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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggactaaacatatttaagtcaccactctaaccagtactattattgtgtctcatcagatttcactggttcttctaagttgcaacttatgattgaattgcagGTTGATATTGCAATTCCCGAAGTTTTCGTTGGTGGGTTGCTAGGTTCCATGCTTATATTTGTTTTTAGTGCTTGGGCCTGTTCTGCTGTTGGCAGAACTG

Basic information

species Glycine max
transcript GLYMA08G24120.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G24120.1 (Glycine max), 3'ss of exon 10
lower sequence: LOC_Os02g33490.1 (Oryza sativa), 3'ss of exon 11
ggactaaacatatttaagtcaccactctaaccagtactattattgtgtctcatcagatttcactggttcttctaagttgcaacttatgattgaattgcagGTTGATATTGCAATTCCCGAAGTTTTCGTTGGTGGGTTGCTAGGTTCCATGCTTATATTTGTTTTTAGTGCTTGGGCCTGTTCTGCTGTTGGCAGAACTG
              ||  | |  |||   ||  | |  ||  ||   |    |  | ||  |     | |    | | |     | | || | |||||||||||| || ||||| || || ||||| |||||||| || || ||||| |||||||||||  | |||||||| ||||| ||||||||||||||||||||||
-------------gtattttattacttagacacgcaaaatacttactttctgt--gcttataacatatat----aatggtcttgtgtaat-ggattgcagGTTGACATAGCAATCCCAGAGGTTTTTGTTGGTGGTTTACTTGGTTCAATGCTTATATTCCTGTTTAGTGCATGGGCTTGTTCTGCTGTTGGCAGAACTG

upper sequence: GLYMA08G24120.1 (Glycine max), 3'ss of exon 10
lower sequence: AT1G78920.2 (Arabidopsis thaliana), 3'ss of exon 11
ggactaaacatatttaagtcaccactctaaccagtactattattgtgtctcatcagatttcactggttcttctaagttgcaacttatgattgaattgcagGTTGATATTGCAATTCCCGAAGTTTTCGTTGGTGGGTTGCTAGGTTCCATGCTTATATTTGTTTTTAGTGCTTGGGCCTGTTCTGCTGTTGGCAGAACTG
                 ||    | |       | |   ||  ||| |       ||| |        ||||| |    || | |  |||  |||  |||||||||||||| || || ||||| ||||||||||| ||  | ||| |||||||||| ||  | |||||||||||||| ||  | || |||||  ||||||
-----------------gtag--atttcgttatgcatcgttgctgtattc---tcgatgttgagacaacttctcatactcatcctcggataaaat--cagGTTGATATTGCTATCCCAGAAGTGTTCGTTGGTGGATTATTGGGTGCCATGCTTATTTTCCTCTTTAGTGCTTGGGCATGCGCGGCAGTTGGTCGAACTG

upper sequence: GLYMA08G24120.1 (Glycine max), 3'ss of exon 10
lower sequence: AT1G16780.1 (Arabidopsis thaliana), 3'ss of exon 12
ggactaaacatatttaagtcaccactctaaccagtactattattgtgtctcatcagatttcactggttcttctaagttgcaacttatgattgaattgcagGTTGATATTGCAATTCCCGAAGTTTTCGTTGGTGGGTTGCTAGGTTCCATGCTTATATTTGTTTTTAGTGCTTGGGCCTGTTCTGCTGTTGGCAGAACTG
       |||| ||| | ||     | ||  | |   | |  |  | |  |||   | |    |  |  | || | |     | |   ||  ||   |||||||||||||| || || ||||| ||| |||| |||||  ||||| |||||||||||||  | ||||| |||||||| ||| | || |||||  ||||||
-----gtacattttttactctttggtgtattctg---tttcctcttattccattccactcgcatactcatcctgattcttgtcctcacatctaa--acagGTTGATATTGCGATCCCAGAAGTCTTCATTGGAGGGTTATTAGGTGCCATGCTTATATTCCTGTTTAGCGCTTGGGCTTGTGCAGCAGTTGGTCGAACTG

upper sequence: GLYMA08G24120.1 (Glycine max), 3'ss of exon 10
lower sequence: Vv09s0054g00700.t01 (Vitis vinifera), 3'ss of exon 11
ggactaaacatatttaagtcaccactctaaccagtactattattgtgtctcatcagatttcactggttcttctaagttgcaacttatgattgaattgcagGTTGATATTGCAATTCCCGAAGTTTTCGTTGGTGGGTTGCTAGGTTCCATGCTTATATTTGTTTTTAGTGCTTGGGCCTGTTCTGCTGTTGGCAGAACTG
          ||  |    ||| ||| | | |       | || |||| |        ||| ||   ||       ||  |  |||  ||    || |||||||||||||| ||||| |||||||| |||||||||||| | || || |||||||| ||  | |||||||| ||||| |||||||| |||||| | ||||
---------gtaagtgga-cactactttgatc----tcttcatcgtgttt-----acattctctaactcactgcttttttatgtta--atcaccttacagGTTGATATTGCCATTCCAGAAGTTTTTGTTGGTGGGTTGTTGGGCTCTATGCTTATTTTCCTATTTAGTGCATGGGCATGTTCTGCAGTTGGCCGGACTG

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|58022630|gb|CX709371.1|CX709371
EST:     GTGCTTATATGGATGAGGTTTCTTCATTTGCTCATGAACCTTTTAAACAG                         GTTGATATTGCAATTCCCGAAGTTTTCGTTGGTGGGTTGCTAGGTTCCATG
genomic: GTGCTTATATGGATGAGGTTTCTTCATTTGCTCATGAACCTTTTAAACAGgtgcgcagaa ... tgaattgcagGTTGATATTGCAATTCCCGAAGTTTTCGTTGGTGGGTTGCTAGGTTCCATG
EST: gi|120529405|gb|EH257539.1|EH257539
EST:     GTGCTTATATGGATGAGGTTTCTTCATTTGCTCATGAACCTGTTAAACAG                         GTGGATATTGCAATTCCCGAAGTTTTCGTTGGTGGGTTGCTAGGTTCCATG
genomic: GTGCTTATATGGATGAGGTTTCTTCATTTGCTCATGAACCTTTTAAACAGgtgcgcagaa ... tgaattgcagGTTGATATTGCAATTCCCGAAGTTTTCGTTGGTGGGTTGCTAGGTTCCATG
EST: gi|58022340|gb|CX709081.1|CX709081
EST:     GTGCTTATATGGATGAGGTTTCTTCATTTGCTCATGAACCTTTTAAACAG                         GTTGATATTGCAATTCCCGAAGTTTTCGTTGGTGGGTTGCTAGGTTCCATG
genomic: GTGCTTATATGGATGAGGTTTCTTCATTTGCTCATGAACCTTTTAAACAGgtgcgcagaa ... tgaattgcagGTTGATATTGCAATTCCCGAAGTTTTCGTTGGTGGGTTGCTAGGTTCCATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtctcatcagatttcactggttcttctaagttgcaacttatgattgaattgcagGTTGATATTGCAATTCCCGAAGTTTTCGTTGGTGGGTTGCTAGGTTCCATGCTTATATTTGTTTTTAGTGCTTGGGCCTGTTCTGCTGTTGGCAGAACTG
                                      ttatgatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggactaaacatatttaagtcaccactctaaccagtactattattgtgtctcatcagatttcactggttcttctaagttgcaacttatgattgaattgcagGTTGATATTGCAATTCCCGAAGTTTTCGTTGGTGGGTTGCTAGGTTCCATGCTTATATTTGTTTTTAGTGCTTGGGCCTGTTCTGCTGTTGGCAGAACTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT