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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAAAGCCCAAATTGATGATACCAACGAGTGGATATACGATAGTATAAATAATGGTGTTTATAAATGTGGGTTTGCAAAGAAGCAAGAACCATACAATGAGgttagtagctatttttaaccctttctagcaacagctggtacttaaatgttacatttgtttaaaaactgctgtactcagatgattgcaactgtttacttggcccttcctttttccag

Basic information

species Glycine max
transcript GLYMA20G02490.3
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G02490.3 (Glycine max), 5'ss of exon 4
lower sequence: AT4G19880.2 (Arabidopsis thaliana), 5'ss of exon 4
AAAAGCCCAAATTGATGATACCAACGAGTGGATATACGATAGTATAAATAATGGTGTTTATAAATGTGGGTTTGCAAAGAAGCAAGAACCATACAATGAGgttagt-----agctatttttaaccctttctagcaacagctggtacttaaatgttacatttgtttaaaaactgctgtactcagatgattgcaactgtttacttggcccttcctttttccag
  ||||  |||| ||||| || || || ||||| ||| || | |||||||||||||| |||| ||| |||||||||||||| |||| ||| ||  | ||||| |||     ||| ||   |||  || |    |   |  || || || | |   |      | ||||   |   || || | ||| | |                               
CCAAGCTAAAATCGATGAAACTAATGAATGGATTTACAATGGGATAAATAATGGTGTCTATAGATGCGGGTTTGCAAAGAAACAAGGACCTTATGAGGAGgtaagtgtggaagccatgaataaagctatt--actgtatatgctaattga-tcccatgagaatgtaaagtttatggttcttatatg-tag-------------------------------

upper sequence: GLYMA20G02490.3 (Glycine max), 5'ss of exon 4
lower sequence: AT5G44990.1 (Arabidopsis thaliana), 5'ss of exon 4
AAAAGCCCAAATTGATGATACCAACGAGTGGATATACGATAGTATAAATAATGGTGTTTATAAATGTGGGTTTGCAAAGAAGCAAGAACCATACAATGAGgttagtagctatttttaaccctttctagcaacagctggtacttaaatgttacatttgtttaaaaactgctgtactcagatgattgcaactgtttacttggcccttcctttttccag
   ||||  ||| ||||| || ||||| |||||  ||||| | ||||| || ||||||||||||||||||||||| |  || |||||| | ||  ||| ||| |   |  | |||      ||  || ||| |  ||  | | |||| | |        |   || |  |   |||   |  |||||                             
CCGAGCCATAATCGATGAGACTAACGAATGGATTCACGATGGGATAAACAACGGTGTTTATAAATGTGGGTTTGCTACAAATCAAGAAACTTATGATGTGgtaa--cgtaactttgcgattttcttatcaata-ttgtaattaaaatttgattccaacattttaattatttgtctc---tctttgcag----------------------------

upper sequence: GLYMA20G02490.3 (Glycine max), 5'ss of exon 4
lower sequence: AT5G45020.2 (Arabidopsis thaliana), 5'ss of exon 4
AAAAGCCCAAATTGATGATACCAACGAGTGGATATACGATAGTATAAATAATGGTGTTTATAAATGTGGGTTTGCAAAGAAGCAAGAACCATACAATGAGgttagtagctatttttaaccctttctagcaac--agctggtacttaaatgttacatttgtttaaaaactgctgtactcagatgattgcaactgtttacttggcccttcctttttccag
 | || |  |||  | || || ||||  ||| | | | |  | ||||| || ||||||||||||||||||||||||| ||| |||||||| || ||||||||    |  |||   | |   | |  | ||    | | || | | |||  ||       |||     | |                                                
CAGAGACGTAATCAACGAGACTAACGGATGGGTTTTCAACGGAATAAACAACGGTGTTTATAAATGTGGGTTTGCAAGGAAACAAGAACCCTATAATGAGgt----atatatccctcaatgtcttaaacatttgaacagggattcaaaaattgatcccttttctctccag------------------------------------------------

upper sequence: GLYMA20G02490.3 (Glycine max), 5'ss of exon 4
lower sequence: Vv01s0011g01890.t01 (Vitis vinifera), 5'ss of exon 5
AAAAGCCCAAATTGATGATACCAACGAGTGGATATACGATAGTATAAATAATGGTGTTTATAAATGTGGGTTTGCAAAGAAGCAAGAACCATACAATGAGgttagtagctatttttaaccctttctagcaacagctggtacttaaatgttacatttgtttaaaa--actgctgtactcagatgattgcaactgtt--tacttggcccttcctttttccag
  |  |||| |||||||| |  || || |||||||| || || ||||| ||||| |||||||||||||| ||||| ||||||||||  || ||||||||||| || |  | | || ||        |  || | |   | | ||  | | | | || || ||||  | | || | |     |||||   ||||||  | ||| ||               
GCAGCCCCAGATTGATGAGATTAATGAATGGATATATGACAGGATAAACAATGGGGTTTATAAATGTGGTTTTGCTAAGAAGCAAGGGCCTTACAATGAGgtgagcatttctattcaa--------atgaaaaacc--tccatacttttaataattcttgaaaaggatttctattcctcagtgatttttactgttcctgctttgcag-------------

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|151404135|gb|EV273945.1|EV273945
EST:     ATGGTGTTTATAAATGTGGGTTTGCAAAGAAGCAAGAACCATACAATGAG                         GCTGCAAGACAATTGTACGGGGCTTTGGACAAATGT
genomic: ATGGTGTTTATAAATGTGGGTTTGCAAAGAAGCAAGAACCATACAATGAGgttagtagct ... ctttttccagGCTGCAAGACAATTGTACGGGGCTTTGGACAAATGT
EST: gi|7639431|gb|AW733754.1|AW733754
EST:     ATGGTGTGTATAAATGTGGGTTTGCAAAGAAACAAGAACCATACAATGAG                         GCTGCAAGACAATTGTACGGCGCTTTGGACANATGTGANGATATACTAAGC
genomic: ATGGTGTTTATAAATGTGGGTTTGCAAAGAAGCAAGAACCATACAATGAGgttagtagct ... ctttttccagGCTGCAAGACAATTGTACGGGGCTTTGGACAAATGTGAGGATATACTAAGC
EST: gi|120490909|gb|EH219076.1|EH219076
EST:     ATAAATGTGGGTTTGCAAAGAAGCAAGAACCATACAATGAG                         GCTGCAAGACAATTGTACGGGGCTTTGGACAAATGTGAGGATATACTAAGC
genomic: ATAAATGTGGGTTTGCAAAGAAGCAAGAACCATACAATGAGgttagtagct ... ctttttccagGCTGCAAGACAATTGTACGGGGCTTTGGACAAATGTGAGGATATACTAAGC
EST: gi|209728830|gb|BW655472.1|BW655472
EST:     ATGGTGTTTATAAATGTGGGTTTGCAAAGAAGCAAGAACCATACAATGAG                         GCTGCAAGACAATTGTACGGGGCTTTGGACAAATGTGAGGATATACTAAGC
genomic: ATGGTGTTTATAAATGTGGGTTTGCAAAGAAGCAAGAACCATACAATGAGgttagtagct ... ctttttccagGCTGCAAGACAATTGTACGGGGCTTTGGACAAATGTGAGGATATACTAAGC
EST: gi|209728829|gb|BW655471.1|BW655471
EST:     ATGGTGTTTATAAATGTGGGTTTGCAAAGAAGCAAGAACCATACAATGAG                         GCTGCAAGACAATTGTACGGGGCTTTGGACAAATGTGAGGATATACTAAGC
genomic: ATGGTGTTTATAAATGTGGGTTTGCAAAGAAGCAAGAACCATACAATGAGgttagtagct ... ctttttccagGCTGCAAGACAATTGTACGGGGCTTTGGACAAATGTGAGGATATACTAAGC
EST: gi|9204775|gb|BE330999.1|BE330999
EST:     ATGGTGTTTATAAATGTGGGTTTGCAAAGAAGCAAGAACCATACAATGAG                         GCTGCAAGACAATTGTACGGGGCTATGGACAAATGTGAGGATATACTAAGC
genomic: ATGGTGTTTATAAATGTGGGTTTGCAAAGAAGCAAGAACCATACAATGAGgttagtagct ... ctttttccagGCTGCAAGACAATTGTACGGGGCTTTGGACAAATGTGAGGATATACTAAGC
EST: gi|192313119|gb|FK004695.1|FK004695
EST:     ATGGTGTTTATAAATGTGGGTTTGCAAAGAAGCAAGAACCATACAATGAG                         GCTGCAAGACAATTGTACGGGGCTTTGGACAAATGTGAGGATATACTAAGC
genomic: ATGGTGTTTATAAATGTGGGTTTGCAAAGAAGCAAGAACCATACAATGAGgttagtagct ... ctttttccagGCTGCAAGACAATTGTACGGGGCTTTGGACAAATGTGAGGATATACTAAGC
EST: gi|120490911|gb|EH219078.1|EH219078
EST:     ATAAATGTGGGTTTGCAAAGAAGCAAGAACCATACAATGAG                         GCTGCAAGACAATTGTACGGGGCTTTGGACAAATGTGAGGATATACTAAGC
genomic: ATAAATGTGGGTTTGCAAAGAAGCAAGAACCATACAATGAGgttagtagct ... ctttttccagGCTGCAAGACAATTGTACGGGGCTTTGGACAAATGTGAGGATATACTAAGC
EST: gi|120491353|gb|EH219520.1|EH219520
EST:     GGTGTTTATAAATGTGGGTTTGCAAAGAAAGCA-GAACCCATACA-TGAG                         GCTGCAAGACAATTGTACGGGGCTTTGGACAA-TGTGA
genomic: GGTGTTTATAAATGTGGGTTTGCAAAGAA-GCAAGAACC-ATACAATGAGgttagtagct ... ctttttccagGCTGCAAGACAATTGTACGGGGCTTTGGACAAATGTGA
EST: gi|192307449|gb|FK000777.1|FK000777
EST:     ATGGTGTTTATAAATGTGGGTTTGCAAAGAAGCAAGAACCATACAATGAG                         GCTGCAAGACAATTGTACGGGGCTTTGGACAAATGTGAGGATATACTAAGC
genomic: ATGGTGTTTATAAATGTGGGTTTGCAAAGAAGCAAGAACCATACAATGAGgttagtagct ... ctttttccagGCTGCAAGACAATTGTACGGGGCTTTGGACAAATGTGAGGATATACTAAGC
EST: gi|120491356|gb|EH219523.1|EH219523
EST:     AATGTGGGTTTGCAAAGAAGCAAGAACCATACAATGAG                         GCTGCAAGACAATTGTACGGGGCTTTGGACAAATGTGAGGATATACTAAGC
genomic: AATGTGGGTTTGCAAAGAAGCAAGAACCATACAATGAGgttagtagct ... ctttttccagGCTGCAAGACAATTGTACGGGGCTTTGGACAAATGTGAGGATATACTAAGC
EST: gi|9902544|gb|BE611512.1|BE611512
EST:     ATGGTGTTTATAAATGTGGGTTTGCAAAGACGCAAGAACCATACAATGAG                         GCTGCAAGACAA
genomic: ATGGTGTTTATAAATGTGGGTTTGCAAAGAAGCAAGAACCATACAATGAGgttagtagct ... ctttttccagGCTGCAAGACAA
EST: gi|192313120|gb|FK004696.1|FK004696
EST:     ATGGTGTTTATAAATGTGGGTTTGCAAAGAAGCAAGAACCATACAATGAG                         GCTGCAAGACAATTGTACGGGGCTTTGGACAAATGTGAGGATATACTAAGC
genomic: ATGGTGTTTATAAATGTGGGTTTGCAAAGAAGCAAGAACCATACAATGAGgttagtagct ... ctttttccagGCTGCAAGACAATTGTACGGGGCTTTGGACAAATGTGAGGATATACTAAGC
EST: gi|15201916|gb|BI425126.1|BI425126
EST:     ATGGTGTTTATAAATGTGGGTTTGCAAAGAAGCAAGAACCATACAATGAG                         GCTGCAAGACAATTGTACGGGGCTTTGGACAAATGTGAGGATATACTAAGC
genomic: ATGGTGTTTATAAATGTGGGTTTGCAAAGAAGCAAGAACCATACAATGAGgttagtagct ... ctttttccagGCTGCAAGACAATTGTACGGGGCTTTGGACAAATGTGAGGATATACTAAGC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAAAGCCCAAATTGATGATACCAACGAGTGGATATACGATAGTATAAATAATGGTGTTTATAAATGTGGGTTTGCAAAGAAGCAAGAACCATACAATGAGgttagtagctatttttaaccctttctagcaacagctggtacttaaatgttacatttgtttaaaaactgctgtactcagatgattgcaactgtttacttggcccttcctttttccag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC