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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aacctgttgaatcgtttcgttttgcaaatctacgttcggtgcagtatagtattgtagtttgtaagctaacgcgtctcgattcttatctcggactttgcagAGAAATAGTTTCGAGCAACTTTGTATAAACTATGCAAATGAGAGGCTGCAGCAACATTTCAACCGTCACCTTTTTAAGCTTGAGCAAGAA

Basic information

species Physcomitrella patens
transcript PP1S199_21V6.1
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S199_21V6.1 (Physcomitrella patens), 3'ss of exon 13
lower sequence: GRMZM2G057380_T01 (Zea mays), 3'ss of exon 13
aacctgttgaatcgtttcgttttgcaaatctacgttcggtgcagtatagtattgtagtttgtaagctaacgcgtctcgattcttatctcggactttgcagAGAAATAGTTTCGAGCAACTTTGTATAAACTATGCAAATGAGAGGCTGCAGCAACATTTCAACCGTCACCTTTTTAAGCTTGAGCAAGAA
                  || | | | || | | ||  ||  ||||  |  ||     |||  |  |     ||    ||  ||   |    | || ||||  ||| |||| |||||| |||||||||| ||||| ||||||||||||||||| || |||||| | || ||| | || ||  | || || 
------------------gtatggaatatttgcattttgtttagtactgatttac---ttggcatttcctcagttgtaatatttggttaaaccattacagAAGAATGGTTTTGAGCAATTTTGTATAAATTATGCCAATGAGAGGCTGCAGCAGCACTTCAACAGACATCTTCTCAAACTACAACAGGAG

upper sequence: PP1S199_21V6.1 (Physcomitrella patens), 3'ss of exon 13
lower sequence: GRMZM2G113202_T01 (Zea mays), 3'ss of exon 13
aacctgttgaatcgtttcgttttgcaaatctacgttcggtgcagtatagtattgtagtttgtaagctaacgcgtctcgattcttatctcggactttgcagAGAAATAGTTTCGAGCAACTTTGTATAAACTATGCAAATGAGAGGCTGCAGCAACATTTCAACCGTCACCTTTTTAAGCTTGAGCAAGAA
           |  |    ||||    | |||   |   ||   |||| ||||  | |   ||   | ||     ||     |||||      ||||||||  || ||||| || ||  | || || || ||||| ||||| ||| |||||||||||||||| |||||  | ||||||||||||||||| 
----------gtaatgcacttttctttacctaaagt---tgtcatata-tattaaattccatatagttac----ttctgacattatcata---tttgcagAAGAACAGTTTTGAACAGTTCTGCATTAATTATGCTAATGAAAGGTTGCAGCAACATTTCAATCGTCATTTGTTTAAGCTTGAGCAAGAG

upper sequence: PP1S199_21V6.1 (Physcomitrella patens), 3'ss of exon 13
lower sequence: GRMZM2G139583_T02 (Zea mays), 3'ss of exon 13
-------aacctgttgaatcgtttcgttttgcaaatctacgttcggtgcagtatagtattgtagtttgtaagctaacgcgtctcgattcttatctcggactttgcagAGAAATAGTTTCGAGCAACTTTGTATAAACTATGCAAATGAGAGGCTGCAGCAACATTTCAACCGTCACCTTTTTAAGCTTGAGCAAGAA
        ||  |||        ||       |  ||| |   |   |  ||    ||||  | |   |   || ||  |   | ||| |||  |      |||||||  || ||||| || ||  | || || || ||||| ||||| ||| |||| ||||||||||| |||||  | ||||||||||||||||| 
cagaccccactcgtttgggatcctccggcactaggtctgcccccaaagttgtcatatattaaattgcatgtacttactggcgac-attattacat------ttgcagAAGAACAGTTTTGAACAGTTCTGCATCAATTATGCTAATGAAAGGTTGCAACAACATTTCAATCGTCATTTATTTAAGCTTGAGCAAGAG

upper sequence: PP1S199_21V6.1 (Physcomitrella patens), 3'ss of exon 13
lower sequence: GLYMA12G34780.1 (Glycine max), 3'ss of exon 16
aacctgttgaatcgtttcgttttgcaaatctacgttcggtgcagtatagtattgtagtttgtaagctaacgcgtctcgattcttatctcggactttgcagAGAAATAGTTTCGAGCAACTTTGTATAAACTATGCAAATGAGAGGCTGCAGCAACATTTCAACCGTCACCTTTTTAAGCTTGAGCAAGAA
       |     ||||   ||  |   | ||   | | |||   ||||     |||  | |  | |||    |    ||| ||||       |||| |||  || || || || ||| |||||||||||||||| ||||||||||| || ||||||||||| || || || ||||| |||||||| || 
------gtatgcagtttgtattaacgtgttta---ttgatgcttcatag----atagactctttgttaatagtttattatttttat-------tttgtagAATAACAGCTTTGAACAATTTTGTATAAACTATGCCAATGAGAGGCTTCAACAACATTTCAATCGGCATCTGTTTAAACTTGAGCAGGAG

upper sequence: PP1S199_21V6.1 (Physcomitrella patens), 3'ss of exon 13
lower sequence: GLYMA13G35790.1 (Glycine max), 3'ss of exon 15
aacctgttgaatcgtttcgttttgcaaatctacgttcggtgcagtatagtattgtagtttgtaagctaacgcgtctcgattcttatctcggactttgcagAGAAATAGTTTCGAGCAACTTTGTATAAACTATGCAAATGAGAGGCTGCAGCAACATTTCAACCGTCACCTTTTTAAGCTTGAGCAAGAA
       |  |  ||||   ||  |   | ||   | | |||   ||||        |||||| |   |  |   | | || |||| |    ||||| |||  || || || || ||| |||||||||||||||| ||||||||||| || ||||||||||| || || || ||||| |||||||| || 
------gtatacagtttgtattaacgtgttta---ttgatgcttcatagatagactctttgtatgt--attctaatagtttattattttt--ctttgtagAATAACAGCTTTGAACAATTTTGTATAAACTATGCCAATGAGAGGCTTCAACAACATTTCAATCGGCATCTGTTTAAACTTGAGCAGGAG

upper sequence: PP1S199_21V6.1 (Physcomitrella patens), 3'ss of exon 13
lower sequence: AT4G27370.1 (Arabidopsis thaliana), 3'ss of exon 12
aacctgttgaatcgtttcgttttgcaaatctacgttcggtgcagtatagtattgtagtttgtaagctaacgcgtctcgattcttatctcggactttgcagAGAAATAGTTTCGAGCAACTTTGTATAAACTATGCAAATGAGAGGCTGCAGCAACATTTCAACCGTCACCTTTTTAAGCTTGAGCAAGAA
                    || | ||  ||  | |||  |   |||||| |     | | |    |   | ||   |||       |||   |||  ||   ||||||||||| ||| |||| ||||||||||||||||| || |||||||||||||||||||| || || ||||| ||||| ||||| 
-------------------gttcgtaa--ctgtgctcgaggttttatagtctcaatttcttttgatt---gtgtaaggatcaggtcttcgtggttt-tagGATAATAGTTTCGAACAATTTTGCATAAACTATGCAAATGAAAGACTGCAGCAACATTTCAACCGACATCTATTTAAACTTGAACAAGAG

upper sequence: PP1S199_21V6.1 (Physcomitrella patens), 3'ss of exon 13
lower sequence: AT1G50360.1 (Arabidopsis thaliana), 3'ss of exon 14
--------------aacctgttgaatcgtttcgttttgcaaatctacgt------tcggtgcagtata------gtattgtagtttgtaa----gctaacgcgtctcg----attcttatctcggactttgcagAGAAATAGTTTCGAGCAACTTTGTATAAACTATGCAAATGAGAGGCTGCAGCAACATTTCAACCGTCACCTTTTTAAGCTTGAGCAAGAA
              |  ||       |||||   |     ||  ||| |      || |  || || |      || ||  | ||||||     | |||   |  | |    ||   ||      |  ||||||| ||||||||| |||||  | |||||||| ||||||||||||||  |||||||||| ||||||||||| || || ||||||||||| || 
gtatgctggtttttagtctccctttgcgttttactgcatgaacttacataagctatctgcacattacatcttctgtgttacattttgtaccaatgttaatttggtttgctgaataaatactatacatgttgcagAAAAATAGTTTTGAGCAGTTCTGTATAAATTATGCAAATGAGAGATTGCAGCAACACTTCAACCGTCATCTCTTCAAGCTTGAGCAGGAG

upper sequence: PP1S199_21V6.1 (Physcomitrella patens), 3'ss of exon 13
lower sequence: AT3G19960.1 (Arabidopsis thaliana), 3'ss of exon 14
-------------------------------------------------------------------------------------aacctgttgaatcgtttcgttttgcaaatctacgt-tcggtgcagtatagtattgtagtttgtaagctaacgcgtctcgat--tcttatctcggacttt---------gcagAGAAATAGTTTCGAGCAACTTTGTATAAACTATGCAAATGAGAGGCTGCAGCAACATTTCAACCGTCACCTTTTTAAGCTTGAGCAAGAA
                                                                                     |   |    ||  ||  |   | | | | ||   | ||  ||   | | || ||    ||| |    | | | ||||   |  | |  | |  ||||||         ||||| |||||| ||||||||  | |||||||| ||||||||||||||  |||||||||| || |||||||| || || ||||| |||||||| 
gtatgttcctgttctctggctctctgagctttctcctgaaaaagattacaattgctaccagctatcattagaccttcagtttgcaatgataccaaacagtgccaaatagtagaactctatatctatgtgcttttgtgtttccatttcttgatttatgtgtcttattgatttgctatacgactttcattcctctgcagAAAAATAGCTTCGAGCAGTTCTGTATAAATTATGCAAATGAGAGATTGCAGCAACACTTTAACCGTCATCTATTCAAGCTGGAGCAAGAG

upper sequence: PP1S199_21V6.1 (Physcomitrella patens), 3'ss of exon 13
lower sequence: Vv19s0014g03640.t01 (Vitis vinifera), 3'ss of exon 14
aacctgttgaatcgt-ttcgttttgcaaatctacgttcggtgcagtatagtattgtagtttgtaagctaacgcgt-ctcgattcttatctcggactttgcagAGAAATAGTTTCGAGCAACTTTGTATAAACTATGCAAATGAGAGGCTGCAGCAACATTTCAACCGTCACCTTTTTAAGCTTGAGCAAGAA
             || | |  ||  ||  | |  | |  ||   || |  || || | | || |   |||| |   |  |  ||||||||   | ||| ||||  || || || || ||||| ||||||||||||||||||||||||||||| || |||||||| ||||| ||  |||| || || || || 
-------------gtatacaattcacatttatctgcttagtcatgtttc-taatggaatatg-attataacactcacaaggatcttatcttcaaattttcagAAGAACAGCTTTGAACAACTCTGTATAAACTATGCAAATGAGAGGCTGCAACAGCATTTCAATCGTCATCTACTTAAACTCGAACAGGAG

upper sequence: PP1S199_21V6.1 (Physcomitrella patens), 3'ss of exon 13
lower sequence: Vv10s0071g00210.t01 (Vitis vinifera), 3'ss of exon 13
-----aacctgttgaatcgtttcgttttgcaaatctacgttcggtgcagtatagtattgtagtttgtaagctaacgcgtctcgat-tcttat-ctcggactttgcagAGAAATAGTTTCGAGCAACTTTGTATAAACTATGCAAATGAGAGGCTGCAGCAACATTTCAACCGTCACCTTTTTAAGCTTGAGCAAGAA
     |   | || | |   | |  |    || | | | |||    || |     |||||      |||  | |    | |  || |   ||  || |  ||| ||||||||||| || |||||  | || ||||| ||||||||||||||| ||||||| || || ||||||||  | || ||| | |||||||| 
gtatgatattatttagtttctgctgtaaataatttttcattccccccattccc-cattgtccccc-taaatttataaatattcatgttacatattctgtttttccagAGAAATAGCTTTGAGCAGTTCTGCATAAATTATGCAAATGAGAGGTTGCAGCAGCACTTTAACCGTCATTTATTCAAGTTAGAGCAAGAG

upper sequence: PP1S199_21V6.1 (Physcomitrella patens), 3'ss of exon 13
lower sequence: EFJ20281 (Selaginella moellendorffii), 3'ss of exon 12
aacctgttgaatcgtttcgttttgcaaatctacgttcggtgcagtatagtattgtagtttgtaagctaacgcgtctcgattcttatctcggactttgcagAGAAATAGTTTCGAGCAACTTTGTATAAACTATGCAAATGAGAGGCTGCAGCAACATTTCAACCGTCACCTTTTTAAGCTTGAGCAAGAA
                                           ||   ||    ||||||   || |  ||||  |  | |    | ||      ||||||| |||||||| ||||||||||| ||||||||||||||||| ||  | ||||||||||||||||| ||||| || || || |||||||| 
-------------------------------------------gt-cggtgcgctagttt--tagttttcgcgattttactgagttttc---tactgcagAGTAATAGTTTTGAGCAACTTTGCATAAACTATGCAAATGAAAGATTACAGCAACATTTCAACCGCCACCTGTTCAAACTCGAGCAAGAG

upper sequence: PP1S199_21V6.1 (Physcomitrella patens), 3'ss of exon 13
lower sequence: EFJ25955 (Selaginella moellendorffii), 3'ss of exon 12
aacctgttgaatcgtttcgttttgcaaatctacgttcggtgcagtatagtattgtagtt--tgtaagctaacgcgtctcgattcttatctcggactt-tgcagAGAAATAGTTTCGAGCAACTTTGTATAAACTATGCAAATGAGAGGCTGCAGCAACATTTCAACCGTCACCTTTTTAAGCTTGAGCAAGAA
                                        | |  | |||||   |      |      | ||    | ||   ||  ||   || | || |||  || ||||||||||| || || ||||||||||||||||||||||| || ||   |||||| |  ||||| || ||  ||||||| || 
----------------------------------------gtaaca-agtatcacacacgccgcttctcaccgatctttgacagtttgcttcaacatgtgtagAACAACAGTTTCGAGCAGCTGTGCATAAACTATGCAAATGAGAGGCTTCAACAGTTTTTCAATCACCACCTCTTCAAAATTGAGCAGGAC

upper sequence: PP1S199_21V6.1 (Physcomitrella patens), 3'ss of exon 13
lower sequence: EFJ23280 (Selaginella moellendorffii), 3'ss of exon 12
aacctgttgaatcgtttcgttttgcaaatctacgttcggtgcagtatagtattgtagtttgtaagctaacgcgtctcgattcttatctcggactttgcagAGAAATAGTTTCGAGCAACTTTGTATAAACTATGCAAATGAGAGGCTGCAGCAACATTTCAACCGTCACCTTTTTAAGCTTGAGCAAGAA
                                   |||||||  |     ||| ||||||         ||||  |  | |    | ||      ||||||| |||||||| ||||||||||| ||||||||||||||||| ||  | ||||||||||||||||| ||||| || || || |||||||| 
----------------------------------gtcggtgcgct----cattttagtttt--------cgcgattttactgagttttc---tactgcagAGTAATAGTTTTGAGCAACTTTGCATAAACTATGCAAATGAAAGATTACAGCAACATTTCAACCGCCACCTGTTCAAACTCGAGCAAGAG

upper sequence: PP1S199_21V6.1 (Physcomitrella patens), 3'ss of exon 13
lower sequence: EFJ05534 (Selaginella moellendorffii), 3'ss of exon 12
aacctgttgaatcgtttcgttttgcaaatctacgttcggtgcagtatagtat-tgtagtttgtaagctaacgcgtctcgattcttatctcggactttgcagAGAAATAGTTTCGAGCAACTTTGTATAAACTATGCAAATGAGAGGCTGCAGCAACATTTCAACCGTCACCTTTTTAAGCTTGAGCAAGAA
                                          |||||   |   |  | || | | | | |   | |      ||   ||    | || |||  || ||||||||||| || || ||||||||||||||||||||||| || ||   |||||| |  ||||| || ||  ||||||| || 
-----------------------------------gtaaca-agtatcacacacgccgcttctcaccgatc---tttaacagtttgcttcaacatgtgtagAACAACAGTTTCGAGCAGCTGTGCATAAACTATGCAAATGAGAGGCTTCAACAGTTTTTCAATCACCACCTCTTCAAAATTGAGCAGGAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atagtattgtagtttgtaagctaacgcgtctcgattcttatctcggactttgcagAGAAATAGTTTCGAGCAACTTTGTATAAACTATGCAAATGAGAGGCTGCAGCAACATTTCAACCGTCACCTTTTTAAGCTTGAGCAAGAA
                  agctaac  putative branch site (score: 2)
                                 attcttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aacctgttgaatcgtttcgttttgcaaatctacgttcggtgcagtatagtattgtagtttgtaagctaacgcgtctcgattcttatctcggactttgcagAGAAATAGTTTCGAGCAACTTTGTATAAACTATGCAAATGAGAGGCTGCAGCAACATTTCAACCGTCACCTTTTTAAGCTTGAGCAAGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - tgttgaa