Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaattgctcattttagaggaattgcatccttattgtacaaattaattaattaatataccctatgtagcccttacatggttggtgattttgtgacacacagAACATCCAAGGTTTCATGTGGGATGAGGAGAAAGTGAACAATGAGCTAAAGACCTACATGACCAAAGGTTTCAAAGATGTGAAGGAAATGTGCAAAACCC

Basic information

species Glycine max
transcript GLYMA16G04560.2
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G04560.2 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os03g58040.3 (Oryza sativa), 3'ss of exon 9
-----aaattgctcattttagaggaattgcatccttattgtacaaattaattaattaatataccctatgtagcccttacatg-----gttggtgattttgtgac--acacagAACATCCAAGGTTTCATGTGGGATGAGGAGAAAGTGAACAATGAGCTAAAGACCTACATGACCAAAGGTTTCAAAGATGTGAAGGAAATGTGCAAAACCC
       | ||| || | |    |   |  || |  | |  | |  | ||  | | |   ||  | | |   |   | ||||     | || || | |||||       |||||||| || |||||||||||||| |||||||| |||||||||||||| |||||||||||||||   || ||||  ||||||||||| |||||||  | ||
gtaagttactgcacaatctccctgtgctaaattcagagtaaaaatgtaaagcagtcaggttaagcaa-gagactgatgcatgaagctgctgctgttcttgtggtttgttcagAACATTCAGGGTTTCATGTGGGACGAGGAGAAGGTGAACAATGAGCTGAAGACCTACATGACCCGTGGGTTCAGGGATGTGAAGGAGATGTGCAGGAGCC

upper sequence: GLYMA16G04560.2 (Glycine max), 3'ss of exon 9
lower sequence: AT3G03910.1 (Arabidopsis thaliana), 3'ss of exon 8
aaattgctcattttagaggaattgca--tccttattgtacaaattaattaattaatataccctatgtagcccttaca-tggttggtgattttgtgacacacagAACATCCAAGGTTTCATGTGGGATGAGGAGAAAGTGAACAATGAGCTAAAGACCTACATGACCAAAGGTTTCAAAGATGTGAAGGAAATGTGCAAAACCC
                | || | | |  ||   | ||||  |  ||||  | |   |  ||  |      |   ||| || || ||| | |          ||||||| ||||| ||||||||||||||||| || ||||| |  ||||||||||||||||||||    || ||||||||  |||| ||||||||  | || |
--------------gtaagactcgaaaatcaagactgtatgacctaatcgaatctaaagcc--actcgatcaaaacactgatttgtgttatatctgtgtgaagAACATACAAGGATTCATGTGGGATGAGGAAAAGGTGAATAGGGAGCTAAAGACCTACATGACTCGCGGGTTCAAAGACTTGAAAGAAATGTGTCAGACGC

upper sequence: GLYMA16G04560.2 (Glycine max), 3'ss of exon 9
lower sequence: AT5G18170.1 (Arabidopsis thaliana), 3'ss of exon 8
-aaattgctcattttagaggaattgcatccttattgtacaaattaattaattaatataccctatgtagcccttacatggttggtgattttgtgacacacagAACATCCAAGGTTTCATGTGGGATGAGGAGAAAGTGAACAATGAGCTAAAGACCTACATGACCAAAGGTTTCAAAGATGTGAAGGAAATGTGCAAAACCC
  |  |     | |   |  || |  | | ||     || || || |  |  ||   | || || | |  |  |  | |||| |  |   || |    |||||||| ||||| || |||||||| || ||||| |||||| ||||||||||||| ||||||||      |||||| ||  |||| || ||||||||||| |
gtatgtatgagtctctcaacaact-tacctttgacagaccaagtactcgaacaa---aaccgattttgatcagat-tagttgtt--tccggtaatgtgcagAACATTCAAGGCTTTATGTGGGAGGAAGAGAAGGTGAACGATGAGCTAAAGACTTACATGACTCGCTCTTTCAAGGACTTGAAAGAGATGTGCAAAACTC

upper sequence: GLYMA16G04560.2 (Glycine max), 3'ss of exon 9
lower sequence: Vv08s0007g07400.t01 (Vitis vinifera), 3'ss of exon 10
aaattgctcattttagaggaattgcatccttattgtacaaattaattaattaatataccc---tatgtagcccttacatggttggtgattttgtgacacacagAACATCCAAGGTTTCATGTGGGATGAGGAGAAAGTGAACAATGAGCTAAAGACCTACATGACCAAAGGTTTCAAAGATGTGAAGGAAATGTGCAAAACCC
    ||||     |  |   | ||     || || || ||| | |  ||| ||| | | |   | || |        |   | |||| |||||||||   |||||||| ||||||||||||||||||||||||||||| |||||||| ||   ||| |||||||||| ||| ||||||||||||||||| ||||||| |||||
-tgatgctagagctgtaatgaatgttgaatt-ttataaaaactgac-aatgaatgtgcacacatttgcatggtagtaaaactcggtggttttgtgacttgcagAACATTCAAGGTTTCATGTGGGATGAGGAGAAAGTAAACAATGAACTGCGGACGTACATGACCAGAGGGTTCAAAGATGTGAAGGAGATGTGCAGAACCC

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|8401465|gb|BE057161.1|BE057161
EST:     TATTTGCAAATTCAGGAGGCGTTACAGTTAGCTACTTTGAGTGGGTTCAG                         AACATCCAAGGTTTCATGTGGGATGAGGAGAAAGTGAACAATGAGCTAAAG
genomic: TATTTGCAAATTCAGGAGGCGTTACAGTTAGCTACTTTGAGTGGGTTCAGgtaactatta ... tgacacacagAACATCCAAGGTTTCATGTGGGATGAGGAGAAAGTGAACAATGAGCTAAAG
EST: gi|21994949|gb|BQ786477.1|BQ786477
EST:     TATTTGCAAATTCAGGAGGCGTTACAGTTAGCTACTTTGAGTGGGTTCAG                         AACATCCAAGGTTTCATGTGGGATGAGGAGAAAGTGAACAATGAGCTAAAG
genomic: TATTTGCAAATTCAGGAGGCGTTACAGTTAGCTACTTTGAGTGGGTTCAGgtaactatta ... tgacacacagAACATCCAAGGTTTCATGTGGGATGAGGAGAAAGTGAACAATGAGCTAAAG
EST: gi|26058522|gb|CA801436.1|CA801436
EST:     TATTTGCAAATTCAGGAGGCGTTACAGTTAGCTACTTTGAGTGGGTTCAG                         ACCATCCAAGGTTTCATGTGG
genomic: TATTTGCAAATTCAGGAGGCGTTACAGTTAGCTACTTTGAGTGGGTTCAGgtaactatta ... tgacacacagAACATCCAAGGTTTCATGTGG
EST: gi|22541194|gb|BU091037.1|BU091037
EST:     TATTTGCAAATTCAGGAGGCGTTACAGTTAGCTACTTTGAGTGGGTTCAG                         AACATCCAACGTTTCATGTGGGATGAGGAGAAAGTGAACAATGAGCTAAAG
genomic: TATTTGCAAATTCAGGAGGCGTTACAGTTAGCTACTTTGAGTGGGTTCAGgtaactatta ... tgacacacagAACATCCAAGGTTTCATGTGGGATGAGGAGAAAGTGAACAATGAGCTAAAG
EST: gi|8404383|gb|BE060017.1|BE060017
EST:     TATTTGCAAATTCAGGAGGCGTTACAGTTAGCTACTTTGAGTGGGTTCAG                         AACATCCAAGGTTTCATGTGGGATGAGGAGAAAGTGAACAATGAGCTAAAG
genomic: TATTTGCAAATTCAGGAGGCGTTACAGTTAGCTACTTTGAGTGGGTTCAGgtaactatta ... tgacacacagAACATCCAAGGTTTCATGTGGGATGAGGAGAAAGTGAACAATGAGCTAAAG
EST: gi|12689220|gb|BG155556.1|BG155556
EST:     TTTGAGTGGGTTCAG                         AACATCCAAGGTTTCATGTGGGATGAGGAGAAAGTGAACAATGAGCTAAAG
genomic: TTTGAGTGGGTTCAGgtaactatta ... tgacacacagAACATCCAAGGTTTCATGTGGGATGAGGAGAAAGTGAACAATGAGCTAAAG
EST: gi|16346792|gb|BI972387.1|BI972387
EST:     ATATTGCAAATTCAGGAGGCGTTACAGTTAGCTACTTTGAGTGGGTTCAG                         AACATCCAAGGTTTCATGTGGGATGAGGAGAAAGTGAACAATGAGCTAAAG
genomic: AT-TTGCAAATTCAGGAGGCGTTACAGTTAGCTACTTTGAGTGGGTTCAGgtaactatta ... tgacacacagAACATCCAAGGTTTCATGTGGGATGAGGAGAAAGTGAACAATGAGCTAAAG
EST: gi|213614864|gb|DB978311.1|DB978311
EST:     TATTTGCAAATTAAGGATTCATTACAGTTAGCTACTTTGAGTGGGTTCAG                         AACATCCAAGGTTTCATGTGGGATGAGGAGAAAGTGAACAATGAGCTAAAG
genomic: TATTTGCAAATTCAGGAGGCGTTACAGTTAGCTACTTTGAGTGGGTTCAGgtaactatta ... tgacacacagAACATCCAAGGTTTCATGTGGGATGAGGAGAAAGTGAACAATGAGCTAAAG
EST: gi|8403457|gb|BE059091.1|BE059091
EST:     TATTTGCAAATTCAGGAGGCGTTACAGTTAGCTACTTTGAGTGGGTTCAG                         AACATCCAAGGTTTCATGTGGGATGAGGAGAAAGTGAACAATGAGCTAAAG
genomic: TATTTGCAAATTCAGGAGGCGTTACAGTTAGCTACTTTGAGTGGGTTCAGgtaactatta ... tgacacacagAACATCCAAGGTTTCATGTGGGATGAGGAGAAAGTGAACAATGAGCTAAAG
EST: gi|13252589|gb|BG363492.1|BG363492
EST:     TATTTGCAAATTCAGGAGGCGTTACAGTTAGCTACTTTGAGTGGGTTCAG                         AACATCCAAGGTTTCATGTGGGATGAGGAGAAAGTGAACAATGAGCTAAAG
genomic: TATTTGCAAATTCAGGAGGCGTTACAGTTAGCTACTTTGAGTGGGTTCAGgtaactatta ... tgacacacagAACATCCAAGGTTTCATGTGGGATGAGGAGAAAGTGAACAATGAGCTAAAG
EST: gi|8827932|gb|BE211662.1|BE211662
EST:     TATTTGCAAATTCAGGAGGCGTTACAGTTAGCTACTTTGAGTGGGTTCAG                         AACATCCAAGGTTTCATGTGGGATGAGGAGAAAGTGAACAATGAGCTAAAG
genomic: TATTTGCAAATTCAGGAGGCGTTACAGTTAGCTACTTTGAGTGGGTTCAGgtaactatta ... tgacacacagAACATCCAAGGTTTCATGTGGGATGAGGAGAAAGTGAACAATGAGCTAAAG
EST: gi|6200845|gb|AW152945.1|AW152945
EST:     TATTTGCAAATTCAGGAGGCGTTACAGTTAGCTACTTTGAGTGGGTTCAG                         AACATCCAAGGTTTCATGTGGGATGAGGAGAAAGTGAACAATGAGCTAAAG
genomic: TATTTGCAAATTCAGGAGGCGTTACAGTTAGCTACTTTGAGTGGGTTCAGgtaactatta ... tgacacacagAACATCCAAGGTTTCATGTGGGATGAGGAGAAAGTGAACAATGAGCTAAAG
EST: gi|192308766|gb|FG999791.1|FG999791
EST:     TATTTGCAAATTCAGGAGGCGTTACAGTTAGCTACTTTGAGTGGGTTCAG                         AACATCCAAGGTTTCATGTGGGATGAGGAGAAAGTGAACAATGAGCTAAAG
genomic: TATTTGCAAATTCAGGAGGCGTTACAGTTAGCTACTTTGAGTGGGTTCAGgtaactatta ... tgacacacagAACATCCAAGGTTTCATGTGGGATGAGGAGAAAGTGAACAATGAGCTAAAG
EST: gi|151413195|gb|EV283003.1|EV283003
EST:     TATTTGCAAATTCAGGAGGCGTTACAGTTAGCTACTTTGAGTGGGTTCAG                         AACATCCAAGGTTTCATGTGGGATGAGGAGAAAGTGAACAATGAGCTAAAG
genomic: TATTTGCAAATTCAGGAGGCGTTACAGTTAGCTACTTTGAGTGGGTTCAGgtaactatta ... tgacacacagAACATCCAAGGTTTCATGTGGGATGAGGAGAAAGTGAACAATGAGCTAAAG
EST: gi|8402782|gb|BE058416.1|BE058416
EST:     TATTTGCAAATTCAGGAGGCGTTACAGTTAGCTACTTTGAGTGGGTTCAG                         AACATCCAAGGTTTCATGTGGGATGAGGAGAAAGTGAACAATGAGCTAAAG
genomic: TATTTGCAAATTCAGGAGGCGTTACAGTTAGCTACTTTGAGTGGGTTCAGgtaactatta ... tgacacacagAACATCCAAGGTTTCATGTGGGATGAGGAGAAAGTGAACAATGAGCTAAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttaattaatataccctatgtagcccttacatggttggtgattttgtgacacacagAACATCCAAGGTTTCATGTGGGATGAGGAGAAAGTGAACAATGAGCTAAAGACCTACATGACCAAAGGTTTCAAAGATGTGAAGGAAATGTGCAAAACCC
                      cccttac  putative branch site (score: 3)
     taatata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaattgctcattttagaggaattgcatccttattgtacaaattaattaattaatataccctatgtagcccttacatggttggtgattttgtgacacacagAACATCCAAGGTTTCATGTGGGATGAGGAGAAAGTGAACAATGAGCTAAAGACCTACATGACCAAAGGTTTCAAAGATGTGAAGGAAATGTGCAAAACCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA