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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaattgatctgttagaccttgtggttccccttcaaaagtttgatagcattggaaaatattgagtagtttttggctggtctgatttatgttctgtggtgtaataaatttcattatgcatgtgttacattacagGTGCTAATGATGTCTCAATGATCCAAATGGCTGATGTTGGAGTTGGCATCAGTGGACAAGAGGGTCGGCAAGCTGTAATGGCATCTGATTTTGCAATGGG

Basic information

species Glycine max
transcript GLYMA04G16040.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA04G16040.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os01g17010.1 (Oryza sativa), 3'ss of exon 4
gtaattgatctgttagaccttgtggttccccttcaaaagtttgatagcattggaaaatattgagtagtttttggctggtctgatttatgttctgtggtgtaataaatttcattatgcatgtgttacattacagGTGCTAATGATGTCTCAATGATCCAAATGGCTGATGTTGGAGTTGGCATCAGTGGACAAGAGGGTCGGCAAGCTGTAATGGCATCTGATTTTGCAATGGG
                     ||  |   || ||     | || ||  || || | ||| |       || ||   |  |  |||||||| |     ||| ||| ||   |  ||  || | ||    | ||||||| |||||||| |||||||| ||||||||||||||||| |||||||||||||| ||||| || ||||| |||||||||||||| |||||||| |||||
---------------------gtattattccctcctggttctgctattat-ggcatataata------ttctgtgagaaccaatttatgtac----atgtgatatatgcta--attaatcttttgttgttcagGTGCAAATGATGTTTCAATGATTCAAATGGCTGATGTTGGTGTTGGCATCAGTGGTCAAGAAGGACGGCAGGCTGTAATGGCATCAGATTTTGCGATGGG

upper sequence: GLYMA04G16040.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os03g20949.1 (Oryza sativa), 3'ss of exon 4
gtaattgatctgttagaccttgtggttccccttcaaaagtttgatagcattggaaaatattgagtagtttttggctggtctgatttatgttctgtggtgtaataaatttcattatgcatgtgttacattacagGTGCTAATGATGTCTCAATGATCCAAATGGCTGATGTTGGAGTTGGCATCAGTGGACAAGAGGGTCGGCAAGCTGTAATGGCATCTGATTTTGCAATGGG
                                   | |||||  |    | |  ||||||| || | ||  |   || | |  | ||| ||      | | | ||                ||  | || ||||||| |||||||| || ||||| |||||||||||||||||  ||||||||||||||||||| ||  |||||||||| |||||||| ||            
---------------------------------gtacagtttttttttctcgccaaatattcaggaattact---tgatttactatatttttctcaatctgaaaag-------------agGTACCTTTCCAGGTGCAAATGATGTATCCATGATTCAAATGGCTGATGTTGGTATTGGCATCAGTGGACAAGAAGGAAGGCAAGCTGTTATGGCATCAGA------------

upper sequence: GLYMA04G16040.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM5G840699_T01 (Zea mays), 3'ss of exon 4
gtaattgatctgttagaccttgtggttccccttcaaaagtttgatagcattggaaaatattgagtagtttttggctggtctgatttatgttctgtggtgtaataaatttcattatgcatgtgttacattacagGTGCTAATGATGTCTCAATGATCCAAATGGCTGATGTTGGAGTTGGCATCAGTGGACAAGAGGGTCGGCAAGCTGTAATGGCATCTGATTTTGCAATGGG
                    | |  |||||         | | ||     || |   ||||   ||   | |   || | || || |  |    || | || | |||||| |||     | |||      |||| || |||||||| |||||||| |||||||||||||||||  ||||||||||||| ||||| ||||| |||||||| |||||||| |||||| | |||||
-------------------gtattattccctcctgcttctcttattatggtgtattttattctctatgatct---tgatatg-ttcaaatc---tgatata-tgaatttccttaccttggcgtt------cagGCGCAAATGATGTTTCAATGATTCAAATGGCTGATGTTGGGATTGGCATCAGTGGCCAAGAAGGTCGACAAGCTGTTATGGCATCAGATTTTTCTATGGG

upper sequence: GLYMA04G16040.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G407825_T01 (Zea mays), 3'ss of exon 4
gtaattgatctgttagaccttgtggttccccttcaaaagtttgatagcattggaaaatattgagtagtttttggctggtctgatttatgttctgtggtgtaataaatttcattatgcatgtgttacattacagGTGCTAATGATGTCTCAATGATCCAAATGGCTGATGTTGGAGTTGGCATCAGTGGACAAGAGGGTCGGCAAGCTGTAATGGCATCTGATTTTGCAATGGG
                      |  ||||   | ||||  | |    ||  ||||     | || | ||  |      | || ||||| |||    ||  || |||| | |  |   |   |||    | ||||||| |||||||| || ||||| ||||||||||| |||||  | ||||||||||| ||||||||  |||||||||| ||||| || |||||||| |||||
---------------------attattccaacttaaaatgtagg--acaaaggaagtagctcagaacttcata-----tatgttttatcttcacgagt-caaaaaatatgaaaacatacacgtt----ttcagGTGCAAATGATGTATCCATGATTCAAATGGCTGACGTTGGCATCGGCATCAGTGGGCAAGAGGGAAGGCAAGCTGTTATGGCCTCAGATTTTGCCATGGG

upper sequence: GLYMA04G16040.1 (Glycine max), 3'ss of exon 4
lower sequence: AT5G04930.1 (Arabidopsis thaliana), 3'ss of exon 4
gtaattgatctgttagaccttgtggttccccttcaaaagtttgatagcattggaaaatattgagta-gtttttggctggtctgatttatgttctgtggtgtaataaatt--tcattatgcatgtgttacatt---acagGTGCTAATGATGTCTCAATGATCCAAATGGCTGATGTTGGAGTTGGCATCAGTGGACAAGAGGGTCGGCAAGCTGTAATGGCATCTGATTTTGCAATGGG
                     ||  |  |||  |     |||           ||| || |  |   | |  || ||   | ||   | ||||| |||| |  ||  ||  || |     |||  ||   ||   |||||||| ||||||||||| ||||| ||||||||||||||||| || || || || |||||||| ||||| |||||||| |||||||||||||| ||||||||
---------------------gtaatgaccccactcttcttt-------ccaaaaagtagtctgcctgatcctgtctaaacagaccca-gttctttggttttttattttcatcttctcatatgctttgtgttttgacagGTGCCAATGATGTCTCCATGATTCAAATGGCTGATGTTGGGGTAGGGATAAGCGGACAAGAAGGTCGCCAAGCTGTGATGGCATCTGATTTCGCAATGGG

upper sequence: GLYMA04G16040.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv13s0047g01210.t01 (Vitis vinifera), 3'ss of exon 4
---gtaattgatctgttagacc--ttgtggttccccttcaaaagtttgatagcattggaaaat-attgagtagtttttggctggtctgatttatgttctgtggtgtaataaatttcattatgcatgtgttacattacagGTGCTAATGATGTCTCAATGATCCAAATGGCTGATGTTGGAGTTGGCATCAGTGGACAAGAGGGTCGGCAAGCTGTAATGGCATCTGATTTTGCAATGGG
      |||  |||   |      ||  |  |        |   ||    |  |    ||||| |    | |        ||| |||| | | || | | | |  |||    ||  | | |  ||  | |   |  |||||||||||||||| |||||||| |||||||||||||| ||| |||| |||||||| |||||||| || |||||||| |||||||| ||||||||||||||
gtgagtattattcttccaatttatttaagactgataacttatgcttgcccaagaccaaaaaattagaagggaaaaaaaatctgatctgttgtttggttt-taggctaacgc-ttgaaatttctattggatgattcccagGTGCTAATGATGTTTCAATGATACAAATGGCTGATGTGGGAATTGGTATCAGTGGCCAAGAGGGCCGTCAAGCTGTCATGGCATCAGATTTTGCAATGGG

upper sequence: GLYMA04G16040.1 (Glycine max), 3'ss of exon 4
lower sequence: PP1S38_368V6.1 (Physcomitrella patens), 3'ss of exon 5
gtaattgatctgttagaccttgtggttccccttcaaaagtttgata-gcattggaaaatattgagtagtttttggctggtctgatttatgttctg-tggtgtaataaatttcattatgcatgtgttacattacagGTGCTAATGATGTCTCAATGATCCAAATGGCTGATGTTGGAGTTGGCATCAGTGGACAAGAGGGTCGGCAAGCTGTAATGGCATCTGATTTTGCAATGGG
                                  ||  |||  ||  |  || |||  |  | || ||    |  ||||  | |  || |||||| | |||||    |||| ||  ||    |  |  ||  ||||||| || || ||||| ||||| |||||||| || || ||||| ||||||||||| || || ||  |||| ||||| ||||| |||||||| ||||| ||
--------------------------------ataagtgttgaatctgtcttagaaggtgat-agcagcagcta-ctggcatcaagtacgttctggtagtgtagatcatttaat-gtgtcgtttctttatcgcagGTGCAAACGACGTCTCGATGATACAAATGGCCGACGTCGGAGTGGGCATCAGTGGGCAGGAAGGGAGGCAGGCTGTCATGGCCTCTGATTTCGCAATTGG

upper sequence: GLYMA04G16040.1 (Glycine max), 3'ss of exon 4
lower sequence: PP1S39_64V6.1 (Physcomitrella patens), 3'ss of exon 6
gtaattgatctgttagaccttgtggttccccttcaaaagtttgatagcattggaaaatattgagtagtttttggctggtctgatttatgttctgtggtgtaataaatttcattatgcatg---tgttacattacagGTGCTAATGATGTCTCAATGATCCAAATGGCTGATGTTGGAGTTGGCATCAGTGGACAAGAGGGTCGGCAAGCTGTAATGGCATCTGATTTTGCAATGGG
                               |||       |  ||  | | |||  | || |  |   ||  | |  ||| |  | ||| || | ||| | |  ||| |||    || |   || ||   | |||| || || || || |||||||| ||||||||||||||||||||||||||||| || || || || || ||||| || ||||| |||||||||||||||||
-------------------------------ttcgtgttactagta--agttgaagctcttca--aaacttcaggttctcttacatgtgt-ctttagtgcactttattacatgtcacaaggcttgctattgttcagGGGCAAACGACGTGTCAATGATACAAATGGCTGATGTTGGAGTTGGCATCAGCGGGCAGGAAGGGCGACAAGCAGTTATGGCGTCTGATTTTGCAATGGG

upper sequence: GLYMA04G16040.1 (Glycine max), 3'ss of exon 4
lower sequence: EFJ23939 (Selaginella moellendorffii), 3'ss of exon 5
gtaattgatctgttagaccttgtggttccccttcaaaagtttgatagcattggaaaatattgagtagtttttggctggtctgatttatgttctgtggtgtaataaatttcattatgcatgtgttacattacagGTGCTAATGATGTCTCAATGATCCAAATGGCTGATGTTGGAGTTGGCATCAGTGGACAAGAGGGTCGGCAAGCTGTAATGGCATCTGATTTTGCAATGGG
                                                                       |        |  |||| |   | |  || ||||| ||   ||    |    |||   |  |||||| ||||| ||  | ||||| || ||||| || || || ||||| || || |||||||| || |||||||| || |||||||| ||||||||||||  
----------------------------------------------------------------------gtaatcatctttgtttaggagatctcttg-aataatttctctt---taatctttaatctttagGTGCGAATGACGTAGCCATGATTCAGATGGCGGACGTAGGCGTTGGTATAAGCGGACAAGAAGGCCGGCAAGCAGTGATGGCATCGGATTTTGCAATGCC

upper sequence: GLYMA04G16040.1 (Glycine max), 3'ss of exon 4
lower sequence: EFJ16263 (Selaginella moellendorffii), 3'ss of exon 6
gtaattgatctgttagaccttgtggttccccttcaaaagtttgatagcattggaaaatattgagtagtttttggctggtctgatttatgttctgtggtgtaataaatttcattatgcatgtgttacattacagGTGCTAATGATGTCTCAATGATCCAAATGGCTGATGTTGGAGTTGGCATCAGTGGACAAGAGGGTCGGCAAGCTGTAATGGCATCTGATTTTGCAATGGG
                                                            |||||  |||||      | ||| || |||    | |   | |   ||||||| | |    |||    | |||| || ||||||||||| ||||| || |  || ||||||||| ||||  | ||||| || || ||||||||||| || ||||||||||| |||||| ||||
-----------------------------------------------------------gtgagtgattttttttctttttgacttttgtggcctag--aagtggttttcatt-tcccgaagttgtgct-cagGAGCCAATGATGTCTCCATGATACAGACAGCAGATGTTGGAATTGGATTGAGTGGCCAGGAAGGTCGGCAAGCAGTCATGGCATCTGACTTTGCATTGGG

upper sequence: GLYMA04G16040.1 (Glycine max), 3'ss of exon 4
lower sequence: EFJ21562 (Selaginella moellendorffii), 3'ss of exon 5
gtaattgatctgttagaccttgtggttccccttcaaaagtttgatagcattggaaaatattgagtagtttttggctggtctgatttatgttctgtggtgtaataaatttcattatgcatgtgttacattacagGTGCTAATGATGTCTCAATGATCCAAATGGCTGATGTTGGAGTTGGCATCAGTGGACAAGAGGGTCGGCAAGCTGTAATGGCATCTGATTTTGCAATGGG
                                                                       |        |  |||| |   | |  || ||||| ||   ||    |    |||   |  |||||| ||||| ||  | ||||| || ||||| || || || ||||| || || |||||||| || |||||||| || |||||||| ||||||||||||  
----------------------------------------------------------------------gtaatcatctttgtttaggagttctcttg-aataatttctctt---taatctttaatctttagGTGCGAATGACGTAGCCATGATTCAGATGGCGGACGTAGGCGTTGGTATAAGCGGACAAGAAGGCCGGCAAGCAGTGATGGCATCGGATTTTGCAATGCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctgatttatgttctgtggtgtaataaatttcattatgcatgtgttacattacagGTGCTAATGATGTCTCAATGATCCAAATGGCTGATGTTGGAGTTGGCATCAGTGGACAAGAGGGTCGGCAAGCTGTAATGGCATCTGATTTTGCAATGGG
 gtctgat  putative branch site (score: 4)
                   tgtaataaatttcatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaattgatctgttagaccttgtggttccccttcaaaagtttgatagcattggaaaatattgagtagtttttggctggtctgatttatgttctgtggtgtaataaatttcattatgcatgtgttacattacagGTGCTAATGATGTCTCAATGATCCAAATGGCTGATGTTGGAGTTGGCATCAGTGGACAAGAGGGTCGGCAAGCTGTAATGGCATCTGATTTTGCAATGGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG