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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...caattttgctgtagtatttgtttggtttgacacagatataaccacagtaggtgatggctaaaatggaaatatgatttcttttgtattttcattttttcagGGGAAAGTGGTTGTAATCAGGGGAGAGGGACCCAAGGGTGGTCCGGGAATGCCTGAGATGTTAACACCAACAAGTGCAATAATGGGTGCAGGTCTTGGAA

Basic information

species Glycine max
transcript GLYMA13G27810.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G27810.1 (Glycine max), 3'ss of exon 10
lower sequence: LOC_Os08g44530.1 (Oryza sativa), 3'ss of exon 10
caattttgctgtagtatttgtttggtttgacacagatataaccacagtaggtgatggctaaaatggaaatatgat-ttcttttgtattttcattttttcagGGGAAAGTGGTTGTAATCAGGGGAGAGGGACCCAAGGGTGGTCCGGGAATGCCTGAGATGTTAACACCAACAAGTGCAATAATGGGTGCAGGTCTTGGAA
  ||||   | ||   | |          |  ||    |   |   |      |||  ||   | |   |    |  |||  ||   |   ||     |||||||| || || || ||  | ||||| ||||| || ||||| || || |||||||| ||| | || ||||| ||||||||||||||||| |||||||| |
-tatttccttttacgctcttgacaagggaatgcattagttcactgggacaaccatgcatagtcttgttctgaattactctgctggcatgcaatcacaacagGGGAAGGTAGTAGTGATACGAGGAGAAGGACCGAAAGGTGGACCAGGGATGCCTGAAATGCTGACTCCAACTAGTGCAATAATGGGTGCTGGTCTTGGGA

upper sequence: GLYMA13G27810.1 (Glycine max), 3'ss of exon 10
lower sequence: AC234528.1_FGT005 (Zea mays), 3'ss of exon 10
-------------------------------------------------------------------------------caattttgctgtagtatttgtttggtttgacacagatataaccacagtaggtgatggctaaaatggaaatatgatttcttttgtattttcattttttcagGGGAAAGTGGTTGTAATCAGGGGAGAGGGACCCAAGGGTGGTCCGGGAATGCCTGAGATGTTAACACCAACAAGTGCAATAATGGGTGCAGGTCTTGGAA
                                                                               ||   ||||  |  | ||   |  |   |    | ||||     |||    ||     |   |||  || || ||||  ||  | |  |  |||   ||||| || || || |||||| | ||||| ||||| || || || || || |||||||| ||||| || ||||||||||||||||||||||| ||||| ||||
gtaatatgtgcgatgcaagtattttctgcatgtgccactgtcgctattgcttgccatttcttcctttttatttggagagcacgattgcctttttcttctctctgcgagtggaacatattgtttcagagcatgc--attcgtatgacaa-atcattttattgctctgatggtttcaacagGGAAAGGTAGTAGTAATCCGAGGAGAAGGACCAAAAGGAGGGCCAGGGATGCCTGAAATGTTGACTCCAACAAGTGCAATAATGGGTGCTGGTCTCGGAA

upper sequence: GLYMA13G27810.1 (Glycine max), 3'ss of exon 10
lower sequence: GRMZM2G014069_T01 (Zea mays), 3'ss of exon 10
-----------------------------------------------------------------------caattttgctgtagtatttgtttggtt-tgacacagatataaccacagtaggtgatggctaaaatggaaatatgatttcttttgtattttcattttttcagGGGAAAGTGGTTGTAATCAGGGGAGAGGGACCCAAGGGTGGTCCGGGAATGCCTGAGATGTTAACACCAACAAGTGCAATAATGGGTGCAGGTCTTGGAA
                                                                         |  ||||  |    | | | || |  ||  | | ||     || || | ||  ||  |      || | || ||||  ||  | |  |  |||   ||||| || || || || ||| | ||||| ||||| || || || || || ||||| || ||||| || |||||||| |||||||||||||| ||||||||||
gtaatatgtgcagtgcaagtattttctgcatttgctactgccgctattgaatgccatttcttcctttttttgtagattgccttttcttctctctgatagtggaatatattgtttcagagcaagttttgcattcttatgacaaatcattttattgctctgatggtttcaacagGGAAAGGTAGTAGTGATCCGAGGAGAAGGACCAAAAGGCGGGCCAGGGATGCCCGAAATGTTGACTCCAACAAGCGCAATAATGGGTGCTGGTCTTGGAA

upper sequence: GLYMA13G27810.1 (Glycine max), 3'ss of exon 10
lower sequence: AT3G23940.1 (Arabidopsis thaliana), 3'ss of exon 10
caattttgctgtagtatttgtttggtttgacacagatataaccacagtaggtgatggctaaaatggaaatatgatttcttttgtattttcattt-tttcagGGGAAAGTGGTTGTAATCAGGGGAGAGGGACCCAAGGGTGGTCCGGGAATGCCTGAGATGTTAACACCAACAAGTGCAATAATGGGTGCAGGTCTTGGAA
             ||| || |    | ||| |   |  | | | ||| || || |        |  | || |  | |||  || | | |    | |||||||| |  |||||||| ||||| |||||||| || || || ||||| || |||||||||||||| ||||| |||||||||||||||||||| ||||||||||
-------------gtaatt-tcctttctgatatgaagttcatctcaggagctggt--------tatatatcttttatctgatgaaatgtatcgtgtttcagGGAACTGTGGTTGTTATCAGAGGAGAGGGGCCTAAAGGAGGTCCAGGTATGCCTGAGATGTTGACACCGACAAGTGCAATAATGGGTGCCGGTCTTGGAA

upper sequence: GLYMA13G27810.1 (Glycine max), 3'ss of exon 10
lower sequence: Vv05s0051g00830.t01 (Vitis vinifera), 3'ss of exon 10
---caattttgctgtagtatttgtttggtttgacacagatataaccacagtaggtgatggctaaaatggaa-atatgatttcttttgtattt-tcattttttcagGGGAAAGTGGTTGTAATCAGGGGAGAGGGACCCAAGGGTGGTCCGGGAATGCCTGAGATGTTAACACCAACAAGTGCAATAATGGGTGCAGGTCTTGGAA
    | |||| || |  ||| ||| |   | || |      |    | | | | |  |    ||||||| | || | |||| ||   | | | | ||  |||||||||||||| ||| | || || ||||||||||||||||| || || ||||||||||| ||||| || |||||||| ||||||||||| ||||||||||| |
tcatattttttctattttatgtgtctcact-gataggatggtg--tataattgat--tcatcaaaatgggatatctaattttttgcttttctgttatactttcagGGGAAAGTAGTTATTATTAGAGGAGAGGGACCCAAGGGGGGGCCAGGAATGCCTGAAATGTTGACTCCAACAAGCGCAATAATGGGAGCAGGTCTTGGGA

upper sequence: GLYMA13G27810.1 (Glycine max), 3'ss of exon 10
lower sequence: EFJ36479 (Selaginella moellendorffii), 3'ss of exon 9
caattttgctgtagtatttgtttggtttgacacagatataaccacagtaggtgatggctaaaatggaaatatgatt-tcttttgtattt--tcattttttcagGGGAAAGTGGTTGTAATCAGGGGAGAGGGACCCAAGGGTGGTCCGGGAATGCCTGAGATGTTAACACCAACAAGTGCAATAATGGGTGCAGGTCTTGGAA
                                              ||      || | |||    | |||||||  ||  | ||  ||  | |  |  ||||||    ||| |||| ||||||||||| || ||||| |||||||||||||||||||||||| |||| || |||||||| || |||||||| ||  | || |
----------------------------------------------gttctctctgtccaaagca-agatatgataatcactggtgattggtgaaatactcagGGCTCCGTGATTGTTATCAGGGGAGAAGGTCCCAAAGGTGGTCCGGGAATGCCTGAGATGCTAACTCCTACAAGTGCGATCATGGGTGCTGGCTTGGGGA

upper sequence: GLYMA13G27810.1 (Glycine max), 3'ss of exon 10
lower sequence: EFJ18570 (Selaginella moellendorffii), 3'ss of exon 10
caattttgctgtagtatttgtttggtttgacacagatataaccacagtaggtgatggctaaaatggaaatatgatt-tcttttgtattt--tcattttttcagGGGAAAGTGGTTGTAATCAGGGGAGAGGGACCCAAGGGTGGTCCGGGAATGCCTGAGATGTTAACACCAACAAGTGCAATAATGGGTGCAGGTCTTGGAA--
                                      ||  |    |     ||| | ||||   | |||||||  ||  | ||  |   | |  |  ||||||    ||| |||| ||||||||||| || ||||| |||||||||||||||||||||||| |||| || |||||||| || |||||||| ||  | || |  
-------------------------------------gtatacttttttctctatgtccaaaaca-agatatgataatcactggtgatcggtgaaatgctcagggctccgtgattgttatcagGGGAGAAGGTCCCAAAGGTGGTCCGGGAATGCCTGAGATGCTAACTCCTACAAGTGCGATCATGGGTGCTGGCTTGGGGAAG

upper sequence: GLYMA13G27810.1 (Glycine max), 3'ss of exon 10
lower sequence: EFJ18571 (Selaginella moellendorffii), 3'ss of exon 11
caattttgctgtagtatttgtttggtttgacacagatataaccacagtaggtgatggctaaaatggaaatatgatttcttttgtattttcattttttcagGGGAAAGTGGTTGTAATCAGGGGAGAGGGACCCAAGGGTGGTCCGGGAATGCCTGAGATGTTAACACCAACAAGTGCAATAATGGGTGCAGGTCTTGGAA
                   ||||  |||        | |  ||| || | |  |||              || ||  ||  ||     | |  |  ||||||    ||| |||| ||||||||||| || ||||| |||||||||||||||||||||||| |||| || |||||||| || |||||||| ||  | || |
-------------------gtttacttt--tttctctctgtccaaagcaagatatg--------------ataatcactggtgatcggtgaaatactcagGGCTCCGTGATTGTTATCAGGGGAGAAGGTCCCAAAGGTGGTCCGGGAATGCCTGAGATGCTAACTCCTACAAGTGCGATCATGGGTGCTGGCTTGGGGA

upper sequence: GLYMA13G27810.1 (Glycine max), 3'ss of exon 10
lower sequence: EFJ36478 (Selaginella moellendorffii), 3'ss of exon 10
caattttgctgtagtatttgtttggtttgacacagatataaccacagtaggtgatggctaaaatggaaatatgatt-tcttttgtattt--tcattttttcagGGGAAAGTGGTTGTAATCAGGGGAGAGGGACCCAAGGGTGGTCCGGGAATGCCTGAGATGTTAACACCAACAAGTGCAATAATGGGTGCAGGTCTTGGAA
                                      ||  |    |      || | |||    | |||||||  ||  | ||  |   | |  |  ||||||    ||| |||| ||||||||||| || ||||| |||||||||||||||||||||||| |||| || |||||||| || |||||||| ||  | || |
-------------------------------------gtatacttttttctctctgtccaaagca-agatatgataatcactggtgatcggtgaaatactcagGGCGCCGTGATTGTTATCAGGGGAGAAGGTCCCAAAGGTGGTCCGGGAATGCCTGAGATGCTAACTCCTACAAGTGCGATCATGGGTGCTGGCTTGGGGA

upper sequence: GLYMA13G27810.1 (Glycine max), 3'ss of exon 10
lower sequence: EFJ36482 (Selaginella moellendorffii), 3'ss of exon 3
----------------caattttgctgtagtatttgtttggtttgacacagatataac-cacag---taggtgatggctaaaatggaaatatg---atttcttttgtattttcattttttcagGGGAAAGTGGTTGTAATCAGG------GGAGAGGGACCCAAGGGTGGT--CCGGGAATGCCTGAGATGTTAACACCAACAAGTGCAATAATGGGTGCAGGTCTTGGAA-----------------------
                  | |     | |  || |   |   | |  |  | |  ||  | |||   |  ||||| | ||  | ||   |  |   ||  ||    |  |  ||  |      ||||   ||| ||  |||         ||   |||  ||||  |   |   ||   |||     |||  | | |  | | | || | | ||    ||  | |   | |                       
gtatgctttttttctctcagtccagagcaagatataagtcactggtgatcggtgaaattctcagggctccgtgattgttatgagggtggtccgggaatgcctgagatgctaacacctacaagtgggatcatggatggtatctaatttctagGTTGGGGGTCCAATCGCCTTAGTCGAAGATGGTCATGATAATGAGA--AGCGACTG-ATTGATCTCGGCGTGGCCGAGGACGAGCTAGCGGCACGAAAGAAAG

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|208239155|gb|GE037191.1|GE037191
EST:     GAGAGGAGGCAATGATTGCTGCCATTTCAGAGGATCCTTCGAGTTTTAAG                         GGGAAAGTGGTTGTAATCAGGGGAGAGGGACCCAAGGGTGGTCCGGGAATG
genomic: GAGAGGAGGCAATGATTGCTGCCATTTCAGAGGATCCTTCGAGTTTTAAGgtatttcttt ... attttttcagGGGAAAGTGGTTGTAATCAGGGGAGAGGGACCCAAGGGTGGTCCGGGAATG
EST: gi|193485361|gb|FK452473.1|FK452473
EST:     AGGATCCTTCGAG-TTTAA-                         GGGAAAGTGGTTGTAATCAGGGGAGAGGGACCCAAGGGTGGTCCGGGAATG
genomic: AGGATCCTTCGAGTTTTAAGgtatttcttt ... attttttcagGGGAAAGTGGTTGTAATCAGGGGAGAGGGACCCAAGGGTGGTCCGGGAATG
EST: gi|23734787|gb|BU765638.1|BU765638
EST:     GAGAGGAGGCAATGATTGCTGCCATTTCAGAGGATCCTTCGAGTTTTAAG                         GGGAAAGTGGTTGTAATCAGGGGAGAGGGACCCAAGGGTGGTCCGGGAATG
genomic: GAGAGGAGGCAATGATTGCTGCCATTTCAGAGGATCCTTCGAGTTTTAAGgtatttcttt ... attttttcagGGGAAAGTGGTTGTAATCAGGGGAGAGGGACCCAAGGGTGGTCCGGGAATG
EST: gi|193477699|gb|FK442288.1|FK442288
EST:     GAGAGGAGGCAATGATTGCTGCCATTTCAGAGGATCCTTCGAG-TTTAA-                         GGGAAAGTGGTTGTAATCAGGGGAGAGGGACCCAAGGGTGGTCCGGGAATG
genomic: GAGAGGAGGCAATGATTGCTGCCATTTCAGAGGATCCTTCGAGTTTTAAGgtatttcttt ... attttttcagGGGAAAGTGGTTGTAATCAGGGGAGAGGGACCCAAGGGTGGTCCGGGAATG
EST: gi|207820136|gb|GD790014.1|GD790014
EST:     GAGAGGAGGCAATGATTGCTGCCATTTCAGAGGATCCTTCGAGTTTTAAG                         GGGAAAGTGGTTGTAA
genomic: GAGAGGAGGCAATGATTGCTGCCATTTCAGAGGATCCTTCGAGTTTTAAGgtatttcttt ... attttttcagGGGAAAGTGGTTGTAA
EST: gi|208038473|gb|GD833239.1|GD833239
EST:     GAGAGGAGGCAATGATTGCTGCCATTTCAGAGGATCCTTCGAGTTTTAAG                         GGGAAAGTGGTTGTAATCAGGGGAGAGGGACCCAAGGGTGGTCCGGGAATG
genomic: GAGAGGAGGCAATGATTGCTGCCATTTCAGAGGATCCTTCGAGTTTTAAGgtatttcttt ... attttttcagGGGAAAGTGGTTGTAATCAGGGGAGAGGGACCCAAGGGTGGTCCGGGAATG
EST: gi|151400516|gb|EV270330.1|EV270330
EST:     GAGAGGAGGCAATGATTGCTGCCATTTCAGAGGATCCTTCGAGTTTTAAG                         GGGAAAGTGGTTGTAATCAGGGGAGAGGGACCCAAGGGTGGTCCGGGAATG
genomic: GAGAGGAGGCAATGATTGCTGCCATTTCAGAGGATCCTTCGAGTTTTAAGgtatttcttt ... attttttcagGGGAAAGTGGTTGTAATCAGGGGAGAGGGACCCAAGGGTGGTCCGGGAATG
EST: gi|208287754|gb|GE081765.1|GE081765
EST:     GAGAGGAGGCAATGATTGCTGCCATTTCAGAGGATCCTTCGAGTTTTAAG                         GGGAAAGTGGTTGCAATCAGGGGAGAGGGACCCAAGGGTGGTCCGGGAATG
genomic: GAGAGGAGGCAATGATTGCTGCCATTTCAGAGGATCCTTCGAGTTTTAAGgtatttcttt ... attttttcagGGGAAAGTGGTTGTAATCAGGGGAGAGGGACCCAAGGGTGGTCCGGGAATG
EST: gi|16281629|gb|BI944586.1|BI944586
EST:     GAGAGGAGGCAATGATTGCTGCCATTTCAGAGGATCCTTCGAGTTTTAAG                         GGGAAAGTGGTTGTAATCAGGGGAGAGGGACCCAAGGGTGGTCCGGGAATG
genomic: GAGAGGAGGCAATGATTGCTGCCATTTCAGAGGATCCTTCGAGTTTTAAGgtatttcttt ... attttttcagGGGAAAGTGGTTGTAATCAGGGGAGAGGGACCCAAGGGTGGTCCGGGAATG
EST: gi|24136426|gb|BU926936.1|BU926936
EST:     GAGAGGAGGCAATGATTGCTGCCATTTCAGAGGATCCTTCGAGTTTTAAG                         GGGAAAGTGGTTGTAATCAGGGGAGAGGGACCCAAGGGTGGTCCGGGAATG
genomic: GAGAGGAGGCAATGATTGCTGCCATTTCAGAGGATCCTTCGAGTTTTAAGgtatttcttt ... attttttcagGGGAAAGTGGTTGTAATCAGGGGAGAGGGACCCAAGGGTGGTCCGGGAATG
EST: gi|208141207|gb|GD938251.1|GD938251
EST:     GAGAGGAGGCAATGATTGCTGCCATTTCAGAGGATCCTTCGAGTTTTAAG                         GGGAAAGTGGTTGTAATCAGGGGAGAGGGACCCAAGGGTGGTCCGGGAATG
genomic: GAGAGGAGGCAATGATTGCTGCCATTTCAGAGGATCCTTCGAGTTTTAAGgtatttcttt ... attttttcagGGGAAAGTGGTTGTAATCAGGGGAGAGGGACCCAAGGGTGGTCCGGGAATG
EST: gi|207822724|gb|GD793959.1|GD793959
EST:     GAGAGGAGGCAATGATTGCTGCCATTTCAGAGGATCCTTCGAGTTTTAAG                         GGGAAAGTGGTTGTAATCAGGGGAGAGGGACCCAAGGGTGGTCCGGGAATG
genomic: GAGAGGAGGCAATGATTGCTGCCATTTCAGAGGATCCTTCGAGTTTTAAGgtatttcttt ... attttttcagGGGAAAGTGGTTGTAATCAGGGGAGAGGGACCCAAGGGTGGTCCGGGAATG
EST: gi|151401192|gb|EV271006.1|EV271006
EST:     GAGAGGAGGCAATGATTGCTGCCATTTCAGAGGATCCTTCGAGTTTTAAG                         GGGAAAGTGGTTGTAATCAGGGGAGAGGGACCCAAGGGTGGTCCGGGAATG
genomic: GAGAGGAGGCAATGATTGCTGCCATTTCAGAGGATCCTTCGAGTTTTAAGgtatttcttt ... attttttcagGGGAAAGTGGTTGTAATCAGGGGAGAGGGACCCAAGGGTGGTCCGGGAATG
EST: gi|209715558|gb|BW682198.1|BW682198
EST:     CGAGTTTTAAG                         GGGAAAGTGGTTGTAATCAGGGGAGAGGGACCCAAGGGTGGTCCGGGAATG
genomic: CGAGTTTTAAGgtatttcttt ... attttttcagGGGAAAGTGGTTGTAATCAGGGGAGAGGGACCCAAGGGTGGTCCGGGAATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtaggtgatggctaaaatggaaatatgatttcttttgtattttcattttttcagGGGAAAGTGGTTGTAATCAGGGGAGAGGGACCCAAGGGTGGTCCGGGAATGCCTGAGATGTTAACACCAACAAGTGCAATAATGGGTGCAGGTCTTGGAA
          ggctaaa  putative branch site (score: 3)
                             tttcttttgtattttc  putative PPT
                     aaatatgatttctttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
caattttgctgtagtatttgtttggtttgacacagatataaccacagtaggtgatggctaaaatggaaatatgatttcttttgtattttcattttttcagGGGAAAGTGGTTGTAATCAGGGGAGAGGGACCCAAGGGTGGTCCGGGAATGCCTGAGATGTTAACACCAACAAGTGCAATAATGGGTGCAGGTCTTGGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - tgctgta
- - - - - - - - -ttgtttg
- - - - - - - - - - - - - -tgacaca
- - - - - - - - - - - - - - - - - - - -aaccaca
- - - - - - - - - - - - - - - - - - - - - - - - -ggtgatg