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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttctatgcatcgtttctcataatcttggctagatgctatctatttcttggagtccgtgagcactactaacactttcgtttttggctcttgctccacacagACAAGGCCAAGATGGGAGAGAAGGAATGGTACTTCTTCACGCTGCGAGACCGAAAGTATCCTACGGGAATGCGCACAAACCGAGCCACCGAGGCCGGATA

Basic information

species Selaginella moellendorffii
transcript EFJ37734
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ37734 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: LOC_Os09g32260.2 (Oryza sativa), 3'ss of exon 2
---ttctatgcatcgtttctcataatcttggctagatgctatctatttcttggagtccgtgagcactac-taacactttcgtttttggctcttgctccacacagACAAGGCCAAGATGGGAGAGAAGGAATGGTACTTCTTCACGCTGCGAGACCGAAAGTATCCTACGGGAATGCGCACAAACCGAGCCACCGAGGCCGGATA
   ||||     |         |  ||     |     |  |       |   | ||  |  |  |||  ||  | |||  | |        |||||||    || ||||| || |||||||||||||||||||||||||| |  ||  | || |||||||| || || ||  |||||||||||||||| ||  | || || ||
aggttctgaatgttcaaatatgtggtcacattttttcacacttacacattcacaatctatatgttctatgtattaattttctctaataaatgtgctcca----gAGAAGGCAAAAATGGGAGAGAAGGAATGGTACTTCTTTAGCCTAAGGGATCGAAAGTACCCAACTGGCGTGCGCACAAACCGAGCAACTAATGCTGGTTA

upper sequence: EFJ37734 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: LOC_Os11g03370.1 (Oryza sativa), 3'ss of exon 1
------------------------------------------ttctatgcatcgttt----ctcataatcttgg----ctagatgc-----tatctatttcttgg----agtccgtgagcactactaacactttcgtttttggctc---ttgctccacac---agACAAGGCCAAGATGGGAGAGAAGGAATGGTACTTCTTCACGCTGCGAGACCGAAAGTATCCTACGGGAATGCGCACAAACCGAGCCACCGAGGCCGGATA
                                          |||| |  |  || |       |||    | |     |||||||     |   |   |||||     | |  ||  |  |   ||  | | |  || |||   |   ||  |    |    || |||||| |||||||| ||||| ||||||||||||||||  |     |||   || || || ||||| ||||| || |||||||||||| |||  |||||
gtaagcctcaagtctcatatgcttacatccttaattctcttcttctctctagagtctagactagatagctgtagagatgtagatgcacaattgcttggctcttgatgttaatttgtttgttcatgtatgaatctgattattgatacaaattaatttgaattgaagGCAAGGCGAAGATGGGGGAGAAAGAATGGTACTTCTTCAGCCACAAGGACATGAAATACCCGACGGGGATGCGAACCAACCGAGCCACCAAGGAGGGATA

upper sequence: EFJ37734 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: LOC_Os03g42630.1 (Oryza sativa), 3'ss of exon 1
--ttctatgcat-cgtttctcataatcttggctagatgctatctatttcttggagtccgtgagcactactaacactttcgtttttggctcttgctccacacagACAAGGCCAAGATGGGAGAGAAGGAATGGTACTTCTTCACGCTGCGAGACCGAAAGTATCCTACGGGAATGCGCACAAACCGAGCCACCGAGGCCGGATA
   ||  ||||| | |     | ||   ||   |  | | |   | |   | || ||  |      |||  |      |  | |||     ||    |  ||| |||||| |  ||||| |||||||| |||||||||||||   |||| ||||| ||||| || ||||| || ||||| ||||| ||||| ||  |||| ||
atatcactgcatgcatacactacaaa--tgcacacgtacaaatgaatgaattga-tcaatcgttcttacacatgaacgcaatgttgatggatgtgatatgcagGCAAGGCAAGCATGGGGGAGAAGGAGTGGTACTTCTTCAGCATGCGCGACCGCAAGTACCCGACGGGGATCCGCACCAACCGCGCCACGGACTCCGGCTA

upper sequence: EFJ37734 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: GRMZM2G031001_T01 (Zea mays), 3'ss of exon 1
--------------------------------------------------------------------ttctatgcatcgtttctcataatcttggctagatgctatctatttcttggagtccgtg--agcactactaacactttcgtttttggctcttgctccacacagACAAGGCCAAGATGGGAGAGAAGGAATGGTACTTCTTCACGCTGCGAG-ACCGAAAGTATCCTACGGGAATGCGCACAAACCGAGCCACCGAGGCCGGATA
                                                                    || | ||  |   | ||  || |  | |       || ||| |    |||    | ||   ||   | |   |||       |||  | ||| |     ||| || |||||||||||| |||||||| ||||||||||||  ||  | || | || ||||| || ||||| | ||| || ||||| ||||| ||| |||| ||
gttagcactgcgcgctactgcttgatacgtcctcacctcaaagagccaaatagacctgcacctcttttttttttgactttgtgcttgtactagtagtacttctctttctctcggctgggaatcatggcggcctaaatttaactgggaagcttgcgttttgatttctccagGCAGGGCCAAGATGGGGGAGAAGGAGTGGTACTTCTTC-TGCCACAAGGATCGCAAGTACCCGACGGGCACGCGGACCAACCGCGCCACGGAGACCGGCTA

upper sequence: EFJ37734 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: GRMZM2G159500_T01 (Zea mays), 3'ss of exon 1
------------------------------------------ttctatgcatcgtttctcataat-cttggctagatgctatctatttcttggagtccgtgagc--actactaacactttcgtttttggctcttgctccacacagACAAGGCCAAGATGGGAGAGAAGGAATGGTACTTCTTCACGCTGCGAG-ACCGAAAGTATCCTACGGGAATGCGCACAAACCGAGCCACCGAGGCCGGATA
                                            ||   | |  |||| | |  | |||       |  ||  | |    ||||  || ||  |  || |  || |     |   || ||  | | |     ||| || |||||||||||| |||||||| ||||||||||||  ||  | || | || ||||| || ||||| | ||| || ||||| ||||| ||| |||| ||
gttagtacttgctgctactgcatcgacgcctcatagctctaaacctgcaccttttttccccttgtgcttctactagtagtacttctcggctggaaaccatgccctaaccaaaaaaaggacggaactttgcgttggatttctccagGCAGGGCCAAGATGGGGGAGAAGGAGTGGTACTTCTTC-TGCCACAAGGATCGCAAGTACCCGACGGGCACGCGGACCAACCGCGCCACGGAGACCGGCTA

upper sequence: EFJ37734 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: GLYMA06G08440.1 (Glycine max), 3'ss of exon 1
-ttctatgcatcgtttctcataatcttggctagatgctatctatttcttggagtccgtgagcact-actaacactttcgtttttggctcttgctccacacagACAAGGCCAAGATGGGAGAGAAGGAATGGTACTTCTTCACGCTGCGAGACCGAAAGTATCCTACGGGAATGCGCACAAACCGAGCCACCGAGGCCGGATA
 ||   ||     | |   ||||| |   |  | |  ||| || |  || || |   |     || |  || |  ||  | | |   | || |   | | ||  ||||| ||||||||||| || ||||||||||||||||  ||| ||||||| || || || |||||  || | ||||| ||||| ||  | ||||| ||
ctttcttgtgatatatgg-ataatatatacgtgcta-tatataataatttgaatgtatatattctcatcaataaattattctataattttttcatgaaatagGGAAGGCAAAGATGGGAGAAAAAGAATGGTACTTCTTCAGTCTGAGAGACCGTAAATACCCAACGGGTGTGAGAACAAATCGAGCAACTAACGCCGGGTA

upper sequence: EFJ37734 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: AT5G53950.1 (Arabidopsis thaliana), 3'ss of exon 1
ttctatgcatcgtttctcataatcttggctagatgctatctatttcttggagtccgtgagcactactaacactttcgtttttggctcttgct-ccacacagACAAGGCCAAGATGGGAGAGAAGGAATGGTACTTCTTCACGCTGCGAGACCGAAAGTATCCTACGGGAATGCGCACAAACCGAGCCACCGAGGCCGGATA
                   |||        | |  ||| ||  | |||| ||| | |  | | |         |    | ||  ||||   |   ||  ||  |  || |||||||||||||| |||||||||||||| |  || || ||||| |||||||| |||||| || | || ||| |||| || ||||| || ||
------------------gtaagaaaatacaaa-actaact--tacttgtagttcttttgtaattaaggtttctgaaatctttactctcaatgttacttagGGAGAGCTAAGATGGGAGAGAAAGAATGGTACTTCTTTAGCCTCCGTGACCGGAAGTATCCGACGGGACTGAGAACTAACAGAGCAACTGAGGCTGGTTA

upper sequence: EFJ37734 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: Vv19s0014g02200.t01 (Vitis vinifera), 3'ss of exon 1
ttctatgcatcgtttctcataatcttggctagatgctatctatttcttggagtccgtgagcactactaacactttcgtttttggctcttgc-tccacacagACAAGGCCAAGATGGGAGAGAAGGAATGGTACTTCTTCACGCTGCGAGACCGAAAGTATCCTACGGGAATGCGCACAAACCGAGCCACCGAGGCCGGATA
         | | | | ||    | |  |    | | || |  |         ||       | | |||   | | |   ||   | |  | | || ||||| || || ||||||||||||||||| |||||||||||||  || || || || |||||||| || ||  | || || ||||| ||||| || || || ||
--------gttggtac-cacctacctacccttctac-attttctctcaaacacccacacaatccattaat-ttatagccattttttttaacatacaaacagAAAAAGCAAAGATGGGAGAGAAGGAGTGGTACTTCTTCAGCCTCCGCGATCGGAAGTATCCAACTGGCCTCCGAACCAACCGGGCCACAGAAGCTGGCTA

upper sequence: EFJ37734 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: Vv08s0007g07640.t01 (Vitis vinifera), 3'ss of exon 1
ttctatgcatcgtttctcataatcttgg-ctagatgctatcta-tttcttggagtccgt-----gagcactactaacactttcgtttttggctcttgctccacacagACAAGGCCAAGATGGGAGAGAAGGAATGGTACTTCTTCACGCTGCGAGACCGAAAGTATCCTACGGGAATGCGCACAAACCGAGCCACCGAGGCCGGATA
      | |   | ||||   |||||   ||    | | | |  ||| ||||| |  ||     | ||  || |   | | |  | || | ||  || |    ||||| || || ||||||||||||||||||||||| |||||    | | ||||  | ||||||||||| || ||| | || || ||||| |||||  | |||||
------gtaatctctctctctatctttctctgtgagttctttggttttttggatttggtatttggggcgttatttctaatcttttattggact--tgatt-gtacagAGAAAGCAAAGATGGGAGAGAAGGAATGGTATTTCTTTTGCCAGAGAGATAGGAAGTATCCTACAGGCATGAGAACGAATCGAGCTACCGAATCTGGATA

upper sequence: EFJ37734 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: PP1S279_85V6.1 (Physcomitrella patens), 3'ss of exon 1
--------------------------------------------ttctatgcatcgt----ttctcataatcttgg-ctagatgctatctatttcttggagtccgtgagcactactaacactttcgtttttggctc----ttgctccac------------acagACAAGGCCAAGATGGGAGAGAAGGAATGGTACTTCTTCACGCTGCGAGACCGAAAGTATCCTACGGGAATGCGCACAAACCGAGCCACCGAGGCCGGATA
                                              |||   || ||    |||   || |      |  ||| | |  | |    |    | ||   |  ||||  |    ||  ||| |||        ||||||               |||| ||||||||| | |||||||||||||||||||||||||  ||||| |||||||| || || || ||   ||| || ||| ||||||| ||    |||||
gtatttttttcttttcgcattatccttcagaacatttggtgtagacctaacaattgtgttattcgtgtagtaggaaacctgatacgaaatttagtgtaagattcgcatgatctacagaatgctttatttgtgggataaagctgctccgtctcgatgattttgcagATAAGGCCAAGGTTGGAGAGAAGGAATGGTACTTCTTCAGTCTGCGTGACCGAAAATACCCAACCGGCCAGCGAACTAACAGAGCCACTGATAAGGGATA

upper sequence: EFJ37734 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: PP1S327_64V6.1 (Physcomitrella patens), 3'ss of exon 1
----------------------------ttctatg-catcgtttctcataatcttggctagatg-ctatctatttcttggagtccgtgagcactactaacactttcgtttttggctcttgctccacacagACAAGGCCAAGATGGGAGAGAAGGAATGGTACTTCTTCACGCTGCGAGACCGAAAGTATCCTACGGGAATGCGCACAAACCGAGCCACCGAGGCCGGATA
                            |  | ||   | || |    |  ||     | | ||   || |       |  |  |   | || |   |  | |||| |   |||    || ||    |||| || || ||| | || |||||||| |||||||||||||  ||||| || || |||||||| ||||||||||| |||||  ||||||||||    || ||
gtgacacaaactcccaatccttccagtatcatctggtgtagtgtgctgtcctccgaatttggtgatcatgtgaactgagatggaccgaatcattgaaattagtttcctcggtgggaaatgatct-tgcagAGAAAGCGAAGTTAGGGGAGAAGGAGTGGTACTTCTTCAGCCTGCGGGATCGCAAGTATCCGACGGGAATGCGAACAAATAGAGCCACCGAAAAGGGTTA

upper sequence: EFJ37734 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: PP1S259_58V6.1 (Physcomitrella patens), 3'ss of exon 1
--------------------------------------------------------------------------ttctatgcatcgtttct-cataatcttggctagatgctatctatttcttggagtccgtgagcactactaacactttcgtttttggctcttgctccacacagACAAGGCCAAGATGGGAGAGAAGGAATGGTACTTCTTCACGCTGCGAGACCGAAAGTATCCTACGGGAATGCGCACAAACCGAGCCACCGAGGCCGGATA
                                                                          ||  |  |  |||| ||  | ||  || | |   ||||||||     ||       |||  |   | | |     | || | | | |     | |   |||| || || ||  | || |||||||||||||| |||||||  ||||||||| | |||||||| ||||| || || || ||| ||||||| |||   || ||
gtacgctactcacacgcgatccttcaattcatcggaacaatcgatgtagacgtctagaaatagtactcacgtgattggagactccgttgctgtacaaattttgttg--tgctatctcgagattattacgtgtggcctaaatttaggaagttgtatattggtgacaattc-tgcagAGAAAGCGAAAGTAGGGGAGAAGGAATGGTATTTCTTCAGCCTGCGAGACAGGAAGTATCCAACGGGGATACGAACCAACAGAGCCACTGAGAAGGGGTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttggagtccgtgagcactactaacactttcgtttttggctcttgctccacacagACAAGGCCAAGATGGGAGAGAAGGAATGGTACTTCTTCACGCTGCGAGACCGAAAGTATCCTACGGGAATGCGCACAAACCGAGCCACCGAGGCCGGATA
                  tactaac  putative branch site (score: 0)
                                       ctcttgctcc  putative PPT
                                ttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttctatgcatcgtttctcataatcttggctagatgctatctatttcttggagtccgtgagcactactaacactttcgtttttggctcttgctccacacagACAAGGCCAAGATGGGAGAGAAGGAATGGTACTTCTTCACGCTGCGAGACCGAAAGTATCCTACGGGAATGCGCACAAACCGAGCCACCGAGGCCGGATA

ttctatg
- - - - - -gtttctc
- - - - - - - - - - - -cttggct
- - - - - - - - - - - - - - - - -tgctatc
- - - - - - - - - - - - - - - - - - - - -atttctt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - tgagcac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gctcttg