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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tagtagatctgaatactagtttttgtgagaactacgtattggactttactttagggtttatttggggtgactctgatggaggcttgcatgggttttctagGTGAACGTTCCGAAAACCAAGAAGTCCTTCTGTCCAGGGAAGGCGTGCAAGAAGCACACCCTCCACAAGGTCACCCAGTACAAGAAGGGAAAGGATAGTT

Basic information

species Physcomitrella patens
transcript PP1S22_326V6.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S22_326V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: LOC_Os07g26740.1 (Oryza sativa), 3'ss of exon 1
tagta-gat-ctgaatactagtttttgtgagaactacg-tattggactttactttagggtttatttggggtgactctgatggaggcttgcatgggttttctagGTGAACGTTCCGAAAACCAAGAAGTCCTTCTGTCCAGGGAAGGCGTGCAAGAAGCACACCCTCCACAAGGTCACCCAGTACAAGAAGGGAAAGGATAGTT
|| |  |||  || | |  ||   ||   |      |  ||||     ||| | |    | ||||   |  |  |   ||  | | |  ||  | |||| ||||||||||| || ||||| |||||| | | ||||      ||||  |||| |||||||||||| |||||||| |||||||||||||| |||||||||||  
taatctgatattgcaaataaggcattagaaagtgagcactatttatgcttaatgtcatctgtattcttgtagtattgaat--atgttatcactg-ttttttagGTGAACGTGCCAAAAACTAAGAAGACTTACTGTAAGAACAAGGAATGCAGGAAGCACACCCTACACAAGGTTACCCAGTACAAGAAAGGAAAGGATAGCC

upper sequence: PP1S22_326V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: LOC_Os07g33880.1 (Oryza sativa), 3'ss of exon 1
---ta-gtagatctgaatactagtttttgtgagaactacgtattggactttactttagggtttatttggggtgactctgatggaggcttgcatgggttttctagGTGAACGTTCCGAAAACCAAGAAGTCCTTCTGTCCAGGGAAGGCGTGCAAGAAGCACACCCTCCACAAGGTCACCCAGTACAAGAAGGGAAAGGATAGTT
   || | | || ||| || |  || |    ||  || ||   |  | |  || ||  |  ||  ||  | ||| |    | |   |     ||  || | |||||||||||||| || ||||||||| ||| |||       |||| ||||| |||||||||||| ||||||||||| |||||||||||||| ||||| ||  
aattatgcacatttgattattgtttat----aggcctgcgatgtccattccacattcagtatttgttaagctgagtgcttttgtttcaaatttgttttgtatagGTGAACGTTCCCAAGACCAAGAAGACCTACTGCAAGAACAAGGAGTGCAGGAAGCACACCCTTCACAAGGTCACTCAGTACAAGAAGGGTAAGGACAGCC

upper sequence: PP1S22_326V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: LOC_Os07g33898.1 (Oryza sativa), 3'ss of exon 1
--tagtagatctgaatactagtttttg----tgagaactacgtattggactttactttagggtttatttggggtgactctgatggaggcttgcatgggttttctagGTGAACGTTCCGAAAACCAAGAAGTCCTTCTGTCCAGGGAAGGCGTGCAAGAAGCACACCCTCCACAAGGTCACCCAGTACAAGAAGGGAAAGGATAGTT
  |  |   | || | | | | || ||    | | |     |   ||  |||| |  ||     ||||||   | | | || |  |   || | |  || |   ||||||||||||| || ||||||||| ||| |||       |||| ||||| |||||||||||| ||||||||||| |||||||||||||| ||||| ||  
gcttctgattatgcacatttgattgtgttgtttataggcctgctatgtgctttccaataaccagtatttgt--taaatttgtttcatattt-cttatgtat---agGTGAACGTTCCCAAGACCAAGAAGACCTACTGCAAGAACAAGGAGTGCAGGAAGCACACCCTTCACAAGGTCACTCAGTACAAGAAGGGTAAGGACAGCC

upper sequence: PP1S22_326V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: LOC_Os07g33860.1 (Oryza sativa), 3'ss of exon 1
-------------------------------------------------------------tagtagatctgaatacta--gtttttgtgagaactacgtattggactttactttagggtttatttggggtgactctgatggaggcttgcatgggttttctagGTGAACGTTCCGAAAACCAAGAAGTCCTTCTGTCCAGGGAAGGCGTGCAAGAAGCACACCCTCCACAAGGTCACCCAGTACAAGAAGGGAAAGGATAGTT
                                                              |    ||    || | |  ||| ||   ||  || ||   |  | |  || ||  |  ||  ||  | |||||    | |   |     ||  || | |||||||||||||| || ||||||||| ||| |||       |||| ||||| |||||||||||| ||||||||||| |||||||||||||| ||||| ||  
gttttaaccattggtttgctgaatgtgtcttcagtgttgaaaaatttggacacatttgcttcaaattatgcacattcgactgttgtttataggcctgcgatgtccattccacattcagtatttgttaagctgactgcttttgtttcaaatttgttttgtatagGTGAACGTTCCCAAGACCAAGAAGACCTACTGCAAGAACAAGGAGTGCAGGAAGCACACCCTTCACAAGGTCACTCAGTACAAGAAGGGTAAGGACAGCC

upper sequence: PP1S22_326V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GRMZM2G160351_T01 (Zea mays), 3'ss of exon 1
tagtagatctgaatactagtttttgtgagaactacgtattggactttactttagggtttattt-ggggtgactct-----gatgga--ggcttgcatgggttttctagGTGAACGTTCCGAAAACCAAGAAGTCCTTCTGTCCAGGGAAGGCGTGCAAGAAGCACACCCTCCACAAGGTCACCCAGTACAAGAAGGGAAAGGATAGTT
     |  || || | | |||  | |   |  |   ||||   | | |||||   ||||||||     ||| |||     |||| |      || |    ||| |||||||||||||||||||||||||||| ||| ||||      ||||  |||| |||||||||||| |||||||| |||||||||||||| || ||||||||  
----gggactaaa-atttgttcatatattactt---tatttagcatgacttttcagtttattttatattgattctttgtggatgaattatgctgtacacatttcctagGTGAACGTTCCGAAAACCAAGAAGACCTACTGTAAGAACAAGGAATGCAGGAAGCACACCCTGCACAAGGTTACCCAGTACAAGAAAGGTAAGGATAGCC

upper sequence: PP1S22_326V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GRMZM2G009412_T01 (Zea mays), 3'ss of exon 1
tagtagatctgaatactagtttttgtgagaactacgtattggact-ttactttagggtttatttggggtgactctgatggaggcttgcatgggttttctagGTGAACGTTCCGAAAACCAAGAAGTCCTTCTGTCCAGGGAAGGCGTGCAAGAAGCACACCCTCCACAAGGTCACCCAGTACAAGAAGGGAAAGGATAGTT
    ||  |   ||       ||  | |    |  || ||    |  ||       |    ||||   | ||  |        ||| ||   ||| | |||||||||||||| || ||||||||| ||| |||       |||| ||||||||||||||| ||||||||||| || |||||||||||||| ||||||||  
-tacagccccatatggagaacttgcttatgctttggtcttcagttgctaaggatatgcaattttgttttaacctttgcaatttctttcacatgttatatagGTGAACGTTCCTAAGACCAAGAAGACCTACTGCAAGAACAAGGAGTGCAAGAAGCACACTCTCCACAAGGTTACTCAGTACAAGAAGGGTAAGGATAGCC

upper sequence: PP1S22_326V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GRMZM2G125527_T02 (Zea mays), 3'ss of exon 1
tagtagatctgaatactagtttttgtgaga---actacgtattggactttactttagggt-ttatttggggtgactctgatggaggcttgcatgggttttctagGTGAACGTTCCGAAAACCAAGAAGTCCTTCTGTCCAGGGAAGGCGTGCAAGAAGCACACCCTCCACAAGGTCACCCAGTACAAGAAGGGAAAGGATAGTT
|        |  | | |  ||||| |   |   ||| |    | ||  |   | |    | || |||    | ||       |    || ||   ||| |  ||||||||||||| || ||||||||| | | |||       || | ||||||||||||||| ||||||||||| || ||||| |||||||| ||||||||  
tgaccctcatagaaagtgttttttattcaattgactgctctctagagatggatatgaaatgttgttt----taacatgtgcagtttgtttcacatgttatacagGTGAACGTTCCTAAGACCAAGAAGACGTACTGCAAGAACAAAGAGTGCAAGAAGCACACACTCCACAAGGTGACTCAGTATAAGAAGGGCAAGGATAGCC

upper sequence: PP1S22_326V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GRMZM2G103059_T01 (Zea mays), 3'ss of exon 1
----------------------------------------------------tagtaga---tctgaatactagtttttgtgagaactacgtattggactttactttagggtttatttggggtg--actctgatg---gaggcttg---catgggttttctagGTGAACGTTCCGAAAACCAAGAAGTCCTTCTGTCCAGGGAAGGCGTGCAAGAAGCACACCCTCCACAAGGTCACCCAGTACAAGAAGGGAAAGGATAGTT
                                                     | | ||   ||  |||| || ||| |       |         ||||   |||   | |  || ||   ||    | | |     |  | |||   ||   ||| | |||||||||||||| || ||||||||| | | |||       || | |||||||||||||||| |||||||||| || ||||| |||||||| ||||||||  
gtgtgcatcaaacacatacttctagccccatgcccccatgttaaaagtgtttcaattgaccctccaaataataatttatccagatgcctaaagaaagact---cttggagatggatatgaaatgttgttttaacatgtgtagtttgtttcacatgttatatagGTGAACGTTCCTAAGACCAAGAAGACGTACTGCAAGAACAAAGAGTGCAAGAAGCACACCGTCCACAAGGTGACTCAGTATAAGAAGGGCAAGGATAGCA

upper sequence: PP1S22_326V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GLYMA05G24930.1 (Glycine max), 3'ss of exon 1
tagtagatctgaatactagtttttgtgagaactacgtattggactttactttagggtttatttggggtgactctgatggaggcttgcatgggttttctagGTGAACGTTCCGAAAACCAAGAAGTCCTTCTGTCCAGGGAAGGCGTGCAAGAAGCACACCCTCCACAAGGTCACCCAGTACAAGAAGGGAAAGGATAGTT
  |||        | | |  ||        |   |  ||  |  |||  || |     | ||   | |  |  | || |    |||  ||    ||  |||||||||||||||| || |||||| ||| |||     | |||| ||||| ||||||||| ||||||||||||||||| ||||||||||| ||||| ||  
--gtaagctcatcttcaatcttcatccctcaactctcatccg--tttgattgaacaactctt---gatttcaattatcgttttttgtttg---cttgcagGTGAACGTTCCGAAGACAAAGAAGACCTACTGCAAGAGCAAGGAGTGCAGGAAGCACACGCTCCACAAGGTCACCCAATACAAGAAGGGCAAGGACAGCA

upper sequence: PP1S22_326V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GLYMA08G08030.1 (Glycine max), 3'ss of exon 1
tagtagatctgaatactagtttttgtgagaactacgtattggactttactttagggtttatttggggtgactctgatggaggcttgcatgggttttctagGTGAACGTTCCGAAAACCAAGAAGTCCTTCTGTCCAGGGAAGGCGTGCAAGAAGCACACCCTCCACAAGGTCACCCAGTACAAGAAGGGAAAGGATAGTT
          | |  ||  | ||  | |   ||    ||  |  || | |  |   ||| |       || |   ||   || |||  ||   |||  |||||||||||||||| || |||||| ||| |||     | |||| ||||| ||||||||| ||||||||||||||||| ||||||||||| ||||| ||  
----------gtaacctcatcttcttcaactct---catccg-tttgattgcacaatttct-------gatttcaattatggtttgtttg---tttgcagGTGAACGTTCCGAAGACAAAGAAGACCTACTGCAAGAGCAAGGAGTGCAGGAAGCACACGCTCCACAAGGTCACCCAATACAAGAAGGGCAAGGACAGCA

upper sequence: PP1S22_326V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GLYMA15G05670.1 (Glycine max), 3'ss of exon 1
tagtagatctgaatactagtttttgtgagaactacgtattggactttactttagggtttatttggggtgactctgatggaggcttgcatgggt--tttctagGTGAACGTTCCGAAAACCAAGAAGTCCTTCTGTCCAGGGAAGGCGTGCAAGAAGCACACCCTCCACAAGGTCACCCAGTACAAGAAGGGAAAGGATAGTT
 | ||| | ||| |       ||  ||   | |  ||  |||    ||   | |    | ||     ||  | |       | |    ||  |  |   |||||||||||||||||||| |||||| | | |||     | |||| ||||| ||||||||| || |||||||| ||||| ||||||||||| ||||||||  
-attaggtttgattgaattggttattggttatttggtcatggttgctatgctggaaaatgtt-aaaatgcttttttcttttgttgttgtgaataataaatagGTGAACGTTCCGAAAACAAAGAAGACATACTGCAAGAGTAAGGAGTGCAGGAAGCACACGCTGCACAAGGTTACCCAATACAAGAAGGGTAAGGATAGCA

upper sequence: PP1S22_326V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GLYMA08G19320.2 (Glycine max), 3'ss of exon 1
----tagtagatctgaa-tactagtttttgtgagaactacgtattggactttactttagggtttatttggggtgactctgatggaggcttgcatgggttttctagGTGAACGTTCCGAAAACCAAGAAGTCCTTCTGTCCAGGGAAGGCGTGCAAGAAGCACACCCTCCACAAGGTCACCCAGTACAAGAAGGGAAAGGATAGTT
     | ||||| |||| |    |  || || |  |   ||| || |    |||  |         ||    ||  | |  |      |||  ||   |    ||||||||||||||||||| |||||| | | |||     | |||| ||||| |||||||||||| |||||||| ||||| ||||||||||| || |||||  
agtgaattagatttgaaattgcggaattggttattaggtcgtgtttggtagtacgctgcaaaaatgttaaaatgcttttcct-----tttgtttgttgtgaacagGTGAACGTTCCGAAAACAAAGAAGACATACTGCAAGAGTAAGGAGTGCAGGAAGCACACCCTGCACAAGGTTACCCAATACAAGAAGGGTAAAGATAGCA

upper sequence: PP1S22_326V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: EFJ05955 (Selaginella moellendorffii), 3'ss of exon 1
tagtagatctgaatactagtttttgtgagaactacgtattggactttactttagggtttatttggggtgactctgatggaggcttgcatgggttttctagGTGAACGTTCCGAAAACCAAGAAGTCCTTCTGTCCAGGGAAGGCGTGCAAGAAGCACACCCTCCACAAGGTCACCCAGTACAAGAAGGGAAAGGATAGTT
                                        | |  ||  |    ||        |      |||  | ||    | |           |||||||||| || || || |||||||||||||| | |||||||   |||  ||||||||| |||||||||||||| |||||||||||||| ||||| ||  
----------------------------------------gtatgttcttgcgaggcgctcgctgctcagatct--tagatctctccccaatgccgacagGTGAACGTCCCCAAGACGAAGAAGTCCTTCTGCCAAGGGAAGAATTGCCGGAAGCACACGCTCCACAAGGTCACGCAGTACAAGAAGGGCAAGGACAGCC

upper sequence: PP1S22_326V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: EFJ07113 (Selaginella moellendorffii), 3'ss of exon 1
tagtagatctgaatactagtttttgtgagaactacgtattggactttactttagggtttatttggggtgactctgatggaggcttgcatgggttttctagGTGAACGTTCCGAAAACCAAGAAGTCCTTCTGTCCAGGGAAGGCGTGCAAGAAGCACACCCTCCACAAGGTCACCCAGTACAAGAAGGGAAAGGATAGTT
                                        | |  ||  |    ||        |      |||  | ||    | |           |||||||||| || || || |||||||||||||| | |||||||   |||  ||||||||| |||||||||||||| |||||||||||||| ||||| ||  
----------------------------------------gtatgttcttgcgaggcgctcgctgctcagatct--tagatctctccccaatgccgacagGTGAACGTGCCCAAGACGAAGAAGTCCTTCTGCCAAGGGAAGAATTGCCGGAAGCACACGCTCCACAAGGTCACGCAGTACAAGAAGGGCAAGGACAGCC

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|18368682|gb|BJ200767.1|BJ200767
EST:     TCGAGCGGTAGCGAGGCCAGTTGAGGCGATTTCTGAACGTAATCACGATG                         GTGAACGTTCCGAAAACCAAGAAGTCCTTCTGTCCAGGGAAGGCGTGCAAG
genomic: TCGAGCGGTAGCGAGGCCAGTTGAGGCGATTTCTGAACGTAATCACGATGgtaagtgcga ... ggttttctagGTGAACGTTCCGAAAACCAAGAAGTCCTTCTGTCCAGGGAAGGCGTGCAAG
EST: gi|162262338|gb|FC437665.1|FC437665
EST:     TCGAGCGGTAGCGAGGCCAGTTGAGGCGATTTCTGAACGTAATCACGATG                         GTGAACGTTCCGAAAACCAAGAAGTCCTTCTGTCCAGGGAAGGCGTGCAAG
genomic: TCGAGCGGTAGCGAGGCCAGTTGAGGCGATTTCTGAACGTAATCACGATGgtaagtgcga ... ggttttctagGTGAACGTTCCGAAAACCAAGAAGTCCTTCTGTCCAGGGAAGGCGTGCAAG
EST: gi|162228552|gb|FC404150.1|FC404150
EST:     TCGAGCGGTAGCGAGGCCAGTTGAGGCGATTTCTGAACGTAATCACGATG                         GTGAACGTTCCGAAAACCAAGAAGTCCTTCTGTCCAGGGAAGGCGTGCAAG
genomic: TCGAGCGGTAGCGAGGCCAGTTGAGGCGATTTCTGAACGTAATCACGATGgtaagtgcga ... ggttttctagGTGAACGTTCCGAAAACCAAGAAGTCCTTCTGTCCAGGGAAGGCGTGCAAG
EST: gi|18335674|gb|BJ167694.1|BJ167694
EST:     TCGAGCGGTAGCGAGGCCAGTTGAGGCGATTTCTGAACGTAATCACGATG                         GTGAACGTTCCGAAAACCAAGAAGTCCTTCTGTCCAGGGAAGGCGTGCAAG
genomic: TCGAGCGGTAGCGAGGCCAGTTGAGGCGATTTCTGAACGTAATCACGATGgtaagtgcga ... ggttttctagGTGAACGTTCCGAAAACCAAGAAGTCCTTCTGTCCAGGGAAGGCGTGCAAG
EST: gi|18360736|gb|BJ192799.1|BJ192799
EST:     TCGAGCGGTAGCGAGGCCAGTTGAGGCGATTTCTGAACGTAATCACGATG                         GTGAACGTTCCGAAAACCAAGAAGTCCTTCTGTCCAGGGAAGGCGTGCAAG
genomic: TCGAGCGGTAGCGAGGCCAGTTGAGGCGATTTCTGAACGTAATCACGATGgtaagtgcga ... ggttttctagGTGAACGTTCCGAAAACCAAGAAGTCCTTCTGTCCAGGGAAGGCGTGCAAG
EST: gi|162225415|gb|FC401193.1|FC401193
EST:     GAACGTAATCACGATG                         GTGAACGTTCCGAAAACCAAGAAGTCCTTCTGTCCAGGGAAGGCGTGCAAG
genomic: GAACGTAATCACGATGgtaagtgcga ... ggttttctagGTGAACGTTCCGAAAACCAAGAAGTCCTTCTGTCCAGGGAAGGCGTGCAAG
EST: gi|67575316|gb|BJ948140.1|BJ948140
EST:     TCGAGCGGTAGCGAGGCCAGTTGAGGCGATTTCTGAACGTAATCACGATG                         GTGAACGTTCCGAAAACCAAGAAGTCCTTCTGTCCAGGGAAGGCGTGCAAG
genomic: TCGAGCGGTAGCGAGGCCAGTTGAGGCGATTTCTGAACGTAATCACGATGgtaagtgcga ... ggttttctagGTGAACGTTCCGAAAACCAAGAAGTCCTTCTGTCCAGGGAAGGCGTGCAAG
EST: gi|67698779|gb|BJ959012.1|BJ959012
EST:     TCGAGCGGTAGCGAGGCCAGTTGAGGCGATTTCTGAACGTAATCACGATG                         GTGAACGTTCCGAAAACCAAGAAGTCCTTCTGTCCAGGGAAGGCGTGCAAG
genomic: TCGAGCGGTAGCGAGGCCAGTTGAGGCGATTTCTGAACGTAATCACGATGgtaagtgcga ... ggttttctagGTGAACGTTCCGAAAACCAAGAAGTCCTTCTGTCCAGGGAAGGCGTGCAAG
EST: gi|18327408|gb|BJ159410.1|BJ159410
EST:     TCGAGCGGTAGCGAGGCCAGTTGAGGCGATTTCTGAACGTAATCACGATG                         GTGAACGTTCCGAAAACCAAGAAGTCCTTCTGTCCAGGGAAGGCGTGCAAG
genomic: TCGAGCGGTAGCGAGGCCAGTTGAGGCGATTTCTGAACGTAATCACGATGgtaagtgcga ... ggttttctagGTGAACGTTCCGAAAACCAAGAAGTCCTTCTGTCCAGGGAAGGCGTGCAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttactttagggtttatttggggtgactctgatggaggcttgcatgggttttctagGTGAACGTTCCGAAAACCAAGAAGTCCTTCTGTCCAGGGAAGGCGTGCAAGAAGCACACCCTCCACAAGGTCACCCAGTACAAGAAGGGAAAGGATAGTT
                         ctctgat  putative branch site (score: 4)
                                               ttttct  putative PPT
           tttattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tagtagatctgaatactagtttttgtgagaactacgtattggactttactttagggtttatttggggtgactctgatggaggcttgcatgggttttctagGTGAACGTTCCGAAAACCAAGAAGTCCTTCTGTCCAGGGAAGGCGTGCAAGAAGCACACCCTCCACAAGGTCACCCAGTACAAGAAGGGAAAGGATAGTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG