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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtcttggtggattcagatccatgagcaagtttactgaaacgaaatctatttgacctctgcttgctaataaatcatcataaaattttcccattcagaagtgccattggctttccaataatattctaagacgcaggtttctgacgatcttcccataatgtggcagGTCAAGGGCTTTGAGGCCATAAAAGGCATGGTTCTGGAGCCTTTGCCGTTTGACGTGGAGCGTAACCTAGTAACCCCAACCTTCAAGCTCAAGAGACCGC

Basic information

species Physcomitrella patens
transcript PP1S218_19V6.1
intron # 18
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|162209089|gb|FC385113.1|FC385113
EST:     CTGTAGCGCACATTATGGCTGCTGTAAACGCTACCGGAAAGGAAAAGAAA                         GTCAAGGGCTTTGAGGCCATAAAAGGCATGGTTCTGGAGCCTTTGCCGTTT
genomic: CTGTAGCGCACATTATGGCTGCTGTAAACGCTACCGGAAAGGAAAAGAAAgtaagtcttg ... aatgtggcagGTCAAGGGCTTTGAGGCCATAAAAGGCATGGTTCTGGAGCCTTTGCCGTTT
EST: gi|37845863|gb|BJ603871.1|BJ603871
EST:     CTGTAGCGCACATTATGGCTGCTGTAAACGCTACCGGAAAGGAAAAGAAA                         GTCAAGGGCTTTGAGGCCATAAAAGGCATGGTTCTGGAGCCTTTGCCGTTT
genomic: CTGTAGCGCACATTATGGCTGCTGTAAACGCTACCGGAAAGGAAAAGAAAgtaagtcttg ... aatgtggcagGTCAAGGGCTTTGAGGCCATAAAAGGCATGGTTCTGGAGCCTTTGCCGTTT
EST: gi|162164428|gb|FC341047.1|FC341047
EST:     CTGTAGCGCACATTATGGCTGCTGTAAACGCTACCGGAAAGGAAAAGAAA                         GTCAAGGGCTTTGAGGCCATAAAAGGCATGGTTCTGGAGCCTTTGCCGTTT
genomic: CTGTAGCGCACATTATGGCTGCTGTAAACGCTACCGGAAAGGAAAAGAAAgtaagtcttg ... aatgtggcagGTCAAGGGCTTTGAGGCCATAAAAGGCATGGTTCTGGAGCCTTTGCCGTTT
EST: gi|162208184|gb|FC384301.1|FC384301
EST:     CTGTAGCGCACATTATGGCTGCTGTAAACGCTACCGGAAAGGAAAAGAAA                         GTCAAGGGCTTTGAGGCCATAAAAGGCATGGTTCTGGAGCCTTTGCCGTTT
genomic: CTGTAGCGCACATTATGGCTGCTGTAAACGCTACCGGAAAGGAAAAGAAAgtaagtcttg ... aatgtggcagGTCAAGGGCTTTGAGGCCATAAAAGGCATGGTTCTGGAGCCTTTGCCGTTT
EST: gi|7647930|gb|AW738913.1|AW738913
EST:     CTGTAGCGCACATTATGGCTGCTGTAAACGCTACCGGAAAGGAAAAGAAA                         GTCAAGGGCTTTGAGGCCATAAAAGGCATGGTTCTGGAGCCTTTGCCGTTT
genomic: CTGTAGCGCACATTATGGCTGCTGTAAACGCTACCGGAAAGGAAAAGAAAgtaagtcttg ... aatgtggcagGTCAAGGGCTTTGAGGCCATAAAAGGCATGGTTCTGGAGCCTTTGCCGTTT
EST: gi|162162560|gb|FC338654.1|FC338654
EST:     CTGTAGCGCACATTATGGCTGCTGTAAACGCTACCGGAAAGGAAAAGAAA                         GTCAAGGGCTTTGAGGCCATAAAAGGCATGGTTCTGGAGCCTTTGCCGTTT
genomic: CTGTAGCGCACATTATGGCTGCTGTAAACGCTACCGGAAAGGAAAAGAAAgtaagtcttg ... aatgtggcagGTCAAGGGCTTTGAGGCCATAAAAGGCATGGTTCTGGAGCCTTTGCCGTTT
EST: gi|18335322|gb|BJ167340.1|BJ167340
EST:     CTGTAGCGCACATTATGGCTGCTGTAAACGCTACCGGAAAGGAAAAGAAA                         GTCAAGGGCTTTGAGGCCATAAAAGGCATGGTTCTGGAGCCTTTGCCGTTT
genomic: CTGTAGCGCACATTATGGCTGCTGTAAACGCTACCGGAAAGGAAAAGAAAgtaagtcttg ... aatgtggcagGTCAAGGGCTTTGAGGCCATAAAAGGCATGGTTCTGGAGCCTTTGCCGTTT
EST: gi|162150967|gb|FC327863.1|FC327863
EST:     CTGTAGCGCACATTATGGCTGCTGTAAACGCTACCGGAAAGGAAAAGAAA                         GTCAAGGGCTTTGAGGCCATAAAAGGCATGGTTCTGGAGCCTTTGCCGTTT
genomic: CTGTAGCGCACATTATGGCTGCTGTAAACGCTACCGGAAAGGAAAAGAAAgtaagtcttg ... aatgtggcagGTCAAGGGCTTTGAGGCCATAAAAGGCATGGTTCTGGAGCCTTTGCCGTTT
EST: gi|18341336|gb|BJ173371.1|BJ173371
EST:     CTGTAGCGCACATTATGGCTGCTGTAAACGCTACCGGAAAGGAAAAGAAA                         GTCAAGGGCTTTGAGGCCATAAAAGGCATGGTTCTGGAGCCTTTGCCGTTT
genomic: CTGTAGCGCACATTATGGCTGCTGTAAACGCTACCGGAAAGGAAAAGAAAgtaagtcttg ... aatgtggcagGTCAAGGGCTTTGAGGCCATAAAAGGCATGGTTCTGGAGCCTTTGCCGTTT
EST: gi|162167279|gb|FC342844.1|FC342844
EST:     CTGTAGCGCACATTATGGCTGCTGTAAACGCTACCGGAAAGGAAAAGAAA                         GTCAAGGGCTTTGAGGCCATAAAAGGCATGGTTCTGGAGCCTTTGCCGTTT
genomic: CTGTAGCGCACATTATGGCTGCTGTAAACGCTACCGGAAAGGAAAAGAAAgtaagtcttg ... aatgtggcagGTCAAGGGCTTTGAGGCCATAAAAGGCATGGTTCTGGAGCCTTTGCCGTTT
EST: gi|162167701|gb|FC344015.1|FC344015
EST:     CTGTAGCGCACATTATGGCTGCTGTAAACGCTACCGGAAAGGAAAAGAAA                         GTCAAGGGCTTTGAGGCCATAAAAGGCATGGTTCTGGAGCCTTTGCCGTTT
genomic: CTGTAGCGCACATTATGGCTGCTGTAAACGCTACCGGAAAGGAAAAGAAAgtaagtcttg ... aatgtggcagGTCAAGGGCTTTGAGGCCATAAAAGGCATGGTTCTGGAGCCTTTGCCGTTT
EST: gi|37832751|gb|BJ590763.1|BJ590763
EST:     CTGTAGCGCACATTATGGCTGCTGTAAACGCTACCGGAAAGGAAAAGAAA                         GTCAAGGGCTTTGAGGCCATAAAAGGCATGGTTCTGGAGCCTTTGCCGTTT
genomic: CTGTAGCGCACATTATGGCTGCTGTAAACGCTACCGGAAAGGAAAAGAAAgtaagtcttg ... aatgtggcagGTCAAGGGCTTTGAGGCCATAAAAGGCATGGTTCTGGAGCCTTTGCCGTTT
EST: gi|37847919|gb|BJ605927.1|BJ605927
EST:     CTGTAGCGCACATTATGGCTGCTGTAAACGCTACCGGAAAGGAAAAGAAA                         GTCAAGGGCTTTGAGGCCATAAAAGGCATGGTTCTGGAGCCTTTGCCGTTT
genomic: CTGTAGCGCACATTATGGCTGCTGTAAACGCTACCGGAAAGGAAAAGAAAgtaagtcttg ... aatgtggcagGTCAAGGGCTTTGAGGCCATAAAAGGCATGGTTCTGGAGCCTTTGCCGTTT
EST: gi|162199025|gb|FC372376.1|FC372376
EST:     CTGTAGCGCACATTATGGCTGCTGTAAACGCTACCGGAAAGGAAAAGAAA                         GTCAAGGGCTTTGAGGCCATAAAAGGCATGGTTCTGGAGCCTTTGCCGTTT
genomic: CTGTAGCGCACATTATGGCTGCTGTAAACGCTACCGGAAAGGAAAAGAAAgtaagtcttg ... aatgtggcagGTCAAGGGCTTTGAGGCCATAAAAGGCATGGTTCTGGAGCCTTTGCCGTTT
EST: gi|162183786|gb|FC360703.1|FC360703
EST:     CTGTAGCGCACATTATGGCTGCTGTAAACGCTACCGGAAAGGAAAAGAAA                         GTCAAGGGCTTTGAGGCCATAAAAGGCATGGTTCTGGAGCCTTTGCCGTTT
genomic: CTGTAGCGCACATTATGGCTGCTGTAAACGCTACCGGAAAGGAAAAGAAAgtaagtcttg ... aatgtggcagGTCAAGGGCTTTGAGGCCATAAAAGGCATGGTTCTGGAGCCTTTGCCGTTT
EST: gi|37822902|gb|BJ580968.1|BJ580968
EST:     CTGTAGCGCACATTATGGCTGCTGTAAACGCTACCGGAAAGGAAAAGAAA                         GTCAAGGGCTTTGAGGCCATAAAAGGCATGGTTCTGGAGCCTTTGCCGTTT
genomic: CTGTAGCGCACATTATGGCTGCTGTAAACGCTACCGGAAAGGAAAAGAAAgtaagtcttg ... aatgtggcagGTCAAGGGCTTTGAGGCCATAAAAGGCATGGTTCTGGAGCCTTTGCCGTTT
EST: gi|37832894|gb|BJ590906.1|BJ590906
EST:     CTGTAGCGCACATTATGGCTGCTGTAAACGCTACCGGAAAGGAAAAGAAA                         GTCAAGGGCTTTGAGGCCATAAAAGGCATGGTTCTGGAGCCTTTGCCGTTT
genomic: CTGTAGCGCACATTATGGCTGCTGTAAACGCTACCGGAAAGGAAAAGAAAgtaagtcttg ... aatgtggcagGTCAAGGGCTTTGAGGCCATAAAAGGCATGGTTCTGGAGCCTTTGCCGTTT
EST: gi|162185787|gb|FC362343.1|FC362343
EST:     CTGTAGCGCACATTATGGCTGCTGTAAACGCTACCGGAAAGGAAAAGAAA                         GTCAAGGGCTTTGAGGCCATAAAAGGCATGGTTCTGGAGCCTTTGCCGTTT
genomic: CTGTAGCGCACATTATGGCTGCTGTAAACGCTACCGGAAAGGAAAAGAAAgtaagtcttg ... aatgtggcagGTCAAGGGCTTTGAGGCCATAAAAGGCATGGTTCTGGAGCCTTTGCCGTTT
EST: gi|37829067|gb|BJ587079.1|BJ587079
EST:     CTGTAGCGCACATTATGGCTGCTGTAAACGCTACCGGAAAGGAAAAGAAA                         GTCAAGGGCTTTGAGGCCATAAAAGGCATGGTTCTGGAGCCTTTGCCGTTT
genomic: CTGTAGCGCACATTATGGCTGCTGTAAACGCTACCGGAAAGGAAAAGAAAgtaagtcttg ... aatgtggcagGTCAAGGGCTTTGAGGCCATAAAAGGCATGGTTCTGGAGCCTTTGCCGTTT
EST: gi|162199026|gb|FC372377.1|FC372377
EST:     CTGTAGCGCACATTATGGCTGCTGTAAACGCTACCGGAAAGGAAAAGAAA                         GTCAAGGGCTTTGAGGCCATAAAAGGCATGGTTCTGGAGCCTTTGCCGTTT
genomic: CTGTAGCGCACATTATGGCTGCTGTAAACGCTACCGGAAAGGAAAAGAAAgtaagtcttg ... aatgtggcagGTCAAGGGCTTTGAGGCCATAAAAGGCATGGTTCTGGAGCCTTTGCCGTTT
EST: gi|162171310|gb|FC347235.1|FC347235
EST:     CTGTAGCGCACATTATGGCTGCTGTAAACGCTACCGGAAAGGAAAAGAAA                         GTCAAGGGCTTTGAGGCCATAAAAGGCATGGTTCTGGAGCCTTTGCCGTTT
genomic: CTGTAGCGCACATTATGGCTGCTGTAAACGCTACCGGAAAGGAAAAGAAAgtaagtcttg ... aatgtggcagGTCAAGGGCTTTGAGGCCATAAAAGGCATGGTTCTGGAGCCTTTGCCGTTT
EST: gi|162170149|gb|FC347061.1|FC347061
EST:     CTGTAGCGCACATTATGGCTGCTGTAAACGCTACCGGAAAGGAAAAGAAA                         GTCAAGGGCTTTGAGGCCATAAAAGGCATGGTTCTGGAGCCTTTGCCGTTT
genomic: CTGTAGCGCACATTATGGCTGCTGTAAACGCTACCGGAAAGGAAAAGAAAgtaagtcttg ... aatgtggcagGTCAAGGGCTTTGAGGCCATAAAAGGCATGGTTCTGGAGCCTTTGCCGTTT
EST: gi|162235484|gb|FC411307.1|FC411307
EST:     CTGTAGCGCACATTATGGCTGCTGTAAACGCTACCGGAAAGGAAAAGAAA                         GTCAAGGGCTTTGAGGCCATAAAAGGCATGGTTCTGGAGCCTTTGCCGTTT
genomic: CTGTAGCGCACATTATGGCTGCTGTAAACGCTACCGGAAAGGAAAAGAAAgtaagtcttg ... aatgtggcagGTCAAGGGCTTTGAGGCCATAAAAGGCATGGTTCTGGAGCCTTTGCCGTTT
EST: gi|37825298|gb|BJ583364.1|BJ583364
EST:     CTGTAGCGCACATTATGGCTGCTGTAAACGCTACCGGAAAGGAAAAGAAA                         GTCAAGGGCTTTGAGGCCATAAAAGGCATGGTTCTGGAGCCTTTGCCGTTT
genomic: CTGTAGCGCACATTATGGCTGCTGTAAACGCTACCGGAAAGGAAAAGAAAgtaagtcttg ... aatgtggcagGTCAAGGGCTTTGAGGCCATAAAAGGCATGGTTCTGGAGCCTTTGCCGTTT
EST: gi|37825233|gb|BJ583299.1|BJ583299
EST:     CTGTAGCGCACATTATGGCTGCTGTAAACGCTACCGGAAAGGAAAAGAAA                         GTCAAGGGCTTTGAGGCCATAAAAGGCATGGTTCTGGAGCCTTTGCCGTTT
genomic: CTGTAGCGCACATTATGGCTGCTGTAAACGCTACCGGAAAGGAAAAGAAAgtaagtcttg ... aatgtggcagGTCAAGGGCTTTGAGGCCATAAAAGGCATGGTTCTGGAGCCTTTGCCGTTT
EST: gi|162209090|gb|FC385114.1|FC385114
EST:     CTGTAGCGCACATTATGGCTGCTGTAAACGCTACCGGAAAGGAAAAGAAA                         GTCAAGGGCTTTGAGGCCATAAAAGGCATGGTTCTGGAGCCTTTGCCGTTT
genomic: CTGTAGCGCACATTATGGCTGCTGTAAACGCTACCGGAAAGGAAAAGAAAgtaagtcttg ... aatgtggcagGTCAAGGGCTTTGAGGCCATAAAAGGCATGGTTCTGGAGCCTTTGCCGTTT
EST: gi|162212203|gb|FC388313.1|FC388313
EST:     CTGTAGCGCACATTATGGCTGCTGTAAACGCTACCGGAAAGGAAAAGAAA                         GTCAAGGGCTTTGAGGCCATAAAAGGCATGGTTCTGGAGCCTTTGCCGTTT
genomic: CTGTAGCGCACATTATGGCTGCTGTAAACGCTACCGGAAAGGAAAAGAAAgtaagtcttg ... aatgtggcagGTCAAGGGCTTTGAGGCCATAAAAGGCATGGTTCTGGAGCCTTTGCCGTTT
EST: gi|162177506|gb|FC353767.1|FC353767
EST:     CTGTAGCGCACATTATGGCTGCTGTAAACGCTACCGGAAAGGAAAAGAAA                         GTCAAGGGCTTTGAGGCCATAAAAGGCATGGTTCTGGAGCCTTTGCCGTTT
genomic: CTGTAGCGCACATTATGGCTGCTGTAAACGCTACCGGAAAGGAAAAGAAAgtaagtcttg ... aatgtggcagGTCAAGGGCTTTGAGGCCATAAAAGGCATGGTTCTGGAGCCTTTGCCGTTT
EST: gi|7583607|gb|AW699516.1|AW699516
EST:     CTGTAGCGCACATTATGGCTGCTGTAAACGCTACCGGAAAGGAAAAGAAA                         GTCAAGGGCTTTGAGGCCATAAAAGGCATGGTTCTGGAGCCTTTGCCGTTT
genomic: CTGTAGCGCACATTATGGCTGCTGTAAACGCTACCGGAAAGGAAAAGAAAgtaagtcttg ... aatgtggcagGTCAAGGGCTTTGAGGCCATAAAAGGCATGGTTCTGGAGCCTTTGCCGTTT
EST: gi|162170150|gb|FC347062.1|FC347062
EST:     CTGTAGCGCACATTATGGCTGCTGTAAACGCTACCGGAAAGGAAAAGAAA                         GTCAAGGGCTTTGAGGCCATAAAAGGCATGGTTCTGGAGCCTTTGCCGTTT
genomic: CTGTAGCGCACATTATGGCTGCTGTAAACGCTACCGGAAAGGAAAAGAAAgtaagtcttg ... aatgtggcagGTCAAGGGCTTTGAGGCCATAAAAGGCATGGTTCTGGAGCCTTTGCCGTTT
EST: gi|162213631|gb|FC389711.1|FC389711
EST:     CTGTAGCGCACATTATGGCTGCTGTAAACGCTACCGGAAAGGAAAAGAAA                         GTCAAGGGCTTTGAGGCCATAAAAGGCATGGTTCTGGAGCCTTTGCCGTTT
genomic: CTGTAGCGCACATTATGGCTGCTGTAAACGCTACCGGAAAGGAAAAGAAAgtaagtcttg ... aatgtggcagGTCAAGGGCTTTGAGGCCATAAAAGGCATGGTTCTGGAGCCTTTGCCGTTT
EST: gi|37851878|gb|BJ609886.1|BJ609886
EST:     CTGTAGCGCACATTATGGCTGCTGTAAACGCTACCGGAAAGGAAAAGAAA                         GTCAAGGGCTTTGAGGCCATAAAAGGCATGGTTCTGGAGCCTTTGCCGTTT
genomic: CTGTAGCGCACATTATGGCTGCTGTAAACGCTACCGGAAAGGAAAAGAAAgtaagtcttg ... aatgtggcagGTCAAGGGCTTTGAGGCCATAAAAGGCATGGTTCTGGAGCCTTTGCCGTTT
EST: gi|162213632|gb|FC389712.1|FC389712
EST:     CTGTAGCGCACATTATGGCTGCTGTAAACGCTACCGGAAAGGAAAAGAAA                         GTCAAGGGCTTTGAGGCCATAAAAGGCATGGTTCTGGAGCCTTTGCCGTTT
genomic: CTGTAGCGCACATTATGGCTGCTGTAAACGCTACCGGAAAGGAAAAGAAAgtaagtcttg ... aatgtggcagGTCAAGGGCTTTGAGGCCATAAAAGGCATGGTTCTGGAGCCTTTGCCGTTT
EST: gi|162199212|gb|FC375048.1|FC375048
EST:     CTGTAGCGCACATTATGGCTGCTGTAAACGCTACCGGAAAGGAAAAGAAA                         GTCAAGGGCTTTGAGGCCATAAAAGGCATGGTTCTGGAGCCTTTGCCGTTT
genomic: CTGTAGCGCACATTATGGCTGCTGTAAACGCTACCGGAAAGGAAAAGAAAgtaagtcttg ... aatgtggcagGTCAAGGGCTTTGAGGCCATAAAAGGCATGGTTCTGGAGCCTTTGCCGTTT

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), 31 (downstream exon)
Score: 5

AAGCAATGGTGTTGAAGGGAACTTTGCTCAAATTTGCAAAGATCCAAAGGCTGTAGCGCACATTATGGCTGCTGTAAACGCTACCGGAAAGGAAAAGAAAgtaagtcttg ... aatgtggcagGTCAAGGGCTTTGAGGCCATAAAAGGCATGGTTCTGGAGCCTTTGCCGTTTGACGTGGAGCGTAACCTAGTAACCCCAACCTTCAAGCTCAAGAGACCGC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttccaataatattctaagacgcaggtttctgacgatcttcccataatgtggcagGTCAAGGGCTTTGAGGCCATAAAAGGCATGGTTCTGGAGCCTTTGCCGTTTGACGTGGAGCGTAACCTAGTAACCCCAACCTTCAAGCTCAAGAGACCGC
                           ttctgac  putative branch site (score: 5)
     aataatattctaaga  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtcttggtggattcagatccatgagcaagtttactgaaacgaaatctatttgacctctgcttgctaataaatcatcataaaattttcccattcagaagtgccattggctttccaataatattctaagacgcaggtttctgacgatcttcccataatgtggcagGTCAAGGGCTTTGAGGCCATAAAAGGCATGGTTCTGGAGCCTTTGCCGTTTGACGTGGAGCGTAACCTAGTAACCCCAACCTTCAAGCTCAAGAGACCGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA