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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcagtctacttcgttaccatcttaagatctatattcgcttaatatgaacggtgtcgccaggatgaggtaatattacctttgttgatggaattcatgtttaacatggtgtgcagGCATTTAAAGCAAAATATAGACTTCCATTCACTTTGCTCAGTGACGACGGCAACAAGCTGCGCAAGGACTGGGGTGTGCCAAGTGACCTCTTCGGAGCCC

Basic information

species Physcomitrella patens
transcript PP1S95_45V6.1
intron # 2
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|67569415|gb|BJ942239.1|BJ942239
EST:     CAGGTGCTGAGGTTGTTGGAGTGAGTGGTGACACTCCCGAATCCCACAAG                         GCATTTAAAGCAAAATATAGACTTCCATTCACTTTGCTCAGTGACGACGGC
genomic: CAGGTGCTGAGGTTGTTGGAGTGAGTGGTGACACTCCCGAATCCCACAAGgtcagtctac ... tggtgtgcagGCATTTAAAGCAAAATATAGACTTCCATTCACTTTGCTCAGTGACGACGGC
EST: gi|208375116|gb|DC944855.1|DC944855
EST:     CAGGTGCTGAGGTTGTTGGAGTGAGTGGTGACACTCCCGAATCCCACAAG                         GCATTTAAAGCAAAATATAGACTTCCATTCACTTTGCTCAGTGACGACGGC
genomic: CAGGTGCTGAGGTTGTTGGAGTGAGTGGTGACACTCCCGAATCCCACAAGgtcagtctac ... tggtgtgcagGCATTTAAAGCAAAATATAGACTTCCATTCACTTTGCTCAGTGACGACGGC
EST: gi|208397835|gb|DC912030.1|DC912030
EST:     CAGGTGCTGAGGTTGTTGGAGTGAGTGGTGACACTCCCGAATCCCACAAG                         GCATTTAAAGCAAAATATAGACTTCCATTCACTTTGCTCAGTGACGACGGC
genomic: CAGGTGCTGAGGTTGTTGGAGTGAGTGGTGACACTCCCGAATCCCACAAGgtcagtctac ... tggtgtgcagGCATTTAAAGCAAAATATAGACTTCCATTCACTTTGCTCAGTGACGACGGC
EST: gi|162269655|gb|FC445588.1|FC445588
EST:     CAGGTGCTGAGGTTGTTGGAGTGAGTGGTGACACTCCCGAATCCCACAAG                         GCATTTAAAGCAAAATATAGACTTCCATTCACTTTGCTCAGTGACGACGGC
genomic: CAGGTGCTGAGGTTGTTGGAGTGAGTGGTGACACTCCCGAATCCCACAAGgtcagtctac ... tggtgtgcagGCATTTAAAGCAAAATATAGACTTCCATTCACTTTGCTCAGTGACGACGGC
EST: gi|162279906|gb|FC455190.1|FC455190
EST:     CAGGTGCTGAGGTTGTTGGAGTGAGTGGTGACACTCCCGAATCCCACAAG                         GCATTTAAAGCAAAATATAGACTTCCATTCACTTTGCTCAGTGACGACGGC
genomic: CAGGTGCTGAGGTTGTTGGAGTGAGTGGTGACACTCCCGAATCCCACAAGgtcagtctac ... tggtgtgcagGCATTTAAAGCAAAATATAGACTTCCATTCACTTTGCTCAGTGACGACGGC
EST: gi|162213415|gb|FC389092.1|FC389092
EST:     CAGGTGCTGAGGTTGTTGGAGTGAGTGGTGACACTCCCGAATCCCACAAG                         GCATTTAAAGCAAAATATAGACTTCCATTCACTTTGCTCAGTGACGACGGC
genomic: CAGGTGCTGAGGTTGTTGGAGTGAGTGGTGACACTCCCGAATCCCACAAGgtcagtctac ... tggtgtgcagGCATTTAAAGCAAAATATAGACTTCCATTCACTTTGCTCAGTGACGACGGC
EST: gi|208364380|gb|DC950681.1|DC950681
EST:     CAGGTGCTGAGGTTGTTGGAGTGAGTGGTGACACTCCCGAATCCCACAAG                         GCATTTAAAGCAAAATATAGACTTCCATTCACTTTGCTCAGTGACGACGGC
genomic: CAGGTGCTGAGGTTGTTGGAGTGAGTGGTGACACTCCCGAATCCCACAAGgtcagtctac ... tggtgtgcagGCATTTAAAGCAAAATATAGACTTCCATTCACTTTGCTCAGTGACGACGGC
EST: gi|19790520|gb|BQ041917.1|BQ041917
EST:     CAGGTGCTGAGGTTGTTGGAGTGAGTGGTGACACTCCCGAATCCCACAAG                         GCATTTAAAGCAAAATATAGACTTCCATTCACTTTG
genomic: CAGGTGCTGAGGTTGTTGGAGTGAGTGGTGACACTCCCGAATCCCACAAGgtcagtctac ... tggtgtgcagGCATTTAAAGCAAAATATAGACTTCCATTCACTTTG
EST: gi|208382790|gb|DC903834.1|DC903834
EST:     CAGGTGCTGAGGTTGTTGGAGTGAGTGGTGACACTCCCGAATCCCACAAG                         GCATTTAAAGCAAAATATAGACTTCCATTCACTTTGCTCAGTGACGACGGC
genomic: CAGGTGCTGAGGTTGTTGGAGTGAGTGGTGACACTCCCGAATCCCACAAGgtcagtctac ... tggtgtgcagGCATTTAAAGCAAAATATAGACTTCCATTCACTTTGCTCAGTGACGACGGC
EST: gi|208351001|gb|DC917732.1|DC917732
EST:     CAGGTGCTGAGGTTGTTGGAGTGAGTGGTGACACTCCCGAATCCCACAAG                         GCATTTAAAGCAAAATATAGACTTCCATTCACTTTGCTCAGTGACGACGGC
genomic: CAGGTGCTGAGGTTGTTGGAGTGAGTGGTGACACTCCCGAATCCCACAAGgtcagtctac ... tggtgtgcagGCATTTAAAGCAAAATATAGACTTCCATTCACTTTGCTCAGTGACGACGGC
EST: gi|208363733|gb|DC954704.1|DC954704
EST:     CAGGTGCTGAGGTTGTTGGAGTGAGTGGTGACACTCCCGAATCCCACAAG                         GCATTTAAAGCAAAATATAGACTTCCATTCACTTTGCTCAGTGACGACGGC
genomic: CAGGTGCTGAGGTTGTTGGAGTGAGTGGTGACACTCCCGAATCCCACAAGgtcagtctac ... tggtgtgcagGCATTTAAAGCAAAATATAGACTTCCATTCACTTTGCTCAGTGACGACGGC
EST: gi|162173048|gb|FC348660.1|FC348660
EST:     CAGGTGCTGAGGTTGTTGGAGTGAGTGGTGACACTCCCGAATCCCACAAG                         GCATTTAAAGCAAAATATAGACTTCCATTCACTTTGCTCAGTGACGACGGC
genomic: CAGGTGCTGAGGTTGTTGGAGTGAGTGGTGACACTCCCGAATCCCACAAGgtcagtctac ... tggtgtgcagGCATTTAAAGCAAAATATAGACTTCCATTCACTTTGCTCAGTGACGACGGC
EST: gi|162238382|gb|FC415898.1|FC415898
EST:     CAGGTGCTGAGGTTGTTGGAGTGAGTGGTGACACTCCCGAATCCCACAAG                         GCATTTAAAGCAAAATATAGACTTCCATTCACTTTGCTCAGTGACGACGGC
genomic: CAGGTGCTGAGGTTGTTGGAGTGAGTGGTGACACTCCCGAATCCCACAAGgtcagtctac ... tggtgtgcagGCATTTAAAGCAAAATATAGACTTCCATTCACTTTGCTCAGTGACGACGGC
EST: gi|208361271|gb|DC930324.1|DC930324
EST:     CAGGTGCTGAGGTTGTTGGAGTGAGTGGTGACACTCCCGAATCCCACAAG                         GCATTTAAAGCAAAATATAGACTTCCATTCACTTTGCTCAGTGACGACGGC
genomic: CAGGTGCTGAGGTTGTTGGAGTGAGTGGTGACACTCCCGAATCCCACAAGgtcagtctac ... tggtgtgcagGCATTTAAAGCAAAATATAGACTTCCATTCACTTTGCTCAGTGACGACGGC
EST: gi|162269654|gb|FC445587.1|FC445587
EST:     CAGGTGCTGAGGTTGTTGGAGTGAGTGGTGACACTCCCGAATCCCACAAG                         GCATTTAAAGCAAAATATAGACTTCCATTCACTTTGCTCAGTGACGACGGC
genomic: CAGGTGCTGAGGTTGTTGGAGTGAGTGGTGACACTCCCGAATCCCACAAGgtcagtctac ... tggtgtgcagGCATTTAAAGCAAAATATAGACTTCCATTCACTTTGCTCAGTGACGACGGC
EST: gi|208345604|gb|DC909288.1|DC909288
EST:     CAGGTGCTGAGGTTGTTGGAGTGAGTGGTGACACTCCCGAATCCCACAAG                         GCATTTAAAGCAAAATATAGACTTCCATTCACTTTGCTCAGTGACGACGGC
genomic: CAGGTGCTGAGGTTGTTGGAGTGAGTGGTGACACTCCCGAATCCCACAAGgtcagtctac ... tggtgtgcagGCATTTAAAGCAAAATATAGACTTCCATTCACTTTGCTCAGTGACGACGGC
EST: gi|100430029|gb|BY978211.1|BY978211
EST:     CAGGTGCTGAGGTTGTTGGAGTGAGTGGTGACACTCCCGAATCCCACAAG                         GCATTTAAAGCAAAATATAGACTTCCATTCACTTTGCTCAGTGACGACGGC
genomic: CAGGTGCTGAGGTTGTTGGAGTGAGTGGTGACACTCCCGAATCCCACAAGgtcagtctac ... tggtgtgcagGCATTTAAAGCAAAATATAGACTTCCATTCACTTTGCTCAGTGACGACGGC
EST: gi|208351999|gb|DC925808.1|DC925808
EST:     CAGGTGCTGAGGTTGTTGGAGTGAGTGGTGACACTCCCGAATCCCACAAG                         GCATTTAAAGCAAAATATAGACTTCCATTCACTTTGCTCAGTGACGACGGC
genomic: CAGGTGCTGAGGTTGTTGGAGTGAGTGGTGACACTCCCGAATCCCACAAGgtcagtctac ... tggtgtgcagGCATTTAAAGCAAAATATAGACTTCCATTCACTTTGCTCAGTGACGACGGC
EST: gi|19789802|gb|BQ041522.1|BQ041522
EST:     CAGGTGCTGAGGTTGTTGGAGTGAGTGGTGACACTCCCGAATCCCACAAG                         GCATTTAAAGCAAAATATAGACTTCCATTCACTTTGCTCAGTGACGACGGC
genomic: CAGGTGCTGAGGTTGTTGGAGTGAGTGGTGACACTCCCGAATCCCACAAGgtcagtctac ... tggtgtgcagGCATTTAAAGCAAAATATAGACTTCCATTCACTTTGCTCAGTGACGACGGC
EST: gi|162238381|gb|FC415897.1|FC415897
EST:     CAGGTGCTGAGGTTGTTGGAGTGAGTGGTGACACTCCCGAATCCCACAAG                         GCATTTAAAGCAAAATATAGACTTCCATTCACTTTGCTCAGTGACGACGGC
genomic: CAGGTGCTGAGGTTGTTGGAGTGAGTGGTGACACTCCCGAATCCCACAAGgtcagtctac ... tggtgtgcagGCATTTAAAGCAAAATATAGACTTCCATTCACTTTGCTCAGTGACGACGGC
EST: gi|208364092|gb|DC947252.1|DC947252
EST:     CAGGTGCTGAGGTTGTTGGAGTGAGTGGTGACACTCCCGAATCCCACAAG                         GCATTTAAAGCAAAATATAGACTTCCATTCACTTTGCTCAGTGACGACGGC
genomic: CAGGTGCTGAGGTTGTTGGAGTGAGTGGTGACACTCCCGAATCCCACAAGgtcagtctac ... tggtgtgcagGCATTTAAAGCAAAATATAGACTTCCATTCACTTTGCTCAGTGACGACGGC
EST: gi|67692676|gb|BJ952909.1|BJ952909
EST:     CAGGTGCTGAGGTTGTTGGAGTGAGTGGTGACACTCCCGAATCCCACAAG                         GCATTTAAAGCAAAATATAGACTTCCATTCACTTTGCTCAGTGACGACGGC
genomic: CAGGTGCTGAGGTTGTTGGAGTGAGTGGTGACACTCCCGAATCCCACAAGgtcagtctac ... tggtgtgcagGCATTTAAAGCAAAATATAGACTTCCATTCACTTTGCTCAGTGACGACGGC
EST: gi|162173047|gb|FC348659.1|FC348659
EST:     CAGGTGCTGAGGTTGTTGGAGTGAGTGGTGACACTCCCGAATCCCACAAG                         GCATTTAAAGCAAAATATAGACTTCCATTCACTTTGCTCAGTGACGACGGC
genomic: CAGGTGCTGAGGTTGTTGGAGTGAGTGGTGACACTCCCGAATCCCACAAGgtcagtctac ... tggtgtgcagGCATTTAAAGCAAAATATAGACTTCCATTCACTTTGCTCAGTGACGACGGC
EST: gi|208381565|gb|DC923151.1|DC923151
EST:     CAGGTGCTGAGGTTGTTGGAGTGAGTGGTGACACTCCCGAATCCCACAAG                         GCATTTAAAGCAAAATATAGACTTCCATTCACTTTGCTCAGTGACGACGGC
genomic: CAGGTGCTGAGGTTGTTGGAGTGAGTGGTGACACTCCCGAATCCCACAAGgtcagtctac ... tggtgtgcagGCATTTAAAGCAAAATATAGACTTCCATTCACTTTGCTCAGTGACGACGGC
EST: gi|208391468|gb|DC937616.1|DC937616
EST:     CAGGTGCTGAGGTTGTTGGAGTGAGTGGTGACACTCCCGAATCCCACAAG                         GCATTTAAAGCAAAATATAGACTTCCATTCACTTTGCTCAGTGACGACGGC
genomic: CAGGTGCTGAGGTTGTTGGAGTGAGTGGTGACACTCCCGAATCCCACAAGgtcagtctac ... tggtgtgcagGCATTTAAAGCAAAATATAGACTTCCATTCACTTTGCTCAGTGACGACGGC
EST: gi|208387358|gb|DC933109.1|DC933109
EST:     CAGGTGCTGAGGTTGTTGGAGTGAGTGGTGACACTCCCGAATCCCACAAG                         GCATTTAAAGCAAAATATAGACTTCCATTCACTTTGCTCAGTGACGACGGC
genomic: CAGGTGCTGAGGTTGTTGGAGTGAGTGGTGACACTCCCGAATCCCACAAGgtcagtctac ... tggtgtgcagGCATTTAAAGCAAAATATAGACTTCCATTCACTTTGCTCAGTGACGACGGC
EST: gi|15261396|gb|BI436706.1|BI436706
EST:     CAGGTGCTGAGGTTGTTGGAGTGAGTGGTGACACTCCCGAATCCCACAAG                         GCATTTAAAGCAAAATATAGACTTCCATTCACTTTGCTCAGTGACGACGGC
genomic: CAGGTGCTGAGGTTGTTGGAGTGAGTGGTGACACTCCCGAATCCCACAAGgtcagtctac ... tggtgtgcagGCATTTAAAGCAAAATATAGACTTCCATTCACTTTGCTCAGTGACGACGGC

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: 35 (upstream exon), 34 (downstream exon)
Score: 17

CACCAGGCAGGCATGTTCATTTCGCGACTCGTACGAAAAGTTCAAGAAGGCAGGTGCTGAGGTTGTTGGAGTGAGTGGTGACACTCCCGAATCCCACAAGgtcagtctac ... tggtgtgcagGCATTTAAAGCAAAATATAGACTTCCATTCACTTTGCTCAGTGACGACGGCAACAAGCTGCGCAAGGACTGGGGTGTGCCAAGTGACCTCTTCGGAGCCC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aggatgaggtaatattacctttgttgatggaattcatgtttaacatggtgtgcagGCATTTAAAGCAAAATATAGACTTCCATTCACTTTGCTCAGTGACGACGGCAACAAGCTGCGCAAGGACTGGGGTGTGCCAAGTGACCTCTTCGGAGCCC
                                     gtttaac  putative branch site (score: 17)
         taatatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcagtctacttcgttaccatcttaagatctatattcgcttaatatgaacggtgtcgccaggatgaggtaatattacctttgttgatggaattcatgtttaacatggtgtgcagGCATTTAAAGCAAAATATAGACTTCCATTCACTTTGCTCAGTGACGACGGCAACAAGCTGCGCAAGGACTGGGGTGTGCCAAGTGACCTCTTCGGAGCCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC