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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagttttcttttccctaactaacttagatactctcttaatttcatagtaaaaaacatgaatttttatttatctgaaataaaccactgattaagaaacaaattcttttggaacactataatatgctcaattcagATTGTGAGGCAGCTGTGGGCATACATAAAGAAAAACAACCTCCAAGATCCTGGTAACAAAAGAAAGATAATTTGTGATGATGCCCTGCGTTTGGTATTTG

Basic information

species Glycine max
transcript GLYMA17G01230.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA17G01230.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G124502_T01 (Zea mays), 3'ss of exon 2
gtagttttcttttccctaactaacttagatactc--tcttaatttcatagtaaaaaacatgaatttttatttatctgaaataaacc-actgattaagaaacaaattcttttggaacactataatatgctcaattcagATTGTGAGGCAGCTGTGGGCATACATAAAGAAAAACAACCTCCAAGATCCTGGTAACAAAAGAAAGATAATTTGTGATGATGCCCTGCGTTTGGTATTTG
                             ||||   | | | | | |||| ||   |||  | | | || |  ||||  |       | ||||| |     | |   | | | ||    ||| ||  ||  ||||||||||||| |||||| |||||||| || | | | ||||| || |||||||||| | ||||||| ||||| |||||  |||| |  || ||| |||| ||||
----------------------------gtactaaatttcattgtgatagaaatttacac-actctgtactcttctggtactctttgaatgattgactc-tatagagtctagaaaataaatattagtctttattcagATTGTGAAGCAGCTCTGGGCATATATCAGGCAGAACAATCTTCAAGATCCTGATGACAAAAGGAAGATTATTTGCAATGACGAACTTCGTGTGGTTTTTG

upper sequence: GLYMA17G01230.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G035325_T01 (Zea mays), 3'ss of exon 2
gtagttttcttttccctaactaacttagatactctcttaatttcatagtaaaaaacatgaatttttatttatctgaaataaaccactgattaagaaacaaattcttttggaacactataatatgctcaattcagATTGTGAGGCAGCTGTGGGCATACATAAAGAAAAACAACCTCCAAGATCCTGGTAACAAAAGAAAGATAATTTGTGATGATGCCCTGCGTTTGGTATTTG
                             ||||  || |||||| |   || | | ||  |       |   ||  | |     |||  || |   |   | |||   ||||    ||  ||  ||  ||||||||||||| |||||| |||||||| || | | | ||||| || |||||||||| | ||||||| ||||| |||||  |||| |  || ||| |||| ||||
----------------------------gtacta-ctcaatttctttacaatagaaattgacacactctatactctactgg--tactctttgaatgattgactcta--ggaaattaatgttagtcttcattcagATTGTGAAGCAGCTATGGGCATATATCAGGCAGAACAATCTTCAAGATCCTGATGACAAAAGGAAGATCATTTGCAATGACGAACTTCGTGTGGTTTTTG

upper sequence: GLYMA17G01230.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv00s0187g00190.t01 (Vitis vinifera), 3'ss of exon 2
gtagttttcttttccctaactaacttagatactctcttaatttcatagtaaaaaacatgaatttttatttatctgaaataaaccactgattaagaaacaaattcttttggaacactataatatgctcaattcagATTGTGAGGCAGCTGTGGGCATACATAAAGAAAAACAACCTCCAAGATCCTGGTAACAAAAGAAAGATAATTTGTGATGATGCCCTGCGTTTGGTATTTG
       |  ||   || |   |  |  |   |||||| ||     ||    |   || |  |||| |  |   |  ||| |  |    |   |||  ||   |  |||    |||  |   ||||   |||||||||||| |||||| ||||||||||| | |||||||||||||||||||||| |||||||  ||||||||||||||||||||||||| || ||||| ||||
------gttcttattctcatagaaatgaactttctctttatc----aggctcacttatcaggttttgtgaagtagttatagaata----tcttgaagtaa---cccttga---actccaccttgcttggttcagATTGTGAAGCAGCTTTGGGCATACATTAGGAAAAACAACCTCCAAGATCCTAGTAACAAGCGAAAGATAATTTGTGATGATGCCCTCCGCTTGGTGTTTG

upper sequence: GLYMA17G01230.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv00s0187g00240.t01 (Vitis vinifera), 3'ss of exon 2
gtagttttcttttccctaactaacttagatactctcttaatttcatagtaaaaaacatgaatttttatttatctgaaataaaccactgattaagaaacaaattcttttggaacactataatatgctcaattcagATTGTGAGGCAGCTGTGGGCATACATAAAGAAAAACAACCTCCAAGATCCTGGTAACAAAAGAAAGATAATTTGTGATGATGCCCTGCGTTTGGTATTTG
      ||||| | |  |   || | |   ||| |||  || |||   | |     || |  |||| |  |   |  ||| |  |    |   |||  ||   |  |||    |||  |   ||||   |||||||||||| |||||| ||||||||||| | |||||||||||||||||||||| |||||||  ||||||||||||||||||||||||| || ||||| || |
-----gttcttattctcatagaaatga---actttctctatatcaggctcac--ttatcaggttttgtgaagtagttatagaata----tcttgaagtaa---cccttga---actccaccttgcttggttcagATTGTGAAGCAGCTTTGGGCATACATTAGGAAAAACAACCTCCAAGATCCTAGTAACAAGCGAAAGATAATTTGTGATGATGCCCTCCGCTTGGTGTTCG

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|192314883|gb|FK010701.1|FK010701
EST:     CTCCTGAACTTCAGGCGGTTGTTGGTGAGCCGGCAATGCCAAGAACTGAA                         ATTGTGAGGCAGCTGTGGGCATACATAAAGAAAA
genomic: CTCCTGAACTTCAGGCGGTTGTTGGTGAGCCGGCAATGCCAAGAACTGAAgtagttttct ... ctcaattcagATTGTGAGGCAGCTGTGGGCATACATAAAGAAAA
EST: gi|15813315|gb|BI785590.1|BI785590
EST:     CTCCTGAACTTCAGGCGGTTGTTGGTGAGCCGGCAATGCCAAGAACTGAA                         ATTGTGAGGCAGCTGTGGGCATACATAAAGAAAAACAACCTCCAAGATCCT
genomic: CTCCTGAACTTCAGGCGGTTGTTGGTGAGCCGGCAATGCCAAGAACTGAAgtagttttct ... ctcaattcagATTGTGAGGCAGCTGTGGGCATACATAAAGAAAAACAACCTCCAAGATCCT
EST: gi|207749107|gb|GD717739.1|GD717739
EST:     CTCCTGAACTTCAGGCGGTTGTTGGTGAGCCGGCAATGCCAAGAACTGAA                         ATTGTGAGGCAGCTGTGGGCATACA
genomic: CTCCTGAACTTCAGGCGGTTGTTGGTGAGCCGGCAATGCCAAGAACTGAAgtagttttct ... ctcaattcagATTGTGAGGCAGCTGTGGGCATACA
EST: gi|208207075|gb|GE006716.1|GE006716
EST:     CTCCTGAACTTCAGGCGGTTGTTGGTGAGCCGGCAATGCCAAGAACTGAA                         ATTGTGAGGCAGCTGTGGGCATAC
genomic: CTCCTGAACTTCAGGCGGTTGTTGGTGAGCCGGCAATGCCAAGAACTGAAgtagttttct ... ctcaattcagATTGTGAGGCAGCTGTGGGCATAC
EST: gi|151409070|gb|EV278878.1|EV278878
EST:     CTCCTGAACTTCAGGCGGTTGTTGGTGAGCCGGCAATGCCAAGAACTGAA                         ATTGTGAGGCAGCTGTGGGCATACATAAAGAAAAACAACCTCCAAGATCCT
genomic: CTCCTGAACTTCAGGCGGTTGTTGGTGAGCCGGCAATGCCAAGAACTGAAgtagttttct ... ctcaattcagATTGTGAGGCAGCTGTGGGCATACATAAAGAAAAACAACCTCCAAGATCCT
EST: gi|193586598|gb|FK541270.1|FK541270
EST:     CTCCTGAACTTCAGGCGGTTGTTGGTGAGCCGGCAATGCCAAGAACTGAA                         ATTGTGAGGCAGCTGTGGGCATACATAAAGAAAAACAACCTCCAAGATCCT
genomic: CTCCTGAACTTCAGGCGGTTGTTGGTGAGCCGGCAATGCCAAGAACTGAAgtagttttct ... ctcaattcagATTGTGAGGCAGCTGTGGGCATACATAAAGAAAAACAACCTCCAAGATCCT
EST: gi|192329210|gb|FK020129.1|FK020129
EST:     CTCCTGAACTTCAGGCGGTTGTTGGTGAGCCGGCAATGCCAAGAACTGAA                         ATTGTGAGGCAGCTGTGGGCATACATAAAG
genomic: CTCCTGAACTTCAGGCGGTTGTTGGTGAGCCGGCAATGCCAAGAACTGAAgtagttttct ... ctcaattcagATTGTGAGGCAGCTGTGGGCATACATAAAG
EST: gi|17964063|gb|BM270804.1|BM270804
EST:     CTCCTGAACTTCAGGCGGTTGTTGGTGAGCCGGCAATGCCAAGAACTGAA                         ATTGTGAGGCAGCTGTGGGCATACATAAAGAAAAACAACCTCCAAGATCCT
genomic: CTCCTGAACTTCAGGCGGTTGTTGGTGAGCCGGCAATGCCAAGAACTGAAgtagttttct ... ctcaattcagATTGTGAGGCAGCTGTGGGCATACATAAAGAAAAACAACCTCCAAGATCCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaaccactgattaagaaacaaattcttttggaacactataatatgctcaattcagATTGTGAGGCAGCTGTGGGCATACATAAAGAAAAACAACCTCCAAGATCCTGGTAACAAAAGAAAGATAATTTGTGATGATGCCCTGCGTTTGGTATTTG
    cactgat  putative branch site (score: 3)
         attaagaaacaaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtagttttcttttccctaactaacttagatactctcttaatttcatagtaaaaaacatgaatttttatttatctgaaataaaccactgattaagaaacaaattcttttggaacactataatatgctcaattcagATTGTGAGGCAGCTGTGGGCATACATAAAGAAAAACAACCTCCAAGATCCTGGTAACAAAAGAAAGATAATTTGTGATGATGCCCTGCGTTTGGTATTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA