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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GACGACTCATACCTGGAGAGTTACATCAGCACAATTGGTGTCGACTTTgtgagtaaccacatgcactaccagtgtggcatgttgagatattgaatgacctggaggcttttgatttacatgtgaaatgaagcttactgttgtggtggagattcgccaatttggaggtgttcgaagttcatactcacagtaattcatgtactgagtgaaagcaattgtgtgttgcag

Basic information

species Physcomitrella patens
transcript PP1S91_243V6.1
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|208377196|gb|DC932346.1|DC932346
EST:     GGCGACTCATACCTGGAGAGTTACATCAGCGCAATTGGTGTCGACTTT                         AAAATACGTACAGTGGAGCTTGACGGAAAGACTATCAAGTTGCAGATT
genomic: GACGACTCATACCTGGAGAGTTACATCAGCACAATTGGTGTCGACTTTgtgagtaacc ... tgtgttgcagAAAATACGTACAGTGGAGCTTGACGGAAAGACTATCAAGTTGCAGATT
EST: gi|100365370|gb|BY966564.1|BY966564
EST:     GACGACTCATACCTGGAGAGTTACATCAGCACAATTGGTGTCGACTTT                         AAAATACGTACAGTGGAGCTTGACGGAAAGACTATCAAGTTGCAGATT
genomic: GACGACTCATACCTGGAGAGTTACATCAGCACAATTGGTGTCGACTTTgtgagtaacc ... tgtgttgcagAAAATACGTACAGTGGAGCTTGACGGAAAGACTATCAAGTTGCAGATT
EST: gi|208394189|gb|DC933857.1|DC933857
EST:     GACGACTCATACCTGGAGAGTTACATCAGCACAATTGGTGTCGACTTT                         AAAATACGTACAGTGGAGCTTGACGGAAAGACTATCAAGTTGCAGATT
genomic: GACGACTCATACCTGGAGAGTTACATCAGCACAATTGGTGTCGACTTTgtgagtaacc ... tgtgttgcagAAAATACGTACAGTGGAGCTTGACGGAAAGACTATCAAGTTGCAGATT
EST: gi|100427223|gb|BY959037.1|BY959037
EST:     GACGACTCATACCTGGAGAGTTACATCAGCACAATTGGTGTCGACTTT                         AAAATACGTACAGTGGAGCTTGACGGANAGACTATCAAGTTGCAGATT
genomic: GACGACTCATACCTGGAGAGTTACATCAGCACAATTGGTGTCGACTTTgtgagtaacc ... tgtgttgcagAAAATACGTACAGTGGAGCTTGACGGAAAGACTATCAAGTTGCAGATT
EST: gi|162190479|gb|FC365701.1|FC365701
EST:     GACGACTCATACCTGGAGAGTTACATCAGCACAATTGGTGTCGACTTT                         AAAATACGTACAGTGGAGCTTGACGGAAAGACTATCAAGTTGCAGATT
genomic: GACGACTCATACCTGGAGAGTTACATCAGCACAATTGGTGTCGACTTTgtgagtaacc ... tgtgttgcagAAAATACGTACAGTGGAGCTTGACGGAAAGACTATCAAGTTGCAGATT
EST: gi|162150706|gb|FC327602.1|FC327602
EST:     GACGACTCATACCTGGAGAGTTACATCAGCACAATTGGTGTCGACTTT                         AAAATACGTACAGTGGAGCTTGACGGAAAGACTATCAAGTTGCAGATT
genomic: GACGACTCATACCTGGAGAGTTACATCAGCACAATTGGTGTCGACTTTgtgagtaacc ... tgtgttgcagAAAATACGTACAGTGGAGCTTGACGGAAAGACTATCAAGTTGCAGATT
EST: gi|100429270|gb|BY978026.1|BY978026
EST:     GACGACTCATACCTGGAGAGTTACATCAGCACAATTGGTGTCGACTTT                         AAAATACGTACAGTGGAGCTTGACGGAAAGACTATCAAGTTGCAGATT
genomic: GACGACTCATACCTGGAGAGTTACATCAGCACAATTGGTGTCGACTTTgtgagtaacc ... tgtgttgcagAAAATACGTACAGTGGAGCTTGACGGAAAGACTATCAAGTTGCAGATT
EST: gi|100375926|gb|BY968230.1|BY968230
EST:     GACGACTCATACCTGGAGAGTTACATCAGCACAATTGGTGTCGACTTT                         AAAATACGTACAGTGGAGCTTGACGGAAAGACTATCAAGTTGCAGATT
genomic: GACGACTCATACCTGGAGAGTTACATCAGCACAATTGGTGTCGACTTTgtgagtaacc ... tgtgttgcagAAAATACGTACAGTGGAGCTTGACGGAAAGACTATCAAGTTGCAGATT
EST: gi|18342722|gb|BJ174757.1|BJ174757
EST:     GACGACTCATACCTGGAGAGTTACATCAGCACAATTGGTGTCGACTTT                         AAAATACGTACAGTGGAGCTTGACGGAAAGACTATCAAGTTGCAGATT
genomic: GACGACTCATACCTGGAGAGTTACATCAGCACAATTGGTGTCGACTTTgtgagtaacc ... tgtgttgcagAAAATACGTACAGTGGAGCTTGACGGAAAGACTATCAAGTTGCAGATT
EST: gi|208376325|gb|DC940995.1|DC940995
EST:     GACGACTCATACCTGGAGAGTTACATCAGCACAATTGGTGTCGACTTT                         AAAATACGTACAGTGGAGCTTGACGGAAAGACTATCAAGTTGCAGATT
genomic: GACGACTCATACCTGGAGAGTTACATCAGCACAATTGGTGTCGACTTTgtgagtaacc ... tgtgttgcagAAAATACGTACAGTGGAGCTTGACGGAAAGACTATCAAGTTGCAGATT
EST: gi|208366816|gb|DC940130.1|DC940130
EST:     GACGACTCATACCTGGAGAGTTACATCAGCACAATTGGTGTCGACTTT                         AAAATACGTACAGTGGAGCTTGACGGAAAGACTATCAAGTTGCAGATT
genomic: GACGACTCATACCTGGAGAGTTACATCAGCACAATTGGTGTCGACTTTgtgagtaacc ... tgtgttgcagAAAATACGTACAGTGGAGCTTGACGGAAAGACTATCAAGTTGCAGATT
EST: gi|100435552|gb|BY960970.1|BY960970
EST:     GACGACTCATACCTGGAGAGTTACATCAGCACAATTGGTGTCGACTTT                         AAAATACGTACAGTGGAGCTTGACGGANAGACTATCAAGTTGCAGATT
genomic: GACGACTCATACCTGGAGAGTTACATCAGCACAATTGGTGTCGACTTTgtgagtaacc ... tgtgttgcagAAAATACGTACAGTGGAGCTTGACGGAAAGACTATCAAGTTGCAGATT
EST: gi|100405284|gb|BY955448.1|BY955448
EST:     GACGACTCATACCTGGAGAGTTACATCAGCACAATTGGTGTCGACTTT                         AAAATACGTACAGTGGAGCTTGACGGAAAGACTATCAAGTTGCAGATT
genomic: GACGACTCATACCTGGAGAGTTACATCAGCACAATTGGTGTCGACTTTgtgagtaacc ... tgtgttgcagAAAATACGTACAGTGGAGCTTGACGGAAAGACTATCAAGTTGCAGATT
EST: gi|67508428|gb|BJ941295.1|BJ941295
EST:     GACGACTCATACCTGGAGAGTTACATCAGCACAATTGGTGTCGACTTT                         AAAATACGTACAGTGGAGCTTGACGGAAAGACTATCAAGTTGCAGATT
genomic: GACGACTCATACCTGGAGAGTTACATCAGCACAATTGGTGTCGACTTTgtgagtaacc ... tgtgttgcagAAAATACGTACAGTGGAGCTTGACGGAAAGACTATCAAGTTGCAGATT
EST: gi|100388728|gb|BY970876.1|BY970876
EST:     GACGACTCATACCTGGAGAGTTACATCAGCACAATTGGTGTCGACTTT                         AAAATACGTACAGTGGAGCTTGACGGAAAGACTATCAAGTTGCAGATT
genomic: GACGACTCATACCTGGAGAGTTACATCAGCACAATTGGTGTCGACTTTgtgagtaacc ... tgtgttgcagAAAATACGTACAGTGGAGCTTGACGGAAAGACTATCAAGTTGCAGATT
EST: gi|208354508|gb|DC953872.1|DC953872
EST:     GACGACTCATACCTGGAGAGNTACATCAGCACAATTGGTGTCGACTTT                         AAAATACGTACAGTGGAGCTTGACGGAAAGACTATCAAGTTGCAGATT
genomic: GACGACTCATACCTGGAGAGTTACATCAGCACAATTGGTGTCGACTTTgtgagtaacc ... tgtgttgcagAAAATACGTACAGTGGAGCTTGACGGAAAGACTATCAAGTTGCAGATT
EST: gi|208359364|gb|DC939117.1|DC939117
EST:     GACGACTCATACCTGGAGAGTTACATCAGCACAATTGGTGTCGACTTT                         AAAATACGTACAGTGGAGCTTGACGGAAAGACTATCAAGTTGCAGATT
genomic: GACGACTCATACCTGGAGAGTTACATCAGCACAATTGGTGTCGACTTTgtgagtaacc ... tgtgttgcagAAAATACGTACAGTGGAGCTTGACGGAAAGACTATCAAGTTGCAGATT
EST: gi|208369746|gb|DC941008.1|DC941008
EST:     GACGACTCATACCTGGAGAGTTACATCAGCACAATTGGTGTCGACTTT                         AAAATACGTACAGTGGAGCTTGACGGAAAGACTATCAAGTTGCAGATT
genomic: GACGACTCATACCTGGAGAGTTACATCAGCACAATTGGTGTCGACTTTgtgagtaacc ... tgtgttgcagAAAATACGTACAGTGGAGCTTGACGGAAAGACTATCAAGTTGCAGATT
EST: gi|67569192|gb|BJ942016.1|BJ942016
EST:     GACGACTCATACCTGGAGAGTTACATCAGCACAATTGGTGTCGACTTT                         AAAATACGTACAGTGGAGCTTGACGGAAAGACTATCAAGTTGCAGATT
genomic: GACGACTCATACCTGGAGAGTTACATCAGCACAATTGGTGTCGACTTTgtgagtaacc ... tgtgttgcagAAAATACGTACAGTGGAGCTTGACGGAAAGACTATCAAGTTGCAGATT
EST: gi|18330928|gb|BJ162934.1|BJ162934
EST:     GACGACTCATACCTGGAGAGTTACATCAGCACAATTGGTGTCGACTTT                         AAAATACGTACAGTGGAGCTTGACGGAAAGACTATCAAGTTGCAGATT
genomic: GACGACTCATACCTGGAGAGTTACATCAGCACAATTGGTGTCGACTTTgtgagtaacc ... tgtgttgcagAAAATACGTACAGTGGAGCTTGACGGAAAGACTATCAAGTTGCAGATT
EST: gi|67571758|gb|BJ944582.1|BJ944582
EST:     GACGACTCATACCTGGAGAGTTACATCAGCACAATTGGTGTCGACTTT                         AAAATACGTACAGTGGAGCTTGACGGAAAGACTATCAAGTTGCAGATT
genomic: GACGACTCATACCTGGAGAGTTACATCAGCACAATTGGTGTCGACTTTgtgagtaacc ... tgtgttgcagAAAATACGTACAGTGGAGCTTGACGGAAAGACTATCAAGTTGCAGATT

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: 34 (upstream exon), 33 (downstream exon)
Score: 41

GACGACTCATACCTGGAGAGTTACATCAGCACAATTGGTGTCGACTTTgtgagtaacc ... tgtgttgcagAAAATACGTACAGTGGAGCTTGACGGAAAGACTATCAAGTTGCAGATT




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GACGACTCATACCTGGAGAGTTACATCAGCACAATTGGTGTCGACTTTgtgagtaaccacatgcactaccagtgtggcatgttgagatattgaatgacctggaggcttttgatttacatgtgaaatgaagcttactgttgtggtggagattcgccaatttggaggtgttcgaagttcatactcacagtaattcatgtactgagtgaaagcaattgtgtgttgcag

- - - - - -  TGGAGA