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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taatgctatgtatcaagttgcaatagcttgctgtggactgtggtttactctaatggcaggtctatttagcagtgctgaaagtattttgttcacattgcagAAATTTCTGGATAGCTCAAAGTTGAAAAGACATTTTCTCATTCATACAGGGGAGAGGGATTTTGTGTGTCCTCATGAAGGCTGTGGTAAG

Basic information

species Glycine max
transcript GLYMA05G30150.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA05G30150.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os02g34680.1 (Oryza sativa), 3'ss of exon 3
taatgctatgtatcaagttgcaatagcttgctgtggactgt--ggtttactctaatggcaggtctatttagcagt--gctgaaagtattttgttc---------acattgcagAAATTTCTGGATAGCTCAAAGTTGAAAAGACATTTTCTCATTCATACAGGGGAGAGGGATTTTGTGTGTCCTCATGAAGGCTGTGGTAAG
   | ||   | | |  || |  | || |||  ||| || |  || | ||| |          ||  |  |  ||  ||| |   |||||| ||          || |||||||||||| | || ||||| ||| |||| || |||||||| ||||||||||| |||| | | ||||| || ||||||||||||||||| |||
--gtactgcctgtaatctttc--ttgcctgcgttggcctttctggatcactatggcattgctgcttctgggttgttcgctaatgttattttctttttgaatctgactttgcagAAATTTTTAGACAGCTCTAAGCTGAAGAGGCATTTTCTTATTCATACAGGAGAGAAGAACTTTGTCTGCCCTCATGAAGGCTGTGGAAAG

upper sequence: GLYMA05G30150.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM5G885700_T02 (Zea mays), 3'ss of exon 3
----------taatgctatgtatcaagttgcaatagcttgctgtggactgtggtttactctaatggcaggtctatttagcagtgctgaaagtattttgttc-acattgcagAAATTTCTGGATAGCTCAAAGTTGAAAAGACATTTTCTCATTCATACAGGGGAGAGGGATTTTGTGTGTCCTCATGAAGGCTGTGGTAAG
          |||| |   ||  ||      | ||   | | ||   |   ||  |  |   ||  ||| |   || |  | | ||     |  |   |   |  |||||||||||  | ||||| || |||||||| ||||||||||| ||||||||||| || | | |||||||||| || |||||||| ||||| |||
gtactgtttataattcctggtcacatcccagagtaatcttcagtctgcaaaggcatgtttctatttcagttgc-ttgattaatcctttttctgctaaatctgattttgcagAAATTCTTAGATAGTTCTAAGTTGAAGAGACATTTTCTTATTCATACAGGAGAAAAGAATTTTGTGTGCCCACATGAAGGTTGTGGGAAG

upper sequence: GLYMA05G30150.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G140016_T01 (Zea mays), 3'ss of exon 3
--------taatgctatgtatcaagttgcaa--tagcttgctgtggactgtggtttactctaatggcag--gtctatttagcagtgctgaaagtattttgttcacattgcagAAATTTCTGGATAGCTCAAAGTTGAAAAGACATTTTCTCATTCATACAGGGGAGAGGGATTTTGTGTGTCCTCATGAAGGCTGTGGTAAG
        ||    |   | |||  |  ||   ||   | | ||   |   ||  |  ||  ||  |||  |  |   ||    |  |    |||  ||  | |  |||||||||||  | |||||||| |||||||| ||||||||||| || ||||| || |||| | |||||||||| || |||||||| ||||| | |
gtactgtttacccttccttttcacatcccagagtaatcttcagtctgcaaaggcatggtcccatttcagttgcttgactaatcttttttcgggtaaatt--tgattttgcagAAATTCTTAGATAGCTCTAAGTTGAAGAGACATTTTCTTATCCATACTGGAGAGAAGAATTTTGTGTGCCCACATGAAGGTTGTGGGAGG

upper sequence: GLYMA05G30150.1 (Glycine max), 3'ss of exon 3
lower sequence: AT4G06634.3 (Arabidopsis thaliana), 3'ss of exon 3
taatgctatgtatcaagttgcaatagcttgctgtggactgtg-gtttactctaatggcaggtctatttagcagtgctgaaagtattttgttcacattgcagAAATTTCTGGATAGCTCAAAGTTGAAAAGACATTTTCTCATTCATACAGGGGAGAGGGATTTTGTGTGTCCTCATGAAGGCTGTGGTAAG
        | ||  ||  | |  |   ||| | |||  |      | ||| | |||  |  |  |   |||  |  ||    | |||  ||    |  ||||||||||||||||| ||||||||||| ||||||| ||| |||||||| || |||||  ||| | | ||| || ||||||| ||||| |||
-------gtttaataatatcctctc-tttggtttggcttacacactcactttcatgatatattga---agccatcttg----tttttgttttttgtaacagAAATTTCTGGATAGTTCAAAGTTGAAGAGACATTATCTTATTCATACTGGAGAGAGAAATTATATATGTACTTATGAAGGATGTGGAAAG

upper sequence: GLYMA05G30150.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv12s0035g00660.t01 (Vitis vinifera), 3'ss of exon 3
taatgctatgtatcaagttgcaatagcttgctgtggactgtggtttactctaat--ggcaggtctatttagcagtgctgaaagtattttgt--tcacattgcagAAATTTCTGGATAGCTCAAAGTTGAAAAGACATTTTCTCATTCATACAGGGGAGAGGGATTTTGTGTGTCCTCATGAAGGCTGTGGTAAG
       |||| || | || |   |  || || |   ||    ||| ||||  |    ||||   ||    ||||| | ||||  | ||||  | |   ||||||||||| ||||||| |||||| |||||||||| || || ||||||||||| ||||| ||||||||||||||||||||||||||||| |||
-cccataatgtttctattttccccacttttctctcatcta-atttttctctgctccatcaggctgat--gacagtgttaaaagattcttgtatttatgatgcagAAATTTTTGGATAGTTCAAAGCTGAAAAGACACTTCCTGATTCATACAGGAGAGAGAGATTTTGTGTGTCCTCATGAAGGCTGTGGGAAG

upper sequence: GLYMA05G30150.1 (Glycine max), 3'ss of exon 3
lower sequence: PP1S42_134V6.1 (Physcomitrella patens), 3'ss of exon 3
taatgctatgtatcaagttgcaatagcttgctgt-ggactgtggtttactctaatggcaggtctatttagcagtgctgaaagtattt--tgttcacattgcagAAATTTCTGGATAGCTCAAAGTTGAAAAGACATTTTCTCATTCATACAGGGGAGAGGGATTTTGTGTGTCCTCATGAAGGCTGTGGTAAG
      ||| | |    | |  |    ||  | | ||| | ||  ||  |   | |     | | |     | |  ||| |  ||||  |||  || |  |||   ||  | || ||||||||| |||||||||||||||| |||||||| ||||||| | ||||||| |||||   |||||||||||| |||
--tccttatctgttttctagacacgctttattattggaatatgtgttcttaccaagttctctttgtcatcaacttatgataacatttgatgtctacgt-acagCGTTTCGTCGACAGCTCAAAGCTGAAAAGACATTTTCTGATTCATACGGGGGAGAAGCATTTTGTTTGTCCATTTGAAGGCTGTGGCAAG

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|193694541|gb|FK628593.1|FK628593
EST:     TATGTTTGTCACTACGATGGATGTGGAAAG                         AAATTTCTGGATAGCTCAAAGTTGAAAAGACATTTTCTCATTCATACAGGG
genomic: TATGTTTGTCACTACGATGGATGTGGAAAGgtagtggttt ... cacattgcagAAATTTCTGGATAGCTCAAAGTTGAAAAGACATTTTCTCATTCATACAGGG
EST: gi|298195839|gb|HO044230.1|HO044230
EST:     ACATCCATGGAGAGAGGCAGTATGTTTGTCACTACGATGGATGTGGAAAG                         AAATTTCTGGATAGCTCAAAGTTGAAAAGACATTTTCTCATTCATACAGGG
genomic: ACATCCATGGAGAGAGGCAGTATGTTTGTCACTACGATGGATGTGGAAAGgtagtggttt ... cacattgcagAAATTTCTGGATAGCTCAAAGTTGAAAAGACATTTTCTCATTCATACAGGG
EST: gi|193372458|gb|FK337411.1|FK337411
EST:     TATGTTTGTCACTACGATGGATGTGGAAAG                         AAATTTCTGGATAGCTCAAAGTTGAAAAGACATTTTCTCATTCATACAGGG
genomic: TATGTTTGTCACTACGATGGATGTGGAAAGgtagtggttt ... cacattgcagAAATTTCTGGATAGCTCAAAGTTGAAAAGACATTTTCTCATTCATACAGGG
EST: gi|192333661|gb|FK025772.1|FK025772
EST:     ACATCCATGGAGAGAGGCAGTATGTTTGTCACTACGATGGATGTGGAAAG                         AAATTTCTGGATAGCTCAAAGTTGAAAAGACATTTTCTCATTCATACAGGG
genomic: ACATCCATGGAGAGAGGCAGTATGTTTGTCACTACGATGGATGTGGAAAGgtagtggttt ... cacattgcagAAATTTCTGGATAGCTCAAAGTTGAAAAGACATTTTCTCATTCATACAGGG
EST: gi|193646854|gb|FK588833.1|FK588833
EST:     TATGTTTGTCACTACGATGGATGTGGAAAG                         AAATTTCTGGATAGCTCAAAGTTGAAAAGACATTTTCTCATTCATACAGGG
genomic: TATGTTTGTCACTACGATGGATGTGGAAAGgtagtggttt ... cacattgcagAAATTTCTGGATAGCTCAAAGTTGAAAAGACATTTTCTCATTCATACAGGG
EST: gi|193701743|gb|FK640435.1|FK640435
EST:     TATGTTTGTCACTACGATGGATGTGGAAAG                         AAATTTCTGGATAGCTCAAAGTTGAAAAGACATTTTCTCATTCATACAGGG
genomic: TATGTTTGTCACTACGATGGATGTGGAAAGgtagtggttt ... cacattgcagAAATTTCTGGATAGCTCAAAGTTGAAAAGACATTTTCTCATTCATACAGGG
EST: gi|298163204|gb|HO011937.1|HO011937
EST:     ACATCCATGGAGAGAGGCAGTATGTTTGTCACTACGATGGATGTGGAAAG                         AAATTTCTGGATAGCTCAAAGTTGAAAAGACATTTTCTCATTCATACAGGG
genomic: ACATCCATGGAGAGAGGCAGTATGTTTGTCACTACGATGGATGTGGAAAGgtagtggttt ... cacattgcagAAATTTCTGGATAGCTCAAAGTTGAAAAGACATTTTCTCATTCATACAGGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tactctaatggcaggtctatttagcagtgctgaaagtattttgttcacattgcagAAATTTCTGGATAGCTCAAAGTTGAAAAGACATTTTCTCATTCATACAGGGGAGAGGGATTTTGTGTGTCCTCATGAAGGCTGTGGTAAG
  ctctaat  putative branch site (score: 3)
                                      ttttgttc  putative PPT
                                aaagtatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
taatgctatgtatcaagttgcaatagcttgctgtggactgtggtttactctaatggcaggtctatttagcagtgctgaaagtattttgttcacattgcagAAATTTCTGGATAGCTCAAAGTTGAAAAGACATTTTCTCATTCATACAGGGGAGAGGGATTTTGTGTGTCCTCATGAAGGCTGTGGTAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG
- -tgctatg
- - - - - - - -agttgca
- - - - - - - - - - - - -gcttgct
- - - - - - - - - - - - - - - - - - actgtgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - -gcaggtc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgctgaa