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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtgtttgagtgagtggatattattgcatgagagttgatgggctttaagtggggcgtaaagttattttgccttactatgttattcatttttgcttgaacagACACACCTTCACCTCAGCTTCAGCAGACAACATAAAGAAGTTTCGGCTGCCCAAGGGAGAGTTTTTACATAACATGCT

Basic information

species Physcomitrella patens
transcript PP1S169_73V6.2
intron # 12
splice site 3'
intron type U2

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|162203186|gb|FC379283.1|FC379283
EST:     TTAACATTTCACAAGAAGTCTGTGAGAGCATTGGCGATGCATCCTTTTGA                         ACACACCTTCACCTCAGCTTCAGCAGACAACATAAAGAAGTTTCGGCTGCC
genomic: TTAACATTTCACAAGAAGTCTGTGAGAGCATTGGCGATGCATCCTTTTGAgtaagtttca ... gcttgaacagACACACCTTCACCTCAGCTTCAGCAGACAACATAAAGAAGTTTCGGCTGCC
EST: gi|162175454|gb|FC350924.1|FC350924
EST:     TTAACATTTCACAAGAAGTCTGTGAGAGCATTGGCGATGCATCCTTTTGA                         ACACACCTTCACCTCAGCTTCAGCAGACAACATAAAGAAGTTTCGGCTGCC
genomic: TTAACATTTCACAAGAAGTCTGTGAGAGCATTGGCGATGCATCCTTTTGAgtaagtttca ... gcttgaacagACACACCTTCACCTCAGCTTCAGCAGACAACATAAAGAAGTTTCGGCTGCC
EST: gi|37832005|gb|BJ590017.1|BJ590017
EST:     TTAACATTTCACAAGAAGTCTGTGAGAGCATTGGCGATGCATCCTTTTGA                         ACACACCTTCACCTCAGCTTCAGCAGACAACATAAAGAAGTTTCGGCTGCC
genomic: TTAACATTTCACAAGAAGTCTGTGAGAGCATTGGCGATGCATCCTTTTGAgtaagtttca ... gcttgaacagACACACCTTCACCTCAGCTTCAGCAGACAACATAAAGAAGTTTCGGCTGCC
EST: gi|37822469|gb|BJ580535.1|BJ580535
EST:     TTAACATTTCACAAGAAGTCTGTGAGAGCATTGGCGATGCATCCTTTTGA                         ACACACCTTCACCTCAGCTTCAGCAGACAACATAAAGAAGTTTCGGCTGCC
genomic: TTAACATTTCACAAGAAGTCTGTGAGAGCATTGGCGATGCATCCTTTTGAgtaagtttca ... gcttgaacagACACACCTTCACCTCAGCTTCAGCAGACAACATAAAGAAGTTTCGGCTGCC
EST: gi|37823397|gb|BJ581463.1|BJ581463
EST:     TTCACAAGAAGTCTGTGAGAGCATTGGCGATGCATCCTTTTGA                         ACACACNTTCACNTCAGCTTCAGCAGACAACATAAAGAAGTTTCGGCTGCC
genomic: TTCACAAGAAGTCTGTGAGAGCATTGGCGATGCATCCTTTTGAgtaagtttca ... gcttgaacagACACACCTTCACCTCAGCTTCAGCAGACAACATAAAGAAGTTTCGGCTGCC
EST: gi|162183680|gb|FC359908.1|FC359908
EST:     TTAACATTTCACAAGAAGTCTGTGAGAGCATTGGCGATGCATCCTTTTGA                         ACACACCTTCACCTCAGCTTCAGCAGACAACATAAAGAAGTTTCGGCTGCC
genomic: TTAACATTTCACAAGAAGTCTGTGAGAGCATTGGCGATGCATCCTTTTGAgtaagtttca ... gcttgaacagACACACCTTCACCTCAGCTTCAGCAGACAACATAAAGAAGTTTCGGCTGCC
EST: gi|162198129|gb|FC373079.1|FC373079
EST:     TTAACATTTCACAAGAAGTCTGTGAGAGCATTGGCGATGCATCCTTTTGA                         ACACACCTTCACCTCAGCTTCAGCAGACAACATAAAGAAGTTTCGGCTGCC
genomic: TTAACATTTCACAAGAAGTCTGTGAGAGCATTGGCGATGCATCCTTTTGAgtaagtttca ... gcttgaacagACACACCTTCACCTCAGCTTCAGCAGACAACATAAAGAAGTTTCGGCTGCC
EST: gi|37827542|gb|BJ585554.1|BJ585554
EST:     TTAACATTTCACAAGAAGTCTGTGAGAGCATTGGCGATGCATCCTTTTGA                         ACACACCTTCACCTCAGCTTCAGCAGACAACATAAAGAAGTTTCGGCTGCC
genomic: TTAACATTTCACAAGAAGTCTGTGAGAGCATTGGCGATGCATCCTTTTGAgtaagtttca ... gcttgaacagACACACCTTCACCTCAGCTTCAGCAGACAACATAAAGAAGTTTCGGCTGCC
EST: gi|18336709|gb|BJ168732.1|BJ168732
EST:     TTCACAAGAAGTCTGTGAGAGCATTGGCGATGCATCCTTTTGA                         ACACACCTTCACCTCAGCTTCAGCAGACAACATAAAGAAGTTTCGGCTGCC
genomic: TTCACAAGAAGTCTGTGAGAGCATTGGCGATGCATCCTTTTGAgtaagtttca ... gcttgaacagACACACCTTCACCTCAGCTTCAGCAGACAACATAAAGAAGTTTCGGCTGCC
EST: gi|162198130|gb|FC373080.1|FC373080
EST:     TTAACATTTCACAAGAAGTCTGTGAGAGCATTGGCGATGCATCCTTTTGA                         ACACACCTTCACCTCAGCTTCAGCA
genomic: TTAACATTTCACAAGAAGTCTGTGAGAGCATTGGCGATGCATCCTTTTGAgtaagtttca ... gcttgaacagACACACCTTCACCTCAGCTTCAGCA
EST: gi|37829602|gb|BJ587614.1|BJ587614
EST:     TTAACATTTCACAAGAAGTCTGTGAGAGCATTGGCGATGCATCCTTTTGA                         ACACACCTTCACCTCAGCTTCAGCAGACAACATAAAGAAGTTTCGGCTGCC
genomic: TTAACATTTCACAAGAAGTCTGTGAGAGCATTGGCGATGCATCCTTTTGAgtaagtttca ... gcttgaacagACACACCTTCACCTCAGCTTCAGCAGACAACATAAAGAAGTTTCGGCTGCC
EST: gi|37834715|gb|BJ592727.1|BJ592727
EST:     TTAACATTTCACAAGAAGTCTGTGAGAGCATTGGCGATGCATCCTTTTGA                         ACACACCTTCACCTCAGCTTCAGCAGACAACATAAAGAAGTTTCGGCTGCC
genomic: TTAACATTTCACAAGAAGTCTGTGAGAGCATTGGCGATGCATCCTTTTGAgtaagtttca ... gcttgaacagACACACCTTCACCTCAGCTTCAGCAGACAACATAAAGAAGTTTCGGCTGCC
EST: gi|37828539|gb|BJ586551.1|BJ586551
EST:     TTAACATTTCACAAGAAGTCTGTGAGAGCATTGGCGATGCATCCTTTTGA                         ACACACCTTCACCTCAGCTTCAGCAGACAACATAAAGAAGTTTCGGCTGCC
genomic: TTAACATTTCACAAGAAGTCTGTGAGAGCATTGGCGATGCATCCTTTTGAgtaagtttca ... gcttgaacagACACACCTTCACCTCAGCTTCAGCAGACAACATAAAGAAGTTTCGGCTGCC
EST: gi|67720614|gb|BJ970873.1|BJ970873
EST:     TTAACATTTCACAAGAAGTCTGTGAGAGCATTGGCGATGCATCCTTTTGA                         ACACACCTTCACCTCAGCTTCAGCAGACAACATAAAGAAGTTTCGGCTGCC
genomic: TTAACATTTCACAAGAAGTCTGTGAGAGCATTGGCGATGCATCCTTTTGAgtaagtttca ... gcttgaacagACACACCTTCACCTCAGCTTCAGCAGACAACATAAAGAAGTTTCGGCTGCC
EST: gi|162266558|gb|FC442789.1|FC442789
EST:     TTAACATTTCACAAGAAGTCTGTGAGAGCATTGGCGATGCATCCTTTTGA                         ACACACCTTCACCTCAGCTTCAGCAGACAACATAAAGAAGTTTCGGCTGCC
genomic: TTAACATTTCACAAGAAGTCTGTGAGAGCATTGGCGATGCATCCTTTTGAgtaagtttca ... gcttgaacagACACACCTTCACCTCAGCTTCAGCAGACAACATAAAGAAGTTTCGGCTGCC
EST: gi|162160838|gb|FC337660.1|FC337660
EST:     TTAACATTTCACAAGAAGTCTGTGAGAGCATTGGCGATGCATCCTTTTGA                         ACACACCTTCACCTCAGCTTCAGCAGACAACATAAAGAAGTTTCGGCTGCC
genomic: TTAACATTTCACAAGAAGTCTGTGAGAGCATTGGCGATGCATCCTTTTGAgtaagtttca ... gcttgaacagACACACCTTCACCTCAGCTTCAGCAGACAACATAAAGAAGTTTCGGCTGCC
EST: gi|208365406|gb|DC950873.1|DC950873
EST:     TTAACATTTCACAAGAAGTCTGTGAGAGCATTGGCGATGCATCCTTTTGA                         ACACACCTTCACCTCAGCTTCAGCAGACAACATAAAGAAGTTTCGGCTGCC
genomic: TTAACATTTCACAAGAAGTCTGTGAGAGCATTGGCGATGCATCCTTTTGAgtaagtttca ... gcttgaacagACACACCTTCACCTCAGCTTCAGCAGACAACATAAAGAAGTTTCGGCTGCC
EST: gi|37823750|gb|BJ581816.1|BJ581816
EST:     TTAACATTTCACAAGAAGTCTGTGAGAGCATTGGCGATGCATCCTTTTGA                         ACACACCTTCACCTCAGCTTCAGCAGACAACATAAAGAAGTTTCGGCTGCC
genomic: TTAACATTTCACAAGAAGTCTGTGAGAGCATTGGCGATGCATCCTTTTGAgtaagtttca ... gcttgaacagACACACCTTCACCTCAGCTTCAGCAGACAACATAAAGAAGTTTCGGCTGCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aagtggggcgtaaagttattttgccttactatgttattcatttttgcttgaacagACACACCTTCACCTCAGCTTCAGCAGACAACATAAAGAAGTTTCGGCTGCCCAAGGGAGAGTTTTTACATAACATGCT
                      gccttac  putative branch site (score: 3)
                                        tttttgctt  putative PPT
                             tatgttattcattttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgtttgagtgagtggatattattgcatgagagttgatgggctttaagtggggcgtaaagttattttgccttactatgttattcatttttgcttgaacagACACACCTTCACCTCAGCTTCAGCAGACAACATAAAGAAGTTTCGGCTGCCCAAGGGAGAGTTTTTACATAACATGCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT