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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtccttgtctggtcatatgatagattttctactatagttccacttgaatacattttagaaataagaatgatatcttgaattaattttttttttttggcagCAATTGCTCTCTCTGAGGATCATAAGCCAAATAGAAGTGATGAGCGGAAGAGAATTGAGAATGCTGGTGGTGTTGTCATGTGGGCAG

Basic information

species Glycine max
transcript GLYMA13G08090.2
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G08090.2 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os05g50970.1 (Oryza sativa), 3'ss of exon 5
------------------gtccttgtctggtcatatgatagattttctactatagttcca--cttgaatacattttagaaataagaatgatatcttgaatt--aattttttttttttggcagCAATTGCTCTCTCTGAGGATCATAAGCCAAATAGAAGTGATGAGCGGAAGAGAATTGAGAATGCTGGTGGTGTTGTCATGTGGGCAG
                  |   ||||    | || | |||   |   | |  | ||| ||  |||     |  | ||        | || | |     |||    ||   |  | ||   ||| ||||| |||||||||||||| |||||||||||||| |||||| ||||| ||||||||| ||||||||| ||||| |||||||| |
gtgcttctgtttacaaaagatgttgttcatttatttaata--ctggatgcagttgttgcattctttgtggcggtgtacctgctgaattgttgttaaacatttcgtttccctcctatttatagCTATTGCACTCTCTGAGGATCACAAGCCAAATAGAAGCGATGAGAGGAAGCGAATTGAGAGTGCTGGTGGGGTTGTTATGTGGGCTG

upper sequence: GLYMA13G08090.2 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G412937_T01 (Zea mays), 3'ss of exon 5
-----gtccttgtctggtcatatgatagattttctactatagttccacttgaatacattttagaaataagaatgatatcttgaattaattttttttttttggcagCAATTGCTCTCTCTGAGGATCATAAGCCAAATAGAAGTGATGAGCGGAAGAGAATTGAGAATGCTGGTGGTGTTGTCATGTGGGCAG
     |    | | |  |  | ||  || | || | || || | |   |  |      | | ||| |     | | |  |    ||   | | ||||    ||||| ||||| |||||||| ||||| |||||||| |||||||||||| ||||  ||||||||| |||||||||  | || ||||||||||
cattaggatatctgtattgctgtggcaggtcttgt-ctgtaatccagatgtagctgtctgttgaactgtttgtaaaacatcatgttgcctctatttt----gcagCTATTGCGCTCTCTGAAGATCACAAGCCAAACAGAAGTGATGAGAGGAATCGAATTGAGAGTGCTGGTGGGATAGTTATGTGGGCAG

upper sequence: GLYMA13G08090.2 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G158818_T02 (Zea mays), 3'ss of exon 3
------gtccttgtctggtcatatgatagattttctactatagttccacttgaatacattttagaaataagaatgatatcttgaattaattttttttttttggcagCAATTGCTCTCTCTGAGGATCATAAGCCAAATAGAAGTGATGAGCGGAAGAGAATTGAGAATGCTGGTGGTGTTGTCATGTGGGCAG
      ||   | | |  |  | || |   || | | ||||| |||   |  | |    ||| ||| |     |   |  | |  ||   |  |||||    ||||| ||||| |||||||| ||||| ||||| || |||||||||||| ||||  |||| |||| |||||||||  | || |||||||| |
aggatagtatatctgtattgctgtggtc--ttcttttctataattcagatgtagttgtcttttgaactgtttgtagaacatcgtgttgcctccttttt----gcagCTATTGCGCTCTCTGAAGATCACAAGCCGAACAGAAGTGATGAGAGGAAACGAATCGAGAGTGCTGGTGGAATAGTTATGTGGGCTG

upper sequence: GLYMA13G08090.2 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G040642_T02 (Zea mays), 3'ss of exon 5
gtccttgtctggtcatatgatagat-tttctactatagttccacttgaatacattttagaa-ataagaatgatatcttgaattaatttt----ttttttttggcagCAATTGCTCTCTCTGAGGATCATAAGCCAAATAGAAGTGATGAGCGGAAGAGAATTGAGAATGCTGGTGGTGTTGTCATGTGGGCAG
    || | || |  | ||||  |  | | |  | || ||    || ||| ||| |||| |  |          | || ||  ||||||       || || ||||| ||||| |||||||| || ||||| ||||| ||||||||||||| |||  | |||||| ||||||| || |||||  | ||| | |
---attttatgttgttttgattaacatatatgttctattta---tttaatgcatcttaggatgtgttggcttgttgttaaagcaattttgtcacccttatttgcagCTATTGCACTCTCTGATGACCATAAACCAAACAGAAGTGATGAGCAGAAACGGATTGAGGATGCTGGAGGAGTTGTTGTTTGGTCTG

upper sequence: GLYMA13G08090.2 (Glycine max), 3'ss of exon 5
lower sequence: AT5G53140.1 (Arabidopsis thaliana), 3'ss of exon 5
gtccttgtctggtcatatgatagattttctactatagttcca---cttgaatacattttagaaataagaatgatatcttgaattaattttttttttttggcagCAATTGCTCTCTCTGAGGATCATAAGCCAAATAGAAGTGATGAGCGGAAGAGAATTGAGAATGCTGGTGGTGTTGTCATGTGGGCAG
    ||   |  |  |   || |||| |      | ||  ||   |||   |   || |    ||||| |   | |    | ||  |  ||| | ||| ||||| || || || ||||| || ||||||||||||||||| |||||  | ||| ||||||| | ||||||||||||| ||||||||||||
--atttagttaatagtg-aatggattcttatgattggtcacaaacctttgttgtgttctttccataaggactcttttcaaacttcgtgctttatgttttgcagCGATCGCGCTATCTGATGACCATAAGCCAAATAGAAGCGATGAAAGAAAGCGAATTGAAAGTGCTGGTGGTGTTATCATGTGGGCAG

upper sequence: GLYMA13G08090.2 (Glycine max), 3'ss of exon 5
lower sequence: Vv16s0050g02570.t01 (Vitis vinifera), 3'ss of exon 5
gtccttgtctggtcatatgatagattttctactatagttccacttgaatacattttagaaataagaatgatatcttgaattaattttttttttttg----gcagCAATTGCTCTCTCTGAGGATCATAAGCCAAATAGAAGTGATGAGCGGAAGAGAATTGAGAATGCTGGTGGTGTTGTCATGTGGGCAG
 |       ||    | | |||  | |||||| | |  |    ||||  |   |  |   ||       ||  ||  || || ||| |||||  ||     |||||||  |||| |||||||||||||| |||||||||||||| ||||| || |||||||| |||||||| |||||||| ||||||||||
-tgtccacttgaat-ttttatatctgttctaccacatatta--ttgagaattgtcgaatcatgcctggaattcctaaaagtagtttctttttcctgctggacagCAATCCCTCTTTCTGAGGATCATAAACCAAATAGAAGTGACGAGCGAAAAAGAATTGAAAATGCTGGAGGTGTTGTGATGTGGGCAG

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|298196173|gb|HO044564.1|HO044564
EST:     TGTAGCTAATGTTGGAGATTCTAGGACTATAATATCAAAAGCTGGTAAAG                         CAATTGCTCTCTCTGAGGATCATAAGCCAAATAGAAGTGATGAGCGGAAGA
genomic: TGTAGCTAATGTTGGAGATTCTAGGACTATAATATCAAAAGCTGGTAAAGgtactattta ... tttttggcagCAATTGCTCTCTCTGAGGATCATAAGCCAAATAGAAGTGATGAGCGGAAGA
EST: gi|254313836|gb|GR831465.1|GR831465
EST:     TGTAGCTAATGTTGGAGATTCTAGGACTATAATATCAAAAGCTGGTAAAG                         CAATTGCTCTCTCTGAGGATCATAAGCCAAATAGAAGTGA
genomic: TGTAGCTAATGTTGGAGATTCTAGGACTATAATATCAAAAGCTGGTAAAGgtactattta ... tttttggcagCAATTGCTCTCTCTGAGGATCATAAGCCAAATAGAAGTGA
EST: gi|151411248|gb|EV281059.1|EV281059
EST:     TGTAGCTAATGTTGGAGATTCTAGGACTATAATATCAAAAGCTGGTAAAG                         CAATTGCTCTCTCTGAG-ATCATAAGCCAAATAGAAGTGATGAGCGGAAGA
genomic: TGTAGCTAATGTTGGAGATTCTAGGACTATAATATCAAAAGCTGGTAAAGgtactattta ... tttttggcagCAATTGCTCTCTCTGAGGATCATAAGCCAAATAGAAGTGATGAGCGGAAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaatacattttagaaataagaatgatatcttgaattaattttttttttttggcagCAATTGCTCTCTCTGAGGATCATAAGCCAAATAGAAGTGATGAGCGGAAGAGAATTGAGAATGCTGGTGGTGTTGTCATGTGGGCAG
                                aattaat  putative branch site (score: 3)
                                  ttaatttttttttttt  CT-rich tract
      attttagaaataagaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtccttgtctggtcatatgatagattttctactatagttccacttgaatacattttagaaataagaatgatatcttgaattaattttttttttttggcagCAATTGCTCTCTCTGAGGATCATAAGCCAAATAGAAGTGATGAGCGGAAGAGAATTGAGAATGCTGGTGGTGTTGTCATGTGGGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG