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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttggtcttgctatgtgtaagattgttttgtggaatgaaagtgaaactgctcttaatatataacatttgtctcgcttgtttgtgttggtcaaatgtgcagGTGGTTGAGAATATGAAAGCCTTACAAGTTGTTCCCAAGCTCACTCCTGAGGTGATGAAGAGAATTGATGAAGCAATCAACTTAAAGGCATCCAAGTAGC

Basic information

species Physcomitrella patens
transcript PP1S83_53V6.1
intron # 4
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|37842032|gb|BJ600040.1|BJ600040
EST:     AGAATCCCAATGTCAGTTCTGTTATCAGTGGAGCCACCAAACTAGATCAG                         GTGGTTGAGAATATGAAAGCCTTACAAGTTGTTCCCAAGCTCACTCCTGAG
genomic: AGAATCCCAATGTCAGTTCTGTTATCAGTGGAGCCACCAAACTAGATCAGgtacttttaa ... aaatgtgcagGTGGTTGAGAATATGAAAGCCTTACAAGTTGTTCCCAAGCTCACTCCTGAG
EST: gi|208380713|gb|DC919429.1|DC919429
EST:     AGAATCCCAATGTCAGTTCTGTTATCAGTGGAGCCACCAAACTAGATCAG                         GTGGTTGAGAATATGAAAGCCTTACAAGTTGTTCCCAAGCTCACTCCTGAG
genomic: AGAATCCCAATGTCAGTTCTGTTATCAGTGGAGCCACCAAACTAGATCAGgtacttttaa ... aaatgtgcagGTGGTTGAGAATATGAAAGCCTTACAAGTTGTTCCCAAGCTCACTCCTGAG
EST: gi|13251450|gb|BG362353.1|BG362353
EST:     AGAATCCCAATGTCAGTTCTGTTATCAGTGGAGCCACCAAACTAGATCAG                         GTGGGTGAGAATATGAAAGGCCTAACAAGTTGTTCCCAAGCTCACTCCTGA
genomic: AGAATCCCAATGTCAGTTCTGTTATCAGTGGAGCCACCAAACTAGATCAGgtacttttaa ... aaatgtgcagGTGGTTGAGAATATGAAAG-CCTTACAAGTTGTTCCCAAGCTCACTCCTGA
EST: gi|162207556|gb|FC384009.1|FC384009
EST:     AGAATCCCAATGTCAGTTCTGTTATCAGTGGAGCCACCAAACTAGATCAG                         GTGGTTGAGAATATGAAAGCCTTACAAGTTGTTCCCAAGCTCACTCCTGAG
genomic: AGAATCCCAATGTCAGTTCTGTTATCAGTGGAGCCACCAAACTAGATCAGgtacttttaa ... aaatgtgcagGTGGTTGAGAATATGAAAGCCTTACAAGTTGTTCCCAAGCTCACTCCTGAG
EST: gi|162236472|gb|FC412839.1|FC412839
EST:     AGAATCCCAATGTCAGTTCTGTTATCAGTGGAGCCACCAAACTAGATCAG                         GTGGTTGAGAATATGAAAGCCTTACAAGTTGTTCCCAAGCTCACTCCTGAG
genomic: AGAATCCCAATGTCAGTTCTGTTATCAGTGGAGCCACCAAACTAGATCAGgtacttttaa ... aaatgtgcagGTGGTTGAGAATATGAAAGCCTTACAAGTTGTTCCCAAGCTCACTCCTGAG
EST: gi|162260012|gb|FC435315.1|FC435315
EST:     AGAATCCCAATGTCAGTTCTGTTATCAGTGGAGCCACCAAACTAGATCAG                         GTGGTTGAGAATATGAAAGCCTTACAAGTTGTTCCCAAGCTCACTCCTGAG
genomic: AGAATCCCAATGTCAGTTCTGTTATCAGTGGAGCCACCAAACTAGATCAGgtacttttaa ... aaatgtgcagGTGGTTGAGAATATGAAAGCCTTACAAGTTGTTCCCAAGCTCACTCCTGAG
EST: gi|208371173|gb|DC955979.1|DC955979
EST:     AGAATCCCAATGTCAGTTCTGTTATCAGTGGAGCCACCAAACTAGATCAG                         GTGGTTGAGAATATGAAAGCCTTACAAGTTGTTCCCAAGCTCACTCCTGAG
genomic: AGAATCCCAATGTCAGTTCTGTTATCAGTGGAGCCACCAAACTAGATCAGgtacttttaa ... aaatgtgcagGTGGTTGAGAATATGAAAGCCTTACAAGTTGTTCCCAAGCTCACTCCTGAG
EST: gi|22131893|gb|BQ826862.1|BQ826862
EST:     AGAATCCCAATGTCAGTTCTGTTATCAGTGGAGCCACCAAACTAGATCAG                         GTGGTTGAGAATATGAAAGCCTTACAAGTTGTTCCCAAGCTCACTCCTGAG
genomic: AGAATCCCAATGTCAGTTCTGTTATCAGTGGAGCCACCAAACTAGATCAGgtacttttaa ... aaatgtgcagGTGGTTGAGAATATGAAAGCCTTACAAGTTGTTCCCAAGCTCACTCCTGAG
EST: gi|162207555|gb|FC384008.1|FC384008
EST:     AGAATCCCAATGTCAGTTCTGTTATCAGTGGAGCCACCAAACTAGATCAG                         GTGGTTGAGAATATGAAAGCCTTACAAGTTGTTCCCAAGCTCACTCCTGAG
genomic: AGAATCCCAATGTCAGTTCTGTTATCAGTGGAGCCACCAAACTAGATCAGgtacttttaa ... aaatgtgcagGTGGTTGAGAATATGAAAGCCTTACAAGTTGTTCCCAAGCTCACTCCTGAG
EST: gi|208395524|gb|DC928939.1|DC928939
