||  | ||  |  ||||||| |||||||| |||||||| ||||||||||||||||| || ||| | |||
gtcgatatcactgtcctgatacactatgatcatgtctatttctttcaccaataattgtgtagtatctgtattgtactgttgtattg--gctaactctgaacttttggtgtactttcagGCTCGTTTCTTCTTCCAGCAGCTGATATCTGGAGTTAGCTACTGCCATTCCATG

upper sequence: AT3G50500.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA01G39020.2 (Glycine max), 3'ss of exon 3
gtttggattctgatttatcgtactgtgttgtggtattgatgtgtgactactg--atctttaagtt-tttttatgt-atagGCTCGGTTCTTCTTTCAGCAGCTTATATCTGGAGTTAGCTATTGTCATGCAATG
|||   || |   ||  |     |   ||||| ||    | | |  |   ||  |   ||||    || | |||  | ||||||| ||||||||||| || || |||||||| || ||||||||||||||||||
gttcttatacaatttgtttacttttgcttgtgctagctctctatttcctgtgtaactattaacccattgtcatgccacagGCTCGTTTCTTCTTTCAACAACTCATATCTGGGGTCAGCTATTGTCATGCAATG

upper sequence: AT3G50500.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA11G06250.1 (Glycine max), 3'ss of exon 3
----------gtttggattctgatttatcgtactgtgttgtggtattgatgtgtgactactgatctttaagtttttttatgtatagGCTCGGTTCTTCTTTCAGCAGCTTATATCTGGAGTTAGCTATTGTCATGCAATG
            || | ||    ||| | || ||  |||    | ||  ||||| |||| | | |  |   | | |      | ||||||| ||||||||||| || || |||||||| || ||||| ||||||||||||
gttcttatacaatttgtttactttttcttgtgctaggtttctat-ttcctgtgtaactattaacccattgatatgtc-----acagGCTCGTTTCTTCTTTCAACAACTCATATCTGGGGTCAGCTACTGTCATGCAATG

upper sequence: AT3G50500.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA17G20610.4 (Glycine max), 3'ss of exon 3
------gtttggatt-ctgatttatcgtactgtgttgtggtattgatgtgtgacta-------ctgatctttaagtt-tttttatg-tatagGCTCGGTTCTTCTTTCAGCAGCTTATATCTGGAGTTAGCTATTGTCATGCAATG
       |||   ||  | | ||||  |||       || |||   | |||   ||       ||  | | |||    || ||||| |  ||||||| |||||||||||||| || |||||||| || |||||||| ||||| |||
gttcttatttaatttgtttacttattctacacctgaatgctataagtttgtacttattctacgctagtttgtaacccgttgttatgattcagGCTCGATTCTTCTTTCAGCAACTCATATCTGGGGTCAGCTATTGCCATGCTATG

upper sequence: AT3G50500.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv07s0197g00080.t01 (Vitis vinifera), 3'ss of exon 3
gtttggattctgatttatcg----tactgtgttgtggtattgatg-tgtgactactgatctttaagttttttta--tgtatagGCTCGGTTCTTCTTTCAGCAGCTTATATCTGGAGTTAGCTATTGTCATGCAATG
|||     |   |   || |    |  | | || | || ||  || | |  | |  | |  || |   |  ||   | |  ||||||| || |||||||| ||||||||||| || || ||||||||||||||||||
gttcttgattcaacccattgggttttttcttttctagtttttgtgctatttccatggtttcttgacactggttgcttctgcagGCTCGCTTTTTCTTTCAACAGCTTATATCAGGGGTCAGCTATTGTCATGCAATG

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|116422506|gb|EG465098.1|EG465098
EST:     GAGAACTTTATGAGCGGATTTGTAATGCCGGACGGTTTAGTGAAGATGAG                         GCTCGGTTCTTCTTTCAGCAGCTTATATCTGGATTTAGCTATTGTCATGCA
genomic: GAGAACTTTATGAGCGGATTTGTAATGCCGGACGGTTTAGTGAAGATGAGgtttggattc ... ttatgtatagGCTCGGTTCTTCTTTCAGCAGCTTATATCTGGAGTTAGCTATTGTCATGCA
EST: gi|164035085|gb|ES151173.1|ES151173
EST:     GGACGGTTTAGTGAAGATGAG                         GCTCGGTTCTTCTTTCAGCAGCTTATATCTGGAGTTAGCTATTGTCATGCA
genomic: GGACGGTTTAGTGAAGATGAGgtttggattc ... ttatgtatagGCTCGGTTCTTCTTTCAGCAGCTTATATCTGGAGTTAGCTATTGTCATGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

actgtgttgtggtattgatgtgtgactactgatctttaagtttttttatgtatagGCTCGGTTCTTCTTTCAGCAGCTTATATCTGGAGTTAGCTATTGTCATGCAATG
                          tactgat  putative branch site (score: 2)
                                        tttttttat  putative PPT
                               atctttaagttttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttggattctgatttatcgtactgtgttgtggtattgatgtgtgactactgatctttaagtttttttatgtatagGCTCGGTTCTTCTTTCAGCAGCTTATATCTGGAGTTAGCTATTGTCATGCAATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT