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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acgcttcgattagctaagtactgaagaggaaattttggtgcaattttctcatatatttatccgcagtcttgatttaacctagagttatgggtcttggcagCCAGAGGACTGGACCTTTGCCTCTGATCCACTGATTTTTCACAAGGGCAGCGAGCAAGCTCCAAG

Basic information

species Physcomitrella patens
transcript PP1S47_175V6.1
intron # 5
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|100446572|gb|CJ970871.1|CJ970871
EST:     TTAGCTACTCCGCTGTTGGCGCTTGTAGTTACCCACGTCCTCTGGTCCTG                         CCAGAGGACTGGACCTTTGCCTCTGATCCACTGATTTTTCACAAGGGCAGC
genomic: TTAGCTACTCCGCTGTTGGCGCTTGTAGTTACCCACGTCCTCTGGTCCTGgtaagtcatt ... gtcttggcagCCAGAGGACTGGACCTTTGCCTCTGATCCACTGATTTTTCACAAGGGCAGC
EST: gi|208400386|gb|DC925024.1|DC925024
EST:     TTAGCTACTCCGCTGTTGGCGCTTGTAGTTACCCACGTCCTCTGGTCCTG                         CCAGAGGACTGGACCTTTGCCTCTGATCCACTGATTTTTCACAAGGGCAGC
genomic: TTAGCTACTCCGCTGTTGGCGCTTGTAGTTACCCACGTCCTCTGGTCCTGgtaagtcatt ... gtcttggcagCCAGAGGACTGGACCTTTGCCTCTGATCCACTGATTTTTCACAAGGGCAGC
EST: gi|100375388|gb|BY948854.1|BY948854
EST:     AGCTACTCCGCTGTTGGCGCTTGTAGTTACCCACGTCCTCTGGTCCTNNG                         C-AGAG-ACTGGACCTTTTGC-TCTGANTC-ACTGATTTTTCACAAGGGC
genomic: AGCTACTCCGCTGTTGGCGCTTGTAGTTACCCACGTCCTCTGGTCCT--Ggtaagtcatt ... gtcttggcagCCAGAGGACTGGACCTTT-GCCTCTGA-TCCACTGATTTTTCACAAGGGC
EST: gi|208353342|gb|DC946290.1|DC946290
EST:     TTAGCTACTCCGCTGTTGGCGCTTGTAGTTACCCACGTCCTCTGGTCCTG                         CCAGAGGACTGGACCTTTGCCTCTGATCCACTGATTTTTCACAAGGGCAGC
genomic: TTAGCTACTCCGCTGTTGGCGCTTGTAGTTACCCACGTCCTCTGGTCCTGgtaagtcatt ... gtcttggcagCCAGAGGACTGGACCTTTGCCTCTGATCCACTGATTTTTCACAAGGGCAGC
EST: gi|208363065|gb|DC946934.1|DC946934
EST:     TTAGCTACTCCGCTGTTGGCGCTTGTAGTTACCCACGTCCTCTGGTCCTG                         CCAGAGGACTGGACCTTTGCCTCTGATCCACTGATTTTTCACAAGGGCAGC
genomic: TTAGCTACTCCGCTGTTGGCGCTTGTAGTTACCCACGTCCTCTGGTCCTGgtaagtcatt ... gtcttggcagCCAGAGGACTGGACCTTTGCCTCTGATCCACTGATTTTTCACAAGGGCAGC
EST: gi|100379831|gb|BY949966.1|BY949966
EST:     TTAGCTACTCCGCTGTTGGCGCTTGTAGTTACCCACGTCCTCTGGTCCTG                         CCAGAGGACTGGACCTTTGCCTCTGATCCACTGATTTTTTCACA-GGGCAG
genomic: TTAGCTACTCCGCTGTTGGCGCTTGTAGTTACCCACGTCCTCTGGTCCTGgtaagtcatt ... gtcttggcagCCAGAGGACTGGACCTTTGCCTCTGATCCACTGATTTTT-CACAAGGGCAG
EST: gi|67724008|gb|BJ974267.1|BJ974267
EST:     TTAGCTACTCCGCTGTTGGCGCTTGTAGTTACCCACGTCCTCTGGTCCTG                         CCAGAGGACTGGACCTTTGCCTCTGATCCACTGATTTTTCACAAGGGCAGC
genomic: TTAGCTACTCCGCTGTTGGCGCTTGTAGTTACCCACGTCCTCTGGTCCTGgtaagtcatt ... gtcttggcagCCAGAGGACTGGACCTTTGCCTCTGATCCACTGATTTTTCACAAGGGCAGC
EST: gi|208355833|gb|DC930196.1|DC930196
EST:     TTAGCTACTCCGCTGTTGGCGCTTGTAGTTACCCACGTCCTCTGGTCCTG                         CCAGAGGACTGGACCTTTGCCTCTGATCCACTGATTTTTCACAAGGGCAGC
genomic: TTAGCTACTCCGCTGTTGGCGCTTGTAGTTACCCACGTCCTCTGGTCCTGgtaagtcatt ... gtcttggcagCCAGAGGACTGGACCTTTGCCTCTGATCCACTGATTTTTCACAAGGGCAGC
EST: gi|100427879|gb|BY959171.1|BY959171
EST:     CTTACTCCGCTGTTGGGCGCTTGGTGGT-ACCCACGTCCTCCTGGTCCTG                         CCAGAGGACTGGGACCTTTGCC
genomic: CT-ACTCCGCTGTTGG-CGCTTG-TAGTTACCCACGTCCTC-TGGTCCTGgtaagtcatt ... gtcttggcagCCAGAGGACTGG-ACCTTTGCC
EST: gi|67569178|gb|BJ942002.1|BJ942002
EST:     TTAGCTACTCCGCTGTTGGCGCTTGTAGTTACCCACGTCCTCTGGTCCTG                         CCAGAGGACTGGACCTTTGCCTCTGATCCACTGATTTTTCACAAGGGCAGC
genomic: TTAGCTACTCCGCTGTTGGCGCTTGTAGTTACCCACGTCCTCTGGTCCTGgtaagtcatt ... gtcttggcagCCAGAGGACTGGACCTTTGCCTCTGATCCACTGATTTTTCACAAGGGCAGC
EST: gi|208384047|gb|DC911225.1|DC911225
EST:     TTAGCTACTCCGCTGTTGGCGCTTGTAGTTACCCACGTCCTCTGGTCCTG                         CCAGANGACTGGACCTTTGCCTCTGATCCACTGATTTTTCACAAGGGCAGC
genomic: TTAGCTACTCCGCTGTTGGCGCTTGTAGTTACCCACGTCCTCTGGTCCTGgtaagtcatt ... gtcttggcagCCAGAGGACTGGACCTTTGCCTCTGATCCACTGATTTTTCACAAGGGCAGC
EST: gi|208366345|gb|DC943863.1|DC943863
EST:     TTAGCTACTCCGCTGTTGGCGCTTGTAGTTACCCACGTCCTCTGGTCCTG                         CCAGAGGACTGGACCTTTGCCTCTGATCCACTGATTTTTCACAAGGGCAGC
genomic: TTAGCTACTCCGCTGTTGGCGCTTGTAGTTACCCACGTCCTCTGGTCCTGgtaagtcatt ... gtcttggcagCCAGAGGACTGGACCTTTGCCTCTGATCCACTGATTTTTCACAAGGGCAGC
EST: gi|208370373|gb|DC931785.1|DC931785
EST:     TTAGCTACTCCGCTGTTGGCGCTTGTAGTTACCCACGTCCTCTGGTCCTG                         CCAGANGACTGGACCTTTGCCTCTGATCCACTGATTTTTCACAAGGGCAGC
genomic: TTAGCTACTCCGCTGTTGGCGCTTGTAGTTACCCACGTCCTCTGGTCCTGgtaagtcatt ... gtcttggcagCCAGAGGACTGGACCTTTGCCTCTGATCCACTGATTTTTCACAAGGGCAGC
EST: gi|208394403|gb|DC942563.1|DC942563
EST:     TTAGCTACTCCGCTGTTGGCGCTTGTAGTTACCCACGTCCTCTGGTCCTG                         CCAGAGGACTGGACCTTTGCCTCTGATCCACTGATTTTTCACAAGGGCAGC
genomic: TTAGCTACTCCGCTGTTGGCGCTTGTAGTTACCCACGTCCTCTGGTCCTGgtaagtcatt ... gtcttggcagCCAGAGGACTGGACCTTTGCCTCTGATCCACTGATTTTTCACAAGGGCAGC
EST: gi|67692423|gb|BJ952656.1|BJ952656
EST:     TTAGCTACTCCGCTGTTGGCGCTTGTAGTTACCCACGTCCTCTGGTCCTG                         CCAGAGGACTGGACCTTTGCCTCTGATCCACTGATTTTTCACAAGGGCAGC
genomic: TTAGCTACTCCGCTGTTGGCGCTTGTAGTTACCCACGTCCTCTGGTCCTGgtaagtcatt ... gtcttggcagCCAGAGGACTGGACCTTTGCCTCTGATCCACTGATTTTTCACAAGGGCAGC
EST: gi|208389723|gb|DC938299.1|DC938299
EST:     TTAGCTACTCCGCTGTTGGCGCTTGTAGTTACCCACGTCCTCTGGTCCTG                         CCANAGGACTGGACCTTTGCCTCTGATCCACTGATTTTTCACAAGGGCAGC
genomic: TTAGCTACTCCGCTGTTGGCGCTTGTAGTTACCCACGTCCTCTGGTCCTGgtaagtcatt ... gtcttggcagCCAGAGGACTGGACCTTTGCCTCTGATCCACTGATTTTTCACAAGGGCAGC
EST: gi|208391012|gb|DC929331.1|DC929331
EST:     TTAGCTACTCCGCTGTTGGCGCTTGTAGTTACCCACGTCCTCTGGTCCTG                         CCAGAGGACTGGACCTTTGCCTCTGATCCACTGATTTTTCACAAGGGCAGC
genomic: TTAGCTACTCCGCTGTTGGCGCTTGTAGTTACCCACGTCCTCTGGTCCTGgtaagtcatt ... gtcttggcagCCAGAGGACTGGACCTTTGCCTCTGATCCACTGATTTTTCACAAGGGCAGC
EST: gi|67716920|gb|BJ967179.1|BJ967179
EST:     TTAGCTACTCCGCTGTTGGCGCTTGTAGTTACCCACGTCCTCTGGTCCTG                         CCAGANGACTGGACCTTTGCCACTGATCCA
genomic: TTAGCTACTCCGCTGTTGGCGCTTGTAGTTACCCACGTCCTCTGGTCCTGgtaagtcatt ... gtcttggcagCCAGAGGACTGGACCTTTGCCTCTGATCCA
EST: gi|100364611|gb|BY947820.1|BY947820
EST:     AGCTACTCCGCTGTTGGCGCTTGTAGTTACCCACGTCCTCTGGTCCCCTG                         C-AGAG-ACTGGACCTTTGCCTCTGATCCACTGATTTTTCACAAGGGCAG
genomic: AGCTACTCCGCTGTTGGCGCTTGTAGTTACCCACGTCCTCTGGTCC--TGgtaagtcatt ... gtcttggcagCCAGAGGACTGGACCTTTGCCTCTGATCCACTGATTTTTCACAAGGGCAG
EST: gi|208385596|gb|DC937141.1|DC937141
EST:     TTAGCTACTCCGCTGTTGGCGCTTGTAGTTACCCACGTCCTCTGGTCCTG                         CCAGAGGACTGGACCTTTGCCTCTGATCCACTGATTTTTCACAGGGGCAGC
genomic: TTAGCTACTCCGCTGTTGGCGCTTGTAGTTACCCACGTCCTCTGGTCCTGgtaagtcatt ... gtcttggcagCCAGAGGACTGGACCTTTGCCTCTGATCCACTGATTTTTCACAAGGGCAGC
EST: gi|208380443|gb|DC914867.1|DC914867
EST:     TTAGCTACTCCGCTGTTGGCGCTTGTAGTTACCCACGTCCTCTGGTCCTG                         CCAGAGGACTGGACCTTTGCCTCTGATCCACTGATTT
genomic: TTAGCTACTCCGCTGTTGGCGCTTGTAGTTACCCACGTCCTCTGGTCCTGgtaagtcatt ... gtcttggcagCCAGAGGACTGGACCTTTGCCTCTGATCCACTGATTT
EST: gi|208373997|gb|DC944730.1|DC944730
EST:     TTAGCTACTCCGCTGTTGGCGCTTGTAGTTACCCACGTCCTCTGGTCCTG                         CCAGAGGACTGGACCTTTGCCTCTGATCCACTGATTTTTCACAAGGGCAGC
genomic: TTAGCTACTCCGCTGTTGGCGCTTGTAGTTACCCACGTCCTCTGGTCCTGgtaagtcatt ... gtcttggcagCCAGAGGACTGGACCTTTGCCTCTGATCCACTGATTTTTCACAAGGGCAGC
EST: gi|208354200|gb|DC957420.1|DC957420
EST:     TTAGCTACTCCGCTGTTGGCGCTTGTAGTTACCCACGTCCTCTGGTCCTG                         CCAGAGGACTGGACCTTTGCCTCTGATCCACTGATTTTTCACAGGGGCAGC
genomic: TTAGCTACTCCGCTGTTGGCGCTTGTAGTTACCCACGTCCTCTGGTCCTGgtaagtcatt ... gtcttggcagCCAGAGGACTGGACCTTTGCCTCTGATCCACTGATTTTTCACAAGGGCAGC
EST: gi|67725438|gb|BJ975697.1|BJ975697
EST:     TTAGCTACTCCGCTGTTGGCGCTTGTAGTTACCCACGTCCTCTGGTCCTG                         CCAGAGGACTGGACCTTTGCCACTGATCCACTGATTTTTCACAAGGGCAGC
genomic: TTAGCTACTCCGCTGTTGGCGCTTGTAGTTACCCACGTCCTCTGGTCCTGgtaagtcatt ... gtcttggcagCCAGAGGACTGGACCTTTGCCTCTGATCCACTGATTTTTCACAAGGGCAGC
EST: gi|208389767|gb|DC933641.1|DC933641
EST:     TTAGCTACTCCGCTGTTGGCGCTTGTAGTTACCCACGTCCTCTGGTCCTG                         CCAGAGGACTGGACCTTTGCCTCTGATCCACTGATTTTTCACAAGGGCAGC
genomic: TTAGCTACTCCGCTGTTGGCGCTTGTAGTTACCCACGTCCTCTGGTCCTGgtaagtcatt ... gtcttggcagCCAGAGGACTGGACCTTTGCCTCTGATCCACTGATTTTTCACAAGGGCAGC
EST: gi|208361102|gb|DC957553.1|DC957553
EST:     TTAGCTACTCCGCTGTTGGCGCTTGTAGTTACCCACGTCCTCTGGTCCTG                         CCAGAGGACTGGACCTTTGCCTCTGATCCACTGATTTTTCACAAGGGCAGC
genomic: TTAGCTACTCCGCTGTTGGCGCTTGTAGTTACCCACGTCCTCTGGTCCTGgtaagtcatt ... gtcttggcagCCAGAGGACTGGACCTTTGCCTCTGATCCACTGATTTTTCACAAGGGCAGC
EST: gi|162272918|gb|FC448854.1|FC448854
EST:     TTAGCTACTCCGCTGTTGGCGCTTGTAGTTACCCACGTCCTCTGGTCCTG                         CCAGAGGACTGGACCTTTGCCTCTGATCCACTGATTTTTCACAAGGGCAGC
genomic: TTAGCTACTCCGCTGTTGGCGCTTGTAGTTACCCACGTCCTCTGGTCCTGgtaagtcatt ... gtcttggcagCCAGAGGACTGGACCTTTGCCTCTGATCCACTGATTTTTCACAAGGGCAGC
EST: gi|208368388|gb|DC955557.1|DC955557
EST:     TTAGCTACTCCGCTGTTGGCGCTTGTAGTTACCCACGTCCTCTGGTCCTG                         CCAGAGGACTGGACCTTTGCCTCTGATCCACTGATTTTTCACAAGGGCAGC
genomic: TTAGCTACTCCGCTGTTGGCGCTTGTAGTTACCCACGTCCTCTGGTCCTGgtaagtcatt ... gtcttggcagCCAGAGGACTGGACCTTTGCCTCTGATCCACTGATTTTTCACAAGGGCAGC
EST: gi|162275152|gb|FC451739.1|FC451739
EST:     TTAGCTACTCCGCTGTTGGCGCTTGTAGTTACCCACGTCCTCTGGTCCTG                         CCAGAGGACTGGACCTTTGCCTCTGATCCACTGATTTTTCACAAGGGCAGC
genomic: TTAGCTACTCCGCTGTTGGCGCTTGTAGTTACCCACGTCCTCTGGTCCTGgtaagtcatt ... gtcttggcagCCAGAGGACTGGACCTTTGCCTCTGATCCACTGATTTTTCACAAGGGCAGC
EST: gi|162272917|gb|FC448853.1|FC448853
EST:     TTAGCTACTCCGCTGTTGGCGCTTGTAGTTACCCACGTCCTCTGGTCCTG                         CCAGAGGACTGGACCTTTGCCTCTGATCCACTGATTTTTCACAAGGGCAGC
genomic: TTAGCTACTCCGCTGTTGGCGCTTGTAGTTACCCACGTCCTCTGGTCCTGgtaagtcatt ... gtcttggcagCCAGAGGACTGGACCTTTGCCTCTGATCCACTGATTTTTCACAAGGGCAGC
EST: gi|208368823|gb|DC951347.1|DC951347
EST:     TTAGCTACTCCGCTGTTGGCGCTTGTAGTTACCCACGTCCTCTGGTCCTG                         CCAGAGGACTGGACCTTTGCCTCTGATCCACTGATTTTTCACAAGGGCAGC
genomic: TTAGCTACTCCGCTGTTGGCGCTTGTAGTTACCCACGTCCTCTGGTCCTGgtaagtcatt ... gtcttggcagCCAGAGGACTGGACCTTTGCCTCTGATCCACTGATTTTTCACAAGGGCAGC
EST: gi|208387707|gb|DC937272.1|DC937272
EST:     TTAGCTACTCCGCTGTTGGCGCTTGTAGTTACCCACGTCCTCTGGTCCTG                         CCAGAGGACTGGACCTTTGCCTCTGATCCACTGATTTTTCACAAGGGCAGC
genomic: TTAGCTACTCCGCTGTTGGCGCTTGTAGTTACCCACGTCCTCTGGTCCTGgtaagtcatt ... gtcttggcagCCAGAGGACTGGACCTTTGCCTCTGATCCACTGATTTTTCACAAGGGCAGC

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: 33 (upstream exon), 35 (downstream exon)
Score: 12

GACAGAGGCAATTTGATAGGTGTTAGCTACTCCGCTGTTGGCGCTTGTAGTTACCCACGTCCTCTGGTCCTGgtaagtcatt ... gtcttggcagCCAGAGGACTGGACCTTTGCCTCTGATCCACTGATTTTTCACAAGGGCAGCGAGCAAGCTCCAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttctcatatatttatccgcagtcttgatttaacctagagttatgggtcttggcagCCAGAGGACTGGACCTTTGCCTCTGATCCACTGATTTTTCACAAGGGCAGCGAGCAAGCTCCAAG
                          atttaac  putative branch site (score: 12)
     atatatttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acgcttcgattagctaagtactgaagaggaaattttggtgcaattttctcatatatttatccgcagtcttgatttaacctagagttatgggtcttggcagCCAGAGGACTGGACCTTTGCCTCTGATCCACTGATTTTTCACAAGGGCAGCGAGCAAGCTCCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - -tggtgca