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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gatgagagattctgtcaacccttgtgaatggtcgacatgatacaacattgttatttttaattttttaatttttaaaattagtcaatcggtgggtctgcagGTGGTCACAGATTGCAACACAACTCCCAGGCCGCACGGACAACGAGATCAAGAACTTCTGGAACTCATGCATCAAGAAGAAGCTCCGCAGCATGGGAATC

Basic information

species Physcomitrella patens
transcript PP1S211_139V6.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S211_139V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: LOC_Os01g36460.1 (Oryza sativa), 3'ss of exon 2
gatgagagattctgtcaacccttgtgaatggtcgacatgatacaacattg--ttatttttaattttttaatttttaaaattagtcaatcggtgggtctgcagGTGGTCACAGATTGCAACACAACTCCCAGGCCGCACGGACAACGAGATCAAGAACTTCTGGAACTCATGCATCAAGAAGAAGCTCCG-CAGCATGGGAATC
   |   ||     |    || | |       ||| ||| |   ||       |      |   |   ||| |||  |  | |      |    ||   ||||||||| ||||||||  | || || || ||||| |||||||||||||||||||||||||||||||| ||| |||||||||||||||| ||||  || |   
--cgcatgagctgatagtgccgttttggctaccgaaatgttgttacgagagtctgacaacacgatcccaatgtttgcacatggatttgtgaattgtgatcagGTGGTCCCAGATTGCGGCGCAGCTGCCCGGCCGGACGGACAACGAGATCAAGAACTTCTGGAACTCGTGCCTCAAGAAGAAGCTCCGGCAGCGCGGCATC-

upper sequence: PP1S211_139V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: LOC_Os07g31470.1 (Oryza sativa), 3'ss of exon 2
gatgagagattctgtcaacccttgtgaatgg-tcgacatgatacaacattgttatttttaattttttaatttttaaaatt--agtcaat--cggtgggtctgcagGTGGTCACAGATTGCAACACAACTCCCAGGCCGCACGGACAACGAGATCAAGAACTTCTGGAACTCATGCATCAAGAAGAAGCTCCGCAGCATGGGAATC
  |    |    ||   |   | | | |||| ||  | |       | || ||   || || |  ||  |   |  |  |     | ||  | ||| |||| ||||||| | ||||| || |  || || ||||| ||||||||||||||| | ||||| ||||||||||| ||||||||||||||||||  |     |||  ||
-ttcttgggccatgcgta---tggcgcatggctctgctttgctttgcttttttggattgaactggttggtgcatggagctcagaacgattcccgtgtgtct-cagGTGGGCGCAGATCGCCAAGCACCTGCCAGGGCGCACGGACAACGAGGTGAAGAATTTCTGGAACTCGTGCATCAAGAAGAAGCTCATCGCGCAGGGGCTC

upper sequence: PP1S211_139V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: LOC_Os07g44090.3 (Oryza sativa), 3'ss of exon 2
-----------------------------------------------gatgagagattctgtcaacccttgtgaatggtcgacatgatacaacattgttattt--ttaattttttaatttttaaaattagtcaatcggtgggtctgcagGTGGTCACAGATTGCAACACAACTCCCAGGCCGCACGGACAACGAGATCAAGAACTTCTGGAACTCATGCATCAAGAAGAAGCTCCGC-AGCATGGGAATC
                                                |  ||  |||     |   ||  | | |  |  | |   |  |  |||  ||  |  |||||   | ||      |||||| |||    |        ||||||||| ||||||||  | || || || || || |||||||||||| ||||||||||||||||||| | ||||||||||||||| ||| |||  || |   
gtaattaactcaaacaaatccatatacacattactactagattatcatactagtaatttaactacttctcttaattaatt-atagcttggatgatttctagctaattaatcaatcaaacag-gaaattaatcagcttgaattgaatcagGTGGTCTCAGATTGCGGCTCAGCTGCCGGGTCGGACGGACAACGAGGTCAAGAACTTCTGGAACTCTTACATCAAGAAGAAGCTTCGCCAGCGCGGCATC-

upper sequence: PP1S211_139V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: LOC_Os07g44090.1 (Oryza sativa), 3'ss of exon 1
gatgagagattctgtcaacccttgtgaatggtcgacatgatacaacattgttattt--ttaattttttaatttttaaaattagtcaatcggtgggtctgcagGTGGTCACAGATTGCAACACAACTCCCAGGCCGCACGGACAACGAGATCAAGAACTTCTGGAACTCATGCATCAAGAAGAAGCTCCGC-AGCATGGGAATC
 |  ||  |||     |   ||  | | |  |  | |   |  |  |||  ||  |  |||||   | ||      |||||| |||    |        ||||||||| ||||||||  | || || || || || |||||||||||| ||||||||||||||||||| | ||||||||||||||| ||| |||  || |   
tactagtaatttaactacttctcttaattaatt-atagcttggatgatttctagctaattaatcaatcaaacag-gaaattaatcagcttgaattgaatcagGTGGTCTCAGATTGCGGCTCAGCTGCCGGGTCGGACGGACAACGAGGTCAAGAACTTCTGGAACTCTTACATCAAGAAGAAGCTTCGCCAGCGCGGCATC-

upper sequence: PP1S211_139V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: LOC_Os05g46610.1 (Oryza sativa), 3'ss of exon 2
------------------------------gatgagagattctgtcaacccttgtgaatggtcgacatgatacaacattgttatttttaattttttaatttttaaaattagtcaatcggtgggtctgcagGTGGTCACAGATTGCAACACAACTCCCAGGCCGCACGGACAACGAGATCAAGAACTTCTGGAACTCATGCATCAAGAAGAAGCTCCG-CAGCATGGGAATC
                                |    ||   ||    |  |  || |  | || || |  |       |||  |   |    |  |   ||| |        ||| |||| |  ||||||||||| ||||| ||  | ||  | || ||  | ||||||||||||||||||||||||||||||   ||| |||||||||||||||| || |  ||     
gtcggtttcatgtcttggattctgcattgccgtttcggagcttgcttgctttcttgcaatggcggca-gccatggag--gttggtcggagggataaaggatttgagggggaataat-ggtgtgg-tgcagGTGGTCGCAGATCGCGTCGCACTTGCCGGGGAGGACGGACAACGAGATCAAGAACTTCTGGAACAGCTGCCTCAAGAAGAAGCTCCGGCAACGCGGCCTC-

upper sequence: PP1S211_139V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: LOC_Os08g05520.1 (Oryza sativa), 3'ss of exon 2
gatgagagattctgtcaacccttgtgaatggtcgacat-gatacaacattgttatttttaattttttaatttttaaaattagtcaatcggtgggtctg-cagGTGGTCACAGATTGCAACACAACTCCCAGGCCGCACGGACAACGAGATCAAGAACTTCTGGAACTCATGCATCAAGAAGAAGCTCCGCAGCATGGGAATC
  |||   |||    |||    ||    ||      ||   || |  |    ||     |||  || | |  ||| ||||| |      ||   |||| ||||||| | || ||||| |  || || || ||||| || ||||||||||||||||||| |||||| ||||| |||||||||||| | ||||    ||     
--tgattaatttgaccaagatatgatggtgtgtagtatcagtatataaaccatagagagaataattaactaattataattaatgttgttgtctctctgacagGTGGGCCCACATTGCCAGCCACCTGCCTGGCCGGACCGACAACGAGATCAAGAACTACTGGAATTCATGGATCAAGAAGAAGATTCGCAAGCCGGCGGCG

upper sequence: PP1S211_139V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: LOC_Os01g50720.1 (Oryza sativa), 3'ss of exon 2
---------gatgagagattctgt--caacccttgtgaatggtcgacatgatacaacattgttatttttaattttttaatttttaa-aattagtc-aatcggtgggtc--------tgcagGTGGTCACAGATTGCAACACAACTCCCAGGCCGCACGGACAACGAGATCAAGAACTTCTGGAACTCATGCATCAAGAAGAAGCTCCG-CAGCATGGGAATC
          |     | | | |    ||  | |   | |  |      |   |||  | ||| | |  |  |  ||  ||    | || | | |  ||| | | | |        ||||||||||| || || ||  | ||  | || ||  | ||||||||||||||||||||||||||||||   ||| |||||||||||||  | ||||  || |   
gttcgtacgtactgccgctccggcaataatgcgtaccagtactattttcgtcgcaatgtggttgtgtggaggtgatttgttagcgataagtggcctgatcagcgaggcgaatccgatgcagGTGGTCGCAAATCGCGTCGCACTTGCCGGGGAGGACGGACAACGAGATCAAGAACTTCTGGAACAGCTGCCTCAAGAAGAAGCTGAGGCAGCGCGGCATC-

upper sequence: PP1S211_139V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: LOC_Os05g04820.1 (Oryza sativa), 3'ss of exon 3
---gatgagagattctgtcaacccttgtgaa-tggtcgacatgatacaacattgttat-ttttaattttttaatttttaaaattagtcaatcggtgggtctgcagGTGGTCACAGATTGCAACACAACTCCCAGGCCGCACGGACAACGAGATCAAGAACTTCTGGAACTCATGCATCAAGAAGAAGCTCCGCAGCATGGGAATC
    |    |   ||  |   | ||    || |    |||  |  ||  ||  |  |   ||| ||   | || |   | |     || ||   |   |  | |||||||| ||||||||| | || || || ||  | || |||||||||||||||||  ||||||| || ||||||||||||||||||||    |  || || 
gtaaacttcaatctcaattggcactaccaaaattcaggactagtaactgcaaggcaacactttgatacatcaactaacacagcccttctatttttccatgagaagGTGGTCTCAGATTGCAGCTCAGCTGCCTGGGAGGACTGACAACGAGATCAAGAATCTCTGGAATTCTTGCATCAAGAAGAAGCTCCGGCAGAAAGGCATT

upper sequence: PP1S211_139V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: LOC_Os12g33070.1 (Oryza sativa), 3'ss of exon 1
gatgagagattctgtcaacccttgtgaatgg---tcgacatgatacaacattgttatttttaattttttaatttttaaaatta-gtcaatcggtgggtctgcagGTGGTCACAGATTGCAACACAACTCCCAGGCCGCACGGACAACGAGATCAAGAACTTCTGGAACTCATGCATCAAGAAGAAGCTCCGCAGCATGGGAATC
    | || |   |  || | | |  |||     | |||| || ||| |    ||  |      |    ||| |     | || | |    ||      ||||||||||| ||||| ||  | |  || || || ||||| |||||||||||||||||||||||||||||   ||||||||||   |||   | |        |
---catagctatagctaagcttggataataattcttgaca-gaaacatctcgtttgctcactgatgaaaaatctaccgtactacgacgcatggaattattgcagGTGGTCTCAGATCGCTGCCCGGCTACCGGGGCGCACCGACAACGAGATCAAGAACTTCTGGAACTCCACCATCAAGAAGCGCCTCAAGATCTCCTCCTCC

upper sequence: PP1S211_139V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: LOC_Os01g18240.1 (Oryza sativa), 3'ss of exon 2
---gatgagagattctgtcaacccttgtgaatggtcgacatgatacaacattgttatttttaat-tttttaatttttaaaattagtcaatcggtgggtctgcagGTGGTCACAGATTGCAACACAACTCCCAGGCCGCACGGACAACGAGATCAAGAACTTCTGGAACTCATGCATCAAGAAGAAGCTCCGCAGCATGGGAATC
    ||  || | ||  |    |  ||  |  | |    ||   |  || |  | |  |  |   |  |  | || |    ||  |       |   |  |||||||||| || ||||||||||  || || ||  | || ||||| |||||||||||  ||||||| |||||||||||||||||||| ||    |  || || 
gtaaatttga-actcaattg--cactgctagagtttaggatttaattacctcatcaaatcgagcctcctctaattatggccttttttttcacatcaatgagcagGTGGTCTCAAATTGCAACACGGCTGCCTGGAAGAACTGACAATGAGATCAAGAATCTCTGGAATTCATGCATCAAGAAGAAGCTGCGGCAGAAAGGCATT

upper sequence: PP1S211_139V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: LOC_Os01g07450.1 (Oryza sativa), 3'ss of exon 1
gatgagagatt-ctgtcaacccttgtgaatggtcgacatgatacaacattgttatttttaattttttaatttttaaaattagtcaatcggtg-------ggtctgcagGTGGTCACAGATTGCAACACAACTCCCAGGCCGCACGGACAACGAGATCAAGAACTTCTGGAACTCATGCATCAAGAAGAAGCTCCGCAGCATGGGAATC-
|  |  |||||  ||          ||  || | ||      |  | |   ||  ||| |    |  | ||  |     | |||  |  |||       | | ||||| ||||||||||| ||  |    || || ||  |  ||||||||||||||||||||||||||||| |  |  |    |||||||||||    | || | || 
gtagctagattattgctcgattaattgtttgctggattaatcatgaaacgattgatttgatcaatggagttcgtgttcatcgtccgtgcgtgttgccgtgttgtgcagCTGGTCACAGATCGCGGCGAGGCTGCCGGGGAGGTCGGACAACGAGATCAAGAACTTCTGGAACGCGCGGCTGCGCAAGAAGCTCCGGCAGACGG-AGTCG

upper sequence: PP1S211_139V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: LOC_Os01g51260.1 (Oryza sativa), 3'ss of exon 2
--gatgagagattctgtcaacccttgtgaatggtcgacatgatacaacattgttatttttaattttttaatttttaaaattagtcaatcggtgggtctgcagGTGGTCACAGATTGCAACACAACTCCCAGGCCGCACGGACAACGAGATCAAGAACTTCTGGAACTCATGCATCAAGAAGAAGCTCCGCAGCATGGGAATC
  |||  ||||    |  |      |  ||||    |   |||  |   |||   |   |||  | |    | | |   | | ||| |   | |   ||||||||| | |||||||| |  || || || ||  | || ||||| ||| |||||||||||||||||||   ||||||||||||||||  |  |  ||   | 
ttgatctgagacaaagg-acggggcgcaaatgtggcaatcgatcgagatttgagctggctaacatatgctgtgtcactgtgattcactgcattg-catgcagGTGGGCTCAGATTGCCAAGCACCTACCTGGTAGAACAGACAATGAGGTCAAGAACTTCTGGAACTCCACCATCAAGAAGAAGCTCATCTCCCAGGCCGTG

upper sequence: PP1S211_139V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: LOC_Os01g07430.1 (Oryza sativa), 3'ss of exon 2
gatgagagattc-tgtcaacccttgtgaatggtc-gacatgatacaacattgttatttttaattttttaattt---ttaaaattagtcaatcggtg-ggtctgcagGTGGTCACAGATTGCAACACAACTCCCAGGCCGCACGGACAACGAGATCAAGAACTTCTGGAACTCATGCATCAAGAAGAAGC--TCCGCAGCATGGGAATC
      | || | |||  |   |  ||  |  || ||     ||    |   ||   |||| || |     ||   || |   | |   ||  ||| || ||||||||||||   ||| ||  |  |  | || ||| | |||||||||||||||||||||| |||||| ||  |||||| ||||   |  ||||| ||    | |  
------aaatccgtgttcattttcatggttaatccgattctctagctgaactttcgatttagttatcagtgttgatttgatcatggatgatatgtgtgggctgcagGTGGTCGGTGATCGCGGCGAAGATGCCGGGCAGGACGGACAACGAGATCAAGAACTACTGGAATTCCCGCATCAGGAAGCGTCAGTCCGCCGCCGCCGGA--

upper sequence: PP1S211_139V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GRMZM2G064744_T01 (Zea mays), 3'ss of exon 2
----------------------------------------------------------------------------------gatgagagattctgtcaacccttgtgaatggtcg-acatgatacaacattgttattt-ttaattttttaatttttaaaattagtcaatcggtgggtctgcagGTGGTCACAGATTGCAACACAACTCCCAGGCCGCACGGACAACGAGATCAAGAACTTCTGGAACTCATGCATCAAGAAGAAGCTCCG-CAGCATGGGAATC
                                                                                  |||  |  |  | | ||| |  ||  |||  ||  ||      |  |    |||  |   |      |||     |  ||  |    |   ||   |  ||||||||| ||||| ||  | || || || ||  | ||||||||||||||||| |||||||||||||| |||||||||||||||||||| ||||| ||| |||
gtaatttaactggtaatagcaagcaacagttaacacgcatgcatatggcatggcagcatgcagaggctgccacacttgtgctgatctgttacacagacaaacaatgccaataatctcactcagagctcctagcttacatgccagccacataacacacatcatgtgcttgtgcctgatccatcagGTGGTCCCAGATCGCGTCGCAGCTGCCGGGGAGGACGGACAACGAGATCAAAAACTTCTGGAACTCGTGCATCAAGAAGAAGCTCCGGCAGCA-GGGCATC

upper sequence: PP1S211_139V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GRMZM2G172327_T01 (Zea mays), 3'ss of exon 2
-----------------gatgagagattctgtcaacccttgtgaatggtcgacatgatacaacattgttatttttaattttttaattttta------aaattagtcaat--cggtg-ggtctgcagGTGGTCACAGATTGCAACACAACTCCCAGGCCGCACGGACAACGAGATCAAGAACTTCTGGAACTCATGCATCAAGAAGAAGCTCCGCAGCATGGGAATC
                   |    |  | | |    || ||  ||     |||         |  || |    |   |  | |  | | |             | |||   || |        ||| ||| | ||||| || |  || || || || |||||||| |||||| ||||||||||||||||||| ||||||||||||||||||  |     |||  ||
gtacgtacgggcatacttcttgccgtctatcttgctccctgctaactagtgactcaccggggccatggtgccatgcctcgtctggtctgtgcgcggcgcgcatgccaactccgatccaactcacagATGGGCGCAGATCGCCAAGCACCTGCCCGGGCGCACGGATAACGAGGTCAAGAACTTCTGGAACTCGTGCATCAAGAAGAAGCTCATCGCGCAGGGCCTC

upper sequence: PP1S211_139V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GRMZM2G147698_T01 (Zea mays), 3'ss of exon 2
gatgagagattctgtcaacccttgtgaatggtcgacatgatacaacattgttatttttaattttttaatttttaaaattagtcaatcggtgggtctgcagGTGGTCACAGATTGCAACACAACTCCCAGGCCGCACGGACAACGAGATCAAGAACTTCTGGAACTCATGCATCAAGAAGAAGCTCCGCAGCATGGGAATC
                            |   |   ||  |    ||| | |   |         ||||    ||      | ||  | |   |   ||||||||| ||||||||  | || || || ||||| |||||||||||| ||||||||||||||||||| | ||||||||||| |||| |       || |||
---------------------------gtaagcttaattttcatgcatggatgcatggcgagcagtaatggagaacgaatctgaacggttacatggccagGTGGTCTCAGATTGCGGCCCAGCTGCCTGGCCGGACGGACAACGAGGTCAAGAACTTCTGGAACTCGTACATCAAGAAGAGGCTCAGGGAGCGCGGCATC

upper sequence: PP1S211_139V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GRMZM2G325907_T01 (Zea mays), 3'ss of exon 2
-gatgagagattctgtcaacccttgtgaatggtcgacatgatacaacattgttatttttaattttttaatttttaaaatta-gtcaatcggtggg---tctgcagGTGGTCACAGATTGCAACACAACTCCCAGGCCGCACGGACAACGAGATCAAGAACTTCTGGAACTCATGCATCAAGAAGAAGCTCCGCAGCATGGGAATC
 ||  |   |  ||   || ||    |||||    || |     | | | | || ||   || | |  ||    | |   | |||   ||||      ||||||||||| | || ||||| |  ||  | || || || |||||||||||||||||||||| ||||||||| || |||||||||||| |||| |    ||  || 
tgaaaatgaaggcta--aatccaaaggaatgcaacacctaggctagc-tagctagtt--gatgtgtacatgaccacagccatgtcccccggttctctctctgcagGTGGGCCCACATTGCCAGCCACTTGCCCGGGCGGACGGACAACGAGATCAAGAACTACTGGAACTCGTGGATCAAGAAGAAGATCCGGAAGCCGGCGATG

upper sequence: PP1S211_139V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GRMZM2G003406_T01 (Zea mays), 3'ss of exon 2
-gatgagagattctgtcaacccttgtgaatggtcgacatgatacaacattgttatttttaatttttta-atttttaaaattagtcaatcggtgggtctgcagGTGGTCACAGATTGCAACACAACTCCCAGGCCGCACGGACAACGAGATCAAGAACTTCTGGAACTCATGCATCAAGAAGAAGCTCCG-CAGCATGGGAATC
  | |    || |  ||    |     ||  |    | | |  || |   ||                     | ||  |   ||  |  | ||||  |||||||||| ||||| ||  | ||  | || ||||| ||||||||||||||||||||||||||||||   ||| ||||||||||||| || ||||  || |   
gtacgtacaatgcgttccggaccaaccaactgatctccttacccagcgcagtgggcggcggcgcgcggcggcatcaatgtatttcttttcgcgggt--gcagGTGGTCGCAGATCGCGTCGCACTTGCCGGGCCGGACGGACAACGAGATCAAGAACTTCTGGAACAGCTGCCTCAAGAAGAAGCTGCGTCAGCGCGGCATC-

upper sequence: PP1S211_139V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GRMZM2G150841_T01 (Zea mays), 3'ss of exon 2
-------------------------------------gatgagagattctgtcaacccttgtgaatggtcgacatgatacaac-attgttatttttaattt-tttaatt-----tttaaaattagtcaatcggtgggtctg-------cagGTGGTCACAGATTGCAACACAACTCCCAGGCCGCACGGACAACGAGATCAAGAACTTCTGGAACTCATGCATCAAGAAGAAGCTCCG-CAGCATGGGAATC
                                     |||    |   | | ||     | | | |  |   |    | | |  ||  | ||   | ||   |  |||      | |||   |  ||  |  |   ||  |       ||||||||| ||||||||  | || || || || || |||||||||||| | ||||||||||||||||| | | |||||||||||||||| ||||  ||||   
gtaggtggtgccacagtggcaggccatgcatacagcagatccccggcccggccagtttcttttatttattagctgtgtgcgatgatgatgatgaatgatccatccaatcggggatgtaattctgttcgttttgcacgtacgaatgacacagGTGGTCTCAGATTGCTTCGCAGCTGCCGGGGCGGACGGACAACGAGGTGAAGAACTTCTGGAACTCGTACGTCAAGAAGAAGCTCCGGCAGCGCGGGATC-

upper sequence: PP1S211_139V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GRMZM2G175232_T01 (Zea mays), 3'ss of exon 2
---------------------------------------------------------------------------------------------gatgagagattctgtcaacccttgtgaatggtcgacatgatacaacattgtt-atttttaattttttaatttttaaaattagtcaatcggt--gggtctgcagGTGGTCACAGATTGCAACACAACTCCCAGGCCGCACGGACAACGAGATCAAGAACTTCTGGAACTCATGCATCAAGAAGAAGCTCCG-CAGCATGGGAATC
                                                                                             |  | | |     |   |    |  | ||  || |  |   |   ||||||  |||   |     ||| |   ||| |  ||  ||| | |    |  ||||||||||| ||||| ||  | ||  | || || || ||||||||||||||||||||||||||||||   ||| | |||||||||||||| ||||  || |   
gtgggtacggtgacagccgaggcaatgcgttccgttcatccaattccagcctcgaatgaatccatctcccgcgcgtccgcaatgcgggcggaggccgcggggggggggagatagcta-gcattatcaatttatcatttcattgtccattggcagcgccttactgactaata--agcgaattgatccacgcatgcagGTGGTCGCAGATCGCGTCGCACTTGCCGGGGCGGACGGACAACGAGATCAAGAACTTCTGGAACAGCTGCCTGAAGAAGAAGCTCCGGCAGCGCGGCATC-

upper sequence: PP1S211_139V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GRMZM2G052606_T01 (Zea mays), 3'ss of exon 1
-gatgagagattctgtcaacccttgtgaatggtcgacatgatacaacattgttatttttaattttttaatttttaaaattagtcaatcggtgggtctgcagGTGGTCACAGATTGCAACACAACTCCCAGGCCGCACGGACAACGAGATCAAGAACTTCTGGAACTCATGCATCAAGAAGAAGCTCCGCAGCA--TGGGAATC
  | |   |      | |  | || |   ||   || | ||| |   || | |  |||   |  | | |  |  |   | | |       |     | ||||||||| ||||||||  | |   | || || ||||| |||||||||||||||||||||||||||||   ||||||||||  ||||   | ||  | || |  
gtacgtacgtacgcatgacactttctctctgacagaaa-gatcctggatcgatcgtttgcttactgtgaaatcaaccctcacttgcgacattatattccagGTGGTCTCAGATTGCTGCCCGGTTGCCGGGGCGCACCGACAACGAGATCAAGAACTTCTGGAACTCCACCATCAAGAAGCGGCTCAAGAACAGCTCGGCA--

upper sequence: PP1S211_139V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GRMZM2G088783_T01 (Zea mays), 3'ss of exon 2
gatgagagattctgtcaacccttgtgaatggtcgacatgatacaacattgttatttttaattttttaatttttaaaattagtcaatcggtgggtctgcagGTGGTCACAGATTGCAACACAACTCCCAGGCCGCACGGACAACGAGATCAAGAACTTCTGGAACTCATGCATCAAGAAGAAGCTCCGCAGCATGGGAATC
 ||  |      |   |||     ||   | | |  |  |   ||           |  |   |  |  |    |||   |     |  ||      ||||||| | ||||| || |  || || || ||  | |||||||||||| | |||||||||||||||||   ||||||||||||||||  |  |  ||   | 
catatgtcgccttaataacttgcttgggagtttgggacaaaggaaagagacgcgaatggaaaatgcagctagctaaaaatgcgtgccactgcacacacagGTGGGCCCAGATCGCCAAGCATCTGCCTGGTAGAACGGACAACGAGGTGAAGAACTTCTGGAACTCCACCATCAAGAAGAAGCTCATCTCCCAGGCCGTG

upper sequence: PP1S211_139V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GRMZM2G017520_T01 (Zea mays), 3'ss of exon 2
---gatgagagattctgtcaacccttgtgaatggtcgacatgatacaacattgttatttttaa--------ttttttaat------ttttaaaattagtcaatcggtgggtctgcagGTGGTCACAGATTGCAACACAACTCCCAGGCCGCACGGACAACGAGATCAAGAACTTCTGGAACTCATGCATCAAGAAGAAGCTCCGCAGCATGGGAATC
    |  ||  |  |    || | |     |      |  |   |||      ||  ||  ||        | ||||||       ||||    ||  |       |   |   ||||||||| ||||||||||||    | || ||  | || ||||||||||| |||||  ||||||||||  |||||||||||||||||||    |  || || 
gtaaaaaagctaagcccaaaatcatcacagacacagaattttgcacaggccgattgcttccaagcaagctttcttttaaccaggcctttttctttttttttccacatccatggacagGTGGTCTCAGATTGCAACAAGGTTGCCTGGAAGAACTGACAACGAGATTAAGAATCTCTGGAACTCGAGCATCAAGAAGAAGCTCCGGCAGAAAGGCATT

upper sequence: PP1S211_139V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GRMZM2G052377_T01 (Zea mays), 3'ss of exon 2
------------------------------------gatgagagattctgtcaaccc--ttgtgaatggtcgacatgatacaacattgttatttttaatttt----ttaatttttaa--aattagtcaatcggtgggtctgc-agGTGGTCACAGATTGCAACACAACTCCCAGGCCGCACGGACAACGAGATCAAGAACTTCTGGAACTCATGCATCAAGAAGAAGCTCCGCAGCATGGGAATC
                                         |  |||   ||| |    ||  | |||| |  |       |||                |     |  ||| | ||  |||| |    ||  |   | |   || ||||| || || ||  |    || || ||  |  ||||||||||||||||||||||||||||| |  |  |    |||||| ||||    | ||    |
gtaactgacctccgctctgctgaacagcagatgtgcctcccgtcattgcctcagcttaattacgcatggccatctcatagtaacccgaccgacccggccgtcgtcgtcgattgtgaactaatttgatggtcattatctgtattagCTGGTCCCAAATCGCGGCGAGGCTGCCGGGGAGGTCGGACAACGAGATCAAGAACTTCTGGAACGCGCGGCTGCGCAAGAAGATCCGGCAGAAGGAGGCC

upper sequence: PP1S211_139V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GRMZM2G127490_T01 (Zea mays), 3'ss of exon 2
-----------gatgagagattctgtcaacccttgtgaatg-gtcgacatgatacaaca-ttgttatttttaattttttaatttttaaaattagtcaatcggtgggtctgcagGTGGTCACAGATTGCAACACAACTCCCAGGCCGCACGGACAACGAGATCAAGAACTTCTGGAACTCATGCATCAAGAAGAAGCTCCGCAGCATGGGAATC
             ||||| ||  | |||    |   || ||  |  |    |  || || ||| || |||||  |     || ||   | ||      ||  || |     |||||||| || |||||| | || || |||||  | || || || |||||||||||  | |||||||| |||||||||||||||||| |    |  || || 
gtaaatttaagcctgagaaatagtatcagaattcaagactgcatacatgcaaagcagcagttggtaattttagct----gatattagcacttcacttttccatgaga----agGTGGTCTCAAATTGCAGCTCAGCTGCCAGGGAGGACTGATAATGAGATCAAGAATCTATGGAACTCGTGCATCAAGAAGAAGCTCAGGCAGAAAGGCATT

upper sequence: PP1S211_139V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GRMZM2G171781_T01 (Zea mays), 3'ss of exon 2
---gatgagagattctgtcaacccttgtgaa-----tggtcgacatg-atacaacattgttatttttaattttttaatttttaaaattagtcaatcggtgggtctgcagGTGGTCACAGATTGCAACACAACTCCCAGGCCGCACGGACAACGAGATCAAGAACTTCTGGAACTCATGCATCAAGAAGAAGCTCCGCAGCATGGGAATC
    ||  ||         ||    | | |      | | |  |||   | |||    |   ||  ||||||      | |||  | |  | | |   |   |  | |||||||| || |||||| | || || |||||  | || || || |||||||||||  | |||||||| |||||||||||||||||  |    |  || || 
gtaaatttgaagcctgaagaagtagtatcagaattctagactgcatatgtgcaaagcagcagttggtaatttagctgatattagcact--ttactttttccatgagaagGTGGTCTCAAATTGCAGCGCAGCTGCCAGGGAGGACTGATAATGAGATCAAGAATCTATGGAACTCGTGCATCAAGAAGAAGCTGAGGCAGAAAGGCATT

upper sequence: PP1S211_139V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GLYMA13G27310.1 (Glycine max), 3'ss of exon 1
-------gatgagagattctgtcaacccttgtgaatggtcgacatgatacaacattgttatttttaattttttaatttttaaaattagtcaatcggtgggtctgcagGTGGTCACAGATTGCAACACAACTCCCAGGCCGCACGGACAACGAGATCAAGAACTTCTGGAACTCATGCATCAAGAAGAAGCTCCGCAGCATGGGAATC-
         |  || ||   ||  ||  || |   |||  ||| |  ||     ||  | | ||   || |||||| | |  || || |      ||   ||| ||||||||| ||||||||| |||| ||||| |||||||| ||||| ||||| ||||| |||||||||||   |||  |  | ||| |    ||||      || 
aactctaagtaggatatgtagtatacgattatct-tgg--gacttagtatttgctttctttcttctcttctttaatctcttcaaatattg---ttgtaaatct-cagGTGGTCTCAGATTGCAGCACATCTCCCTGGCCGCACAGACAATGAGATTAAGAATTTCTGGAACTC-CACATTGAAGAAAAGGTTGAAAGCAAACACTTCT

upper sequence: PP1S211_139V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GLYMA12G36630.1 (Glycine max), 3'ss of exon 1
gatgagagattctgtcaacccttgtgaatggtcgacatgatacaacattgttatttttaattttttaatttttaaaattagtcaat--cggtgggtctgcagGTGGTCACAGATTGCAACACAACTCCCAGGCCGCACGGACAACGAGATCAAGAACTTCTGGAACTCATGCATCAAGAAGAAGCTCCGCAGCATGGGAATC-
 || |||  |      |     ||||     |    ||  |     ||| ||   |||  || ||   || || ||  |  || ||  | ||       ||||||||| ||||||||| | |  ||||| |||||||| ||||| ||||| ||||| |||||||||||   |||  |  | ||| |    | |       || 
-attagaactctatgtaggatatgtggtatatgagtatattg-ggtattatttgctttctttcttctcttctttaatcttttccatttctgtaaaatctcagGTGGTCTCAGATTGCAGCGCGTCTCCCTGGCCGCACAGACAATGAGATTAAGAATTTCTGGAACTC-CACATTGAAGAAAAGGTTGAAAACTAACACTTCC

upper sequence: PP1S211_139V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GLYMA08G17370.1 (Glycine max), 3'ss of exon 2
gatgagagattctgtcaacccttgtgaatggtcg---acatgatacaacattgttatttttaattttttaatttttaaaattagtcaatcggtgggtctgcagGTGGTCACAGATTGCAACACAACTCCCAGGCCGCACGGACAACGAGATCAAGAACTTCTGGAACTCATGCATCAAGAAGAAGCTCCGCAGCATGGGAATC-
||   ||  |  |    |      |||  ||  |   | || || ||        |  |  | | | || ||   |   ||  || | | |||    |||||| ||| |||| || || |  || || |||||  | || ||||| ||| ||||||| ||||||||||||||||| || |||||||||     ||   |  |  
gacatgatttaattatcatatacatgagaggatgtgtatataattcagtgcaaggacatgca-tatattcatcaatgccatgtgtta-ttggtcta-ctgcagATGGGCACAAATAGCCAAGCACCTACCAGGAAGAACAGACAATGAGGTCAAGAATTTCTGGAACTCATGCATAAAAAAGAAGCTC-ATTTCACAAGGCTTA

upper sequence: PP1S211_139V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GLYMA05G02550.1 (Glycine max), 3'ss of exon 2
-------------------gatgag--agattc-tgtcaacccttgtgaatggtcgacatgatacaacattgttatttttaattttttaattttta-aaattagtcaatcggtgggtctgcagGTGGTCACAGATTGCAACACAACTCCCAGGCCGCACGGACAACGAGATCAAGAACTTCTGGAACTCATGCATCAAGAAGAAGCTCC-GCAGCATGGGAATC
                   ||| |    ||||| | | || |    |   |     |  | | | ||||     ||   ||  | || | |  ||   || | ||   ||  |       ||||||| | || || ||| ||||  | |||||  | || ||||| ||||| ||||||||||||||||||||  | ||||||||||| | | |||| |||| | 
gtaacatatattgaaggatgatcaatatgattcatataaaacaaattctttttcttatgttagataacaagaaaatggctatatattgattggttgtgaaatggtttttctttttaatatcagGTGGGCTCAAATAGCAGCACAGTTACCAGGGAGAACAGACAATGAGATTAAGAACTTCTGGAACTCATGTTTAAAGAAGAAGCTTCTGAAGCAAGGGATT-

upper sequence: PP1S211_139V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GLYMA13G07020.1 (Glycine max), 3'ss of exon 2
gatgagagattctgtcaacccttgtgaatggtcgacatgatacaacat-tgttatt----tttaattttttaatttttaaaattagtcaatcggtgggtctgcagGTGGTCACAGATTGCAACACAACTCCCAGGCCGCACGGACAACGAGATCAAGAACTTCTGGAACTCATGCATCAAGAAGAAGCTCCGCA-GCATGGGAATC
  | |   ||   |  |||| |  |  | |||  |  |  |  || || |||| ||    |||  ||| |    ||||||   |   |||   ||   ||| ||| ||||| ||||||||  |||  ||||| || ||||| ||||| ||||||||||| |||||||||||     | ||||| | | |    | | |    ||| 
--taattaataaag--aaccatgatacaaggtatatgtattgaaatatgtgttgtttccatttgttttctcttcttttaaccatttccaagttgtaaatct-cagATGGTCTCAGATTGCGGCACGTCTCCCTGGTCGCACAGACAATGAGATCAAGAATTTCTGGAACTCCACTCTGAAGAAAAGGTTGAAAATGAACAACAAT-

upper sequence: PP1S211_139V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: AT1G09540.1 (Arabidopsis thaliana), 3'ss of exon 2
-----------------------------------------------------------------------------gatgagagattctgtcaacccttgtgaatggt--cgacatgatacaacattgttatttttaattttttaatttttaaaattagtcaatcggtgggtctgcagGTGGTCACAGATTGCAACACAACTCCCAGGCCGCACGGACAACGAGATCAAGAACTTCTGGAACTCATGCATCAAGAAGAAGCTCCGCAGCATGGGAATC
                                                                             | |       |||||       | ||    ||    |||    |  |  ||  | | || |   |  |   ||||    || |    || ||   |   ||| ||||||||||||||  ||   || || ||  | || |||||||||||||||||  | ||||||||| ||||||||||||| ||       |  || || 
gtaataattagttatcaacaataatgctgtctaagaaaaaatatcatagaaaacagaggatcatgtttatgttttcagcttcattcctctgttttttgctctgctctgttttaacagaggatcaagtttatgtcttaagcctcctctgtttttggctttg---gtctgtttatactcagATGGTCACAGATTGCGTCAAGGCTTCCGGGTAGAACCGACAACGAGATCAAGAATCTATGGAACTCAAGCATCAAGAAGAAACTGAAACAAAGAGGCATT

upper sequence: PP1S211_139V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: AT1G57560.1 (Arabidopsis thaliana), 3'ss of exon 2
gatgagagattctgtcaacccttgtgaatggtcgacatgatacaacattgttatttttaattttttaatttttaaaattagtcaatcggtgggtctgcagGTGGTCACAGATTGCAACACAACTCCCAGGCCGCACGGACAACGAGATCAAGAACTTCTGGAACTCATGCATCAAGAAGAAGCTCCGCAGCATGGGAATC
                      |   |||       |  ||    |  |||| | |  ||     || ||| | ||||    |  |      || | ||| ||||| || |||||  |    || || ||  | || ||||||||||| |||||||| ||||| || ||||| |||||||||||    |  |  || || 
---------------------gtaacaatcacaattacaattattctctgtt-tctgaaacagagtattttctgaaatcc-cctgttatcttgtat-cagATGGTCGCAAATTGCTGCGAGGCTTCCCGGGAGAACCGACAACGAGATAAAGAACTTGTGGAATTCGTGCATTAAGAAGAAGCTGATGAAGAAAGGCATT

upper sequence: PP1S211_139V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: AT5G26660.1 (Arabidopsis thaliana), 3'ss of exon 2
gatgagagattctgtcaacccttgtgaatggtcgacatgatacaacat-tgttatttttaattttttaatttttaaaa---------ttagtcaatcggtgggtctgcagGTGGTCACAGATTGCAACACAACTCCCAGGCCGCACGGACAACGAGATCAAGAACTTCTGGAACTCATGCATCAAGAAGAAGCTCCGCAGCATGGGAATC
| | |   |||    |||| | | |  || ||    |   || ||  | | || | | ||  | | ||  | ||||||         || ||  ||   ||  | || || ||||| || || ||||| |   | || ||  | || |||||||||||||| ||||| |||||||||||  | |||||||||||  | || |  || || 
gttcattaatttg--caacacatttatatagttttgaatttataatgtatattgtgtatatatatatatatgttaaaaaaaaaatctttggttcat-attgaatatgtagATGGTCTCAAATCGCAACGCGGTTACCGGGAAGAACAGACAACGAGATCAAAAACTTTTGGAACTCATGTCTTAAGAAGAAGCTGAGAAGAAAAGGCATT

upper sequence: PP1S211_139V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: AT5G12870.1 (Arabidopsis thaliana), 3'ss of exon 1
gatgagagattctgtcaa-cccttgtgaatggtcgacatg-atacaacattgttatttttaattttttaa-tttttaaaattagtcaatcggtgggtctgcagGTGGTCACAGATTGCAACACAACTCCCAGGCCGCACGGACAACGAGATCAAGAACTTCTGGAACTCATGCATCAAGAAGAAGCTCCGCAGCATGGGAATC
   |    | ||| | |  ||| ||  ||   |  ||  | |||||   |   ||   | |  |  ||||  | ||  | |   | | ||   |  |    |||||||| ||||||||| ||| | | || || || || || |||||||||||||| ||||||||||||   || ||||| | |||    |  |||      
---ggatcactctctaattcccatgcaaaccatgcactggtatacattttacataacatcatctcattaaactattctactctcttattcttcgatttcatagGTGGTCTCAGATTGCAGCACGATTGCCTGGTCGGACCGATAACGAGATCAAGAATTTCTGGAACTCAACAATAAAGAAAAGGCTAAAGAAGATGTCCGAT

upper sequence: PP1S211_139V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: Vv17s0000g09080.t01 (Vitis vinifera), 3'ss of exon 2
gatgagagattctgtcaacccttgtgaatggtcgacatgatacaacattgttatttttaattttttaatttttaaaattagtcaatcggt--gggtctgcagGTGGTCACAGATTGCAACACAACTCCCAGGCCGCACGGACAACGAGATCAAGAACTTCTGGAACTCATGCATCAAGAAGAAGCT-CCGCAGCATGGGAATC
       |  |     ||| |    |||   ||  || |||     ||| ||  | | ||   || || |      |||  |  ||   |  ||   ||||||||| | ||||||||| ||||| | |||||  | || ||||| ||||| |||||||| |||||||||||| | ||||||||||| | | |||| || |   
-------gtatggaaaaacaccccagaaccctct-caggatttccaatttttggtatgaaaaattgaaatg--ggtattcatggattctttgggaattgcagGTGGGCTCAGATTGCAGCACAATTGCCAGGAAGAACAGACAATGAGATTAAGAACTTTTGGAACTCATGCTTGAAGAAGAAGCTACTGAAGCAAGGCATG-

upper sequence: PP1S211_139V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: Vv19s0085g00940.t01 (Vitis vinifera), 3'ss of exon 2
gatgagagattctgtcaacccttgt--gaatggtcgacatgatacaacattgttatttttaattttttaatttt---taaaattagtcaatcggtgggtct--gcagGTGGTCACAGATTGCAACACAACTCCCAGGCCGCACGGACAACGAGATCAAGAACTTCTGGAACTCATGCATCAAGAAGAAGCTCCGCAGCATGGGAATC-
|  | ||   |||  |||    |    | |||    |  |   |  | |||    || |     |||| ||||    | || ||  ||  |   ||  | |  |||| ||| | ||||| || |  || || || ||  | || ||||| ||| | ||||| ||||||||||||||||| |||||||||||      ||   |  |  
gtagggatgatctcacaatatatacaaggatgagtaaggtagaaagaaattagatttctctgcattttcatttcatgttaatttcctctctttatgtatatatgcagATGGGCTCAGATAGCTAAGCATCTACCTGGGAGAACAGACAATGAGGTGAAGAATTTCTGGAACTCATGCATTAAGAAGAAGCTG-ATTTCACAAGGCTTG

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 23 (upstream exon), 13 (downstream exon)
Score: 1

TGCGATGGATCAACTACTTGAGACCAGATTTGAAACGAGGGGTATTCTCCGCGACAGAAGAAAGTTTGATAATAGACTGGCATGCTGCACTTGGCAACAGgtctaaatct ... gggtctgcagGTGGTCACAGATTGCAACACAACTCCCAGGCCGCACGGACAACGAGATCAAGAACTTCTGGAACTCATGCATCAAGAAGAAGCTCCGCAGCATGGGAATC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cattgttatttttaattttttaatttttaaaattagtcaatcggtgggtctgcagGTGGTCACAGATTGCAACACAACTCCCAGGCCGCACGGACAACGAGATCAAGAACTTCTGGAACTCATGCATCAAGAAGAAGCTCCGCAGCATGGGAATC
                 ttttaat  putative branch site (score: 1)
     ttatttttaatttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gatgagagattctgtcaacccttgtgaatggtcgacatgatacaacattgttatttttaattttttaatttttaaaattagtcaatcggtgggtctgcagGTGGTCACAGATTGCAACACAACTCCCAGGCCGCACGGACAACGAGATCAAGAACTTCTGGAACTCATGCATCAAGAAGAAGCTCCGCAGCATGGGAATC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC