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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAAGCTTTGAAAAAGAATATATTTAAATTGTTAACTGAAAGAGTGACCACCACCGAGCTTCAATTGGGCAATAGgttcgtcgaattcgcatccttacaaccttgaatgccggagtactatgttttattttattttatgtatgggctgaaggtattcatacaattttgtacttcgattatttttctcacacctttaacgaacagtggtcttgttgcgtcacaattgtgtgcag

Basic information

species Physcomitrella patens
transcript PP1S98_142V6.1
intron # 3
splice site 5'
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|18358653|gb|BJ190712.1|BJ190712
EST:     AAATTGTTAACTGAAAGAGTGACCACCACCGAGCTTCAATTGGGCAATAG                         TCGCCCTGCAGTACTCATGATTGT
genomic: AAATTGTTAACTGAAAGAGTGACCACCACCGAGCTTCAATTGGGCAATAGgttcgtcgaa ... ttgtgtgcagTCGCCCTGCAGTACTCATGATTGT
EST: gi|208381435|gb|DC927871.1|DC927871
EST:     AANTTGTNAACTGAAAGAGTGACCACCNCCGAGCTTCANTTGGGCAATAG                         TCGCCCNGCAGTACTCANGATTGTCGGTGTAAATGGAGGAGGAAAAACCAC
genomic: AAATTGTTAACTGAAAGAGTGACCACCACCGAGCTTCAATTGGGCAATAGgttcgtcgaa ... ttgtgtgcagTCGCCCTGCAGTACTCATGATTGTCGGTGTAAATGGAGGAGGAAAAACCAC
EST: gi|100406046|gb|BY991512.1|BY991512
EST:     AAATTGTTAACTGAAAGAGTGACCACCACCGAGCTTCAATTGGGCAATAG                         TCGCCCTGCAGTACTCATGATTGTCGGTGTAAATGGAGGAGGAAAAACCAC
genomic: AAATTGTTAACTGAAAGAGTGACCACCACCGAGCTTCAATTGGGCAATAGgttcgtcgaa ... ttgtgtgcagTCGCCCTGCAGTACTCATGATTGTCGGTGTAAATGGAGGAGGAAAAACCAC
EST: gi|208354010|gb|DC914122.1|DC914122
EST:     AAATTGTTAACTGAAAGAGTGACCACCACCGAGCTTCAATTGGGCAATAG                         TCGCCCTGCAGTACTCATGATTGTCGGTGTAAATGGAGGANGAAAAACCAC
genomic: AAATTGTTAACTGAAAGAGTGACCACCACCGAGCTTCAATTGGGCAATAGgttcgtcgaa ... ttgtgtgcagTCGCCCTGCAGTACTCATGATTGTCGGTGTAAATGGAGGAGGAAAAACCAC
EST: gi|100362534|gb|BY947402.1|BY947402
EST:     AATTGTTAACTGAAAGAGTGACCACCACCGAGCTTNCA-TTGGGCAATAG                         TCGCCCTGCAGTACTCATGATTGTCGGTGTAAATGGAGGAGGAAAAAC-AC
genomic: AATTGTTAACTGAAAGAGTGACCACCACCGAGCTT-CAATTGGGCAATAGgttcgtcgaa ... ttgtgtgcagTCGCCCTGCAGTACTCATGATTGTCGGTGTAAATGGAGGAGGAAAAACCAC
EST: gi|100436742|gb|BY979503.1|BY979503
EST:     AAATTGTTAACTGAAAGAGTGACCACCACCGAGCTTCAATTGGGCAATAG                         TCGCCCTGCAGTACTCATGATTGTCGGTGTAAATGGAGGAGGAAAAACCAC
genomic: AAATTGTTAACTGAAAGAGTGACCACCACCGAGCTTCAATTGGGCAATAGgttcgtcgaa ... ttgtgtgcagTCGCCCTGCAGTACTCATGATTGTCGGTGTAAATGGAGGAGGAAAAACCAC
EST: gi|100424608|gb|BY976725.1|BY976725
EST:     AAATTGTTAACTGAAAGAGTGACCACCACCGAGCTTCAATTGGGCAATAG                         TCGCCCTGCAGTACTCATGATTGTCGGTGTAAATGGAGGAGGAAAAAC-AC
genomic: AAATTGTTAACTGAAAGAGTGACCACCACCGAGCTTCAATTGGGCAATAGgttcgtcgaa ... ttgtgtgcagTCGCCCTGCAGTACTCATGATTGTCGGTGTAAATGGAGGAGGAAAAACCAC
EST: gi|100405617|gb|BY973767.1|BY973767
EST:     AAATTGTTAACTGAAAGAGTGACCACCACCGAGCTTCAATTGGGCAATAG                         TCGCCCTGCAGTACTCATGATTGTCGGTGT
genomic: AAATTGTTAACTGAAAGAGTGACCACCACCGAGCTTCAATTGGGCAATAGgttcgtcgaa ... ttgtgtgcagTCGCCCTGCAGTACTCATGATTGTCGGTGT
EST: gi|67574460|gb|BJ947284.1|BJ947284
EST:     AAATTGTTAACTGAAAGAGTGACCACCACCGAGCTTCAATTGGGCAATAG                         TCGCCCTGCAGTACTCATGATTGTCGGTGTAAATGGAGGAGGAAAAACCAC
genomic: AAATTGTTAACTGAAAGAGTGACCACCACCGAGCTTCAATTGGGCAATAGgttcgtcgaa ... ttgtgtgcagTCGCCCTGCAGTACTCATGATTGTCGGTGTAAATGGAGGAGGAAAAACCAC
EST: gi|162166212|gb|FC342623.1|FC342623
EST:     AAATTGTTAACTGAAAGAGTGACCACCACCGAGCTTCAATTGGGCAATAG                         TCGCCCTGCAGTACTCATGATTGTCGGTGTAAATGGAGGAGGAAAAACCAC
genomic: AAATTGTTAACTGAAAGAGTGACCACCACCGAGCTTCAATTGGGCAATAGgttcgtcgaa ... ttgtgtgcagTCGCCCTGCAGTACTCATGATTGTCGGTGTAAATGGAGGAGGAAAAACCAC
EST: gi|100391599|gb|BY989465.1|BY989465
EST:     AATTGTTAACTGAAAGAGTGACCACCACCGAGCTTNCA-TTGGGCAATAG                         TCGCCCTGCAGTACTCATGATTGTCGGTGTAAATGGAGGAGGAAAA-CCAC
genomic: AATTGTTAACTGAAAGAGTGACCACCACCGAGCTT-CAATTGGGCAATAGgttcgtcgaa ... ttgtgtgcagTCGCCCTGCAGTACTCATGATTGTCGGTGTAAATGGAGGAGGAAAAACCAC
EST: gi|208353643|gb|DC938752.1|DC938752
EST:     AAATTGTTAACTGAAAGAGTGACCACCACCGAGCTTCAATTGGGCAATAG                         TCGCCCTGCAGTACTCATGATTGTCGGTGTAAATGGAGGAGGAAAAACCAC
genomic: AAATTGTTAACTGAAAGAGTGACCACCACCGAGCTTCAATTGGGCAATAGgttcgtcgaa ... ttgtgtgcagTCGCCCTGCAGTACTCATGATTGTCGGTGTAAATGGAGGAGGAAAAACCAC
EST: gi|18361896|gb|BJ193963.1|BJ193963
EST:     AAATTGTTAACTGAAAGAGTGACCACCACCGAGCTTCAATTGGGCAATAG                         TCGCCCTGCAGTACTCATG
genomic: AAATTGTTAACTGAAAGAGTGACCACCACCGAGCTTCAATTGGGCAATAGgttcgtcgaa ... ttgtgtgcagTCGCCCTGCAGTACTCATG

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: 35 (upstream exon), 24 (downstream exon)
Score: 6

GAAGCTTTGAAAAAGAATATATTTAAATTGTTAACTGAAAGAGTGACCACCACCGAGCTTCAATTGGGCAATAGgttcgtcgaa ... ttgtgtgcagTCGCCCTGCAGTACTCATGATTGTCGGTGTAAATGGAGGAGGAAAAACCACCACTCTTG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAAGCTTTGAAAAAGAATATATTTAAATTGTTAACTGAAAGAGTGACCACCACCGAGCTTCAATTGGGCAATAGgttcgtcgaattcgcatccttacaaccttgaatgccggagtactatgttttattttattttatgtatgggctgaaggtattcatacaattttgtacttcgattatttttctcacacctttaacgaacagtggtcttgttgcgtcacaattgtgtgcag

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