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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aacaccttgaagtgtcttgcggggttgattataccttctagcgctttgctgctccattctgctcgtctcactgattttgtatttatttgaatgatttcagCTCGTGTTCTCTTCTTCAGCAACTGTATATGGTTGGCCAAAGGAAGTTCCATGCACAGAAGAGTTCCCTCTGTCAGCAATGAACCCATATGGACGAACTA

Basic information

species Glycine max
transcript GLYMA11G01940.3
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G01940.3 (Glycine max), 3'ss of exon 3
lower sequence: AT4G10960.1 (Arabidopsis thaliana), 3'ss of exon 3
aacaccttgaagtgtcttgcggggttg-attataccttctagcgctttgctgctccattctgctcgtctcactgattttgtatttatttgaatgatttcagCTCGTGTTCTCTTCTTCAGCAACTGTATATGGTTGGCCAAAGGAAGTTCCATGCACAGAAGAGTTCCCTCTGTCAGCAATGAACCCATATGGACGAACTA
         | || |  |  |    |  |  | |  ||| |   | ||  | ||    |       |     |||||   || || ||    || || ||||| ||||| || || ||||||||||| ||||| |  ||||| |||||||| || ||||| ||||| ||  | || ||  ||||||||||||||||||| |
-------gtatgtataatttgccactacacaacaagttcgaatccatttttactttgcttgatcaattctcatgattagctactt-ttactctgtttccagCTTGTGTTTTCATCATCAGCAACTGTGTATGGCTCTCCAAAAGAAGTTCCTTGTACAGAGGAGTTTCCAATTTCTGCTTTGAACCCATATGGACGAACAA

upper sequence: GLYMA11G01940.3 (Glycine max), 3'ss of exon 3
lower sequence: Vv02s0025g01560.t01 (Vitis vinifera), 3'ss of exon 3
aacaccttgaagtgtctt-gcggggttgattatacctt--ctagcgctttgctgctccattctgctcgtctcactgattttgtatttatttgaatgatttcagCTCGTGTTCTCTTCTTCAGCAACTGTATATGGTTGGCCAAAGGAAGTTCCATGCACAGAAGAGTTCCCTCTGTCAGCAATGAACCCATATGGACGAACTA
  |    |    ||| ||  |   |||  || |    |  ||     | |||  |||  ||||  |     |||||| ||   | || |    |  ||||||||| || || || || ||||| ||||| ||||||||||||||||| |||||||| |||||||||||||| || |  ||||  || ||||||||||||||||
tcctttattttttgtttttaccacgtttcttgtgatattactgtttatgtgcaactctgttctaatgtctccactgacttctaaattctc---aacatttcagCTTGTTTTTTCATCATCAGCTACTGTTTATGGTTGGCCAAAGGAGGTTCCATGTACAGAAGAGTTCCCACTATGTGCAACAAATCCATATGGACGAACTA

upper sequence: GLYMA11G01940.3 (Glycine max), 3'ss of exon 3
lower sequence: Vv02s0025g01580.t01 (Vitis vinifera), 3'ss of exon 3
-aacaccttgaagtgtcttgcggggttgattatacctt--ctagcgctttgctgctccattctgctcgtctcactgattttgtatttatttgaatgatttcagCTCGTGTTCTCTTCTTCAGCAACTGTATATGGTTGGCCAAAGGAAGTTCCATGCACAGAAGAGTTCCCTCTGTCAGCAATGAACCCATATGGACGAACTA
  |  | |     | | ||     |||  || |    |  ||     | |||  |||  |||   |    ||||||||||   |||| |   ||| ||||||||| || || || || ||||| ||||| ||||||||||||||||| |||||||| |||||||||||||| || |  ||    || |||||||||||||| |
agatgcatgccttttttttagcatgtttcttgtgatgttactgtttatatgcaactctgttcaaatgtcttcactgatttctaatttctc--aat-atttcagCTTGTTTTTTCATCATCAGCTACTGTTTATGGTTGGCCAAAGGAGGTTCCATGTACAGAAGAGTTCCCGCTATGTGCTGCAAATCCATATGGACGAACCA

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|19346734|gb|BM891614.1|BM891614
EST:     CTGGGACAATCACTCTATTGGAAGTCATGGCTGCCCATGGATGCAAGAAG                         CTCGTGTTCTCTTCTTCAGCAACTGTATATGGTTGGCCAAAGGAAGTTCCA
genomic: CTGGGACAATCACTCTATTGGAAGTCATGGCTGCCCATGGATGCAAGAAGgtaaaatcct ... atgatttcagCTCGTGTTCTCTTCTTCAGCAACTGTATATGGTTGGCCAAAGGAAGTTCCA
EST: gi|58025113|gb|CX711854.1|CX711854
EST:     CTGGGACAATCACTCTATTGGAAGTCATGGCTGCCCATGGATGCAAGAAG                         CTCGTGTTCTCTTCTTCAGCAACTGTATATGGTTGGCCAAAGGAAGTTCCA
genomic: CTGGGACAATCACTCTATTGGAAGTCATGGCTGCCCATGGATGCAAGAAGgtaaaatcct ... atgatttcagCTCGTGTTCTCTTCTTCAGCAACTGTATATGGTTGGCCAAAGGAAGTTCCA
EST: gi|11275167|gb|BF325490.1|BF325490
EST:     CTGGGACAATCACTCTATTG-AAGTCATGGCTGCCCATGGATGCAAGAAG                         CT-GTGTTCTCTTCT-CAGCA-CTGTATATGGTGGGCCAAAG-AAGT-CCA
genomic: CTGGGACAATCACTCTATTGGAAGTCATGGCTGCCCATGGATGCAAGAAGgtaaaatcct ... atgatttcagCTCGTGTTCTCTTCTTCAGCAACTGTATATGGTTGGCCAAAGGAAGTTCCA
EST: gi|213598812|gb|DB968283.1|DB968283
EST:     CTGGGACAATCACTCTATTGGAAGTCATGGCTGCCCATGGATGCAAGAAG                         CTCGTGTTCTCTTCTTCAGCAACTGTATATGGTTGGCCAAAGGAAGT-CCA
genomic: CTGGGACAATCACTCTATTGGAAGTCATGGCTGCCCATGGATGCAAGAAGgtaaaatcct ... atgatttcagCTCGTGTTCTCTTCTTCAGCAACTGTATATGGTTGGCCAAAGGAAGTTCCA
EST: gi|19346921|gb|BM891809.1|BM891809
EST:     CTGGGACAATCACTCTATTGGAAGTCATGGCTGCCCATGGATGCAAGAAG                         CTCGTGTTCTCTTCTTCAGCAACTGTATATGGTTGGCCAAAGGAAGTTCCA
genomic: CTGGGACAATCACTCTATTGGAAGTCATGGCTGCCCATGGATGCAAGAAGgtaaaatcct ... atgatttcagCTCGTGTTCTCTTCTTCAGCAACTGTATATGGTTGGCCAAAGGAAGTTCCA
EST: gi|17022573|gb|BM093607.1|BM093607
EST:     CTGGGACAATCACTCTATTGGAAGTCATGGCTGCCCATGGATGCAAGAAG                         CTCGTGTTCTCTTCTTCAGCAACTGTATATGGTTGGCCAAAGGAAGTTCCA
genomic: CTGGGACAATCACTCTATTGGAAGTCATGGCTGCCCATGGATGCAAGAAGgtaaaatcct ... atgatttcagCTCGTGTTCTCTTCTTCAGCAACTGTATATGGTTGGCCAAAGGAAGTTCCA
EST: gi|8283435|gb|BE020996.1|BE020996
EST:     CTGGGACAATCACTCTATTGGAAGTCATGGCTGCCCATGGATGCAAGAAG                         CTCGTGTTCTCTTCTTCAGCAACTGTATATGGTTGGCCAAAGGAAGTTCCA
genomic: CTGGGACAATCACTCTATTGGAAGTCATGGCTGCCCATGGATGCAAGAAGgtaaaatcct ... atgatttcagCTCGTGTTCTCTTCTTCAGCAACTGTATATGGTTGGCCAAAGGAAGTTCCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgctgctccattctgctcgtctcactgattttgtatttatttgaatgatttcagCTCGTGTTCTCTTCTTCAGCAACTGTATATGGTTGGCCAAAGGAAGTTCCATGCACAGAAGAGTTCCCTCTGTCAGCAATGAACCCATATGGACGAACTA
                       cactgat  putative branch site (score: 3)
                            attttgtatttatttg  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aacaccttgaagtgtcttgcggggttgattataccttctagcgctttgctgctccattctgctcgtctcactgattttgtatttatttgaatgatttcagCTCGTGTTCTCTTCTTCAGCAACTGTATATGGTTGGCCAAAGGAAGTTCCATGCACAGAAGAGTTCCCTCTGTCAGCAATGAACCCATATGGACGAACTA

- caccttg
- - - - - - tgtcttg
- - - - - - - - - - ggggttg
- - - - - - - - - - - - - - - - -ccttcta
- - - - - - - - - - - - - - - - - - - - - - tttgctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctcactg