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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tattttagtgtgttttagacttagtgtattgttcaatagttatcattcaattgtcgatagcctagtttgttgtgttaatgtctattattcaaatctgcagGCTGAGAAGATAGGATTGGACTACATGGATGTCGAGGCCTTGAAGAAGCTTAACAAAAACAAGAAATTGGTGAAAAAACTAGCCAAAAAATATCATGCCT

Basic information

species Glycine max
transcript GLYMA12G31040.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA12G31040.2 (Glycine max), 3'ss of exon 2
lower sequence: AT2G27530.1 (Arabidopsis thaliana), 3'ss of exon 3
tattttagtgtgttttagacttagtgtattgttcaatagttatcattcaattgtcgatagcctagtttgttgtgttaatgtctattattcaaatctgcagGCTGAGAAGATAGGATTGGACTACATGGATGTCGAGGCCTTGAAGAAGCTTAACAAAAACAAGAAATTGGTGAAAAAACTAGCCAAAAAATATCATGCCT
         ||| || | |  |  | || | ||   |   | |  ||   ||     | |    | |||       | ||| |  | ||    |    |||| ||||| || ||| |     |||||||||| ||||| ||||| ||||||||||| ||||||||  | || || || || || ||    || ||||| |
---------gtgattgaaatctc-tatact-ttttgtgtatcttgtttggtttgaattggt---gattgacacaa-agtgtttgatgtttgttttgatagGCAGAGAAAATGGGACTTAGTAACATGGATGTTGAGGCTTTGAAAAAGCTTAACAAGAACAAGAAGCTTGTTAAGAAGCTTGCTAAGTCTTACCATGCTT

upper sequence: GLYMA12G31040.2 (Glycine max), 3'ss of exon 2
lower sequence: Vv06s0080g00400.t01 (Vitis vinifera), 3'ss of exon 5
-tattttagtgtgttttagacttagtgtattgttcaatagttatcattcaattgtcg-atagcctagtttgttgtgttaa--tgtctattattcaaatctgcagGCTGAGAAGATAGGATTGGACTACATGGATGTCGAGGCCTTGAAGAAGCTTAACAAAAACAAGAAATTGGTGAAAAAACTAGCCAAAAAATATCATGCCT
 ||  ||    | ||  ||  | ||  | |  || | |  |  | ||| | || | | ||    | |||  ||   | |   ||| | |||    ||  | ||||| || |||||||| ||||| ||||||||||| || |   | || ||||| ||||| ||||||||| |||| || ||||| ||||| ||||| |||||||
gtacctt----tattccagcttaagattttaattgagtcttatttatttattttttgcattagtttgttctttccttaaggttgtttgttaaattaaattacagGCAGAAAAGATAGGCTTGGAATACATGGATGTGGAAGGGCTAAAAAAGCTGAACAAGAACAAGAAACTGGTCAAGAAACTTGCCAAGAAATACCATGCCT
















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|31309902|gb|CD395105.1|CD395105
EST:     TGAAGATTTGTATGCTTGGAGATGCCCAACACGTTGAAGAG                         GCTGAGAAGATAGGATTGGACTACATGGATGTTGAGGCCTTGAAGAAGCTT
genomic: TGAAGATTTGTATGCTTGGAGATGCCCAACACGTTGAAGAGgtaataagct ... aaatctgcagGCTGAGAAGATAGGATTGGACTACATGGATGTCGAGGCCTTGAAGAAGCTT
EST: gi|207709585|gb|GD691599.1|GD691599
EST:     GCCCCAAGATGAAGATTTGTATGCTTGGAGATGCCCAACACGTTGAAGAG                         GCTGAGAAGATAGGATTGGACTACATGGATGTCGAGGCCTTGAAGAAG
genomic: GCCCCAAGATGAAGATTTGTATGCTTGGAGATGCCCAACACGTTGAAGAGgtaataagct ... aaatctgcagGCTGAGAAGATAGGATTGGACTACATGGATGTCGAGGCCTTGAAGAAG
EST: gi|151413165|gb|EV282973.1|EV282973
EST:     GCCCCAAGATGAAGATTTGTATGCTTGGAGATGCCCAACACGTTGAAGAG                         GCTGAGAAGATAGGATTGGACTACATGGATGTCGAGGCCTTGAAGAAGCTT
genomic: GCCCCAAGATGAAGATTTGTATGCTTGGAGATGCCCAACACGTTGAAGAGgtaataagct ... aaatctgcagGCTGAGAAGATAGGATTGGACTACATGGATGTCGAGGCCTTGAAGAAGCTT
EST: gi|207745327|gb|GD716311.1|GD716311
EST:     GCCCCAAGATGAAGATTTGTATGCTTGGAGATGCCCAACACGTTGAAGAG                         GCTGAGAAGATAGGATTGGACTACATGGATGTCGAGGCCTTGAAGAAGCTT
genomic: GCCCCAAGATGAAGATTTGTATGCTTGGAGATGCCCAACACGTTGAAGAGgtaataagct ... aaatctgcagGCTGAGAAGATAGGATTGGACTACATGGATGTCGAGGCCTTGAAGAAGCTT
EST: gi|192315373|gb|FK009637.1|FK009637
EST:     GCCCCAAGATGAAGATTTGTATGCTTGGAGATGCCCAACACGTTGAAGAG                         GCTGAGAAGATAGGATTGGACTACATGGATGTCGAGGCCTTGAAGAAGCTT
genomic: GCCCCAAGATGAAGATTTGTATGCTTGGAGATGCCCAACACGTTGAAGAGgtaataagct ... aaatctgcagGCTGAGAAGATAGGATTGGACTACATGGATGTCGAGGCCTTGAAGAAGCTT
EST: gi|207715980|gb|GD699372.1|GD699372
EST:     GCCCCAAGATGAAGATTTGTATGCTTGGAGATGCCCAACACGTTGAAGAG                         GCTGAGAAGATAGGATTGGACTACATGGATGTCGAGGCCTTGAAGAAGCTT
genomic: GCCCCAAGATGAAGATTTGTATGCTTGGAGATGCCCAACACGTTGAAGAGgtaataagct ... aaatctgcagGCTGAGAAGATAGGATTGGACTACATGGATGTCGAGGCCTTGAAGAAGCTT
EST: gi|207751720|gb|GD722621.1|GD722621
EST:     GCCCCAAGATGAAGATTTGTATGCTTGGAGATGCCCAACACGTTGAAGAG                         GCTGAGAAGATAGGATTGGACTACATGG
genomic: GCCCCAAGATGAAGATTTGTATGCTTGGAGATGCCCAACACGTTGAAGAGgtaataagct ... aaatctgcagGCTGAGAAGATAGGATTGGACTACATGG
EST: gi|19934524|gb|BQ079554.1|BQ079554
EST:     GCCCCAAGATGAAGATTTGTATGCTTGGAGATGCCCAACACGTTGAAGAG                         GCTGAGAAGATAGGATTGGACTACATGGATGTCGAGGCCTTGAAGAAGCTT
genomic: GCCCCAAGATGAAGATTTGTATGCTTGGAGATGCCCAACACGTTGAAGAGgtaataagct ... aaatctgcagGCTGAGAAGATAGGATTGGACTACATGGATGTCGAGGCCTTGAAGAAGCTT
EST: gi|298169144|gb|HO020504.1|HO020504
EST:     GCCCCAAGATGAAGATTTGTATGCTTGGAGATGCCCAACATGTTGAAGAG                         GCTGAGAAGATAGGATTGGACTACATGGATGTTGAGGCCTTGAAGAAGCTT
genomic: GCCCCAAGATGAAGATTTGTATGCTTGGAGATGCCCAACACGTTGAAGAGgtaataagct ... aaatctgcagGCTGAGAAGATAGGATTGGACTACATGGATGTCGAGGCCTTGAAGAAGCTT
EST: gi|254329947|gb|GR839500.1|GR839500
EST:     GAAGATTTGTATGCTTGGAGATGCCCAACACGTTGAAGAG                         GCTGAGAAGATAGGATTGGACTACATGGATGTCGAGGCCTTGAAGAAGCTT
genomic: GAAGATTTGTATGCTTGGAGATGCCCAACACGTTGAAGAGgtaataagct ... aaatctgcagGCTGAGAAGATAGGATTGGACTACATGGATGTCGAGGCCTTGAAGAAGCTT
EST: gi|120495150|gb|EH223317.1|EH223317
EST:     GCCCCAAGATGAAGATTTGTATGCTTGGAGATGCCCAACACGTTGAAGAG                         GCTGAGAAGATAGGATTGGACTACATGGATGTCGAGGCCTTGAAGAAGCTT
genomic: GCCCCAAGATGAAGATTTGTATGCTTGGAGATGCCCAACACGTTGAAGAGgtaataagct ... aaatctgcagGCTGAGAAGATAGGATTGGACTACATGGATGTCGAGGCCTTGAAGAAGCTT
EST: gi|192315372|gb|FK009636.1|FK009636
EST:     GCCCCAAGATGAAGATTTGTATGCTTGGAGATGCCCAACACGTTGAAGAG                         GCTGAGAAGATAGGATTGGACTACATGGATGTCGAGGCCTTGAAGAAGCTT
genomic: GCCCCAAGATGAAGATTTGTATGCTTGGAGATGCCCAACACGTTGAAGAGgtaataagct ... aaatctgcagGCTGAGAAGATAGGATTGGACTACATGGATGTCGAGGCCTTGAAGAAGCTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcaattgtcgatagcctagtttgttgtgttaatgtctattattcaaatctgcagGCTGAGAAGATAGGATTGGACTACATGGATGTCGAGGCCTTGAAGAAGCTTAACAAAAACAAGAAATTGGTGAAAAAACTAGCCAAAAAATATCATGCCT
                           tgttaat  putative branch site (score: 3)
                             ttaatgtctattatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tattttagtgtgttttagacttagtgtattgttcaatagttatcattcaattgtcgatagcctagtttgttgtgttaatgtctattattcaaatctgcagGCTGAGAAGATAGGATTGGACTACATGGATGTCGAGGCCTTGAAGAAGCTTAACAAAAACAAGAAATTGGTGAAAAAACTAGCCAAAAAATATCATGCCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA