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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agcaattgctgtatgttgttttctccagttttactgcagtagtgaaatttaagttgcattggtgttgctcacttttattattattgttatttttgttcagGACTACATAGACAGCATGGAAGGTGCAACCTTGTCTGGCAGACAAGCTTCGGCCTATATCTGTGATGCAGGGGAAGGATTAGTGGCATTGCGGAAGAAGC

Basic information

species Glycine max
transcript GLYMA20G37170.2
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G37170.1 (Glycine max), 3'ss of exon 13
lower sequence: AT3G04870.1 (Arabidopsis thaliana), 3'ss of exon 12
--agcaattgctgtatgttgttttct--ccagttttactgcagt----agtgaaa------------tttaagttgcattggtgttgc--------tcacttttattattattgttatttttgtt-cagGACTACATAGACAGCATGGAAGGTGCAACCTTGTCTGGCAGACAAGCTTCGGCCTATATCTGTGATGCAGGGGAAGGATTAGTGGCATTGCGGAAGAAGC
  | || ||      |  | | ||    |||| |   |   ||     | || ||            |  || |||  |  | |            ||| |   | | || ||  |    ||||| ||||| |||||||| || |||||||| ||||| || || || |||||||||||| | || ||||||||||| || |||| | |||  |   |    |||||||
gtaacatttttcacttactatctttcagccagatccccgatagctacaaatgcaagcaagaacagcctccaaattgtgtctgagaaatccgaaagatcagtgagaattttgtttctggacttgttacagGATTACATAGATAGTATGGAAGGAGCAACATTATCAGGGAGACAAGCTTCGTCATACATCTGTGATGCTGGTGAAGAACTAGCAGAGCTAAACAAGAAGC
















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|193649916|gb|FK594505.1|FK594505
EST:     TGGATCTTACACAAAGCAG                         GACTACATAGACAGCATGGAAGGTGCAACCTTGTCTGGCAGACAAGCTTCG
genomic: TGGATCTTACACAAAGCAGgtagcacctt ... ttttgttcagGACTACATAGACAGCATGGAAGGTGCAACCTTGTCTGGCAGACAAGCTTCG
EST: gi|209724168|gb|BW659702.1|BW659702
EST:     AAAAGACGCCAGTGAAGAATTTCTTTCTTGATGGATCTTACACAAAGCAG                         GACTACATAGACAGCATGGAAGGTGCAACCTTGTCTGGCAGACAAGCTTCG
genomic: AAAAGACGCCAGTGAAGAATTTCTTTCTTGCTGGATCTTACACAAAGCAGgtagcacctt ... ttttgttcagGACTACATAGACAGCATGGAAGGTGCAACCTTGTCTGGCAGACAAGCTTCG
EST: gi|209716761|gb|BW682243.1|BW682243
EST:     AAAAGACGCCAGTGAAGAATTTCTTTCTTGCTGGATCTTACACAAAGCAG                         GACTACATAGACAGCATGGAAGGTGCAACCTTGTCTGGCAGACAAGCTTCG
genomic: AAAAGACGCCAGTGAAGAATTTCTTTCTTGCTGGATCTTACACAAAGCAGgtagcacctt ... ttttgttcagGACTACATAGACAGCATGGAAGGTGCAACCTTGTCTGGCAGACAAGCTTCG
EST: gi|10236984|gb|BE805872.1|BE805872
EST:     AAAAGACGCCAGTGAAGAATTTCTTTCTTGCTGGATCTTACACAAAGCAG                         GACTACATAGACAGCATGGAAGGTGCAACCTTGTCTGGC
genomic: AAAAGACGCCAGTGAAGAATTTCTTTCTTGCTGGATCTTACACAAAGCAGgtagcacctt ... ttttgttcagGACTACATAGACAGCATGGAAGGTGCAACCTTGTCTGGC
EST: gi|120496009|gb|EH224176.1|EH224176
EST:     AAAAGACGCCAGTGAAGAATTTCTTTCTTGCTGGATCTTACACAAAGCAG                         GACTACATAGACAGCATGGAAGGTGCAACCTTGTCTGGCAGACAAGCTTCG
genomic: AAAAGACGCCAGTGAAGAATTTCTTTCTTGCTGGATCTTACACAAAGCAGgtagcacctt ... ttttgttcagGACTACATAGACAGCATGGAAGGTGCAACCTTGTCTGGCAGACAAGCTTCG
EST: gi|213602074|gb|DB981924.1|DB981924
EST:     AAAAGACGCCAGTGAAGAATTTCTTTCTTGCTGGATCTTACACAAAGCAG                         GACTACATAGACAGCATGGAAGGTGCAACCTTGTCTGGCAGACAAGCTTCG
genomic: AAAAGACGCCAGTGAAGAATTTCTTTCTTGCTGGATCTTACACAAAGCAGgtagcacctt ... ttttgttcagGACTACATAGACAGCATGGAAGGTGCAACCTTGTCTGGCAGACAAGCTTCG
EST: gi|214007199|gb|DB986191.1|DB986191
EST:     AAAAGACGCCAGTGAAGAATTTCTTTCTTGCTGGATCTTACACAAAGCAG                         GACTACATAGACAGCATGGAAGGTGCAACCTTGTCTGGCAGACAAGCTTCG
genomic: AAAAGACGCCAGTGAAGAATTTCTTTCTTGCTGGATCTTACACAAAGCAGgtagcacctt ... ttttgttcagGACTACATAGACAGCATGGAAGGTGCAACCTTGTCTGGCAGACAAGCTTCG
EST: gi|254340372|gb|GR858497.1|GR858497
EST:     AAAAGACGCCAGTGAAGAATTTCTTTCTTGCTGGATCTTACACAAAGCAG                         GACTACATAGACAGCATGGAAGGTGCAACCTTGTCTGGCAGACAAGCTTCG
genomic: AAAAGACGCCAGTGAAGAATTTCTTTCTTGCTGGATCTTACACAAAGCAGgtagcacctt ... ttttgttcagGACTACATAGACAGCATGGAAGGTGCAACCTTGTCTGGCAGACAAGCTTCG
EST: gi|207805117|gb|GD780670.1|GD780670
EST:     AAAAGACGCCAGTGAAGAATTTCTTTCTTGCTGGATCTTACACAAAGCAG                         GACTACATAGACAGCATGGAAGGTGCAACCTTGTCTGGCAGACAAGCTTCG
genomic: AAAAGACGCCAGTGAAGAATTTCTTTCTTGCTGGATCTTACACAAAGCAGgtagcacctt ... ttttgttcagGACTACATAGACAGCATGGAAGGTGCAACCTTGTCTGGCAGACAAGCTTCG
EST: gi|23064112|gb|BU578885.1|BU578885
EST:     AAAAGACGCCAGTGAAGAATTTCTTTCTTGCTGGATCTTACACAAAGCAG                         GACTACATAGACAGCATGGAAGGTGCAACCTTGTCTGGCAGACAAGCTTCG
genomic: AAAAGACGCCAGTGAAGAATTTCTTTCTTGCTGGATCTTACACAAAGCAGgtagcacctt ... ttttgttcagGACTACATAGACAGCATGGAAGGTGCAACCTTGTCTGGCAGACAAGCTTCG
EST: gi|15662004|gb|BI699375.1|BI699375
EST:     AAAAGACGCCAGTGAAGAATTTCTTTCTTGCTGGATCTTACACAAAGCAG                         GACTACATAGACAGCATGGAAGGTGCAACCTTGTCTGGCAGACAAGCTTCG
genomic: AAAAGACGCCAGTGAAGAATTTCTTTCTTGCTGGATCTTACACAAAGCAGgtagcacctt ... ttttgttcagGACTACATAGACAGCATGGAAGGTGCAACCTTGTCTGGCAGACAAGCTTCG
EST: gi|10234566|gb|BE803454.1|BE803454
EST:     AAAAGACGCCAGTGAAGAATTTCTTTCTTGCTGGATCTTACACAAAGCAG                         GACTACATAGACAGCATGGAAGGTGCAACCTTGTCTGGCAGACAAGCTTCG
genomic: AAAAGACGCCAGTGAAGAATTTCTTTCTTGCTGGATCTTACACAAAGCAGgtagcacctt ... ttttgttcagGACTACATAGACAGCATGGAAGGTGCAACCTTGTCTGGCAGACAAGCTTCG
EST: gi|151398068|gb|EV267946.1|EV267946
EST:     AAAAGACGCCAGTGAAGAATTTCTTTCTTGCTGGATCTTACACAAAGCAG                         GACTACATAGACAGCATGGAAGGTGCAACCTTGTCTGGCAGACAAGCTTCG
genomic: AAAAGACGCCAGTGAAGAATTTCTTTCTTGCTGGATCTTACACAAAGCAGgtagcacctt ... ttttgttcagGACTACATAGACAGCATGGAAGGTGCAACCTTGTCTGGCAGACAAGCTTCG
EST: gi|209707946|gb|BW657041.1|BW657041
EST:     AAAAGACGCCAGTGAAGAATTTCTTTCTTGCTGGATCTTACACAAAGCAG                         GACTACATAGACAGCATGGAAGGTGCAACCTTGTCTGGCAGACAAGCTTCG
genomic: AAAAGACGCCAGTGAAGAATTTCTTTCTTGCTGGATCTTACACAAAGCAGgtagcacctt ... ttttgttcagGACTACATAGACAGCATGGAAGGTGCAACCTTGTCTGGCAGACAAGCTTCG
EST: gi|209703398|gb|BW676225.1|BW676225
EST:     AAAAGACGCCAGTGAAGAATTTCTTTCTTGCTGGATCTTACACAAAGCAG                         GACTACATAGACAGCATGGAAGGTGCAACCTTGTCTGGCAGACAAGCTTCG
genomic: AAAAGACGCCAGTGAAGAATTTCTTTCTTGCTGGATCTTACACAAAGCAGgtagcacctt ... ttttgttcagGACTACATAGACAGCATGGAAGGTGCAACCTTGTCTGGCAGACAAGCTTCG
EST: gi|120495894|gb|EH224061.1|EH224061
EST:     AAAAGACGCCAGTGAAGAATTTCTTTCTTGCTGGATCTTACACAAAGCAG                         GACTACATAGACAGCATGGAAGGTGCAACCTTGTCTGGCAGACAAGCTTCG
genomic: AAAAGACGCCAGTGAAGAATTTCTTTCTTGCTGGATCTTACACAAAGCAGgtagcacctt ... ttttgttcagGACTACATAGACAGCATGGAAGGTGCAACCTTGTCTGGCAGACAAGCTTCG
EST: gi|23064255|gb|BU579028.1|BU579028
EST:     AAAAGACGCCAGTGAAGAATTTCTTTCTTGCTGGATCTTACACAAAGCAG                         GACTACATAGACAGCATGGAAGGTGCAACCTTGTCTGGCAGACAAGCTTCG
genomic: AAAAGACGCCAGTGAAGAATTTCTTTCTTGCTGGATCTTACACAAAGCAGgtagcacctt ... ttttgttcagGACTACATAGACAGCATGGAAGGTGCAACCTTGTCTGGCAGACAAGCTTCG
EST: gi|120496110|gb|EH224277.1|EH224277
EST:     AAAAGACGCCAGTGAAGAATTTCTTTCTTGCTGGATCTTACACAAAGCAG                         GACTACATAGACAGCATGGAAGGTGCAACCTTGTCTGGCAGACAAGCTTCG
genomic: AAAAGACGCCAGTGAAGAATTTCTTTCTTGCTGGATCTTACACAAAGCAGgtagcacctt ... ttttgttcagGACTACATAGACAGCATGGAAGGTGCAACCTTGTCTGGCAGACAAGCTTCG
EST: gi|213616900|gb|DB978890.1|DB978890
EST:     AAAAGACGCCAGTGAAGAATTACTTTCTTGCTGGATCTTACACAAAGCAG                         GACTACATAGACAGCATGGAAGGTGCAACCTTGTCTGGCAGACAAGCTTCG
genomic: AAAAGACGCCAGTGAAGAATTTCTTTCTTGCTGGATCTTACACAAAGCAGgtagcacctt ... ttttgttcagGACTACATAGACAGCATGGAAGGTGCAACCTTGTCTGGCAGACAAGCTTCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatttaagttgcattggtgttgctcacttttattattattgttatttttgttcagGACTACATAGACAGCATGGAAGGTGCAACCTTGTCTGGCAGACAAGCTTCGGCCTATATCTGTGATGCAGGGGAAGGATTAGTGGCATTGCGGAAGAAGC
                    tgctcac  putative branch site (score: 2)
                                            tttttgttc  putative PPT
                       tcacttttattattat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agcaattgctgtatgttgttttctccagttttactgcagtagtgaaatttaagttgcattggtgttgctcacttttattattattgttatttttgttcagGACTACATAGACAGCATGGAAGGTGCAACCTTGTCTGGCAGACAAGCTTCGGCCTATATCTGTGATGCAGGGGAAGGATTAGTGGCATTGCGGAAGAAGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - tgctgta
- - - - - - -tgttgtt
- - - - - - - - - - -tctccag
- - - - - - - - - - - - - - - -tactgca
- - - - - - - - - - - - - - - - - - - - - - - - - -agttgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ggtgttg