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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TAAGGGTTGGTTCTATATGGTTACCTTGACAGCAAACAATCCAAGCGAGATTTGTCAGATTATGAAAAAGAAGGGCTTTGCATCACGAATTGTTATTCAGgtaattttgatggcatcctgacctactcgcagtacgggttggcccatattcttgtttctaaatatgaacagtgacgtaagataattgtgtgtgtgtgtgt...

Basic information

species Physcomitrella patens
transcript PP1S78_28V6.2
intron # 5
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|208365484|gb|DC954725.1|DC954725
EST:     TTTGTCAGATTATGAAAAAGAAGGGCTTTGCATCACGAATTGTTATTCAG                         CGTTATACAGAGGAAGAGAACTTACATGTACTGAAGTTCTGGAGAGAAGAC
genomic: TTTGTCAGATTATGAAAAAGAAGGGCTTTGCATCACGAATTGTTATTCAGgtaattttga ... atgagtgcagCGTTATACAGAGGAAGAGAACTTACATGTACTGAAGTTCTGGAGAGAAGAC
EST: gi|22132000|gb|BQ826927.1|BQ826927
EST:     TTTGTCAGATTATGAAAAAGAAGGGCTTTGCATCACGAATTGTTATTCAG                         CGTTATACAGAGGAAGAGAACTTACATGTACTGAAGTTCTGGAGAGAAGAC
genomic: TTTGTCAGATTATGAAAAAGAAGGGCTTTGCATCACGAATTGTTATTCAGgtaattttga ... atgagtgcagCGTTATACAGAGGAAGAGAACTTACATGTACTGAAGTTCTGGAGAGAAGAC
EST: gi|37850124|gb|BJ608132.1|BJ608132
EST:     TTTGTCAGATTATGAAAAAGAAGGGCTTTGCATCACGAATTGTTATTCAG                         CGTTATACAGAGGAAGAGAACTTACATGTACTGAAGTTCTGGAGAGAAGAC
genomic: TTTGTCAGATTATGAAAAAGAAGGGCTTTGCATCACGAATTGTTATTCAGgtaattttga ... atgagtgcagCGTTATACAGAGGAAGAGAACTTACATGTACTGAAGTTCTGGAGAGAAGAC
EST: gi|67696122|gb|BJ956355.1|BJ956355
EST:     TTTGTCAGATTATGAAAAAGAAGGGCTTTGCATCACGAATTGTTATTCAG                         CGTTATACAGAGGAAGAGAACTTACATGTACTGAAGTTCTGGAGAGAAGAC
genomic: TTTGTCAGATTATGAAAAAGAAGGGCTTTGCATCACGAATTGTTATTCAGgtaattttga ... atgagtgcagCGTTATACAGAGGAAGAGAACTTACATGTACTGAAGTTCTGGAGAGAAGAC
EST: gi|67696662|gb|BJ956895.1|BJ956895
EST:     TTTGTCAGATTATGAAAAAGAAGGGCTTTGCATCACGAATTGTTATTCAG                         CGTTATACAGAGGAAGAGAACTTACATGTACTGAAGTTCTGGAGAGAAGAC
genomic: TTTGTCAGATTATGAAAAAGAAGGGCTTTGCATCACGAATTGTTATTCAGgtaattttga ... atgagtgcagCGTTATACAGAGGAAGAGAACTTACATGTACTGAAGTTCTGGAGAGAAGAC
EST: gi|37823861|gb|BJ581927.1|BJ581927
EST:     TTTGTCAGATTATGAAAAAGAAGGGCTTTGCATCACGAATTGTTATTCAG                         CGTTATACAGAGGAAGAGAACTTACATGTACTGAAGTTCTGGAGAGAAGAC
genomic: TTTGTCAGATTATGAAAAAGAAGGGCTTTGCATCACGAATTGTTATTCAGgtaattttga ... atgagtgcagCGTTATACAGAGGAAGAGAACTTACATGTACTGAAGTTCTGGAGAGAAGAC
EST: gi|37831093|gb|BJ589105.1|BJ589105
EST:     TTTGTCAGATTATGAAAAAGAAGGGCTTTGCATCACGAATTGTTATTCAG                         CGTTATACAGAGGAAGAGAACTTACATGTACTGAAGTTCTGGAGAGAAGAC
genomic: TTTGTCAGATTATGAAAAAGAAGGGCTTTGCATCACGAATTGTTATTCAGgtaattttga ... atgagtgcagCGTTATACAGAGGAAGAGAACTTACATGTACTGAAGTTCTGGAGAGAAGAC
EST: gi|37846605|gb|BJ604613.1|BJ604613
EST:     TTTGTCAGATTATGAAAAAGAAGGGCTTTGCATCACGAATTGTTATTCAG                         CGTTATACAGAGGAAGAGAACTTACATGTACTGAAGTTCTGGAGAGAAGAC
genomic: TTTGTCAGATTATGAAAAAGAAGGGCTTTGCATCACGAATTGTTATTCAGgtaattttga ... atgagtgcagCGTTATACAGAGGAAGAGAACTTACATGTACTGAAGTTCTGGAGAGAAGAC
EST: gi|162237559|gb|FC413642.1|FC413642
EST:     TTTGTCAGATTATGAAAAAGAAGGGCTTTGCATCACGAATTGTTATTCAG                         CGTTATACAGAGGAAGAGAACTTACATGTACTGAAGTTCTGGAGAGAAGAC
genomic: TTTGTCAGATTATGAAAAAGAAGGGCTTTGCATCACGAATTGTTATTCAGgtaattttga ... atgagtgcagCGTTATACAGAGGAAGAGAACTTACATGTACTGAAGTTCTGGAGAGAAGAC
EST: gi|162237558|gb|FC413641.1|FC413641
EST:     TTTGTCAGATTATGAAAAAGAAGGGCTTTGCATCACGAATTGTTATTCAG                         CGTTATACAGAGGAAGAGAACTTACATGTACTGAAGTTCTGGAGAGAAGAC
genomic: TTTGTCAGATTATGAAAAAGAAGGGCTTTGCATCACGAATTGTTATTCAGgtaattttga ... atgagtgcagCGTTATACAGAGGAAGAGAACTTACATGTACTGAAGTTCTGGAGAGAAGAC
EST: gi|162242864|gb|FC417582.1|FC417582
EST:     TTTGTCAGATTATGAAAAAGAAGGGCTTTGCATCACGAATTGTTATTCAG                         CGTTATACAGAGGAAGAGAACTTACATGTACTGAAGTTCTGGAGAGAAGAC
genomic: TTTGTCAGATTATGAAAAAGAAGGGCTTTGCATCACGAATTGTTATTCAGgtaattttga ... atgagtgcagCGTTATACAGAGGAAGAGAACTTACATGTACTGAAGTTCTGGAGAGAAGAC
EST: gi|162193740|gb|FC371267.1|FC371267
EST:     TTTGTCAGATTATGAAAAAGAAGGGCTTTGCATCACGAATTGTTATTCAG                         CGTTATACAGAGGAAGAGAACTTACATGTACTGAAGTTCTGGAGAGAAGAC
genomic: TTTGTCAGATTATGAAAAAGAAGGGCTTTGCATCACGAATTGTTATTCAGgtaattttga ... atgagtgcagCGTTATACAGAGGAAGAGAACTTACATGTACTGAAGTTCTGGAGAGAAGAC
EST: gi|162223988|gb|FC400346.1|FC400346
EST:     TTTGTCAGATTATGAAAAAGAAGGGCTTTGCATCACGAATTGTTATTCAG                         CGTTATACAGAGGAAGAGAACTTACATGTACTGAAGTTCTGGAGAGAAGAC
genomic: TTTGTCAGATTATGAAAAAGAAGGGCTTTGCATCACGAATTGTTATTCAGgtaattttga ... atgagtgcagCGTTATACAGAGGAAGAGAACTTACATGTACTGAAGTTCTGGAGAGAAGAC
EST: gi|15730155|gb|BI741703.1|BI741703
EST:     TTTGTCAGATTATGAAAAAGAAGGGCTTTGCATCACGAATTGTTATTCAG                         CGTTATACAGAGGAAGAGAACTTACATGTACTGAAGTTCTGGAGAGAAGAC
genomic: TTTGTCAGATTATGAAAAAGAAGGGCTTTGCATCACGAATTGTTATTCAGgtaattttga ... atgagtgcagCGTTATACAGAGGAAGAGAACTTACATGTACTGAAGTTCTGGAGAGAAGAC
EST: gi|37836037|gb|BJ594045.1|BJ594045
EST:     TTTGTCAGATTATGAAAAAGAAGGGCTTTGCATCACGAA--ATTATTCAG                         CGTTATACAGAGGAAGAGAACTTACATGTACTGAAGTTCTGGAGAGAAGAC
genomic: TTTGTCAGATTATGAAAAAGAAGGGCTTTGCATCACGAATTGTTATTCAGgtaattttga ... atgagtgcagCGTTATACAGAGGAAGAGAACTTACATGTACTGAAGTTCTGGAGAGAAGAC
EST: gi|37824564|gb|BJ582630.1|BJ582630
EST:     TTTGTCAGATTATGAAAAAGAAGGGCTTTGCATCACGAATTGTTATTCAG                         CGTTATACAGAGGAAGAGAACTTACATGTACTGAAGTTCTGGAGAGAAGAC
genomic: TTTGTCAGATTATGAAAAAGAAGGGCTTTGCATCACGAATTGTTATTCAGgtaattttga ... atgagtgcagCGTTATACAGAGGAAGAGAACTTACATGTACTGAAGTTCTGGAGAGAAGAC
EST: gi|162223987|gb|FC400345.1|FC400345
EST:     TTTGTCAGATTATGAAAAAGAAGGGCTTTGCATCACGAATTGTTATTCAG                         CGTTATACAGAGGAAGAGAACTTACATGTACTGAAGTTCTGGAGAGAAGAC
genomic: TTTGTCAGATTATGAAAAAGAAGGGCTTTGCATCACGAATTGTTATTCAGgtaattttga ... atgagtgcagCGTTATACAGAGGAAGAGAACTTACATGTACTGAAGTTCTGGAGAGAAGAC
EST: gi|67693877|gb|BJ954110.1|BJ954110
EST:     TTTGTCAGATTATGAAAAAGAAGGGCTTTGCATCACGAATTGTTATTCAG                         CGTTATACAGAGGAAGAGAACTTACATGTACTGAAGTTCTGGAGAGAAGAC
genomic: TTTGTCAGATTATGAAAAAGAAGGGCTTTGCATCACGAATTGTTATTCAGgtaattttga ... atgagtgcagCGTTATACAGAGGAAGAGAACTTACATGTACTGAAGTTCTGGAGAGAAGAC
EST: gi|37826909|gb|BJ584921.1|BJ584921
EST:     TTTGTCAGATTATGAAAAAGAAGGGCTTTGCATCACGAATTGTTATTCAG                         CGTTATACAGAGGAAGAGAACTTACATGTACTGAAGTTCTGGAGAGAAGAC
genomic: TTTGTCAGATTATGAAAAAGAAGGGCTTTGCATCACGAATTGTTATTCAGgtaattttga ... atgagtgcagCGTTATACAGAGGAAGAGAACTTACATGTACTGAAGTTCTGGAGAGAAGAC
EST: gi|67570593|gb|BJ943417.1|BJ943417
EST:     TTTGTCAGATTATGAAAAAGAAGGGCTTTGCATCACGAATTGTTATTCAG                         CGTTATACAGAGGAAGAGAACTTACATGTACTGAAGTTCTGGAGAGAAGAC
genomic: TTTGTCAGATTATGAAAAAGAAGGGCTTTGCATCACGAATTGTTATTCAGgtaattttga ... atgagtgcagCGTTATACAGAGGAAGAGAACTTACATGTACTGAAGTTCTGGAGAGAAGAC
EST: gi|37828120|gb|BJ586132.1|BJ586132
EST:     TTTGTCAGATTATGAAAAAGAAGGGCTTTGCATCACGAATTGTTATTCAG                         CGTTATACAGAGGAAGAGAACTTACATGTACTGAAGTTCTGGAGAGAAGAC
genomic: TTTGTCAGATTATGAAAAAGAAGGGCTTTGCATCACGAATTGTTATTCAGgtaattttga ... atgagtgcagCGTTATACAGAGGAAGAGAACTTACATGTACTGAAGTTCTGGAGAGAAGAC

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), 23 (downstream exon)
Score: 2

TAAGGGTTGGTTCTATATGGTTACCTTGACAGCAAACAATCCAAGCGAGATTTGTCAGATTATGAAAAAGAAGGGCTTTGCATCACGAATTGTTATTCAGgtaattttga ... atgagtgcagCGTTATACAGAGGAAGAGAACTTACATGTACTGAAGTTCTGGAGAGAAGACCTTGCTTTTGATTATGATTACAACGCCGAAACAGGGGGTGGTGGTACTA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TAAGGGTTGGTTCTATATGGTTACCTTGACAGCAAACAATCCAAGCGAGATTTGTCAGATTATGAAAAAGAAGGGCTTTGCATCACGAATTGTTATTCAGgtaattttgatggcatcctgacctactcgcagtacgggttggcccatattcttgtttctaaatatgaacagtgacgtaagataattgtgtgtgtgtgtgt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG