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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCTTCCACGGAATCTTTTGCATGGAGCGTTGGGTCAGAGCCTGGTGCTTCCACGGGAGCTCCGGCGAGTGATGGAGCGCAGGAAAATGGGGCAACCTCAGgtggggcatccagctaggtttatagctctccgtgttttgaaaagtttacgaggaacgtttgttgctgcagaacatcggcaggtcttgttcttgaactgaa...

Basic information

species Physcomitrella patens
transcript PP1S6_148V6.1
intron # 1
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|100429193|gb|BY977987.1|BY977987
EST:     CACGGGAGCTCCGGCGAGTGATGGAGCGCAGGAAAATGGGGCAACCTCAG                         GACTTGGAGCAAGTTTTAAAAACACAAGTGACAAAGACTCGGCAAGCGATG
genomic: CACGGGAGCTCCGGCGAGTGATGGAGCGCAGGAAAATGGGGCAACCTCAGgtggggcatc ... acgtgtgcagGACTTGGAGCAAGTTTTAAAAACACAAGTGACAAAGACTCGGCAAGCGATG
EST: gi|18331661|gb|BJ163672.1|BJ163672
EST:     CACGGGAGCTCCGGCGAGTGATGGAGCGCAGGAAAATGGGGCAACCTCAG                         GACTTGGAGCAAGTTTTAAAAACACAAGTGACAAAGACTCGGCAAGCGATG
genomic: CACGGGAGCTCCGGCGAGTGATGGAGCGCAGGAAAATGGGGCAACCTCAGgtggggcatc ... acgtgtgcagGACTTGGAGCAAGTTTTAAAAACACAAGTGACAAAGACTCGGCAAGCGATG
EST: gi|18347588|gb|BJ179635.1|BJ179635
EST:     CACGGGAGCTCCGGCGAGTGATGGAGCGCAGGAAAATGGGGCAACCTCAG                         GACTTGGAGCAAGTTTTAAAAACACAAGTGACAAAGACTCGGCAAGCGATG
genomic: CACGGGAGCTCCGGCGAGTGATGGAGCGCAGGAAAATGGGGCAACCTCAGgtggggcatc ... acgtgtgcagGACTTGGAGCAAGTTTTAAAAACACAAGTGACAAAGACTCGGCAAGCGATG
EST: gi|100444940|gb|BY982768.1|BY982768
EST:     CACGGGAGCTCCGGCGAGTGATGGAGCGCAGGAAAATGGGGCAACCTCAG                         GACTTGGAGCAAGTTTTAAAAACACAAGTGACAAAGACTCGGCAAGCGATG
genomic: CACGGGAGCTCCGGCGAGTGATGGAGCGCAGGAAAATGGGGCAACCTCAGgtggggcatc ... acgtgtgcagGACTTGGAGCAAGTTTTAAAAACACAAGTGACAAAGACTCGGCAAGCGATG
EST: gi|162273082|gb|FC447776.1|FC447776
EST:     CACGGGAGCTCCGGCGAGTGATGGAGCGCAGGAAAATGGGGCAACCTCAG                         GACTTGGAGCAAGTTTTAAAAACACAAGTGACAAAGACTCGGCAAGCGATG
genomic: CACGGGAGCTCCGGCGAGTGATGGAGCGCAGGAAAATGGGGCAACCTCAGgtggggcatc ... acgtgtgcagGACTTGGAGCAAGTTTTAAAAACACAAGTGACAAAGACTCGGCAAGCGATG
EST: gi|162190184|gb|FC365926.1|FC365926
EST:     CACGGGAGCTCCGGCGAGTGATGGAGCGCAGGAAAATGGGGCAACCTCAG                         GACTTGGAGCAAGTTTTAAAAACACAAGTGACAAAGACTCGGCAAGCGATG
genomic: CACGGGAGCTCCGGCGAGTGATGGAGCGCAGGAAAATGGGGCAACCTCAGgtggggcatc ... acgtgtgcagGACTTGGAGCAAGTTTTAAAAACACAAGTGACAAAGACTCGGCAAGCGATG
EST: gi|162161863|gb|FC337952.1|FC337952
EST:     CACGGGAGCTCCGGCGAGTGATGGAGCGCAGGAAAATGGGGCAACCTCAG                         GACTTGGAGCAAGTTTTAAAAACACAAGTGACAAAGACTCGGCAAGCGATG
genomic: CACGGGAGCTCCGGCGAGTGATGGAGCGCAGGAAAATGGGGCAACCTCAGgtggggcatc ... acgtgtgcagGACTTGGAGCAAGTTTTAAAAACACAAGTGACAAAGACTCGGCAAGCGATG
EST: gi|18326716|gb|BJ158715.1|BJ158715
EST:     CACGGGAGCTCCGGCGAGTGATGGAGCGCAGGAAAATGGGGCAACCTCAG                         GACTTGGAGCAAGTTTTAAAAACACAAGTGACAAAGACTCGGCAAGCGATG
genomic: CACGGGAGCTCCGGCGAGTGATGGAGCGCAGGAAAATGGGGCAACCTCAGgtggggcatc ... acgtgtgcagGACTTGGAGCAAGTTTTAAAAACACAAGTGACAAAGACTCGGCAAGCGATG
EST: gi|208377435|gb|DC927081.1|DC927081
EST:     CACGGGAGCTCCGGCGAGTGATGGAGCGCAGGAAAATGGGGCAACCTCAG                         GACTTGGAGCAAGTTTTAAAAACACAAGTGACAAAGACTCGGCAAGCGATG
genomic: CACGGGAGCTCCGGCGAGTGATGGAGCGCAGGAAAATGGGGCAACCTCAGgtggggcatc ... acgtgtgcagGACTTGGAGCAAGTTTTAAAAACACAAGTGACAAAGACTCGGCAAGCGATG
EST: gi|100441361|gb|BY962650.1|BY962650
EST:     CACGGGAGCTCCGGCGAGTGATGGAGCGCAGGANAATGGGGCAACCTCAG                         GACTTGGAGCAAGTTTTAAAAACACAAGTGACAAAGACTCGGCAAGCGATG
genomic: CACGGGAGCTCCGGCGAGTGATGGAGCGCAGGAAAATGGGGCAACCTCAGgtggggcatc ... acgtgtgcagGACTTGGAGCAAGTTTTAAAAACACAAGTGACAAAGACTCGGCAAGCGATG
EST: gi|162211282|gb|FC387512.1|FC387512
EST:     CACGGGAGCTCCGGCGAGTGATGGAGCGCAGGAAAATGGGGCAACCTCAG                         GACTTGGAGCAAGTTTTAAAAACACAAGTGACAAAGACTCGGCAAGCGATG
genomic: CACGGGAGCTCCGGCGAGTGATGGAGCGCAGGAAAATGGGGCAACCTCAGgtggggcatc ... acgtgtgcagGACTTGGAGCAAGTTTTAAAAACACAAGTGACAAAGACTCGGCAAGCGATG
EST: gi|100376216|gb|BY986078.1|BY986078
EST:     CACGGGAGCTCCGGCGAGTGATGGAGCGCAGGANAATGGGGCAACCTCAG                         GACTTGGAGCAAGTTT-AAAAACACAAGTGACAAAGACTCGGCAAGCGATG
genomic: CACGGGAGCTCCGGCGAGTGATGGAGCGCAGGAAAATGGGGCAACCTCAGgtggggcatc ... acgtgtgcagGACTTGGAGCAAGTTTTAAAAACACAAGTGACAAAGACTCGGCAAGCGATG
EST: gi|162220972|gb|FC396157.1|FC396157
EST:     CACGGGAGCTCCGGCGAGTGATGGAGCGCAGGAAAATGGGGCAACCTCAG                         GACTTGGAGCAAGTTTTAAAAACACAAGTGACAAAGACTCGGCAAGCGATG
genomic: CACGGGAGCTCCGGCGAGTGATGGAGCGCAGGAAAATGGGGCAACCTCAGgtggggcatc ... acgtgtgcagGACTTGGAGCAAGTTTTAAAAACACAAGTGACAAAGACTCGGCAAGCGATG
EST: gi|100363494|gb|BY966417.1|BY966417
EST:     CACGGGAGCTCCGGCGAGTGATGGAGCGCAGGANAATGGGGCAACCTCAG                         GACTTGGAGCAAGTTTTAAAAACACAAGTGACAAAGACTCGGCAAGCGATG
genomic: CACGGGAGCTCCGGCGAGTGATGGAGCGCAGGAAAATGGGGCAACCTCAGgtggggcatc ... acgtgtgcagGACTTGGAGCAAGTTTTAAAAACACAAGTGACAAAGACTCGGCAAGCGATG
EST: gi|208346672|gb|DC913318.1|DC913318
EST:     CACGGGAGCTCCGGCGAGTGATGGAGCGCAGGAAAATGGGGCAACCTCAG                         GACTTGGAGCAAGTTTTAAAAACACAAGTGACAAAGACTCGGCAAGCGATG
genomic: CACGGGAGCTCCGGCGAGTGATGGAGCGCAGGAAAATGGGGCAACCTCAGgtggggcatc ... acgtgtgcagGACTTGGAGCAAGTTTTAAAAACACAAGTGACAAAGACTCGGCAAGCGATG
EST: gi|208384841|gb|DC907454.1|DC907454
EST:     CACGGGAGCTCCGGCGAGTGATGGAGCGCAGGAAAATGGGGCAACCTCAG                         GACTTGGAGCAAGTTTTAAAAACACAAGTGACAAAGACTCGGCAAGCGATG
genomic: CACGGGAGCTCCGGCGAGTGATGGAGCGCAGGAAAATGGGGCAACCTCAGgtggggcatc ... acgtgtgcagGACTTGGAGCAAGTTTTAAAAACACAAGTGACAAAGACTCGGCAAGCGATG
EST: gi|208363381|gb|DC946979.1|DC946979
EST:     GCGAGTGATGGAGCGCAGG-AAATGGGGCAACCTCAG                         GACTTGGAGCAAGTTTT-AAAACACAAGTGACAAAGACTCGGCAAGCGATG
genomic: GCGAGTGATGGAGCGCAGGAAAATGGGGCAACCTCAGgtggggcatc ... acgtgtgcagGACTTGGAGCAAGTTTTAAAAACACAAGTGACAAAGACTCGGCAAGCGATG
EST: gi|162274452|gb|FC450687.1|FC450687
EST:     CACGGGAGCTCCGGCGAGTGATGGAGCGCAGGAAAATGGGGCAACCTCAG                         GACTTGGAGCAAGTTTTAAAAACACAAGTGACAAAGACTCGGCAAGCGATG
genomic: CACGGGAGCTCCGGCGAGTGATGGAGCGCAGGAAAATGGGGCAACCTCAGgtggggcatc ... acgtgtgcagGACTTGGAGCAAGTTTTAAAAACACAAGTGACAAAGACTCGGCAAGCGATG
EST: gi|100447936|gb|CJ972235.1|CJ972235
EST:     CACGGGAGCTCCGGCGAGTGATGGAGCGCAGGAAAATGGGGCAACCTCAG                         GACTTGGAGCAAGTTTTAAAAACACAAGTGACAAGGACTCGGCAAGCGATG
genomic: CACGGGAGCTCCGGCGAGTGATGGAGCGCAGGAAAATGGGGCAACCTCAGgtggggcatc ... acgtgtgcagGACTTGGAGCAAGTTTTAAAAACACAAGTGACAAAGACTCGGCAAGCGATG
EST: gi|208346915|gb|DC905445.1|DC905445
EST:     CACGGGAGCTCCGGCGAGTGATGGAGCGCAGGAAAATGGGGCAACCTCAG                         GACTTGGAGCAAGTTTTAAAAACACAAGTGACAAAGACTCGGCAAGCGATG
genomic: CACGGGAGCTCCGGCGAGTGATGGAGCGCAGGAAAATGGGGCAACCTCAGgtggggcatc ... acgtgtgcagGACTTGGAGCAAGTTTTAAAAACACAAGTGACAAAGACTCGGCAAGCGATG
EST: gi|100451366|gb|CJ974729.1|CJ974729
EST:     CACGGGAGCTCCGGCGAGTGATGGAGCGCAGGAAAATGGGGCAACCTCAG                         GACTTGGAGCAAGTTTTAAAAACACAAGTGACAAAGACTCGGCAAGCGATG
genomic: CACGGGAGCTCCGGCGAGTGATGGAGCGCAGGAAAATGGGGCAACCTCAGgtggggcatc ... acgtgtgcagGACTTGGAGCAAGTTTTAAAAACACAAGTGACAAAGACTCGGCAAGCGATG
EST: gi|100451262|gb|CJ974677.1|CJ974677
EST:     CACGGGAGCTCCGGCGAGTGATGGAGCGCAGGAAAATGGGGCAACCTCAG                         GACTTGGAGCAAGTTTTAAAAACACAAGTGACAAAGACTCGGTAAGCGATG
genomic: CACGGGAGCTCCGGCGAGTGATGGAGCGCAGGAAAATGGGGCAACCTCAGgtggggcatc ... acgtgtgcagGACTTGGAGCAAGTTTTAAAAACACAAGTGACAAAGACTCGGCAAGCGATG
EST: gi|67703490|gb|BJ963723.1|BJ963723
EST:     CACGGGAGCTCCGGCGAGTGATGGAGCGCAGGAAAATGGGGCAACCTCAG                         GACTTGGAGCAAGTTTTAAAAACACAAGTGACAAAGACTCGGCAAGCGATG
genomic: CACGGGAGCTCCGGCGAGTGATGGAGCGCAGGAAAATGGGGCAACCTCAGgtggggcatc ... acgtgtgcagGACTTGGAGCAAGTTTTAAAAACACAAGTGACAAAGACTCGGCAAGCGATG

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: 29 (upstream exon), 34 (downstream exon)
Score: 15

TCTTCCACGGAATCTTTTGCATGGAGCGTTGGGTCAGAGCCTGGTGCTTCCACGGGAGCTCCGGCGAGTGATGGAGCGCAGGAAAATGGGGCAACCTCAGgtggggcatc ... acgtgtgcagGACTTGGAGCAAGTTTTAAAAACACAAGTGACAAAGACTCGGCAAGCGATGAAGAGGCTGTGGACGAGAAGTCCCAGGTTCTCCGTGCGGCCATGTCTCA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCTTCCACGGAATCTTTTGCATGGAGCGTTGGGTCAGAGCCTGGTGCTTCCACGGGAGCTCCGGCGAGTGATGGAGCGCAGGAAAATGGGGCAACCTCAGgtggggcatccagctaggtttatagctctccgtgttttgaaaagtttacgaggaacgtttgttgctgcagaacatcggcaggtcttgttcttgaactgaa

- - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA