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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctcaaaagatagtttgctttattcgttgttatatatgacaactttatatagcaagttaccttcttgatttgttcgtaaggtctgctatcattgtttgcagGGAAGTTGGAAGAAGCTCTTGAGTATTTTACCGAAGCTATAATCTGCAATCCACATTCAGCAATCCTATTCGCCAACCGAG

Basic information

species Physcomitrella patens
transcript PP1S9_386V6.1
intron # 4
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|162275962|gb|FC452030.1|FC452030
EST:     GGACGAGGCTCAGCTCTCGAAAGGCAAAGCAGTGGAAGCTATGGCAGAAG                         GGAAGTTGGAAGAAGCTCTTGAGTATTTTACCGAAGCTATAATCTGCAATC
genomic: GGACGAGGCTCAGCTCTCGAAAGGCAAAGCAGTGGAAGCTATGGCAGAAGgtagttatat ... ttgtttgcagGGAAGTTGGAAGAAGCTCTTGAGTATTTTACCGAAGCTATAATCTGCAATC
EST: gi|18358114|gb|BJ190173.1|BJ190173
EST:     GGACGAGGCTCAGCTCTCGAAAGGCAAAGCAGTGGAAGCTATGGCAGAAG                         GGAAGTTGGAAGAAGCTCTTGAGTATTTTACCGAAGCTATAATCTGCAATC
genomic: GGACGAGGCTCAGCTCTCGAAAGGCAAAGCAGTGGAAGCTATGGCAGAAGgtagttatat ... ttgtttgcagGGAAGTTGGAAGAAGCTCTTGAGTATTTTACCGAAGCTATAATCTGCAATC
EST: gi|100399659|gb|BY972829.1|BY972829
EST:     GGACGAGGCTCAGCTCTCGAAAGGCAAAGCAGTGGAAGCTATGGCAGAAG                         GGAAGTTGGAAGAAGCTCTTGAGTATTTTACCGAAGCTATAATCTGCAATC
genomic: GGACGAGGCTCAGCTCTCGAAAGGCAAAGCAGTGGAAGCTATGGCAGAAGgtagttatat ... ttgtttgcagGGAAGTTGGAAGAAGCTCTTGAGTATTTTACCGAAGCTATAATCTGCAATC
EST: gi|100427615|gb|BY977586.1|BY977586
EST:     GGACGAGGCTCAGCTCTCGAAAGGCAAAGCAGTGGAAGCTATGGCAGAAG                         GGAAGTTGGAAGAAGCTCTTGAGTATTTTACCGAAGCTATAATCTGCAATC
genomic: GGACGAGGCTCAGCTCTCGAAAGGCAAAGCAGTGGAAGCTATGGCAGAAGgtagttatat ... ttgtttgcagGGAAGTTGGAAGAAGCTCTTGAGTATTTTACCGAAGCTATAATCTGCAATC
EST: gi|22492231|gb|BU052154.1|BU052154
EST:     GGACGAGGCTCAGCTCTCGAAAGGCAAAGCAGTGGAAGCTATGGCAGAAG                         GGAAGTTGGAAGAAGCTCTTGAGTATTTTACCGAAGCTATAATCTGCAATC
genomic: GGACGAGGCTCAGCTCTCGAAAGGCAAAGCAGTGGAAGCTATGGCAGAAGgtagttatat ... ttgtttgcagGGAAGTTGGAAGAAGCTCTTGAGTATTTTACCGAAGCTATAATCTGCAATC
EST: gi|208347568|gb|DC912827.1|DC912827
EST:     GGACGAGGCTCAGCTCTCGAAAGGCAAAGCAGTGGAAGCTATGGCAGAAG                         GGAAGTTGGAAGAAGCTCTTGAGTATTTTACCGAAGCTATAATCTGCAATC
genomic: GGACGAGGCTCAGCTCTCGAAAGGCAAAGCAGTGGAAGCTATGGCAGAAGgtagttatat ... ttgtttgcagGGAAGTTGGAAGAAGCTCTTGAGTATTTTACCGAAGCTATAATCTGCAATC
EST: gi|100417743|gb|BY975631.1|BY975631
EST:     GGACGAGGCTCAGCTCTCGAAAGGCAAAGCAGTGGAAGCTATGGCAGAAG                         GGAAGTTGGAAGAAGCTCTTGAGTATTTTACCGAAGCTATAATCTGCAATC
genomic: GGACGAGGCTCAGCTCTCGAAAGGCAAAGCAGTGGAAGCTATGGCAGAAGgtagttatat ... ttgtttgcagGGAAGTTGGAAGAAGCTCTTGAGTATTTTACCGAAGCTATAATCTGCAATC
EST: gi|67717655|gb|BJ967914.1|BJ967914
EST:     GGACGAGGCTCAGCTCTCGAAAGGCAAAGCAGTGGAAGCTATGGCAGAAG                         GGAAGTTGGAAGAAGCTCTTGAGTATTTTACCGAAGCTATAATCTGCAATC
genomic: GGACGAGGCTCAGCTCTCGAAAGGCAAAGCAGTGGAAGCTATGGCAGAAGgtagttatat ... ttgtttgcagGGAAGTTGGAAGAAGCTCTTGAGTATTTTACCGAAGCTATAATCTGCAATC
EST: gi|100416732|gb|BY993060.1|BY993060
EST:     GGACGAGGCTCAGCTCTCGAAAGGCAAAGCAGTGGAAGCTATGGCAGAAG                         GGAAGTTGGAAGAAGCTCTTGAGTATTTTACCGAAGCTATAATCTGCAATC
genomic: GGACGAGGCTCAGCTCTCGAAAGGCAAAGCAGTGGAAGCTATGGCAGAAGgtagttatat ... ttgtttgcagGGAAGTTGGAAGAAGCTCTTGAGTATTTTACCGAAGCTATAATCTGCAATC
EST: gi|18348196|gb|BJ180243.1|BJ180243
EST:     GGACGAGGCTCAGCTCTCGAAAGGCAAAGCAGTGGAAGCTATGGCAGAAG                         GGAAGTTGGAAGAAGCTCTTGAGTATTTTACCGAAGCTATAATCTGCAATC
genomic: GGACGAGGCTCAGCTCTCGAAAGGCAAAGCAGTGGAAGCTATGGCAGAAGgtagttatat ... ttgtttgcagGGAAGTTGGAAGAAGCTCTTGAGTATTTTACCGAAGCTATAATCTGCAATC
EST: gi|100446593|gb|CJ970892.1|CJ970892
EST:     GGACGAGGCTCAGCTCTCGAAAGGCAAAGCAGTGGAAGCTATGGCAGAAG                         GGAAGTTGGAAGAAGCTCTTGAGTATTTTACCGAAGCTATAATCTGCAATC
genomic: GGACGAGGCTCAGCTCTCGAAAGGCAAAGCAGTGGAAGCTATGGCAGAAGgtagttatat ... ttgtttgcagGGAAGTTGGAAGAAGCTCTTGAGTATTTTACCGAAGCTATAATCTGCAATC
EST: gi|162164761|gb|FC340483.1|FC340483
EST:     GGACGAGGCTCAGCTCTCGAAAGTCAAAGCAGTGGAAGCTATGGCAGAAG                         GGAAGTTGGAAGAAGCTCTTGAGTATTTTACCGAAGCTATAATCTGCAATC
genomic: GGACGAGGCTCAGCTCTCGAAAGGCAAAGCAGTGGAAGCTATGGCAGAAGgtagttatat ... ttgtttgcagGGAAGTTGGAAGAAGCTCTTGAGTATTTTACCGAAGCTATAATCTGCAATC
EST: gi|208373792|gb|DC936577.1|DC936577
EST:     GGACGAGGCTCAGCTCTCGAAAGGCAAAGCAGTGGAAGCTATGGCAGAAG                         GGAAGTTGGAAGAAGCTCTTGAGTATTTTACCGAAGCTATAATCTGCAATC
genomic: GGACGAGGCTCAGCTCTCGAAAGGCAAAGCAGTGGAAGCTATGGCAGAAGgtagttatat ... ttgtttgcagGGAAGTTGGAAGAAGCTCTTGAGTATTTTACCGAAGCTATAATCTGCAATC
EST: gi|208349326|gb|DC910385.1|DC910385
EST:     GGACGAGGCTCAGCTCTCGAAAGGCAAAGCAGTGGAAGCTATGGCAGAAG                         GGAAGTTGGAAGAAGCTCTTGAGTATTTTACCGAAGCTATAATCTGCAATC
genomic: GGACGAGGCTCAGCTCTCGAAAGGCAAAGCAGTGGAAGCTATGGCAGAAGgtagttatat ... ttgtttgcagGGAAGTTGGAAGAAGCTCTTGAGTATTTTACCGAAGCTATAATCTGCAATC
EST: gi|208344626|gb|DC912572.1|DC912572
EST:     GGACGAGGCTCAGCTCTCGAAAGGCAAAGCAGTGGAAGCTATGGCAGAAG                         GGAAGTTGGAAGAAGCTCTTGAGTATTTTACCGAAGCTATAATCTGCAATC
genomic: GGACGAGGCTCAGCTCTCGAAAGGCAAAGCAGTGGAAGCTATGGCAGAAGgtagttatat ... ttgtttgcagGGAAGTTGGAAGAAGCTCTTGAGTATTTTACCGAAGCTATAATCTGCAATC
EST: gi|67719577|gb|BJ969836.1|BJ969836
EST:     GGACGAGGCTCAGCTCTCGAAAGGCAAAACAGTGGAAGCTATGGCAGAAG                         GGAAGTTGGAAGAAGCTCTTGAGTACTTTACCGAAGCTATAATCTGCAATC
genomic: GGACGAGGCTCAGCTCTCGAAAGGCAAAGCAGTGGAAGCTATGGCAGAAGgtagttatat ... ttgtttgcagGGAAGTTGGAAGAAGCTCTTGAGTATTTTACCGAAGCTATAATCTGCAATC
EST: gi|67717904|gb|BJ968163.1|BJ968163
EST:     GGACGAGGCTCAGCTCTCGAAAGGCAAAGCAGTGGAAGCTATGGCAGAAG                         GGAAGTTGGAAGAAGCTCTTGAGTATTTTACCGAAGCTATAATCTGCAATC
genomic: GGACGAGGCTCAGCTCTCGAAAGGCAAAGCAGTGGAAGCTATGGCAGAAGgtagttatat ... ttgtttgcagGGAAGTTGGAAGAAGCTCTTGAGTATTTTACCGAAGCTATAATCTGCAATC
EST: gi|100393447|gb|BY953403.1|BY953403
EST:     GGACGAGGCTCAGCTCTCGAAAGGCAAAGCAGTGGAAGCTATGGCAGAAG                         GGAAGTTGGAAGAAGCTCTTGAGTATTTTACCGAAGCTATAATCTGCAATC
genomic: GGACGAGGCTCAGCTCTCGAAAGGCAAAGCAGTGGAAGCTATGGCAGAAGgtagttatat ... ttgtttgcagGGAAGTTGGAAGAAGCTCTTGAGTATTTTACCGAAGCTATAATCTGCAATC
EST: gi|162249194|gb|FC421537.1|FC421537
EST:     GGACGAGGCTCAGCTCTCGAAAGTCAAAGCAGTGGAAGCTATGGCAGAAG                         GGAAGTTGGAAGAAGCTCTTGAGTATTTTACCGAAGCTATAATCTGCAATC
genomic: GGACGAGGCTCAGCTCTCGAAAGGCAAAGCAGTGGAAGCTATGGCAGAAGgtagttatat ... ttgtttgcagGGAAGTTGGAAGAAGCTCTTGAGTATTTTACCGAAGCTATAATCTGCAATC
EST: gi|208358732|gb|DC942926.1|DC942926
EST:     GGACGAGGCTCAGCTCTCGAAAGGCAAAGCAGTGGAAGCTATGGCAGAAG                         GGAAGTTGGAAGAAGCTCTTGAGTATTTTACCGAAGCTATAATCTGCAATC
genomic: GGACGAGGCTCAGCTCTCGAAAGGCAAAGCAGTGGAAGCTATGGCAGAAGgtagttatat ... ttgtttgcagGGAAGTTGGAAGAAGCTCTTGAGTATTTTACCGAAGCTATAATCTGCAATC
EST: gi|100401417|gb|BY990992.1|BY990992
EST:     GGACGAGGCTCAGCTCTCGAAAGGCAAAGCAGTGGAAGCTATGGCAGAAG                         GGAAGTTGGAAGAAGCTCTTGAGTATTTTACCGAAGCTATAATCTGCAATC
genomic: GGACGAGGCTCAGCTCTCGAAAGGCAAAGCAGTGGAAGCTATGGCAGAAGgtagttatat ... ttgtttgcagGGAAGTTGGAAGAAGCTCTTGAGTATTTTACCGAAGCTATAATCTGCAATC
EST: gi|162150303|gb|FC326388.1|FC326388
EST:     GGACGAGGCTCAGCTCTCGAAAGTCAAAGCAGTGGAAGCTATGGCAGAAG                         GGAAGTTGGAAGAAGCTCTTGAGTATTTTACCGAAGCTATAATCTGCAATC
genomic: GGACGAGGCTCAGCTCTCGAAAGGCAAAGCAGTGGAAGCTATGGCAGAAGgtagttatat ... ttgtttgcagGGAAGTTGGAAGAAGCTCTTGAGTATTTTACCGAAGCTATAATCTGCAATC
EST: gi|208368260|gb|DC935643.1|DC935643
EST:     GGACGAGGCTCAGCTCTCGAAAGGCAAAGCAGTGGAAGCTATGGCAGAAG                         GGAAGTTGGAAGAAGCTCTTGAGTATTTTACCGAAGCTATAATCTGCAATC
genomic: GGACGAGGCTCAGCTCTCGAAAGGCAAAGCAGTGGAAGCTATGGCAGAAGgtagttatat ... ttgtttgcagGGAAGTTGGAAGAAGCTCTTGAGTATTTTACCGAAGCTATAATCTGCAATC
EST: gi|18362966|gb|BJ195038.1|BJ195038
EST:     GGACGAGGCTCAGCTCTCGAAAGGCAAAGCAGTGGAAGCTATGGCAGAAG                         GGAAGTTGGAAGAAGCTCTTGAGTATTTTACCGAAGCTATAATCTGCAATC
genomic: GGACGAGGCTCAGCTCTCGAAAGGCAAAGCAGTGGAAGCTATGGCAGAAGgtagttatat ... ttgtttgcagGGAAGTTGGAAGAAGCTCTTGAGTATTTTACCGAAGCTATAATCTGCAATC
EST: gi|67704727|gb|BJ964960.1|BJ964960
EST:     GGACGAGGCTCANCTCTCGAAAGGCAAAGCAGTGGAAGCTATGGCAGAAG                         GGAAGTTGGAAGAAGCTCTTGAGTATTTTACCGAAGCTATAATCTGCAATC
genomic: GGACGAGGCTCAGCTCTCGAAAGGCAAAGCAGTGGAAGCTATGGCAGAAGgtagttatat ... ttgtttgcagGGAAGTTGGAAGAAGCTCTTGAGTATTTTACCGAAGCTATAATCTGCAATC
EST: gi|100428929|gb|BY959504.1|BY959504
EST:     GGACGAGGCTCAGCTCTCGAAGGGCAAAGCAGTGGAAGCTATGGCAGAAG                         GGGAAGTTGGAAGAAGCTCTTGAGTATTTTACCGAAGCTATAATCTGGCA-
genomic: GGACGAGGCTCAGCTCTCGAAAGGCAAAGCAGTGGAAGCTATGGCAGAAGgtagttatat ... ttgtttgcagGG-AAGTTGGAAGAAGCTCTTGAGTATTTTACCGAAGCTATAATCTG-CAA
EST: gi|67719148|gb|BJ969407.1|BJ969407
EST:     GGACGAGGCTCANCTCTCGAAAGGCAAAGCAGTGGAAGCTATGGCANAAG                         GGAANTTGGAAGAAGCTCTTGAGTATTTTACCGAAGCTATAATCTGCAATC
genomic: GGACGAGGCTCAGCTCTCGAAAGGCAAAGCAGTGGAAGCTATGGCAGAAGgtagttatat ... ttgtttgcagGGAAGTTGGAAGAAGCTCTTGAGTATTTTACCGAAGCTATAATCTGCAATC

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: 32 (upstream exon), 28 (downstream exon)
Score: 23

ATGGGTGATCAAGATGTGGAGGTGACAGAGGAGAAGATGGACGAGGCTCAGCTCTCGAAAGGCAAAGCAGTGGAAGCTATGGCAGAAGgtagttatat ... ttgtttgcagGGAAGTTGGAAGAAGCTCTTGAGTATTTTACCGAAGCTATAATCTGCAATCCACATTCAGCAATCCTATTCGCCAACCGAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atatagcaagttaccttcttgatttgttcgtaaggtctgctatcattgtttgcagGGAAGTTGGAAGAAGCTCTTGAGTATTTTACCGAAGCTATAATCTGCAATCCACATTCAGCAATCCTATTCGCCAACCGAG
                tcttgat  putative branch site (score: 23)
                  ttgattt  TA-rich tract