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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gcaagatcatcacactcaagtgccaacctgaagcacgtgcatgtacattgtaatccaaggaagagtattgggcattgctaactgatagcgtccattgcagAGGTATGCAAGATTCCAGGCGACCATTCCGTGAACCAGAACAACTGGTACTTCTTTAGCCATAAGGACAAGAAGTACCCCACCGGCAACCGCGCCAACCG

Basic information

species Physcomitrella patens
transcript PP1S77_42V6.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S77_42V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: LOC_Os08g02300.1 (Oryza sativa), 3'ss of exon 1
--------------------------gcaagatcatcacactc-aagtgccaacctgaagcacgtgcatgtacattgtaatc--caaggaagagtattgggcattgctaactgatagcgtccattgcagAGGTATGCAA-GATTCCAGGCGACCAT---------TCCGTGAACCAGAACAACTGGTACTTCTTTAGCCATAAGGACAAGAAGTACCCCACCGGCAACCGCGCCAACCG---------
                            ||  |     | ||| || |  |||  |  |||      ||  |   || | |   |||  ||  |   |  || | ||||| | || | ||   |   | |  |||     | || |||       |         || | |   |||||| ||||||||||||| ||||| ||||||||||||||||| || || |   |  | ||| |         
gtagctaagctagtattcctcatcatataacctttctcctctccaattctcaatttctagctaccaaatcgatgatggatttatcaatcaatcgagctaagc-tagctaagtaatggtgtgtgtgcaaaatatatattgtggttgcagAGAGGTGTAAGATTGGGTCAGGGCCGCAGAACGACTGGTACTTCTTCAGCCACAAGGACAAGAAGTACCCGACGGGGACGAGGACGAACAGGGCGACGGC

upper sequence: PP1S77_42V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: LOC_Os06g04090.1 (Oryza sativa), 3'ss of exon 1
gcaagatcatcacactcaagtgccaacctgaagcacgtgcatgtacattgtaatccaaggaagagtattgggcattgctaactgatagcgtccattgcagAGGTATGCAAGATTCCAGGCGACCATTCCGTGAAC-CAGAACAACTGGTACTTCTTTAGCCATAAGGACAAGAAGTACCCCACCGGCAACCGCGCCAACCG---------
             ||  || |   || |  |  ||| |  ||  |     |        ||   || |||  || ||     ||   |  ||   | || |  ||||||           ||      |  |  | || ||| ||||||||||||| ||||| ||||||||||||||||| || || |   |  | |||||         
-----------gtacgtaatt---aagcacacacacatcgatcaattcgatcgatttttgacatgttttgatcaatgtggcatgtgtgtatca--tacatacatatgcagAGAGGTGCAGGATTGGGTCAGGGCCGCAAAACGACTGGTACTTCTTCAGCCACAAGGACAAGAAGTACCCGACGGGGACGAGGACGAACCGGGCAACGGC

upper sequence: PP1S77_42V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: LOC_Os06g01480.1 (Oryza sativa), 3'ss of exon 3
-------gcaagatcatcacactcaagtgccaacctgaagcacgtgcatgtacattgtaatccaaggaagagtattgggcattgctaactgatagcgt--ccat---tgcagAGGTATGCAAGATTCCAGGCGACCATTCCGTGAAC---CAGAACAACTGGTACTTCTTTAGCCATAAGGACAAGAAGTACCCCACCGGCAACCGCGCCAACCG
          ||  ||  ||   || |     |  |||   | ||| |      | ||   | ||  |||       |  ||   ||||||  ||  |  ||||   |||||||   |||  |||    ||||      | | | |    |||||| | ||||||||||| ||||| ||||||||||||||||| || || |   |  ||||   
gtcagtactcagtacagtacgtacatgcatgcatatgatagatgtgtacaatattcgtgtgctaattaag----ccagcaataattaactgggagtataaccatgcatgcagAGCGTTGCCGGATCAATGGCGGGTCGGCGGCGGAGGAGCAGAACGAATGGTACTTCTTCAGCCACAAGGACAAGAAGTACCCGACGGGGACGAGGACCAA---

upper sequence: PP1S77_42V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: LOC_Os06g33940.1 (Oryza sativa), 3'ss of exon 2
--------------------gcaa--gatcatcacactcaagtgccaacctgaagc--acgtgcatgta-cattgtaatccaaggaagagtattgggcattgctaactgatagcgtccattgcagAGGTATGCAAGATTCCAGGCGACCATTCCGTGAACCAGAACAACTGGTACTTCTTTAGCCATAAGGACAAGAAGTACCCCACCGGCAACCGCGCCAACCG---------
                     |||    ||| | ||   |  |  |   | | |||   |  ||||| | || ||  ||  |  |  ||   ||   ||| | | | | |||       | | | |  ||   |    | ||||  |     | | |   |||||| | ||||||||||| ||||| ||||||||||||||||| || || |   |  | |||||         
gtaaaattgaaattgagcaatcaatcagtcagctcatctagctagccggccggagctagcaagcatgcaacagtgagattta--gctgaagtttaaacatgg-tgattaatatttcatgtggtatatatacagATCGGTGCAGGATAGGGA-CGGGGCCTCAGAACGAGTGGTACTTCTTCAGCCACAAGGACAAGAAGTACCCGACGGGGACGAGGACGAACCGGGCGACGAC

upper sequence: PP1S77_42V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: LOC_Os02g15340.1 (Oryza sativa), 3'ss of exon 2
--------------------------------------------gcaagatcatcacact--caagtgccaacctgaagcacgtgcatgtacattgt----aatccaaggaagagtattgggcattgctaactgatagcgtccattg-cagAGGTATGCAAGATTCCAGGC-GACCATTCCGTGAAC------------CAGAACAACTGGTACTTCTTTAGCCATAAGGACAAGAAGTACCCCACCGGCAACCGCGCCAACCG---------
                                              || || | || |||  ||| ||   |  |   |   |||| |     || |    ||  ||   ||   | ||     |  ||   |||     |  |||  || |  ||||   |  |  | || || |  | |  ||              ||| |  | ||||||||||| ||||| ||||||||||||||||| || || |   |  |||||||         
gtataaacacatatgcttgctaattaattaactagcacttctttagaaaatgaacaaacttacaaatgtatatgttgtgttggtgcttaatttttttcacaaaatcacctaacgattttaaatttaactttatgaatatattgattaacatatatatggttgcattgatgcagATCGATGCAGGATTGGGACGGGGGCGCAGGAGGAGTGGTACTTCTTCAGCCACAAGGACAAGAAGTACCCGACGGGGACGAGGACCAACCGCGCCACGGT

upper sequence: PP1S77_42V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: LOC_Os02g42970.1 (Oryza sativa), 3'ss of exon 1
gcaagatcatcacactcaagtgccaacctgaagcacgtgcatgtacattgtaatccaaggaagagtattgggcattgctaactgatagcgtccattgcagAGGTATGCAAGATTCCAGGCGACCATTCCGTGAACCAGAACAACTGGTACTTCTTTAGCCATAAGGACAAGAAGTACCCCACCGGCAACCGCGCCAACCG---------
     || | ||  |      |   | | |||| |     |    ||  || |     |  |  | |||| ||||  | |||   || |    |||||||||   |||||||||   |||         |   | |||||  ||||||||||||| ||||| || ||||| |||||||| || |||| |||| |||||||         
--gtaattagcatgcatgcaagttgatc-gaagaatcaaaaaaatcaaagttaggtttgcgattgaattgagcat--ccaacatgta-caaatattgcagAGAAGTGCAAGATT---GGCA------TGGAAGAACAGAATGACTGGTACTTCTTCAGCCACAAAGACAAAAAGTACCCGACGGGCACCCGCACCAACCGGGCCACGGG

upper sequence: PP1S77_42V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GRMZM2G069047_T01 (Zea mays), 3'ss of exon 1
---------------------------------------------------------------gcaagatcatcacactcaag-tgccaacctgaag---------cacgtgcatgtacattg--taatccaaggaagagtattgggcattgctaactga---tagc-gtccattgcagAGGTATGCAAGATTCCAGGCGACCATTCCGTGAACC-AGAACAACTGGTACTTCTTTAGCCATAAGGACAAGAAGTACCCCACCGGCAACCGCGCCAACCG---------
                                                                  | |  |||  |    || ||   |||||| |         |||| ||||| || |    | |||   | | |   ||  |||  || | |  |    |||   || |||      | |||||           || |    || |  || ||||| ||||||||||||| ||||| ||||||||||||||||| || || |  ||| |||||||         
gtacggtatacttaccaccatataccttccatctccgaggtccgagcaaagcatcagctcgtgatcataggatcggatcggagctggtgacctgatggtcatgtcacacgagcatgaacgtgagctgatcatcgtacgtccat--ggcgctgatcatcggggttagttatcgattctgcgtgcatgcagAGAGATGCAAGATCGGGTCGGGTCCCCAGAACGACTGGTACTTCTTCAGCCACAAGGACAAGAAGTACCCGACGGGGACGCGCACCAACCGCGCTACGGC

upper sequence: PP1S77_42V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GRMZM2G171395_T01 (Zea mays), 3'ss of exon 1
----------------------------gcaagatcatcacactcaagtgccaacctgaagcacgtgcatgtacattgtaatccaaggaagagtattgg-gcattgctaactgatagcgtccattgcagAGGT-----ATGCA-AGATTCCAGGCGACCATTCCGTGAACCAGAACAACTGGTACTTCTTTAGCCATAAGGACAAGAAGTACCCCACCGGCAACCGCGCCAACCG---------
                            ||  | |     ||  || || | |  | |     | | ||||  |  ||   |||             |  ||||   |  | |||   |  | | |    |||     ||||| |||      ||  |  ||| |    ||||||| ||||||||||||| ||||| ||||||||||||||||| || || |  ||| |||||||         
gtagtactacgctgttacgcacgcacgcgcttgcttgctgcatacatgt-ctatgcggccatgcatacatgc-ctctgccgtccgtctgccctccccgatgcatatatggccgatcctgatcgtcgagccggtgaccgatgcagAGAAGTGCCGCATCGGTTCGGGCCCCCAGAACGACTGGTACTTCTTCAGCCACAAGGACAAGAAGTACCCGACGGGGACGCGCACCAACCGCGCCACCGC

upper sequence: PP1S77_42V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GRMZM2G092465_T03 (Zea mays), 3'ss of exon 1
--gcaagatcatcacactcaagtgccaacctgaagcacgtgcatgtacattgtaatccaaggaagagtattgggcattgctaactgatagcgtccat-tgcagAGGTATGCAAGATTCCAGGCGACCATTCCGTGAACCAGAACAACTGGTACTTCTTTAGCCATAAGGACAAGAAGTACCCCACCGGCAACCGCGCCAACCG---------
    ||    |||  | |||    |   |   ||  ||  ||    |  |  || | | |  ||      | |         |   || |    |    ||||||  |||||||||     | | |   |||     ||||||| ||||||||||||| ||||| ||||||||||||||||| || || |  ||| |||||||         
atcaaacgcgatcgaattcat---cgcgcgctaactactggctaacaactgctactactactaaagccgctagctccattccatgcatggaaatcgcgcgcagAGAAATGCAAGATC----GGGTCGGGTCC-----CCAGAACGACTGGTACTTCTTCAGCCACAAGGACAAGAAGTACCCGACGGGGACGCGCACCAACCGCGCCACGGC

upper sequence: PP1S77_42V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GRMZM2G178998_T01 (Zea mays), 3'ss of exon 3
----------------------------------------------------------------gcaagatcatcacactcaagtgccaacctgaagca--------cgtgcatgtacattgtaatccaaggaagagtattgggcattgctaactgatagc-----gtccattgcagAGGTATGCAAGATTCCAGGCGACCATTCCGTGAACCAGAACAACTGGTACTTCTTTAGCCATAAGGACAAGAAGTACCCCACCGGCAACCGCGCCAACCG---------
                                                                   ||||    ||||   |  ||     || | ||        | ||      |||| |     |||    |   ||       ||||||| |   |      | ||| |    |  |   || | | ||||         ||   | |||||| | ||||||||||| ||||| ||||||||||||||||| |||||||  ||| ||||| |         
gtacatcaacctaaactcgatttgtactccgagcttgcatgatgagacataaaactgtacttagctgagatatgtacacctcaaagcatgtgtggaacaacaagcttcttgtggagtcattatgcatgaagctcaacggttataagccgctaactcacttctacatatgcatggtgacgaaacagAAAAGTGCAGG-ATTGGAAGCGAAGAGCAGAACGAGTGGTACTTCTTCAGCCACAAGGACAAGAAGTACCCAACCGGCACTCGCACCAACAGAGCGACGAC

upper sequence: PP1S77_42V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GRMZM2G315140_T01 (Zea mays), 3'ss of exon 2
------------------------gcaag--atcatcacactcaagtgccaacctg--aagcacgtgcatgtacat-tgtaatccaaggaagagtattgggc-----attgctaactgata----gcgtccattgcagAGGTATGCAAGATTCCAGGCGACCATTCCGTGAACCAGAACAACTGGTACTTCTTTAGCCATAAGGACAAGAAGTACCCCACCGGCAACCGCGCCAACCG---------
                        |||||   |     || |  |||    |   |  ||  || ||||| || |   ||  | | |   | | |||| | |     ||    || ||  |     | | ||||    | |     |  | | || |          | | | |||||| | ||||||||||| ||||| ||||||||||||||||| || ||||  ||| |||||||         
gcaagaaataaatacattccgaaagcaagtagttgatgcaatggagttggtagtagacaattacatgcatatatacacgtgctgctaattaaa-tattagactcacaatgatcaattggcatcacacatgcatttggaatgggcagAGAAGTGCAAG-ATTGGGATGGAGGAGCAGAACGATTGGTACTTCTTCAGCCACAAGGACAAGAAGTACCCGACGGGCACTCGCACCAACCGGGCGACCAC

upper sequence: PP1S77_42V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GRMZM2G354151_T01 (Zea mays), 3'ss of exon 3
gcaagatcatcacactcaagtgccaacctgaagcacgtgcatgtacattgtaatccaaggaagagtattgggcattgctaactgatagcgtccattgcagAGGTATGCAAGATTCCAGGCGACCATTCCGTGAACCAGAACAACTGGTACTTCTTTAGCCATAAGGACAAGAAGTACCCCACCGGCAACCGCGCCAACCG---------
| ||||  |  ||| | || |   || |      |  |  |  ||||| |    |     || ||      |||||    | ||   || |     ||||||   |||||||| |  | ||        | | | |||||| | ||||||||||| ||||| ||||||||||||||||| || |||| |||| | |||||         
gtaaga--agtacatt-aattctgaaacaagtatatatatacatacatagctg-ctgctaaatagacacatgcattttggaatgg--gcat-----gcagAGAAGTGCAAGAT-CGGGACG--------GAGGAGCAGAACGAGTGGTACTTCTTCAGCCACAAGGACAAGAAGTACCCGACGGGCACCCGCACAAACCGGGCGACCAC

upper sequence: PP1S77_42V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GRMZM2G440219_T01 (Zea mays), 3'ss of exon 1
gcaag-atcatcacactcaagtgccaacctgaagcacgtgcatgtacattgtaatccaaggaagagtattgggcattgctaactgatagcgtccattgcagAGGTATGCAAGATTCCAGGCGACCATTCCGTGAACCAGAACAACTGGTACTTCTTTAGCCATAAGGACAAGAAGTACCCCACCGGCAACCGCGCCAACCG
 |||  ||      ||  |    | |     |   || | | |  | | | |  |  |    |   |  |  |        ||   ||   |   | |||||    ||||   |   ||||     |   | | | |||||| | ||||||||||| ||||| ||||||||||||||||| || |||| |||  |||||||
acaaatattcgagaacggagacactactgctatatacattctttcagagtatggtatatcacatcctcctacgacacatgcac-attattattattagcagACAAGTGCAGACTGGGAGGCCCTGGTGAGGAGGAGCAGAACGAGTGGTACTTCTTCAGCCACAAGGACAAGAAGTACCCGACGGGCACCCGGACCAACCG

upper sequence: PP1S77_42V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GRMZM2G091490_T01 (Zea mays), 3'ss of exon 1
-------------------gcaagatcatcacactcaagtgccaacctgaagcacgtgcatgtacattgtaatccaaggaagagtattgggcat---tgctaactgatag--cgtccattgcagAGGTATGCAAGATTCCAGGCGACCATTCCGTGAACCAGAACAACTGGTACTTCTTTAGCCATAAGGACAAGAAGTACCCCACCGGCAACCGCGCCAACCG---
                   | | ||||     ||  |    |   | |||    |||  || | |||||    |  | | |  | ||    | |   ||   ||     |   | ||  ||||||    |||    |  | ||    | |   |     |||||| ||||||||||||| ||||| ||||||| ||||||||| || || |  ||| |||||||   
gtatgcatccatgcatatagtaggatctgtgtacg-agacacatgcatgatcatcgtctatct-cattgcttgcgcatgcaatgcatgaaacttacatggcgacgaccggactgacccctgcagACAAGTGCCGCGT--CGGGTCGTCGTCAGGCCC-TCAGAACGACTGGTACTTCTTCAGCCACAAGGACAGGAAGTACCCGACGGGGACGCGCACCAACCGCGC

upper sequence: PP1S77_42V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GRMZM2G041746_T01 (Zea mays), 3'ss of exon 2
--------------------------------------------------------------------------------gcaagatc-atcacactcaagtgccaacctgaagcacgtgcatgtacattgtaatccaaggaagagtattgggcattgctaactgatagcgtccattgcagAGGTATGCA--------AGATTCCAGGCGACCATTCCGTGAACCAGAACAACTGGTACTTCTTTAGCCATAAGGACAAGAAGTACCCCACCGGCAACCGCGCCAACCG---------
                                                                                || || |  |||  |      |  | | ||  | |   |  || |   ||| ||  ||| ||    ||     ||    |||    |    |   | | | | | |||||        || | |  |     ||  ||| | | |||||| | ||||||||||| ||||| ||||||||||||||||| || || |   |  | |||||         
gtaagtaaaatacatgtatgtatatgtcattttgtgtgcaaacagctagcaaacatatacttgttatatatatacctgcagcgagctagatctgatgttgctagctagctagacctaattaattttt-ttgcaaatcaaagaga--taactcacacaaataatcttttatatatgtggaacatgcatgcatggcagAAAGGTGCAGGATAGGCA--CCGGGCATCAGAACGAGTGGTACTTCTTCAGCCACAAGGACAAGAAGTACCCGACGGGAACAAGGACGAACCGCGCCACGAC

upper sequence: PP1S77_42V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GRMZM2G104074_T01 (Zea mays), 3'ss of exon 2
gcaagatcatcacactcaagtgccaacctgaagcacgtgcatgtacattgtaatccaaggaagagtat-tgggcattgctaactgatagcgtccatt-----gcagAGGTATGCAAGATTCCAGGCGACCATTCCGTGAACCAGAACAACTGGTACTTCTTTAGCCATAAGGACAAGAAGTACCCCACCGGCAACCGCGCCAACCG---------
             |   |  |   || || ||||      || |   || ||||   |  |  ||||| | || |   |  |   |     |  |||      ||  || | | ||||| | |      || |  | |   || ||| | ||||||||||| ||||| ||||||||||||||||| || || |   |  | |||||         
----------tttaaaaatatatgaatctaaagccaaaatatctc--ttataatttgaaaagaagtatataggtaactcataggaaggttatatatttgtggacaatggca-gAAAGATGCAAAATAGGCACT--GGGCCTCAAAACGAGTGGTACTTCTTCAGCCACAAGGACAAGAAGTACCCAACGGGAACGAGAACGAACCGTGCCACGAC

upper sequence: PP1S77_42V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GLYMA19G44890.1 (Glycine max), 3'ss of exon 1
gcaagatcatcacactcaagtgccaacctgaagcacgtgcatgtacattgtaatccaaggaagagtattgggcattgctaactgatagcgtccattgcagAGGTATGCAAGATTCCAGGCGACCATTCCGTGAACCAGAACAACTGGTACTTCTTTAGCCATAAGGACAAGAAGTACCCCACCGGCAACCGCGCCAACCG---------
                   |||   |  |      |     |    |   ||||     || ||||| ||    |   ||| | ||         ||||||| | ||||| ||   | ||  ||           || ||| | |||||||| || ||||| |||||||||||||||||||| || | |||| |||||||         
-------------------gtgatgattttttttgctca-gtagctaagataatt----gatgagtagtgcatgtaattaattaat------ttgtgcagAGATGTGCAAAATAGGAAGCAGCCCA---------CAAAACGATTGGTACTTGTTCAGCCACAAGGACAAGAAGTACCCCACGGGAAGCCGCACCAACCGCGCCATCAT

upper sequence: PP1S77_42V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GLYMA07G05660.1 (Glycine max), 3'ss of exon 1
-------gcaagatcatcacactcaagtgccaacctgaagcacgtgcatgtacattgtaatccaaggaagagtattgggcattgctaactgatagcgtccattgcagAGGTATGCAAGATTCCAGGCGACCATTCCGTGAACCAGAACAACTGGTACTTCTTTAGCCATAAGGACAAGAAGTACCCCACCGGCAACCGCGCCAACCG---------
            |  ||  || ||| | | ||  ||| |  || || ||  ||    | ||     |  |  | ||     || ||| ||           ||||||||  |||||| ||     |  |||| ||||     |||||  | ||||||||||| ||||| || ||||||||||||||||| || |  ||| |||| ||         
ttggaatattcaaatattgca-tcatgagtcatgctgcatgacatgaat-cacggcatcattttgaggggtttcttttttctttctatct-----ttctttttgcagAGAAATGCAAAAT----AGGAACCACTCCG-----CAGAATGATTGGTACTTCTTCAGCCACAAAGACAAGAAGTACCCCACAGGAACGCGCACCAATCGCGCCACTGC

upper sequence: PP1S77_42V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GLYMA16G02200.1 (Glycine max), 3'ss of exon 1
gcaagatcatcacactcaagtgccaacctgaagcacgtgcatg---tacattgtaat-ccaaggaagagtattg-ggcattgctaactgatagcgtccatt----gcagAGGTATGCAAGATTCCAGGCGACCATTCCGTGAACCAGAACAACTGGTACTTCTTTAGCCATAAGGACAAGAAGTACCCCACCGGCAACCGCGCCAACCG---------
           | | |||| |           |  | ||||||   |  ||       | || | |   | ||| ||  || ||   |  |    |  |||    ||||||  |||||| ||     |  |||| ||||     |||||  | ||||||||||| ||||| || ||||||||||||||||| || |  ||| |||| ||         
---------gaatattcaaatattgcatcatgggtcatgcatgacatgaatcacggcactaatgcaccattttgaggggtttcttttttcttttctttattttttgcagAGAAATGCAAAAT----AGGAACCACTCCG-----CAGAATGATTGGTACTTCTTCAGCCACAAAGACAAGAAGTACCCCACAGGAACGCGCACCAATCGCGCAACTGC

upper sequence: PP1S77_42V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GLYMA11G03340.1 (Glycine max), 3'ss of exon 1
----------------------gcaagatcatcacactcaagtg-ccaacctgaagcacgtgcatgtacattgtaatccaaggaagagtattgggcattgctaactgatagcgtccattgcagAGGTATGCAAGATTCCAGGCGACCATTCCGTGAACCAGAACAACTGGTACTTCTTTAGCCATAAGGACAAGAAGTACCCCACCGGCAACCGCGCCAACCG---------
                      || || |  | |   | ||||  ||||   |||  || |  || || |    | | |     | | |  ||   ||| || | |||||        |  |||  ||||||| ||   | ||||        ||||  | ||  | ||||| |||||||| ||||| ||||||||||||||||| || |  ||  ||||  |         
gtacgtatgatatataagcctagctagcttcttatgattaagtctccaattagaaatacatatatataaaccacagtactgctcacatt--tgtttatttctga-tgata--------tatagAATTATGCAAAATAGGAAGCGA--------TGAAG-AAAATGAATGGTATTTCTTTAGTCATAAAGACAAGAAGTACCCCACTGGGACTCGTACCAATAGAGCTACAAA

upper sequence: PP1S77_42V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: AT1G12260.1 (Arabidopsis thaliana), 3'ss of exon 2
gcaagatcatcacactcaagtgccaacctgaagcacgtgcatgtacattgtaatccaaggaagagtattgggcattgctaactgatagcgtccattg-cagAGGTATGCAAGATTCCAGGCGACCATTCCGTGAACCAGAACAACTGGTACTTCTTTAGCCATAAGGACAAGAAGTACCCCACCGGCAACCGCGCCAACCG---------
    | |   |  |  | |    |    |    ||      ||| |  | |   | ||||||   | ||     |   |   |  | |  |        |||| | ||||| |||      |  |||   |   | ||||   | |||||||||||||||||||| ||||||||||| ||||| || |  ||  ||||  |         
----gtttgcccaatcccaccatctctatccttcattactttgt-ctctatttcctaaggaaagattttaaaagtctttttttattcgtttgtggaaatagAGTTGTGCAAAATT------GGGCAT---GAAGAGCAGAGTGATTGGTACTTCTTTAGCCATAAAGACAAGAAGTATCCCACAGGGACTCGAACCAATAGAGCAACAAA

upper sequence: PP1S77_42V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: AT3G61910.1 (Arabidopsis thaliana), 3'ss of exon 1
--gcaagatcatcacactcaagtgc-caacctgaagcacgtgcatgtacattgtaatccaaggaag--agtattgggcattgctaactgatagcgtccattgcagAGGTATGCAAGATTCCAGGCGACCATTCCGTGAACCAGAACAACTGGTACTTCTTTAGCCATAAGGACAAGAAGTACCCCACCGGCAACCGCGCCAACCG---------
  | ||  |   || | | |  |   |    ||    |     || | ||  ||||   ||   ||  |  | |   ||   ||  ||  |    || || | |||| | || ||||||    |  || |  |||     || ||| | |||||||| | ||||||||||||||||||||| |||||||| |   |  ||||| |         
caggaaattttgcagagtaatatatactttttgtgataataaaatttgca--gtaacaaaattcagtcaaaacttaacacaact--cttgttttttctat-gtagAGATGTGTAAGATT----GGAACGACGCCG-----CAAAACGATTGGTACTTTTATAGCCATAAGGACAAGAAGTATCCCACCGGGACTAGAACCAACAGAGCCACCAC

upper sequence: PP1S77_42V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: AT1G71930.1 (Arabidopsis thaliana), 3'ss of exon 1
gcaagatcatcacactcaagtgccaacctgaagcacgtgcatgtacattgtaatccaaggaagagtattg-ggcattgctaactgatagcgtccattgcagAGGTATGCAAGATTCCAGGCGACCATTCCGTGAACCAGAACAACTGGTACTTCTTTAGCCATAAGGACAAGAAGTACCCCACCGGCAACCGCGCCAACCG---------
  |   || |     |  |  |  |     ||   |    || |  |   |     | | ||||   ||  | ||||  ||  |  |        |||||| |   || ||    | |||  |  |        | || ||| | |||||||||||||| |||||||||| ||||||||| ||||| |   |  |||||||         
atattctcttttttttttaaagaaacataaaatttctaatattttgaccttttgtaatgtaagaaatttatgacattaatatttagttttacat-ttgcagCGAGGTGTAAA---CTAGGGTATGA------AGAGCAAAACGAGTGGTACTTCTTTAGTCATAAGGACAGGAAGTACCCTACCGGGACTAGGACCAACCGAGCCACTGC

upper sequence: PP1S77_42V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: AT1G32770.1 (Arabidopsis thaliana), 3'ss of exon 1
gcaagatcatcacactcaagtgccaacctgaagcacgtgcatgtacattgtaatccaaggaagagtattgggcattgctaactgatagcgtccattgcagAGGTATGCAAGATTCCAGGCGACCATTCCGTGAACCAGAACAACTGGTACTTCTTTAGCCATAAGGACAAGAAGTACCCCACCGGCAACCGCGCCAACCG---------
         | | || | |      |    || | | | ||| |  |  | | ||          | ||    |||  | |   ||    |    |    |  |    | || |  ||    |  |||   |   || ||| ||||||||||||| ||||| |||||||||||||| || ||||| | | |  | |||||         
--------gttaaaccctaaatatgaaaaaaaactctttcatttctac-gaactctctatttctttgttctttatttttgaaccat----tttggtatgcaaatgcagAGGAATGTAGA-ATCGGTTCAACGCCACAAAACGACTGGTACTTCTTCAGCCACAAGGACAAGAAGTATCCAACCGGGACCAGGACGAACCGGGCAACAGT

upper sequence: PP1S77_42V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: AT1G62700.1 (Arabidopsis thaliana), 3'ss of exon 1
gcaagatcatcacactcaagtgccaacctgaagcacgtgcatgtacattgtaatccaagg-aagagtattgggcattgctaactgatagcgtccattgcagAGGTATGCAAGATTCCAGGCGACCATTCCGTGAACCAGAACAACTGGTACTTCTTTAGCCATAAGGACAAGAAGTACCCCACCGGCAACCGCGCCAACCG---------
|          | |  | |    |   ||  || |     ||     || |  |  ||   |||  |   |    ||| |   |  | | |   |||  |||| ||||||||||   |  |||           | |||| | | |||||||||||||| ||||| ||||||||||| ||||| || |  ||  ||||  |         
gtttagcaggaaaatcctatcatctctctttagtagtgatatccttgttttggtataaattaaggcttacgattgttgttttttctttgtgataatt-tagAGTTATGCAAGATAGGAAACGA---------AGAGCAGAGCGAATGGTACTTCTTTAGTCATAAAGACAAGAAGTATCCCACGGGAACTCGAACCAATAGAGCCACGAA

upper sequence: PP1S77_42V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: EFJ30650 (Selaginella moellendorffii), 3'ss of exon 1
gcaagatcatcacactcaagtgccaacctgaagcacgtgcatgtacattgtaatccaaggaagagtattgggcattgctaactgatagcgtcc----attgcagAGGTATGCAAGATTCCAGGCGACCATTCCGTGAACCAGAACAACTGGTACTTCTTTAGCCATAAGGACAAGAAGTACCCCACCGGCAACCGCGCCAACCG---------
                              | ||||  || |  || |||     |||  |    | |||       ||  ||||     |||     |  |||||  ||| | ||||  |         || |   | || | | | |||||||| || ||||| |||||||||||||||||||| || |  ||  ||||| |         
----------------------------gtaggcactcgcttccaccttg---ctcaaaaacatcttttgctggcccctggctgaatctctcctgttgtcacagAGAAATGTAGGATTGGA---------TCAGCAGAGCAAACCGAGTGGTACTTTTTCAGCCACAAGGACAAGAAGTACCCCACAGGAACACGAACCAACAGAGCAACCAC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcaagatcatcacactcaagtgccaacctgaagcacgtgcatgtacattgtaatccaaggaagagtattgggcattgctaactgatagcgtccattgcagAGGTATGCAAGATTCCAGGCGACCATTCCGTGAACCAGAACAACTGGTACTTCTTTAGCCATAAGGACAAGAAGTACCCCACCGGCAACCGCGCCAACCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT
- - - - - - - - - - - - - - - - -cacgtgc