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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttctgttaagcttttggtaaatagaaataattatgtatccttaacttgtcttgcaaatatcttatttactagacctaaatctagtctttgttgtttcagTGGCATGGGTCCCGATTTTCGAGTTTTGGTTCGAAAAAGCAGGAAACAAGCTGAGCAGTATCATCGGTTATATAAA

Basic information

species Glycine max
transcript GLYMA01G25940.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA01G25940.3 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os02g42320.1 (Oryza sativa), 3'ss of exon 3
tttctgttaagcttttggtaaatagaaat---aattatgtatccttaacttgtcttgcaaatatcttatttac-tagacctaaatctagtctttgttgtttcagTGGCATGGGTCCCGATTTTCGAGTTTTGGTTCGAAAAAGCAGGAAACAAGCTGAGCAGTATCATCGGTTATATAAA
|||   |||    || | |   || |  |   |  |   |    ||||  |   |||||| |   | ||  |  |  || ||  | |   |||     ||||||||| |||||||||||||| || ||| | ||  |||||||  ||||||||||  |||||||| ||||||| || || 
tttaaattatttgttagtttgttacatctctcagcttgctgctgttaatatcagttgcaattcaataatacatgtttacttacctgtgcacttc----tttcagTGGGATGGGTCCCGATTTCCGTGTTCTTGTGAGAAAAAGTCGGAAACAAGCACAGCAGTATTATCGGTTGTACAAG

upper sequence: GLYMA01G25940.3 (Glycine max), 3'ss of exon 5
lower sequence: AT1G16470.1 (Arabidopsis thaliana), 3'ss of exon 5
tttctgttaagcttttggtaaatagaaataattatgtatccttaacttgtcttgcaaatatcttatttactagacctaaatctagtctttgttgtttcagTGGCATGGGTCCCGATTTTCGAGTTTTGGTTCGAAAAAGCAGGAAACAAGCTGAGCAGTATCATCGGTTATATAAA
     |||      |   | | |  || |  |||  | |  ||   || |  ||  | || ||||   ||||    |   |  | | | |  | |   |||||||||||||| |||||||||||| | ||| | || || |||||||| |||||||| |||| |||  | || |||
-----gtttgctcatcatttattttaagtttttagttgtttttg-tttttgatgtta-tagcttaaggactaactttttctgcattttcttctatga-agTGGCATGGGTCCTGATTTTCGAGTTCTTGTTAGGAAGAGTAGGAAACAGGCTGAGCAATATCTTCGTCTGTACAAA

upper sequence: GLYMA01G25940.3 (Glycine max), 3'ss of exon 5
lower sequence: Vv01s0011g01960.t01 (Vitis vinifera), 3'ss of exon 4
---------------tttctgttaagcttttggtaaataga------aataattatgtatccttaact----tgtcttgcaaat-------atctta-tttactagacctaaatctagtctttgttgttt---------cagTGGCATGGGTCCCGATTTTCGAGTTTTGGTTCGAAAAAGCAGGAAACAAGCTGAGCAGTATCATCGGTTATATAAA
               |  || |||    || || | ||  |      |||  |||||| ||| |   |    ||| |  || ||       ||| || | | |  |   ||| | |  ||  ||||||||         ||| ||||||||||| |||| |||||||||||||||||| || ||||| || || |||||||||||  || ||||||| 
gtttgatctttgtgctgcctcttagttattagggagattaagtatttaatgtttatgtttccctgcttgtggtgtttcacacattaacttgatcctaatctgcatgttttaatttttatcaatgttgttttattttttgcagCGGCATGGGTCCTGATTCTCGAGTTTTGGTTCGAAAGAGTAGGAAGCAGGCAGAGCAGTATCACAGGCTATATAAG

upper sequence: GLYMA01G25940.3 (Glycine max), 3'ss of exon 5
lower sequence: PP1S2_595V6.1 (Physcomitrella patens), 3'ss of exon 4
---tttctgttaagct--tttggtaaatagaaataattatgtatccttaacttgtcttgcaaatatcttatttactagacctaaatctagtctttgttgtttcagTGGCATGGGTCCCGATTTTCGAGTTTTGGTTCGAAAAAGCAGGAAACAAGCTGAGCAGTATCATCGGTTATATAAA
       | | |  ||  |||| |   |    |   || ||   | ||    | |    |  ||  ||||  |  ||| | || || | |     |  ||||||| || ||||||||||||| ||| ||||||||||| |||||| |||| |||||  |    ||||| ||  | ||  | 
aagaacgtatcattctagtttgatctttctggaaccttgtgcgccattctgattttaccctcattacttacatcgtagtcatatatgtgg-----gaggtttcagCGGTATGGGTCCCGATTCTCGTGTTTTGGTTCGCAAAAGCCGGAAGCAAGCACAAACATATCAGCGACTTTACCAG

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|192309680|gb|FG999893.1|FG999893
EST:     GTCCAGAAAATTCAGTTATCAACACCAAATATAGGTGTCGTATATAG                         TGGCATGGGTCCCGATTTTCGAGTTTTGGTTCGAAAAAGCAGGAAACAAGC
genomic: GTCCAGAAAATTCAGTTATTAACACCAAATATAGGTGTCGTATATAGgtttgtttct ... gttgtttcagTGGCATGGGTCCCGATTTTCGAGTTTTGGTTCGAAAAAGCAGGAAACAAGC
EST: gi|24206299|gb|BU965552.1|BU965552
EST:     GTCCAGAAAATTCAGTTATTAACACCAAATATAGGTGTCGTATATAG                         TGGCATGGGTCCCGATTTTCGAGTTTTGGTTCGAAAAAGCAGGAAACAAGC
genomic: GTCCAGAAAATTCAGTTATTAACACCAAATATAGGTGTCGTATATAGgtttgtttct ... gttgtttcagTGGCATGGGTCCCGATTTTCGAGTTTTGGTTCGAAAAAGCAGGAAACAAGC
EST: gi|15204528|gb|BI427296.1|BI427296
EST:     GTCCAGAAAATTCAGTTATTAACACCAAATATAGGTGTCGTATATAG                         TGGCATGGGTCCCGATTTTCGAGTTTTGGTTCGAAAAAGCAGGAAACAAGC
genomic: GTCCAGAAAATTCAGTTATTAACACCAAATATAGGTGTCGTATATAGgtttgtttct ... gttgtttcagTGGCATGGGTCCCGATTTTCGAGTTTTGGTTCGAAAAAGCAGGAAACAAGC
EST: gi|9564578|gb|BE474087.1|BE474087
EST:     GTCCAGAAAATTCAGTTATTAACACCAAATATAGGTGTCGTATATAG                         TGGCATGGGTCCCGATTTTCGAGTTTTGGTTCGAAAAAGCAGGAAACAAGC
genomic: GTCCAGAAAATTCAGTTATTAACACCAAATATAGGTGTCGTATATAGgtttgtttct ... gttgtttcagTGGCATGGGTCCCGATTTTCGAGTTTTGGTTCGAAAAAGCAGGAAACAAGC
EST: gi|213598011|gb|DB972199.1|DB972199
EST:     GTCCAGAAAATTCAGTTATTAACACCAAATATAGGTGTCGTATATAG                         TGGCATGGGTCCCGATTTTCGAGTTTTGGTTCGAAAAAGCAGGAAACAAGC
genomic: GTCCAGAAAATTCAGTTATTAACACCAAATATAGGTGTCGTATATAGgtttgtttct ... gttgtttcagTGGCATGGGTCCCGATTTTCGAGTTTTGGTTCGAAAAAGCAGGAAACAAGC
EST: gi|7924388|gb|AW830414.1|AW830414
EST:     GTCCAGAAAATTCAGTTATTAACACCAAATATAGGTGTCGTATATAG                         TGGCATGGGTCCCGATTTTCGAGTTTTGGTTCGAAAAAGCAGGAAACAAGC
genomic: GTCCAGAAAATTCAGTTATTAACACCAAATATAGGTGTCGTATATAGgtttgtttct ... gttgtttcagTGGCATGGGTCCCGATTTTCGAGTTTTGGTTCGAAAAAGCAGGAAACAAGC
EST: gi|298198188|gb|HO039727.1|HO039727
EST:     GTCCAGAAAATTCAGTTATTAACACCAAATATAGGTGTCGTATATAG                         TGGCATGGGTCCCGATTTTCGAGTTTTGGTTCGAAAAAGCAGGAAACAAGC
genomic: GTCCAGAAAATTCAGTTATTAACACCAAATATAGGTGTCGTATATAGgtttgtttct ... gttgtttcagTGGCATGGGTCCCGATTTTCGAGTTTTGGTTCGAAAAAGCAGGAAACAAGC
EST: gi|21602716|gb|BQ613047.1|BQ613047
EST:     GTCCAGAAAATTCAGTTATTAACACCAAATATAGGTGTCGTATATAG                         TGGCATGGGTCCCGATTTTCGAGTTTTGGTTCGAAAAAGCAGGAAACAAGC
genomic: GTCCAGAAAATTCAGTTATTAACACCAAATATAGGTGTCGTATATAGgtttgtttct ... gttgtttcagTGGCATGGGTCCCGATTTTCGAGTTTTGGTTCGAAAAAGCAGGAAACAAGC
EST: gi|58014614|gb|CX701356.1|CX701356
EST:     GTCCAGAAAATTCAGTTATTAACACCAAATATAGGTGTCGTATATAG                         TGGCATGGGTCCCGATTTTCGAGTTTTGGTTCGAAAAAGCAGGAAACAAGC
genomic: GTCCAGAAAATTCAGTTATTAACACCAAATATAGGTGTCGTATATAGgtttgtttct ... gttgtttcagTGGCATGGGTCCCGATTTTCGAGTTTTGGTTCGAAAAAGCAGGAAACAAGC
EST: gi|192325446|gb|FK018387.1|FK018387
EST:     GTCCAGAAAATTCAGTTATTAACACCAAATATAGGTGTCGTATATAG                         TGGCGTGGGTCCCGATTTTCGAGTTTTGGTTCGAAAAAGCAGGAAACAAGC
genomic: GTCCAGAAAATTCAGTTATTAACACCAAATATAGGTGTCGTATATAGgtttgtttct ... gttgtttcagTGGCATGGGTCCCGATTTTCGAGTTTTGGTTCGAAAAAGCAGGAAACAAGC
EST: gi|18690708|gb|BM519556.1|BM519556
EST:     GTCCAGAAAATTCAGTTATTAACACCAAATATAGGTGTCGTATATAG                         TGGCATGGGTCCCGATTTTCGAGTTTTGGTTCGAAAAAGCAGGAAACAAGC
genomic: GTCCAGAAAATTCAGTTATTAACACCAAATATAGGTGTCGTATATAGgtttgtttct ... gttgtttcagTGGCATGGGTCCCGATTTTCGAGTTTTGGTTCGAAAAAGCAGGAAACAAGC
EST: gi|120494647|gb|EH222814.1|EH222814
EST:     GTCCAGAAAATTCAGTTATTAACACCAAATATAGGTGTCGTATATAG                         TGGCATGGGTCCCGATTTTCGAGTTTTGGTTCGAAAAAGCAGGAAACAAGC
genomic: GTCCAGAAAATTCAGTTATTAACACCAAATATAGGTGTCGTATATAGgtttgtttct ... gttgtttcagTGGCATGGGTCCCGATTTTCGAGTTTTGGTTCGAAAAAGCAGGAAACAAGC
EST: gi|14258901|gb|BG881809.1|BG881809
EST:     GTCCAGAAAATTCAGTTATTAACACCAAATATAGGTGTCGTATATAG                         TGGCATGGGTCCCGATTTTCGAGTTTTGGTTCGAAAAAGCAGGAAACAAGC
genomic: GTCCAGAAAATTCAGTTATTAACACCAAATATAGGTGTCGTATATAGgtttgtttct ... gttgtttcagTGGCATGGGTCCCGATTTTCGAGTTTTGGTTCGAAAAAGCAGGAAACAAGC
EST: gi|8403449|gb|BE059083.1|BE059083
EST:     TCAGTCCAGAAAATTCAGTTATTAACACCAAATATAGGTGTCGTATATAG                         TGGCATGGGTCCCGATTTTCGAGTTTTGGTTCGAAAAAGCAGGAAACAAGC
genomic: TCAGTCCAGAAAATTCAGTTATTAACACCAAATATAGGTGTCGTATATAGgtttgtttct ... gttgtttcagTGGCATGGGTCCCGATTTTCGAGTTTTGGTTCGAAAAAGCAGGAAACAAGC
EST: gi|4313519|gb|AI460638.1|AI460638
EST:     GTCCAGAAAATTCAGTTATTAACACCAAATATAGGTGTCGTATATAG                         TGGCATGGGTCCCGATTTTCGAGTTTTGGTTCGAAAAAGCAGGAAACAAGC
genomic: GTCCAGAAAATTCAGTTATTAACACCAAATATAGGTGTCGTATATAGgtttgtttct ... gttgtttcagTGGCATGGGTCCCGATTTTCGAGTTTTGGTTCGAAAAAGCAGGAAACAAGC
EST: gi|14259203|gb|BG882111.1|BG882111
EST:     GTCCAGAAAATTCAGTTATTAACACCAAATATAGGTGTCGTATATAG                         TGGCATGGGTCCCGATTTTCGAGTTTTGGTTCGAAAAAGCAGGAAACAAGC
genomic: GTCCAGAAAATTCAGTTATTAACACCAAATATAGGTGTCGTATATAGgtttgtttct ... gttgtttcagTGGCATGGGTCCCGATTTTCGAGTTTTGGTTCGAAAAAGCAGGAAACAAGC
EST: gi|7925135|gb|AW831161.1|AW831161
EST:     GTCCAGAAAATTCAGTTATTAACACCAAATATAGGTGTCGTATATAG                         TGGCATGGGTCCCGATTTTCGAGTTTTGGTTCGAAAAAGCAGGAAACAAGC
genomic: GTCCAGAAAATTCAGTTATTAACACCAAATATAGGTGTCGTATATAGgtttgtttct ... gttgtttcagTGGCATGGGTCCCGATTTTCGAGTTTTGGTTCGAAAAAGCAGGAAACAAGC
EST: gi|151406778|gb|EV276593.1|EV276593
EST:     GTCCAGAAAATTCAGTTATTAACACCAAATATAGGTGTCGTATATAG                         TGGCATGGGTCCCGATTTTCGAGTTTTGGTTCGAAAAAGCAGGAAACAAGC
genomic: GTCCAGAAAATTCAGTTATTAACACCAAATATAGGTGTCGTATATAGgtttgtttct ... gttgtttcagTGGCATGGGTCCCGATTTTCGAGTTTTGGTTCGAAAAAGCAGGAAACAAGC
EST: gi|19269188|gb|BM885444.1|BM885444
EST:     GTCCAGAAAATTCAGTTATTAACACCAAATATAGGTGTCGTATATAG                         TGGCATGGGTCCCGATTTTCGAGTTTTGGTTCGAAAAAGCAGGAAACAAGC
genomic: GTCCAGAAAATTCAGTTATTAACACCAAATATAGGTGTCGTATATAGgtttgtttct ... gttgtttcagTGGCATGGGTCCCGATTTTCGAGTTTTGGTTCGAAAAAGCAGGAAACAAGC
EST: gi|4397406|gb|AI496403.1|AI496403
EST:     GTCCAGAAAATTCAGTTATTAACACCAAATATAGGTGTCGTATATAG                         TGGCATGGGTCCCGATTTTCGAGTTTTGGTTCGAAAAAGCAGGAAACAAGC
genomic: GTCCAGAAAATTCAGTTATTAACACCAAATATAGGTGTCGTATATAGgtttgtttct ... gttgtttcagTGGCATGGGTCCCGATTTTCGAGTTTTGGTTCGAAAAAGCAGGAAACAAGC
EST: gi|21889053|gb|BQ742266.1|BQ742266
EST:     GTCCAGAAAATTCAGTTATTAACACCAAATATAGGTGTCGTATATAG                         TGGCATGGGTCCCGATTTTCGAGTTTTGGTTCGAAAAAGCAGGAAACAAGC
genomic: GTCCAGAAAATTCAGTTATTAACACCAAATATAGGTGTCGTATATAGgtttgtttct ... gttgtttcagTGGCATGGGTCCCGATTTTCGAGTTTTGGTTCGAAAAAGCAGGAAACAAGC
EST: gi|19052912|gb|BM731579.1|BM731579
EST:     GTCCAGAAAATTCAGTTATTAACACCAAATATAGGTGTCGTATATAG                         TGGCATGGGTCCCGATTTTCGAGTTTTGGTTCGAAAAAGCAGGAAACAAGC
genomic: GTCCAGAAAATTCAGTTATTAACACCAAATATAGGTGTCGTATATAGgtttgtttct ... gttgtttcagTGGCATGGGTCCCGATTTTCGAGTTTTGGTTCGAAAAAGCAGGAAACAAGC
EST: gi|20448816|gb|BQ252940.1|BQ252940
EST:     GTCCAGAAAATTCAGTTATTAACACCAAATATAGGTGTCGTATATAG                         TGGCATGGGTCCCGATTTTCGAGTTTTGGTTCGAAAAAGCAGGAAACAAGC
genomic: GTCCAGAAAATTCAGTTATTAACACCAAATATAGGTGTCGTATATAGgtttgtttct ... gttgtttcagTGGCATGGGTCCCGATTTTCGAGTTTTGGTTCGAAAAAGCAGGAAACAAGC
EST: gi|192316846|gb|FK010833.1|FK010833
EST:     GTCCAGAAAATTCAGTTATTAACACCAAATATAGGTGTCGTATATAG                         TGGCATGGGTCCCGATTTTCGAGTTTTGGTTCGAAAAAGCAGGAAACAAGC
genomic: GTCCAGAAAATTCAGTTATTAACACCAAATATAGGTGTCGTATATAGgtttgtttct ... gttgtttcagTGGCATGGGTCCCGATTTTCGAGTTTTGGTTCGAAAAAGCAGGAAACAAGC
EST: gi|192326825|gb|FK018922.1|FK018922
EST:     GTCCAGAAAATTCAGTTATTAACACCAAATATAGGTGTCGTATATAG                         TGGCATGGGTCCCGATTTTCGAGTTTTGGTTCGAAAAAGCAGGAAACAAGC
genomic: GTCCAGAAAATTCAGTTATTAACACCAAATATAGGTGTCGTATATAGgtttgtttct ... gttgtttcagTGGCATGGGTCCCGATTTTCGAGTTTTGGTTCGAAAAAGCAGGAAACAAGC
EST: gi|21888974|gb|BQ742187.1|BQ742187
EST:     GTCCAGAAAATTCAGTTATTAACACCAAATATAGGTGTCGTATATAG                         TGGCATGGGTCCCGATTTTCGAGTTTTGGTTCGAAAAAGCAGGAAACAAGC
genomic: GTCCAGAAAATTCAGTTATTAACACCAAATATAGGTGTCGTATATAGgtttgtttct ... gttgtttcagTGGCATGGGTCCCGATTTTCGAGTTTTGGTTCGAAAAAGCAGGAAACAAGC
EST: gi|23735184|gb|BU765862.1|BU765862
EST:     GTCCAGAAAATTCAGTTATTAACACCAAATATAGGTGTCGTATATAG                         TGGCATGGGTCCCGATTTTCGAGTTTTGGTTCGAAAAAGCAGGAAACAAGC
genomic: GTCCAGAAAATTCAGTTATTAACACCAAATATAGGTGTCGTATATAGgtttgtttct ... gttgtttcagTGGCATGGGTCCCGATTTTCGAGTTTTGGTTCGAAAAAGCAGGAAACAAGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttgtcttgcaaatatcttatttactagacctaaatctagtctttgttgtttcagTGGCATGGGTCCCGATTTTCGAGTTTTGGTTCGAAAAAGCAGGAAACAAGCTGAGCAGTATCATCGGTTATATAAA
                            acctaaa  putative branch site (score: 3)
                                        tctttgtt  putative PPT
          aaatatcttatttact  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttctgttaagcttttggtaaatagaaataattatgtatccttaacttgtcttgcaaatatcttatttactagacctaaatctagtctttgttgtttcagTGGCATGGGTCCCGATTTTCGAGTTTTGGTTCGAAAAAGCAGGAAACAAGCTGAGCAGTATCATCGGTTATATAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
-ttctgtt
- - - - - gcttttg
- - - - - - - - - - aatagaaa