EST:     AGAATCCCAATGTCAGTTCTGTTATCAGTGGAGCCACCAAACTAGATCAG                         GTGGTTGAGAATATGAAAGCCTTACAAGTTGTTCCCAAGCTCACTCCTGAG
genomic: AGAATCCCAATGTCAGTTCTGTTATCAGTGGAGCCACCAAACTAGATCAGgtacttttaa ... aaatgtgcagGTGGTTGAGAATATGAAAGCCTTACAAGTTGTTCCCAAGCTCACTCCTGAG
EST: gi|208346033|gb|DC921278.1|DC921278
EST:     AGAATCCCAATGTCAGTTCTGTTATCAGTGGAGCCACCAAACTAGATCAG                         GTGGTTGAGAATATGAAAGCCTTACAAGTTGTTCCCAAGCTCACTCCTGAG
genomic: AGAATCCCAATGTCAGTTCTGTTATCAGTGGAGCCACCAAACTAGATCAGgtacttttaa ... aaatgtgcagGTGGTTGAGAATATGAAAGCCTTACAAGTTGTTCCCAAGCTCACTCCTGAG
EST: gi|162248713|gb|FC424566.1|FC424566
EST:     AGAATCCCAATGTCAGTTCTGTTATCAGTGGAGCCACCAAACTAGATCAG                         GTGGTTGAGAATATGAAAGCCTTACAAGTTGTTCCCAAGCTCACTCCTGAG
genomic: AGAATCCCAATGTCAGTTCTGTTATCAGTGGAGCCACCAAACTAGATCAGgtacttttaa ... aaatgtgcagGTGGTTGAGAATATGAAAGCCTTACAAGTTGTTCCCAAGCTCACTCCTGAG
EST: gi|37840709|gb|BJ598717.1|BJ598717
EST:     AGAATCCCAATGTCAGTTCTGTTATCAGTGGAGCCACCAAACTAGATCAG                         GTGGTTGAGAATATGAAAGCCTTACAAGTTGTTCCCAAGCTCACTCCTGAG
genomic: AGAATCCCAATGTCAGTTCTGTTATCAGTGGAGCCACCAAACTAGATCAGgtacttttaa ... aaatgtgcagGTGGTTGAGAATATGAAAGCCTTACAAGTTGTTCCCAAGCTCACTCCTGAG
EST: gi|162272930|gb|FC448047.1|FC448047
EST:     AGAATCCCAATGTCAGTTCTGTTATCAGTGGAGCCACCAAACTAGATCAG                         GTGGTTGAGAATATGAAAGCCTTACAAGTTGTTCCCAAGCTCACTCCTGAG
genomic: AGAATCCCAATGTCAGTTCTGTTATCAGTGGAGCCACCAAACTAGATCAGgtacttttaa ... aaatgtgcagGTGGTTGAGAATATGAAAGCCTTACAAGTTGTTCCCAAGCTCACTCCTGAG
EST: gi|37845209|gb|BJ603217.1|BJ603217
EST:     AGAATCCCAATGTCAGTTCTGTTATCAGTGGAGCCACCAAACTAGATCAG                         GTGGTTGAGAATATGAAAGCCTTACAAGTTGTTCCCAAGCTCACTCCTGAG
genomic: AGAATCCCAATGTCAGTTCTGTTATCAGTGGAGCCACCAAACTAGATCAGgtacttttaa ... aaatgtgcagGTGGTTGAGAATATGAAAGCCTTACAAGTTGTTCCCAAGCTCACTCCTGAG
EST: gi|208367179|gb|DC947857.1|DC947857
EST:     AGAATCCCAATGTCAGTTCTGTTATCAGTGGAGCCACCAAACTAGATCAG                         GTGGTTGAGAATATGAAAGCCTTACAAGTTGTTCCCAAGCTCACTCCTGAG
genomic: AGAATCCCAATGTCAGTTCTGTTATCAGTGGAGCCACCAAACTAGATCAGgtacttttaa ... aaatgtgcagGTGGTTGAGAATATGAAAGCCTTACAAGTTGTTCCCAAGCTCACTCCTGAG
EST: gi|208366178|gb|DC955279.1|DC955279
EST:     AGAATCCCAATGTCAGTTCTGTTATCAGTGGAGCCACCAAACTAGATCAG                         GTGGTTGAGAATATGAAAGCCTTACAAGTTGTTCCCAAGCTCACTCCTGAG
genomic: AGAATCCCAATGTCAGTTCTGTTATCAGTGGAGCCACCAAACTAGATCAGgtacttttaa ... aaatgtgcagGTGGTTGAGAATATGAAAGCCTTACAAGTTGTTCCCAAGCTCACTCCTGAG
EST: gi|208370555|gb|DC951591.1|DC951591
EST:     AGAATCCCAATGTCAGTTCTGTTATCAGTGGAGCCACCAAACTAGATCAG                         GTGGTTGAGAATATGAAAGCCTTACAAGTTGTTCCCAAGCTCACTCCTGAG
genomic: AGAATCCCAATGTCAGTTCTGTTATCAGTGGAGCCACCAAACTAGATCAGgtacttttaa ... aaatgtgcagGTGGTTGAGAATATGAAAGCCTTACAAGTTGTTCCCAAGCTCACTCCTGAG
EST: gi|162236005|gb|FC412164.1|FC412164
EST:     AGAATCCCAATGTCAGTTCTGTTATCAGTGGAGCCACCAAACTAGATCAG                         GTGGTTGAGAATATGAAAGCCTTACAAGTTGTTCCCAAGCTCACTCCTGAG
genomic: AGAATCCCAATGTCAGTTCTGTTATCAGTGGAGCCACCAAACTAGATCAGgtacttttaa ... aaatgtgcagGTGGTTGAGAATATGAAAGCCTTACAAGTTGTTCCCAAGCTCACTCCTGAG
EST: gi|208355973|gb|DC946189.1|DC946189
EST:     AGAATCCCAATGTCAGTTCTGTTATCAGTGGAGCCACCAAACTAGATCAG                         GTGGTTGAGAATATGAAAGCCTTACAAGTTGTTCCCAAGCTCACTCCTGAG
genomic: AGAATCCCAATGTCAGTTCTGTTATCAGTGGAGCCACCAAACTAGATCAGgtacttttaa ... aaatgtgcagGTGGTTGAGAATATGAAAGCCTTACAAGTTGTTCCCAAGCTCACTCCTGAG

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: 32 (upstream exon), 22 (downstream exon)
Score: 3

CAAGGAGCTTGACGCTTCTTTAGCACAGTTGGCTCTAGCTTGGTGCGTCAAGAATCCCAATGTCAGTTCTGTTATCAGTGGAGCCACCAAACTAGATCAGgtacttttaa ... aaatgtgcagGTGGTTGAGAATATGAAAGCCTTACAAGTTGTTCCCAAGCTCACTCCTGAGGTGATGAAGAGAATTGATGAAGCAATCAACTTAAAGGCATCCAAGTAGC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

actgctcttaatatataacatttgtctcgcttgtttgtgttggtcaaatgtgcagGTGGTTGAGAATATGAAAGCCTTACAAGTTGTTCCCAAGCTCACTCCTGAGGTGATGAAGAGAATTGATGAAGCAATCAACTTAAAGGCATCCAAGTAGC
            atataac  putative branch site (score: 3)
     tcttaatatataacat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttggtcttgctatgtgtaagattgttttgtggaatgaaagtgaaactgctcttaatatataacatttgtctcgcttgtttgtgttggtcaaatgtgcagGTGGTTGAGAATATGAAAGCCTTACAAGTTGTTCCCAAGCTCACTCCTGAGGTGATGAAGAGAATTGATGAAGCAATCAACTTAAAGGCATCCAAGTAGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA