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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctcagggacgacctcgagaggctcaagaagatcaggcaagccattttttcctttcaatctcttacggatggatggattgacttgaggttatcttccttagGGACCACCGTGGTCTTCGTCACTACTGGGGTCTGCGCGTCCGCGGGCAGCACACCAAGACCACCGAACGCCGTGGAAGAACCGTGGGAGTCTCCAAGAAA

Basic information

species Selaginella moellendorffii
transcript EFJ25542
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ25542 (Selaginella moellendorffii), 3'ss of exon 4
lower sequence: LOC_Os07g07709.1 (Oryza sativa), 3'ss of exon 3
-----ctcagggacgacctcgagaggctcaagaagatcaggcaagccattttttcctttcaatctcttacggatggatggattgacttgaggttatcttccttagGGACCACCGTGGTCTTCGTCACTACTGGGGTCTGCGCGTCCGCGGGCAGCACACCAAGACCACCGAACGCCGTGGAAGAACCGTGGGAGTCTCCAAGAAA
     ||    |   ||  | |     || |||  || |   |  |||   |         ||  | ||  | || || ||   |||  |  || |  | |  ||| ||||||||||||| ||||||||||||||||| || |||||||| |||||||||||||| || |   |  | ||||  || || || ||||||||||| 
tgtttctttcagcttactcccaataa-tctagattataata-atcccaagctgaaagaaacatggccta-agttgaatcgaactactccattttgtaatgc--agGAACCACCGTGGTCTCCGTCACTACTGGGGTCTCCGTGTCCGCGGTCAGCACACCAAGACTACTGGCAGGAGGGGAAAGACTGTCGGTGTCTCCAAGAAG

upper sequence: EFJ25542 (Selaginella moellendorffii), 3'ss of exon 4
lower sequence: LOC_Os07g07719.1 (Oryza sativa), 3'ss of exon 2
ctcagggacgacctcgagaggctcaagaagatcaggcaagccattttttcctttcaatct--cttacggatggatggattgacttgaggttatcttc----cttagGGACCACCGTGGTCTTCGTCACTACTGGGGTCTGCGCGTCCGCGGGCAGCACACCAAGACCACCGAACGCCGTGGAAGAACCGTGGGAGTCTCCAAGAAA
         | | | |    ||| |      |  |  ||   |||   | ||   | |    |  |  | |   ||  || | ||||  |    ||      | ||| ||||||||||||| ||||||||||||||||| || ||||| || |||||||||||||| || |   |  | ||||  || || || ||||||||||| 
------cgaggctttggactgctaacttctttgggctaattaattgcattctcagagttgaacaaattgctctttgatttcatttgaactaccttttgtaattcagGAACCACCGTGGTCTCCGTCACTACTGGGGTCTCCGTGTCCGTGGTCAGCACACCAAGACTACTGGCAGGAGGGGAAAGACTGTCGGTGTCTCCAAGAAG

upper sequence: EFJ25542 (Selaginella moellendorffii), 3'ss of exon 4
lower sequence: LOC_Os07g07770.1 (Oryza sativa), 3'ss of exon 2
ctcagggacgacctcgagaggctca-agaagatcaggcaagccattttttcctttcaatctcttacggatggatg-gattga--cttgaggttatcttccttagGGACCACCGTGGTCTTCGTCACTACTGGGGTCTGCGCGTCCGCGGGCAGCACACCAAGACCACCGAACGCCGTGGAAGAACCGTGGGAGTCTCCAAGAAA
     |       |    |  |||| ||  || ||       | ||  || | ||  | ||  ||||  |   ||  || ||  | |    || | |   | ||| ||||||||||||| ||||||||||||||||| || ||||| || |||||||||||||| || |   |  | ||||  || || || ||||||||||| 
----cgagtactttttgtattctcacagttgaacaaattgcgctttgatttcatttgaactactacgattaattgtaatcgaaccatatctttttgtaattcagGAACCACCGTGGTCTCCGTCACTACTGGGGTCTCCGTGTCCGTGGTCAGCACACCAAGACTACTGGCAGGAGGGGAAAGACTGTCGGTGTCTCCAAGAAG

upper sequence: EFJ25542 (Selaginella moellendorffii), 3'ss of exon 4
lower sequence: LOC_Os03g58050.1 (Oryza sativa), 3'ss of exon 3
ctcagggacgacctcgagaggctcaagaag-atcagg-caagccattttttcctttcaatctcttacggatggatgga--ttgacttgaggt-tatcttccttagGGACCACCGTGGTCTTCGTCACTACTGGGGTCTGCGCGTCCGCGGGCAGCACACCAAGACCACCGAACGCCGTGGAAGAACCGTGGGAGTCTCCAAGAAA
     |   |    | ||    |||  | | ||  |  |     |  || |  |  | |||| |||||     ||     |||   | |  | |  |||    ||| |||||||||||||  | ||||||||||| || || || || ||||||||||||||||| |||| | |  | || |  || || || || |||||||| 
-----gtttgttacccaggcattcatcatgtattggatccctttaacttatgttgaccatcttttacgctctcatcacccttgcgctcacttgttccttgtacagGAACCACCGTGGTCTGAGGCACTACTGGGGCCTCCGTGTGCGTGGGCAGCACACCAAGACAACCGGAAGGAGGGGTAAGACTGTCGGTGTGTCCAAGAAG

upper sequence: EFJ25542 (Selaginella moellendorffii), 3'ss of exon 4
lower sequence: GRMZM2G130544_T02 (Zea mays), 3'ss of exon 3
--ctcagggacgacctcgagaggctcaagaagatcaggcaagccattttttcctttcaatctcttacggatggatggattgacttgaggttatcttccttagGGACCACCGTGGTCTTCGTCACTACTGGGGTCTGCGCGTCCGCGGGCAGCACACCAAGACCACCGAACGCCGTGGAAGAACCGTGGGAGTCTCCAAGAAA
  |    |  |    || | |  ||  |      ||   |    |  |  || | | |   |  || |    ||      || ||    || | |||   ||| ||||||||||||| |||||||||||||| || |||||||| || |||||||||||||| || |   | |||||||  ||||| || ||||||||||| 
gtccattgtgcactgtctacactctacattcttgcatcgagaatacatgatcttattatcgtagta-gcccagaccttcagatttttaatt-tgttctgcagGAACCACCGTGGTCTGCGTCACTACTGGGGCCTCCGCGTCCGTGGCCAGCACACCAAGACTACTGGTAGGCGTGGAAAGACCGTTGGTGTCTCCAAGAAG

upper sequence: EFJ25542 (Selaginella moellendorffii), 3'ss of exon 4
lower sequence: GRMZM2G178341_T02 (Zea mays), 3'ss of exon 2
ctcagggacgacctcgagaggctcaagaagatcaggcaagccattttttcctttcaatctcttacg--gatggatggattgacttgaggttatcttccttagGGACCACCGTGGTCTTCGTCACTACTGGGGTCTGCGCGTCCGCGGGCAGCACACCAAGACCACCGAACGCCGTGGAAGAACCGTGGGAGTCTCCAAGAAA
   ||    | |||  | |   | ||       | ||      |  ||   | |  |  || || |   |  |    ||   |      |  |  |    ||| ||||||||||||| |||||||||||||| || || ||||| || ||||||||||||||||| |   | || |||| ||| || || ||||||||||| 
--tagccgtggccttcaaattttaaatttttgtatgctgcatgtcattgtttatgtagttcctaagttaacagtcacatattcgcatcttcttggtttgcagGAACCACCGTGGTCTGCGTCACTACTGGGGCCTCCGTGTCCGTGGCCAGCACACCAAGACCACTGGCAGGCGCGGAAAAACTGTTGGTGTCTCCAAGAAG

upper sequence: EFJ25542 (Selaginella moellendorffii), 3'ss of exon 4
lower sequence: GRMZM2G062911_T01 (Zea mays), 3'ss of exon 3
--ctcagggacgacctcgagaggctcaagaagatcaggcaagccattttttcctttcaatctcttacggatggatggattgacttgaggttatcttccttagGGACCACCGTGGTCTTCGTCACTACTGGGGTCTGCGCGTCCGCGGGCAGCACACCAAGACCACCGAACGCCGTGGAAGAACCGTGGGAGTCTCCAAGAAA
   |||     |  |   |  |    | | |  ||   |||    |  || |  ||     |  |     || |||     ||   |  || | ||    ||| ||||||| ||||| |||||||||| ||| ||||| ||||  || |||||||||||||| || | | | |||||||  || || || || || ||||| 
ttttcatttgtgttcgtaactgttatatgcacttctcccaaaatttgcttgcggtttgtagttgtgttt-tgtatgcgac-acagaaccttgtgttatccagGAACCACCGAGGTCTCCGTCACTACTAGGGCCTGCGTGTCCATGGCCAGCACACCAAGACTACTGGAAGGCGTGGAAAGACTGTTGGTGTGTCAAAGAAG

upper sequence: EFJ25542 (Selaginella moellendorffii), 3'ss of exon 4
lower sequence: AT1G22780.1 (Arabidopsis thaliana), 3'ss of exon 3
-----ctcagggacg---acctcgagaggctcaagaagatcaggcaagccattttttcctttcaatctcttacggatggatggattgacttgaggttatcttccttagGGACCACCGTGGTCTTCGTCACTACTGGGGTCTGCGCGTCCGCGGGCAGCACACCAAGACCACCGAACGCCGTGGAAGAACCGTGGGAGTCTCCAAGAAA
      | |  || |    | | |     |||  |  | || |  || | || |    ||||     |  ||| ||  ||  ||||| |       | |   |   ||  |||| ||||||||  | |||||||||||||| || || || || ||||||||||| ||||||| |||||||||||  || || || || |||||||| 
aatgatttactgatgcatcctttgtttctctcttgttgttctgataatcgatatagaactttg---tttgtactgactga--gattgtcactgtaatgtaaac---agAAACCATCGTGGTCTGAGGCACTACTGGGGTCTCCGTGTACGTGGACAGCACACCAAAACCACCGGACGCCGTGGAAAGACTGTTGGTGTTTCCAAGAAG

upper sequence: EFJ25542 (Selaginella moellendorffii), 3'ss of exon 4
lower sequence: Vv05s0020g03450.t01 (Vitis vinifera), 3'ss of exon 3
--ctcagggacgacctcgagaggctcaagaagatcaggcaagccattttttcctttcaatctcttacggatggatggattgacttgaggttatcttcctt----agGGACCACCGTGGTCTTCGTCACTACTGGGGTCTGCGCGTCCGCGGGCAGCACACCAAGACCACCGAACGCCGTGGAAGAACCGTGGGAGTCTCCAAGAAA
  |||  |  |     | |    || |     |      | |      | |  ||  ||    | |  |  ||   | |     |||  | || |||  |    ||| |||||||||||||||| |||||||||||||| || || ||||| || ||||||||||| || |  ||| | || | ||| || || ||||| || || 
tgctcgtgagcattgccta----cttattttcactgcatatgtatccatctgtttataagaggtgatag--gggcagttaacactgatatcattttcaatggacagGAACCACCGTGGTCTTCGACACTACTGGGGTCTACGTGTACGCGGACAACACACCAAGACAACTGGCCGCAGAGGGAAAACTGTTGGTGTCTCAAAAAAG

upper sequence: EFJ25542 (Selaginella moellendorffii), 3'ss of exon 4
lower sequence: Vv18s0072g00060.t01 (Vitis vinifera), 3'ss of exon 4
----ctcagggacgacctcgagaggctcaagaagatcaggcaagccattttttcctttcaatctcttacgg-atggatggattgacttgaggttatcttccttagGGACCACCGTGGTCTTCGTCACTACTGGGGTCTGCGCGTCCGCGGGCAGCACACCAAGACCACCGAACGCCGTGGAAGAACCGTGGGAGTCTCCAAGAAA
    | | | | | |      | ||    || || |   | | |   |||   |             | |  |      | |   |||||   | |  | |  ||| |||||||||||||  | ||||||||||| || || || ||||| ||||||||||||||||| |  ||  | ||||  || || || ||||| ||||| 
agggcaccgtgtccattgtttgtggt---agtaggttgtgaatgaagtttaggctaggtggggaaacatgatactttcagctaatcttgatactgttatgc--agGAACCACCGTGGTCTGAGGCACTACTGGGGCCTCCGTGTTCGCGGCCAGCACACCAAGACCACAGGTCGTAGAGGAAAGACTGTTGGTGTCTCTAAGAAG

upper sequence: EFJ25542 (Selaginella moellendorffii), 3'ss of exon 4
lower sequence: PP1S72_222V6.2 (Physcomitrella patens), 3'ss of exon 3
ctcagggacgacctcgagaggctcaa--gaagatcaggcaagccattttttc---ctttcaatctcttacggatggatggattgacttgaggttatcttccttagGGACCACCGTGGTCTTCGTCACTACTGGGGTCTGCGCGTCCGCGGGCAGCACACCAAGACCACCGAACGCCGTGGAAGAACCGTGGGAGTCTCCAAGAAA
   ||   |    ||     || |||   | | || |||    ||| ||| |    |||     |||| | ||| | |   | || |||| |||   |   | ||| | ||||||||||||||||| ||||||||  ||||||| || || || ||||||||||| |||| ||| |||||||||||||| || || |||||||| 
--tagtctcattttcttcgagcgcaatgaaggctcgggcttttcatatttgcgatttttgtggttcttcctgataggt---tagagttgatgttgattgattcagGAATCACCGTGGTCTTCGTCATTACTGGGGCTTGCGCGTGCGTGGTCAACACACCAAGACTACCGGACGACGTGGAAGAACCGTTGGTGTGTCCAAGAAG

upper sequence: EFJ25542 (Selaginella moellendorffii), 3'ss of exon 4
lower sequence: PP1S242_94V6.1 (Physcomitrella patens), 3'ss of exon 3
ctcagggacgacctcgagaggctcaagaagatcaggcaagccattttttc---ctttcaatct-cttacggatggatggattgacttgaggttatcttccttagGGACCACCGTGGTCTTCGTCACTACTGGGGTCTGCGCGTCCGCGGGCAGCACACCAAGACCACCGAACGCCGTGGAAGAACCGTGGGAGTCTCCAAGAAA
    ||       |    |   ||  |     ||||    |  || |||     | |   | |  || |   ||  |||| |    || || |||  |    ||| ||||||||||||||||||||||||||||  |||| || ||||| |||||||| ||||| || | ||| |||||||| ||||| || || |||||||| 
---gggtgtcttgtttgtatcatcccggtttacaggttgtcggttctttgaagatctggttttgttttctactgattggagtcgactgtggctattattgc-agGAACCACCGTGGTCTTCGTCACTACTGGGGCTTGCGAGTACGCGGACAGCACACAAAGACTACTGGACGGCGTGGAAGGACCGTCGGTGTGTCCAAGAAG

upper sequence: EFJ25542 (Selaginella moellendorffii), 3'ss of exon 4
lower sequence: PP1S14_433V6.1 (Physcomitrella patens), 3'ss of exon 3
------ctcagggacgacctcgagaggctcaagaagatcaggcaagccattttttcctttcaatctcttacggatggatggattgacttgaggttatcttccttagGGACCACCGTGGTCTTCGTCACTACTGGGGTCTGCGCGTCCGCGGGCAGCACACCAAGACCACCGAACGCCGTGGAAGAACCGTGGGAGTCTCCAAGAAA
       |  |  | |   | || |   | | |     ||  || ||  | | |       | | |  |     ||||      | |||| | | ||       ||| ||||||||||||||||||||||||||||  |||| || || || || ||||||||||| || | | | ||||| |||||||| ||||| |||||||| 
tcatggatatgaaatgtattagatatttttaggcttcgcat-catgcagtatgtgagggcgattatggtcttattggagatgccgtcttgtgatcatgc-----agGAACCACCGTGGTCTTCGTCACTACTGGGGCTTGCGTGTACGTGGTCAACACACCAAGACAACTGGAAGACGTGGTAGAACCGTCGGAGTGTCCAAGAAG

upper sequence: EFJ25542 (Selaginella moellendorffii), 3'ss of exon 4
lower sequence: PP1S215_81V6.1 (Physcomitrella patens), 3'ss of exon 3
ctcagggacgacctcgagaggctcaagaagatcaggcaagccattttttcctt-tcaatctcttacggatggatggattgacttgaggttatcttccttagGGACCACCGTGGTCTTCGTCACTACTGGGGTCTGCGCGTCCGCGGGCAGCACACCAAGACCACCGAACGCCGTGGAAGAACCGTGGGAGTCTCCAAGAAA
 |           | ||     |         ||  |    | ||| |   || | |||  ||      | | || | | | | |  | | | |     ||| ||||||||||||||||||||||||||||  |||| || || || |||||||||||||| || | ||| |||||| | ||||| || || || ||||| 
tttttttcttgtatggatctttttttcgtacacattcttttcttttgtagattcttaattactctaatgttgctgaaatcaatggccgct-tatgttgcagGAACCACCGTGGTCTTCGTCACTACTGGGGCTTGCGTGTACGTGGACAGCACACCAAGACAACTGGACGTCGTGGACGGACCGTTGGTGTGTCTAAGAAG

upper sequence: EFJ25542 (Selaginella moellendorffii), 3'ss of exon 4
lower sequence: PP1S14_438V6.1 (Physcomitrella patens), 3'ss of exon 3
ctcagggacgacctcgagaggctcaagaagatcaggcaagccattttttcctttcaatctcttacggatggatggattgacttgaggttatcttcct-tagGGACCACCGTGGTCTTCGTCACTACTGGGGTCTGCGCGTCCGCGGGCAGCACACCAAGACCACCGAACGCCGTGGAAGAACCGTGGGAGTCTCCAAGAAA
 || | |||     |   |   | |   |   || |       |||     | |    |  |     || ||    ||         |||  ||  |  ||| |||||||||| ||||| |||||||||||  ||||||| || || ||||| |||||||| || |  || |||||||||||||| || || |||||||| 
-tctgagacagttcctcaattgttagtgatcacatgtttttagtttgccattcttgggcggtgttttattgactctttctgaaacatttaatttgttgcagGAACCACCGTGGACTTCGACACTACTGGGGCTTGCGCGTGCGTGGACAGCATACCAAGACTACAGGGCGACGTGGAAGAACCGTCGGTGTGTCCAAGAAG

upper sequence: EFJ25542 (Selaginella moellendorffii), 3'ss of exon 4
lower sequence: PP1S215_71V6.1 (Physcomitrella patens), 3'ss of exon 3
----------------------------------------------------------------------ctcagggac--gacctcgagaggctcaagaagatcaggcaagccattttttcctttcaatc-tcttacggatggatggattgacttgaggttatcttccttagGGACCACCGTGGTCTTCGTCACTACTGGGGTCTGCGCGTCCGCGGGCAGCACACCAAGACCACCGAACGCCGTGGAAGAACCGTGGGAGTCTCCAAGAAA
                                                                      ||   |      ||   |     ||| |    ||   ||  | | ||      |    ||   |||  |    || || |||  ||| ||    |      ||| ||||||||||||||||||||||||||||  |||| || || || || ||||| ||||| || | ||| |||||||| ||||| || || || ||||| 
gttagtgaaattttcttcttccagtttatgattaatgcttattcaaatttatatttacaaatatagatcacttgtgatttgaactatgcagcactctattgcattgcgcctggctttaggcagtgctgattgccttgtgtcatgacggcttggtttgggggatgc------agGAACCACCGTGGTCTTCGTCACTACTGGGGCTTGCGAGTACGTGGTCAACACACGAAGACAACTGGACGTCGTGGAAGGACCGTCGGTGTGTCTAAGAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttcctttcaatctcttacggatggatggattgacttgaggttatcttccttagGGACCACCGTGGTCTTCGTCACTACTGGGGTCTGCGCGTCCGCGGGCAGCACACCAAGACCACCGAACGCCGTGGAAGAACCGTGGGAGTCTCCAAGAAA
                             gattgac  putative branch site (score: 3)
                                          ttatcttcctt  putative PPT
      tttcaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctcagggacgacctcgagaggctcaagaagatcaggcaagccattttttcctttcaatctcttacggatggatggattgacttgaggttatcttccttagGGACCACCGTGGTCTTCGTCACTACTGGGGTCTGCGCGTCCGCGGGCAGCACACCAAGACCACCGAACGCCGTGGAAGAACCGTGGGAGTCTCCAAGAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - cgacctc
- - - - - - - - -gaggctc
- - - - - - - - - - - - aagaaga
- - - - - - - - - - - - - - - - caggcaag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttgactt