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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagttttattttccctaactaacttagatcctctcttaatttcattgtaaaagcatgaattttcatttttctgaaatgaaccactgattaagaaacaaattcttttggaacacttttatatgctcaattcagATTGTGAGGCAGCTGTGGGCATACATAAAGAAAAACAACCTCCAAGATCCTGGTAACAAAAGAAAGATAATTTGTGATGATGCACTGCGTTTGGTATTTG

Basic information

species Glycine max
transcript GLYMA07G39530.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA07G39530.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G124502_T01 (Zea mays), 3'ss of exon 2
gtagttttattttccctaactaacttagatcctctcttaatttcattgtaaaagcatgaattttcatttttctgaaatgaacc---actgattaagaaacaaattct------tttggaacacttttatatg-ctcaattcagATTGTGAGGCAGCTGTGGGCATACATAAAGAAAAACAACCTCCAAGATCCTGGTAACAAAAGAAAGATAATTTGTGATGATGCACTGCGTTTGGTATTTG
                                   || ||||||||||| | ||    ||||| ||   | ||| | |   |    |||  || |   |   | |||      | | ||| |    |||  | ||  ||||||||||||| |||||| |||||||| || | | | ||||| || |||||||||| | ||||||| ||||| |||||  |||| | ||| ||| |||| ||||
--------------------------------gtactaaatttcattgtgatag---aaatttacacact-ctgtactcttctggtactctttgaatgattgactctatagagtctagaaaataaatattagtctttattcagATTGTGAAGCAGCTCTGGGCATATATCAGGCAGAACAATCTTCAAGATCCTGATGACAAAAGGAAGATTATTTGCAATGACGAACTTCGTGTGGTTTTTG

upper sequence: GLYMA07G39530.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G035325_T01 (Zea mays), 3'ss of exon 2
gtagttttattttccctaactaacttagatcctctcttaatttcattgtaaaagcatgaattttcatttttctgaaatgaaccactgattaagaaacaaattcttttggaacacttttatatg-ctcaattcagATTGTGAGGCAGCTGTGGGCATACATAAAGAAAAACAACCTCCAAGATCCTGGTAACAAAAGAAAGATAATTTGTGATGATGCACTGCGTTTGGTATTTG
                             | ||  || |||||| ||  || ||    ||||  ||   | ||  | |  ||   |  |     ||  | |   | | | | | |  | |  | ||  ||||||||||||| |||||| |||||||| || | | | ||||| || |||||||||| | ||||||| ||||| |||||  |||| | ||| ||| |||| ||||
----------------------------gtacta-ctcaatttctttacaatag---aaattgacacact-ctatactctactggtactctttgaatgattgactctaggaaattaatgttagtcttcattcagATTGTGAAGCAGCTATGGGCATATATCAGGCAGAACAATCTTCAAGATCCTGATGACAAAAGGAAGATCATTTGCAATGACGAACTTCGTGTGGTTTTTG

upper sequence: GLYMA07G39530.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv00s0187g00190.t01 (Vitis vinifera), 3'ss of exon 2
gtagttttattttccctaactaacttagatcctctcttaatttcattgtaaaagcatgaattttcatttttctgaaatgaaccactgattaagaaacaaattcttttggaacacttttatatgctcaattcagATTGTGAGGCAGCTGTGGGCATACATAAAGAAAAACAACCTCCAAGATCCTGGTAACAAAAGAAAGATAATTTGTGATGATGCACTGCGTTTGGTATTTG
    | ||||| ||    |   |  |  |   |||||| ||          | ||     | |    |||| |||| | |   |  || ||      |    |  |||    |||      ||||   |||||||||||| |||||| ||||||||||| | |||||||||||||||||||||| |||||||  |||||||||||||||||||||| || || ||||| ||||
--gttcttattctc----atagaaatgaactttctctttatc---------aggctcacttatcaggttttgtgaagt-agttatagaatatcttgaagtaacccttga---actccaccttgcttggttcagATTGTGAAGCAGCTTTGGGCATACATTAGGAAAAACAACCTCCAAGATCCTAGTAACAAGCGAAAGATAATTTGTGATGATGCCCTCCGCTTGGTGTTTG

upper sequence: GLYMA07G39530.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv00s0187g00240.t01 (Vitis vinifera), 3'ss of exon 2
gtagttttattttccctaactaacttagatcctctcttaatttcattgtaaaagcatgaattttcatttttctgaaatgaaccactgattaagaaacaaattcttttggaacacttttatatgctcaattcagATTGTGAGGCAGCTGTGGGCATACATAAAGAAAAACAACCTCCAAGATCCTGGTAACAAAAGAAAGATAATTTGTGATGATGCACTGCGTTTGGTATTTG
               || | |  | ||||      |||    ||  | ||  ||  | | || |||  |||    ||  |   |  || ||      |    |  |||    |||      ||||   |||||||||||| |||||| ||||||||||| | |||||||||||||||||||||| |||||||  |||||||||||||||||||||| || || ||||| || |
------------gttcttattctcatagaaatgaactt----tctctatatcaggctcacttatcaggttttgtgaagtagttatagaatatcttgaagtaacccttga---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|26047410|gb|CA784213.1|CA784213
EST:     CTCCTGAACTTCAGGCAGTTGTTGGTGAGCCGGCAATGCCAAGAACTGAG                         ATTGTGAGGCAGCTGTGGGCATACATAAAGAAAAACAACCTCCAAGATCCT
genomic: CTCCTGAACTTCAGGCAGTTGTTGGTGAGCCGGCAATGCCAAGAACTGAGgtagttttat ... ctcaattcagATTGTGAGGCAGCTGTGGGCATACATAAAGAAAAACAACCTCCAAGATCCT
EST: gi|207804393|gb|GD776362.1|GD776362
EST:     GGTGAGCCGGCAATGCCAAGAACTGAG                         ATTGTGAGGCAGCTGTGGGCATACATAAAGAAAAACAACCTCCAAGATCCT
genomic: GGTGAGCCGGCAATGCCAAGAACTGAGgtagttttat ... ctcaattcagATTGTGAGGCAGCTGTGGGCATACATAAAGAAAAACAACCTCCAAGATCCT
EST: gi|308098694|gb|HO760435.1|HO760435
EST:     CTCCTGAACTTCAGGCAGTTGTTGGTGAGCCGGCAATGCCAAGAACTGAG                         ATTGTGAGGCAGCTGTGGGCATACATAAAGAAAAACAACCTCCAAGATCCT
genomic: CTCCTGAACTTCAGGCAGTTGTTGGTGAGCCGGCAATGCCAAGAACTGAGgtagttttat ... ctcaattcagATTGTGAGGCAGCTGTGGGCATACATAAAGAAAAACAACCTCCAAGATCCT
EST: gi|193583211|gb|FK538831.1|FK538831
EST:     CTCCTGAACTTCAGGCGGTTGTTGGTGAGCCGGCAATGCCAAGAACTGAA                         ATTGTGAGGCAGCTGTGGGCATACATAAAGAAAAACAACCTCCAAGATCCT
genomic: CTCCTGAACTTCAGGCAGTTGTTGGTGAGCCGGCAATGCCAAGAACTGAGgtagttttat ... ctcaattcagATTGTGAGGCAGCTGTGGGCATACATAAAGAAAAACAACCTCCAAGATCCT
EST: gi|298171705|gb|HO021297.1|HO021297
EST:     CTCCTGAACTTCAGGCAGTTGTTGGTGAGCCGGCAATGCCAAGAACTGAG                         ATTGTGAGGCAGCTGTGGGCATACATAA
genomic: CTCCTGAACTTCAGGCAGTTGTTGGTGAGCCGGCAATGCCAAGAACTGAGgtagttttat ... ctcaattcagATTGTGAGGCAGCTGTGGGCATACATAA
EST: gi|192306778|gb|FG998145.1|FG998145
EST:     CTCCTGAACTTCAGGCAGTTGTTGGTGAGCCGGCAATGCCAAGAACTGAG                         ATTGTGAGGCAGCTGTGGGCATACATAAAGAAAAACAACCTCCAAGATCCT
genomic: CTCCTGAACTTCAGGCAGTTGTTGGTGAGCCGGCAATGCCAAGAACTGAGgtagttttat ... ctcaattcagATTGTGAGGCAGCTGTGGGCATACATAAAGAAAAACAACCTCCAAGATCCT
EST: gi|209698471|gb|BW667268.1|BW667268
EST:     CTCCTGAACTTCAGGCAGTTGTTGGTGAGCCGGCAATGCCAAGAACTGAG                         ATTGTGAGGCAGCTGTGGGCATACATAA
genomic: CTCCTGAACTTCAGGCAGTTGTTGGTGAGCCGGCAATGCCAAGAACTGAGgtagttttat ... ctcaattcagATTGTGAGGCAGCTGTGGGCATACATAA
EST: gi|298173846|gb|HO017182.1|HO017182
EST:     CTCCTGAACTTCAGGCAGTTGTTGGTGAGCCGGCAATGCCAAGAACTGAG                         ATTGTGAGGCAGCTGTGGGCATACATAAAGAAAAACAACCTCCAAGATCCT
genomic: CTCCTGAACTTCAGGCAGTTGTTGGTGAGCCGGCAATGCCAAGAACTGAGgtagttttat ... ctcaattcagATTGTGAGGCAGCTGTGGGCATACATAAAGAAAAACAACCTCCAAGATCCT
EST: gi|192305692|gb|FG998364.1|FG998364
EST:     CTCCTGAACTTCAGGCAGTTGTTGGTGAGCCGGCAATGCCAAGAACTGAG                         ATTGTGAGGCAGCTGTGGGCATACA
genomic: CTCCTGAACTTCAGGCAGTTGTTGGTGAGCCGGCAATGCCAAGAACTGAGgtagttttat ... ctcaattcagATTGTGAGGCAGCTGTGGGCATACA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaaccactgattaagaaacaaattcttttggaacacttttatatgctcaattcagATTGTGAGGCAGCTGTGGGCATACATAAAGAAAAACAACCTCCAAGATCCTGGTAACAAAAGAAAGATAATTTGTGATGATGCACTGCGTTTGGTATTTG
    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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtagttttattttccctaactaacttagatcctctcttaatttcattgtaaaagcatgaattttcatttttctgaaatgaaccactgattaagaaacaaattcttttggaacacttttatatgctcaattcagATTGTGAGGCAGCTGTGGGCATACATAAAGAAAAACAACCTCCAAGATCCTGGTAACAAAAGAAAGATAATTTGTGATGATGCACTGCGTTTGGTATTTG

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