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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattaccttactggaaaattattgtccttatgatgcccctttttctttgtaaattttttgtgaactaatttattctttaattcaactaaacatcattgcagGCTGAACTAGACAGGTTCTGTGATGCTCTTATTTCCATTAGACAAGAAATTGCTGAGATTGAGAAAGGAAATGCTGACATTAACAACAATGTACTTAAG

Basic information

species Glycine max
transcript GLYMA17G34690.1
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA17G34690.1 (Glycine max), 3'ss of exon 12
lower sequence: LOC_Os01g51410.2 (Oryza sativa), 3'ss of exon 11
gtattaccttactggaaaattattgtccttatgatgcccctttttctt-tgtaaattttttgtgaactaatttattctttaattcaactaaacatcattgcagGCTGAACTAGACAGGTTCTGTGATGCTCTTATTTCCATTAGACAAGAAATTGCTGAGATTGAGAAAGGAAATGCTGACATTAACAACAATGTACTTAAG
            |  || | ||     | ||  ||   ||||    || |   ||   ||  |    | || |   ||| |  |||  | |      | |||||| |||||||||||||||||||||||||| || || || ||  |||||||||| || || || |  || || || ||  | ||||||||||| || |||
-----------gtaaaacactaaaacacctactatattccttgccattgtaccaaccattctt----ttatatgaacttaatgtcacattatttatttcgcagGCCGAACTAGACAGGTTCTGTGATGCTCTAATCTCAATCAGGGAAGAAATTGCAGAAATCGAAAGTGGCAAAGCAGATGTGAACAACAATGTCCTCAAG

upper sequence: GLYMA17G34690.1 (Glycine max), 3'ss of exon 12
lower sequence: LOC_Os06g40940.2 (Oryza sativa), 3'ss of exon 10
gtattaccttactggaaaattattgtccttatgatgcccctttttctt-tgtaaattttttgtgaactaatttattctttaattcaactaaacatcattgcagGCTGAACTAGACAGGTTCTGTGATGCTCTTATTTCCATTAGACAAGAAATTGCTGAGATTGAGAAAGGAAATGCTGACATTAACAACAATGTACTTAAG-
            |  || | ||     | ||  ||   ||||    || |   ||   ||  |    | || |   ||| |  |||  | ||     | |||||| |||||||| ||||||||||||||||| || || || ||  |||||||||| ||||| || |  || || || ||  | |||||||| || || ||| 
-----------gtaaaacactaaaacacatactatattccttagcattgtaccaaccattctt----ttatatgagcttaatgtcacatcaattatctcgcagGCCGAACTAGATAGGTTCTGTGATGCTCTAATCTCAATCAGGGAAGAAATTGCAGAGATAGAAAGTGGCAAAGCAGATGTGAACAACAACGTCCTCAAGG

upper sequence: GLYMA17G34690.1 (Glycine max), 3'ss of exon 12
lower sequence: LOC_Os06g40940.3 (Oryza sativa), 3'ss of exon 11
gtattaccttactggaaaattattgtccttatgatgcccctttttctt-tgtaaattttttgtgaactaatttattctttaattcaactaaacatcattgcagGCTGAACTAGACAGGTTCTGTGATGCTCTTATTTCCATTAGACAAGAAATTGCTGAGATTGAGAAAGGAAATGCTGACATTAACAACAATGTACTTAAG
            |  || | ||     | ||  ||   ||||    || |   ||   ||  |    | || |   ||| |  |||  | ||     | |||||| |||||||| ||||||||||||||||| || || || ||  |||||||||| ||||| || |  || || || ||  | |||||||| || || |||
-----------gtaaaacactaaaacacatactatattccttagcattgtaccaaccattctt----ttatatgagcttaatgtcacatcaattatctcgcagGCCGAACTAGATAGGTTCTGTGATGCTCTAATCTCAATCAGGGAAGAAATTGCAGAGATAGAAAGTGGCAAAGCAGATGTGAACAACAACGTCCTCAAG

upper sequence: GLYMA17G34690.1 (Glycine max), 3'ss of exon 12
lower sequence: AT4G33010.2 (Arabidopsis thaliana), 3'ss of exon 11
gtattaccttactggaaaattattgtccttatgatgcccctttttctttgtaaattttttgtgaactaatttattctttaattcaactaaacatcattgcagGCTGAACTAGACAGGTTCTGTGATGCTCTTATTTCCATTAGACAAGAAATTGCTGAGATTGAGAAAGGAAATGCTGACATTAACAACAATGTACTTAAG
               || ||   | |    | |||  | | ||  || | |    | |  ||| |  || ||  |    || | ||  | |     |||||||| || |||||||||||||| |||||||| ||||| || ||  ||||||||||  ||||||| ||||||||||| ||  |  | ||||| || || |||
------------gtaaatatggatatatgca-gatctctcattgactctttcttctctcagtgtatcaacttgatg--aaactaaataatattcgtttgcagGCGGAGCTAGACAGGTTCTGCGATGCTCTCATTTCAATCAGGGAAGAAATTGCACAGATTGAAAAAGGAAATGCAGATGTCCAGAACAACGTTCTCAAG

upper sequence: GLYMA17G34690.1 (Glycine max), 3'ss of exon 12
lower sequence: Vv04s0008g01300.t01 (Vitis vinifera), 3'ss of exon 12
gtattaccttactggaaaattattgtccttatgatgcccctttttctttgtaaattttttgtgaactaatttattctttaattcaactaaacatcattgcagGCTGAACTAGACAGGTTCTGTGATGCTCTTATTTCCATTAGACAAGAAATTGCTGAGATTGAGAAAGGAAATGCTGACATTAACAACAATGTACTTAAG
||||  | | ||  |  ||  ||| | |||            | | ||  ||    |||  |   ||| |  ||| || | |     |      | || ||||| ||  |||||||||| |||||||||||||| ||||||||| ||||||||||  |||||||||| ||||| |||||| || |||||||||| || |||
gtat-gcttcaccagggaa--attcttctt------ttttcatcttttcatactcctttcttcttctagtgaatt-ttaagtgtgtttgttttacttttcagGCAGAGTTAGACAGGTTTTGTGATGCTCTTATCTCCATTAGAAAAGAAATTGCACAGATTGAGAATGGAAAAGCTGACGTTCACAACAATGTCCTAAAG

upper sequence: GLYMA17G34690.1 (Glycine max), 3'ss of exon 12
lower sequence: Vv11s0016g02280.t01 (Vitis vinifera), 3'ss of exon 13
gtattaccttactggaaaattattgtccttatgatgcccctttttctttgtaaattttttgtgaactaatttattctttaattcaactaaacatcattgcagGCTGAACTAGACAGGTTCTGTGATGCTCTTATTTCCATTAGACAAGAAATTGCTGAGATTGAGAAAGGAAATGCTGACATTAACAACAATGTACTTAAG
            |  || | ||   | ||  | ||  | | || | ||||| | |||   || ||   |||          || ||||     |  |||||||| ||  ||||||| || |||||||| || || ||||| ||| | ||||||||| ||||||||||||| || |||||   |||||||||||| || |||
----------gtttaaataataaccttctctttatttctcgttctttttgtcagtttaaagtaaatggatt--------gtttgaact---tctttttgcagGCAGAGTTAGACAGATTTTGTGATGCCCTGATATCCATCAGAGAGGAAATTGCTCAGATTGAGAAAGGGAAAGCTGATCCTAACAACAATGTTCTCAAG

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|120493517|gb|EH221684.1|EH221684
EST:     GCCTGGCACACTCATGATTGAGCCAACTGAGAGTGAAAGCAAG                         GCTGAACTAGACAGGTTCTGTGATGCTCTTATTTCCATTAGACAAGAAATT
genomic: GCCTGGCACACTCATGATTGAGCCAACTGAGAGTGAAAGCAAGgtattacctt ... atcattgcagGCTGAACTAGACAGGTTCTGTGATGCTCTTATTTCCATTAGACAAGAAATT
EST: gi|22523580|gb|BU082391.1|BU082391
EST:     GATTGAGCCAACTGAGAGTGAAAGCAAG                         GCTGAACTAGACAGGTTCTGTGATGCTCTTATTTCCATTAGACAAGAAATT
genomic: GATTGAGCCAACTGAGAGTGAAAGCAAGgtattacctt ... atcattgcagGCTGAACTAGACAGGTTCTGTGATGCTCTTATTTCCATTAGACAAGAAATT
EST: gi|26058323|gb|CA801237.1|CA801237
EST:     GGCCTGTGCCTGGCACACTCATGATTGAGCCAACTGAGAGTGAAAGCAAG                         GCTGAACTAGACAGGTTCTGTGATGCTCTTATTTCCATTAGACAAGAAATT
genomic: GGCCTGTGCCTGGCACACTCATGATTGAGCCAACTGAGAGTGAAAGCAAGgtattacctt ... atcattgcagGCTGAACTAGACAGGTTCTGTGATGCTCTTATTTCCATTAGACAAGAAATT
EST: gi|154204736|gb|EV554998.1|EV554998
EST:     GGCCTGTGCCTGGCACACTCATGATTGAGCCAACTGAGAGTGAAAGCAAG                         GCTGAACTAGACAGGTTCTGTGATGCTCTTATTTCCATTAGACAAGAAATT
genomic: GGCCTGTGCCTGGCACACTCATGATTGAGCCAACTGAGAGTGAAAGCAAGgtattacctt ... atcattgcagGCTGAACTAGACAGGTTCTGTGATGCTCTTATTTCCATTAGACAAGAAATT
EST: gi|16342969|gb|BI968564.1|BI968564
EST:     GGCCTGTGCCTGGCACACTCATGATTGAGCCAACTGAGAGTGAAAGCAAG                         GCTGAACTAGACAGGTTCTGTGATGCTCTTATTTCCATTAGACAAGAAATT
genomic: GGCCTGTGCCTGGCACACTCATGATTGAGCCAACTGAGAGTGAAAGCAAGgtattacctt ... atcattgcagGCTGAACTAGACAGGTTCTGTGATGCTCTTATTTCCATTAGACAAGAAATT
EST: gi|120493515|gb|EH221682.1|EH221682
EST:     GGCCTGTGCCTGGCACACTCATGATTGAGCCAACTGAGAGTGAAAGCAAG                         GCTGAACTAGACAGGTTCTGTGATGCTCTTATTTCCATTAGACAAGAAATT
genomic: GGCCTGTGCCTGGCACACTCATGATTGAGCCAACTGAGAGTGAAAGCAAGgtattacctt ... atcattgcagGCTGAACTAGACAGGTTCTGTGATGCTCTTATTTCCATTAGACAAGAAATT
EST: gi|10231306|gb|BE800194.1|BE800194
EST:     GGCCTGTGCCTGGCACACTCATGATTGAGCCAACTGAGAGTGAAAGTAAG                         GCTGAATTAGACAGGTTCTGTGATGTTCTTATTTCCATTAGACAAGAAATT
genomic: GGCCTGTGCCTGGCACACTCATGATTGAGCCAACTGAGAGTGAAAGCAAGgtattacctt ... atcattgcagGCTGAACTAGACAGGTTCTGTGATGCTCTTATTTCCATTAGACAAGAAATT
EST: gi|192295731|gb|FG990825.1|FG990825
EST:     GGCCTGTGCCTGGCACACTCATGATTGAGCCAACTGAGAGTGAAAGCAAG                         GCTGAACTAGACAGGTTCTGTGATGCTCTTATTTCCATTAGACAAGAAATT
genomic: GGCCTGTGCCTGGCACACTCATGATTGAGCCAACTGAGAGTGAAAGCAAGgtattacctt ... atcattgcagGCTGAACTAGACAGGTTCTGTGATGCTCTTATTTCCATTAGACAAGAAATT
EST: gi|120492558|gb|EH220725.1|EH220725
EST:     GGCCTGTGCCTGGCACACTCATGATTGAGCCAACTGAGAGTGAAAGCAAG                         GCTGAACTAGACAGGTTCTGTGATGCTCTTATTTCCATTAGACAAGAAATT
genomic: GGCCTGTGCCTGGCACACTCATGATTGAGCCAACTGAGAGTGAAAGCAAGgtattacctt ... atcattgcagGCTGAACTAGACAGGTTCTGTGATGCTCTTATTTCCATTAGACAAGAAATT
EST: gi|13480387|gb|BG509730.1|BG509730
EST:     GGCCTGTGCCTGGCACACTCATGATTGAGCCAACTGAGAGTGAAAGCAAG                         GCTGAACTAGACAGGTTCTGTGATGCTCTTATTTCCATTAGACAAGAAATT
genomic: GGCCTGTGCCTGGCACACTCATGATTGAGCCAACTGAGAGTGAAAGCAAGgtattacctt ... atcattgcagGCTGAACTAGACAGGTTCTGTGATGCTCTTATTTCCATTAGACAAGAAATT
EST: gi|192315105|gb|FK009929.1|FK009929
EST:     GGCCTGTGCCTGGCACACTCATGATTGAGCCAACTGAGAGTGAAAGCAAG                         GCTGAACTAGACAGGTTCTGTGATGCTCTTATTTCCATTAGACAAGAAATT
genomic: GGCCTGTGCCTGGCACACTCATGATTGAGCCAACTGAGAGTGAAAGCAAGgtattacctt ... atcattgcagGCTGAACTAGACAGGTTCTGTGATGCTCTTATTTCCATTAGACAAGAAATT
EST: gi|192315106|gb|FK009930.1|FK009930
EST:     GGCCTGTGCCTGGCACACTCATGATTGAGCCAACTGAGAGTGAAAGCAAG                         GCTGAACTAGACAGGTTCTGTGATGCTCTTATTTCCATTAGACAAGAAATT
genomic: GGCCTGTGCCTGGCACACTCATGATTGAGCCAACTGAGAGTGAAAGCAAGgtattacctt ... atcattgcagGCTGAACTAGACAGGTTCTGTGATGCTCTTATTTCCATTAGACAAGAAATT
EST: gi|21676476|gb|BQ628827.1|BQ628827
EST:     GGCACACTCATGATTGAGCCAACTGAGAGTGAAAGCAAG                         GCTGAACTAGACAGGTTCTGTGATGCTCTTATTTCCATTAGACAAGAAATT
genomic: GGCACACTCATGATTGAGCCAACTGAGAGTGAAAGCAAGgtattacctt ... atcattgcagGCTGAACTAGACAGGTTCTGTGATGCTCTTATTTCCATTAGACAAGAAATT
EST: gi|117557747|gb|EG702132.1|EG702132
EST:     GGCCTGTGCCTGGCACACTCATGATTGAGCCAACTGAGAGTGAAAGCAAG                         GCTGAACTAGACAGGTTCTGTGATGCTCTTATTTCCATTAGACAAGAAATT
genomic: GGCCTGTGCCTGGCACACTCATGATTGAGCCAACTGAGAGTGAAAGCAAGgtattacctt ... atcattgcagGCTGAACTAGACAGGTTCTGTGATGCTCTTATTTCCATTAGACAAGAAATT
EST: gi|154204730|gb|EV554992.1|EV554992
EST:     GGCCTGTGCCTGGCACACTCATGATTGAGCCAACTGAGAGTGAAAGCAAG                         GCTGAACTAGACAGGTTCTGTGATGCTCTTATTTCCATTAGACAAGAAATT
genomic: GGCCTGTGCCTGGCACACTCATGATTGAGCCAACTGAGAGTGAAAGCAAGgtattacctt ... atcattgcagGCTGAACTAGACAGGTTCTGTGATGCTCTTATTTCCATTAGACAAGAAATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgtaaattttttgtgaactaatttattctttaattcaactaaacatcattgcagGCTGAACTAGACAGGTTCTGTGATGCTCTTATTTCCATTAGACAAGAAATTGCTGAGATTGAGAAAGGAAATGCTGACATTAACAACAATGTACTTAAG
                                     aactaaa  putative branch site (score: 2)
     aattttttgtgaacta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtattaccttactggaaaattattgtccttatgatgcccctttttctttgtaaattttttgtgaactaatttattctttaattcaactaaacatcattgcagGCTGAACTAGACAGGTTCTGTGATGCTCTTATTTCCATTAGACAAGAAATTGCTGAGATTGAGAAAGGAAATGCTGACATTAACAACAATGTACTTAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG