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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatgatggttcctttagaggtctttgagcatgtttgggtgtcatttgtgggtgcttttacattgagcaagacttaatttggatgatgatgtaaatggtttctgtgtgcagCTACCCAGAAGACCGTGGACGGTCCATCTGGAAAGGACTGGCGTGGAGGACGTGGTGCTGGACAGAACATTATTCCCAGCTCAACTGGAGCTGCGAAG

Basic information

species Physcomitrella patens
transcript PP1S309_73V6.2
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S309_73V6.3 (Physcomitrella patens), 3'ss of exon 6
lower sequence: GRMZM2G104632_T01 (Zea mays), 3'ss of exon 9
-gtaatgatggttcctttagaggtctttgagcatgtttgggtgtcatttgtgggtgcttttacattgagcaagacttaatttggatgatgatgtaaatggtttctgtgtgcagCTACCCAGAAGACCGTGGACGGTCCATCTGGAAAGGACTGGCGTGGAGGACGTGGTGCTGGACAGAACATTATTCCCAGCTCAACTGGAGCTGCGAAG
  |    |  |    ||     || | |   | ||||  |   |||||||    |  |  | ||||    || |  |  ||   ||||  |||| | |  || |  ||| ||||||||||||||||||| || ||||| ||    ||||| ||| | ||||||||||||||||  || ||||| ||||||||||| ||||| || || |||
gttggcaactgacttttatccagtgtcta--cctgttaag---tcatttgccatt-ttcgtgcattttcaaaaa--tggttgtcatgaaaatgttact--ttaccatgtccagCTACCCAGAAGACCGTCGATGGTCCTTCGATGAAGGATTGGAGAGGAGGACGTGGTGCTGCCCAAAACATAATTCCCAGCTCCACTGGTGCAGCAAAG

upper sequence: PP1S309_73V6.3 (Physcomitrella patens), 3'ss of exon 6
lower sequence: GRMZM2G051004_T01 (Zea mays), 3'ss of exon 9
gtaatgatggttcctttagaggtctttgagcatgtttgggt---gtcatttgtgggtgcttttacattgagcaagacttaatttggatgatgatgtaaatggtttctgtgtgcagCTACCCAGAAGACCGTGGACGGTCCATCTGGAAAGGACTGGCGTGGAGGACGTGGTGCTGGACAGAACATTATTCCCAGCTCAACTGGAGCTGCGAAG
     | ||||| ||   |   || |  ||  | |    ||   ||||||||    |  |  | ||||   ||| |  |||||   ||||  |||| | ||  | |  ||| |||| |||||||||||||| || ||||| ||    ||||| ||| | ||||||||||||||||| || ||||| ||||| ||||| ||||| || || |||
-----gttggttact--ggctttcatccagtgtctacctgttaagtcatttgccatt-ttcatgcatttt-caaaa--taattgtcatgagcatgttactg--taccatgtccagCCACCCAGAAGACCGTTGATGGTCCTTCAATGAAGGATTGGAGAGGAGGACGTGGTGCTGGCCAAAACATAATTCCTAGCTCCACTGGTGCAGCAAAG

upper sequence: PP1S309_73V6.3 (Physcomitrella patens), 3'ss of exon 6
lower sequence: EFJ15779 (Selaginella moellendorffii), 3'ss of exon 6
gtaatgatggttcctttagaggtctttgagcatgtttgggtgtcatttgtgggtgcttttacattgagcaagacttaatttggatgatgatgtaaatggtttctgtgtgcagCTACCCAGAAGACCGTGGACGGTCCATCTGGAAAGGACTGGCGTGGAGGACGTGGTGCTGGACAGAACATTATTCCCAGCTCAACTGGAGCTGCGAAG--
                                                                              ||  |    | || |   | |||||| | | |||| || ||||| || ||||| ||||| ||||||||||| ||||| || ||||| ||||| || ||||| || || |||||||| || ||||| || |||  
-----------------------------------------------------------------------------gttctgtgcttaatttcttttgtttctttctccagCAACTCAGAAAACTGTGGATGGTCCCTCTGGAAAGGATTGGCGAGGCGGACGAGGTGCCGGCCAGAATATCATCCCCAGCTCTACCGGAGCAGCAAAGGC

upper sequence: PP1S309_73V6.3 (Physcomitrella patens), 3'ss of exon 6
lower sequence: EFJ32914 (Selaginella moellendorffii), 3'ss of exon 8
gtaatgatggttcctttagaggtctttgagcatgtttgggtgtcatttgtgggtgcttttacattgagcaagacttaatttggatgatgatgtaaatggtttctgtgtgcagCTACCCAGAAGACCGTGGACGGTCCATCTGGAAAGGACTGGCGTGGAGGACGTGGTGCTGGACAGAACATTATTCCCAGCTCAACTGGAGCTGCGAAG
                                                    |||||    ||| |||  ||   || ||  |    | || |   | |||||| | | |||| || ||||| || ||||| ||||| ||||||||||| ||||| || ||||| ||||| || ||||| || || |||||||| || ||||| || |||
----------------------------------------------------gtgctaccccatggag--agctctagttctgtgcttaatttcttttgtttctttctccagCAACTCAGAAAACTGTGGATGGTCCCTCTGGAAAGGATTGGCGAGGCGGACGAGGTGCCGGCCAGAATATCATCCCCAGCTCTACCGGAGCAGCAAAG

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|67570882|gb|BJ943706.1|BJ943706
EST:     CAACTTCGGCATTGAGGAAGGGCTCATGACCACTGTGCATGCCACCACTG                         CTACCCAGAAGACCGTGGACGGTCCATCTGGAAAGGACTGGCGT
genomic: CAACTTCGGCATTGAGGAAGGGCTCATGACCACTGTGCATGCCACCACTGgtaatgatgg ... ctgtgtgcagCTACCCAGAAGACCGTGGACGGTCCATCTGGAAAGGACTGGCGT
EST: gi|208369274|gb|DC956065.1|DC956065
EST:     GGCTCATGACCACTGTGCATGCCACCACTG                         CTACCCAGAAGACCGTGGAC-GTCCATCTGGAAAGGACTGGCGTGGAGGAC
genomic: GGCTCATGACCACTGTGCATGCCACCACTGgtaatgatgg ... ctgtgtgcagCTACCCAGAAGACCGTGGACGGTCCATCTGGAAAGGACTGGCGTGGAGGAC
EST: gi|162152341|gb|FC328528.1|FC328528
EST:     CCACTGTGCATGCCACCACTG                         CTACCCAGAAGACCGTGGACGGTCCATCTGGAAAGGACTGGCGTGGAGGAC
genomic: CCACTGTGCATGCCACCACTGgtaatgatgg ... ctgtgtgcagCTACCCAGAAGACCGTGGACGGTCCATCTGGAAAGGACTGGCGTGGAGGAC
EST: gi|67726807|gb|BJ977066.1|BJ977066
EST:     CAACTTCGGCATTGAGGAAGGGCTCATGACCACTGTGCATGCCACCACTG                         CTACCCAGAAGACCGTGGACGGTCCATCTGGAAAGGACTGGCGTGGAGGAC
genomic: CAACTTCGGCATTGAGGAAGGGCTCATGACCACTGTGCATGCCACCACTGgtaatgatgg ... ctgtgtgcagCTACCCAGAAGACCGTGGACGGTCCATCTGGAAAGGACTGGCGTGGAGGAC
EST: gi|208388488|gb|DC957070.1|DC957070
EST:     CAACTTCGGCATTGAGGAAGGGCTCATGACCACTGTGCATGCCACCACTG                         CTACCCAGAAGACCGTGGACGGTCCATCTGGAAAGGACTGGCGTGGAGGAC
genomic: CAACTTCGGCATTGAGGAAGGGCTCATGACCACTGTGCATGCCACCACTGgtaatgatgg ... ctgtgtgcagCTACCCAGAAGACCGTGGACGGTCCATCTGGAAAGGACTGGCGTGGAGGAC
EST: gi|208394113|gb|DC957194.1|DC957194
EST:     CAACTTCGGCATTGAGGAAGGGCTCATGACCACTGTGCATGCCACCACTG                         CTACCCAGAAGACCGTGGACGGTCCATCTGGAAAGGACTGGCGTGGAGGAC
genomic: CAACTTCGGCATTGAGGAAGGGCTCATGACCACTGTGCATGCCACCACTGgtaatgatgg ... ctgtgtgcagCTACCCAGAAGACCGTGGACGGTCCATCTGGAAAGGACTGGCGTGGAGGAC
EST: gi|67726975|gb|BJ977234.1|BJ977234
EST:     CATTGAGGAAGGGCTCATGACCACTGTGCATGCCACCACTG                         CTACCCAGAAGACCGTGGACGGTCCCATCTGGAAAGGACTGGCGTGGAGGA
genomic: CATTGAGGAAGGGCTCATGACCACTGTGCATGCCACCACTGgtaatgatgg ... ctgtgtgcagCTACCCAGAAGACCGTGGACGGT-CCATCTGGAAAGGACTGGCGTGGAGGA
EST: gi|208389399|gb|DC953237.1|DC953237
EST:     TGTGCATGCCACCACTG                         CTA-CCAGAAG-NCGTGGACGGTCCATCTGGAAAGGACTGGCGTGGAGGAC
genomic: TGTGCATGCCACCACTGgtaatgatgg ... ctgtgtgcagCTACCCAGAAGACCGTGGACGGTCCATCTGGAAAGGACTGGCGTGGAGGAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttacattgagcaagacttaatttggatgatgatgtaaatggtttctgtgtgcagCTACCCAGAAGACCGTGGACGGTCCATCTGGAAAGGACTGGCGTGGAGGACGTGGTGCTGGACAGAACATTATTCCCAGCTCAACTGGAGCTGCGAAG
               acttaat  putative branch site (score: 4)
                                          tttctgt  putative PPT
               acttaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatgatggttcctttagaggtctttgagcatgtttgggtgtcatttgtgggtgcttttacattgagcaagacttaatttggatgatgatgtaaatggtttctgtgtgcagCTACCCAGAAGACCGTGGACGGTCCATCTGGAAAGGACTGGCGTGGAGGACGTGGTGCTGGACAGAACATTATTCCCAGCTCAACTGGAGCTGCGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC