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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aacgggcatcgaggctttgtactgttgcgaaggatgagtcggtagacagagggtttagggttctgatgattggatcatgacattgcgattctggatgcagGTTTCTACACCTTTGATAAAGAATGTTCTGCTTCTAGATTCGGAAGGGAAGCGCGTAGCTGTTAAGTATTACTCGGATGACTGGCCTAAGCTTGCTGATA

Basic information

species Physcomitrella patens
transcript PP1S8_105V6.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S8_105V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GLYMA08G20370.1 (Glycine max), 3'ss of exon 1
--------aacgggcatcgaggctttg-tactgttgcgaaggatgagtcggtagacagagggtttagggttctgatgattggatcatgacattgcgattctggatgcagGTTTCTACACCTTTGATAAAGAATGTTCTGCTTCTAGATTCGGAAGGGAAGCGCGTAGCTGTTAAGTATTACTCGGATGACTGGCCTAAGCTTGCTGATA
         | ||      ||  | || || |  ||| | | ||  || | ||   | || | |      | | | || | |    | | ||||  |  ||   || ||| ||     |||| |||||| ||| |||| ||| | || || ||||||||||| || || || ||||||||||| ||||||||||| |       ||  |
tttgctttcatggaggagaagcttgtgatatttgtgcaaggtattggt-gataagtacagtgctc----ctttaacgacttgcgtct-atattgttacact---tgtagGGTTTGTGTCCTTCGATAAAAAATATTCTTCTTTTGGACTCTGAAGGGAAGCGTGTGGCAGTCAAGTATTACTCAGATGACTGGCCAACAAACAATGCAA

upper sequence: PP1S8_105V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GLYMA08G20370.3 (Glycine max), 3'ss of exon 1
aacgggcatcgaggctttgtactgttgcgaaggatgagtcggtagacagagggtttagggttctgatgattggatcatgacattgcgattctggatgcagGTTTCTACACCTTTGATAAAGAATGTTCTGCTTCTAGATTCGGAAGGGAAGCGCGTAGCTGTTAAGTATTACTCGGATGACTGGCCTAAGCTTGCTGATA----------------------------------------------
                               | ||  || | ||   | || | |      | | | || | |    | | ||||  |  ||   || ||| ||     |||| |||||| ||| |||| ||| | || || ||||||||||| || || || ||||||||||| ||||||||||| |       ||  |                                              
-------------------------------gtattggt-gataagtacagtgctc----ctttaacgacttgcgtct-atattgttacact---tgtagggtttgtgtccttcgataaaaaatattcttcttttggactctgaagGGAAGCGTGTGGCAGTCAAGTATTACTCAGATGACTGGCCAACAAACAATGCAAAGTTAGCTTTTGAGAAGTTTGTATTTACTAAGACTGTTAAGACAAA

upper sequence: PP1S8_105V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GLYMA07G01000.1 (Glycine max), 3'ss of exon 1
--------aacgggcatcgaggctttg-tactgttgcgaaggatgagtcggtagacagagggtttagggttctgatgattggatcatgacattgcgattctggatgcagGTTTCTACACCTTTGATAAAGAATGTTCTGCTTCTAGATTCGGAAGGGAAGCGCGTAGCTGTTAAGTATTACTCGGATGACTGGCCTAAGCTTGCTGATA
         | ||      ||  | || || |  ||| | | ||  || | || | | || | |      | | |  | | |    || |  ||   || ||  || ||| ||     |||| |||||| ||| |||| ||| | || || ||||||||||| || || || ||||||||||| ||||||||||| |       ||  |
tttgctttcatggaggagaagcttctgatatttgtgcaaggtattggt-gataaatacagtgctc----ctttaacaacttg----tgtctatgttgttatgcctgtagGGTTTGTGTCCTTCGATAAAAAATATTCTTCTTTTGGACTCTGAAGGGAAGCGTGTGGCAGTCAAGTATTACTCAGATGACTGGCCAACAAACAATGCAA

upper sequence: PP1S8_105V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: AT3G09800.1 (Arabidopsis thaliana), 3'ss of exon 2
-------------------------------aacgggcatcgaggctttgtac-tgttgcgaaggatgagtcggtagacagagggtttagggttctgatg-attggatcat-------gacattgcgattctggatg--cagGTTTCTACACCTTTGATAAAGAATGTTCTGCTTCTAGATTCGGAAGGGAAGCGCGTAGCTGTTAAGTATTACTCGGATGACTGGCCTAAGCTTGCTGATA
                                     |    ||  | |||   ||||||            | |    ||  | ||||   || |  || | |||| | |       ||| || | ||      ||   ||| ||||   |||||| |||||||  |||| |||||||| || ||||| ||||| || ||||| ||||||||||||||||||||||| |    ||| |  |
gtaagtacatatgcattatatgattgtatttcgtattctgttagaatgtgtgtatgttgccgcaatcatacagctttgtaggagttttactctttttttggactggaacttaattactgactttccaatgtacattgaatagGATTCTTGTCCTTTGGTAAAGAAGATTCTTCTTCTAGACTCTGAAGGAAAGCGTGTGGCTGTCAAGTATTACTCGGATGACTGGCCAACTAATGCCGCCA

upper sequence: PP1S8_105V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: AT1G60970.1 (Arabidopsis thaliana), 3'ss of exon 1
--aacgggcatcgaggctttgtactgttgcgaaggatgagtcggtagacagagggtttagggttctgatgattggatcatgacattgcgattctgg-atgcagGTTTCTACACCTTTGATAAAGAATGTTCTGCTTCTAGATTCGGAAGGGAAGCGCGTAGCTGTTAAGTATTACTCGGATGACTGGCCTAAGCTTGCTGATA
  |  |  ||  ||  | | || ||||| |      ||  | |  |     |   | |     |||  | |||  ||  ||   || |  | ||   ||  |||  |   | ||     | || ||  |  ||||| | ||||| ||||| ||||| ||||| |||||||||||||| ||||||||||| |    | | | | 
ttactgttcactgattcat-gttctgttacatcttttggttggtgattttcaatatctcttaatct--ttattctattctgtgttttcattacttacatttagGAATTGCCCCCAAAAGTGAAAAACATCTTGCTTTTGGATTCTGAAGGAAAGCGTGTAGCGGTTAAGTATTACTCAGATGACTGGCCAACAAATTCAGCTC

upper sequence: PP1S8_105V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: AT4G08520.1 (Arabidopsis thaliana), 3'ss of exon 2
aacgggcatcgaggctttgt-actgttgcgaaggatgagtcggtagacagagggtttagggttctgatgattggatcatgacattgcgattctggatg--cagGTTTCTACACCTTTGATAAAGAATGTTCTGCTTCTAGATTCGGAAGGGAAGCGCGTAGCTGTTAAGTATTACTCGGATGACTGGCCTAAGCTTGCTGATA
   |    || |   |   | |    |   ||||||       |   |    | ||     |  |  |  ||  ||  ||||  |  | |     |||   ||| ||||   |||||| |||||||  |||| |||||||| || ||||| ||||| || ||||| ||||||||||| ||||| ||| | |    ||||   |
---gaagttcaaacttacatgatccattttaaggattctcgcttctgcttgtgcttctctctcttagtacttacatgctgactatctggtctacaatgaatagGATTCTTGTCCTTTGGTAAAGAACATTCTTCTTCTAGACTCTGAAGGAAAGCGTGTGGCTGTCAAGTATTACTCCGATGATTGGGCAACTAATGCTTCCA

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|18348987|gb|BJ181036.1|BJ181036
EST:     TTGAAAGCGAGGTGTTGAAGGAGCTGCGGATCGACGCTATTAAAATGGAT                         GTTTCTACACCTTTGATAAAGAATGTTCTGCTTCTAGATTCGGAAGGGAAG
genomic: TTGAAAGCGAGGTGTTGAAGGAGCTGCGGATCGACGCTATTAAAATGGATgtgagtgttt ... ctggatgcagGTTTCTACACCTTTGATAAAGAATGTTCTGCTTCTAGATTCGGAAGGGAAG
EST: gi|19790513|gb|BQ041913.1|BQ041913
EST:     TTGAAAGCGAGGTGTTGAAGGAGCTGCGGATCGACGCTATTAAAATGGAT                         GTTTCTACACCTTTGATAAAGAATGTTCTGCTTCTAGATTCGGAAGGGAAG
genomic: TTGAAAGCGAGGTGTTGAAGGAGCTGCGGATCGACGCTATTAAAATGGATgtgagtgttt ... ctggatgcagGTTTCTACACCTTTGATAAAGAATGTTCTGCTTCTAGATTCGGAAGGGAAG
EST: gi|208382534|gb|DC919758.1|DC919758
EST:     TTGAAAGCGAGGTGTTGAAGGAGCTGCGGATCGACGCTATTAAAATGGAT                         GTTTCTACACCTTTGATAAAGAATGTTCTGCTTCTAGATTCGGAAGGGAAG
genomic: TTGAAAGCGAGGTGTTGAAGGAGCTGCGGATCGACGCTATTAAAATGGATgtgagtgttt ... ctggatgcagGTTTCTACACCTTTGATAAAGAATGTTCTGCTTCTAGATTCGGAAGGGAAG
EST: gi|162221832|gb|FC398399.1|FC398399
EST:     TTGAAAGCGAGGTGTTGAAGGAGCTGCGGATCGACGCTATTAAAATGGAT                         GTTTCTACACCTTTGATAAAGAATGTTCTGCTTCTAGATTCGGAAGGGAAG
genomic: TTGAAAGCGAGGTGTTGAAGGAGCTGCGGATCGACGCTATTAAAATGGATgtgagtgttt ... ctggatgcagGTTTCTACACCTTTGATAAAGAATGTTCTGCTTCTAGATTCGGAAGGGAAG
EST: gi|22491811|gb|BU051734.1|BU051734
EST:     TTGAAAGCGAGGTGTTGAAGGAGCTGCGGATCGACGCTATTAAAATGGAT                         GTTTCTACACCTTTGATAAAGAATGTTCTGCTTCTAGATTCGGAAGGGAAG
genomic: TTGAAAGCGAGGTGTTGAAGGAGCTGCGGATCGACGCTATTAAAATGGATgtgagtgttt ... ctggatgcagGTTTCTACACCTTTGATAAAGAATGTTCTGCTTCTAGATTCGGAAGGGAAG
EST: gi|18339333|gb|BJ171360.1|BJ171360
EST:     ATCGACGCTATTAAAATGGAT                         GTTTCTACACCTTTGATAAAGAATGTTCTGCTTCTAGATTCGGAAGGGAAG
genomic: ATCGACGCTATTAAAATGGATgtgagtgttt ... ctggatgcagGTTTCTACACCTTTGATAAAGAATGTTCTGCTTCTAGATTCGGAAGGGAAG
EST: gi|162222858|gb|FC399320.1|FC399320
EST:     TGAAAGCGAGGTG-TGAAAGGAGCTGCGGATCGACGCTATTAAAATGGAT                         GTTTCTACACCTTTGATAAAGAATGTTCTGCTTCTAGATTCGGAAGGGAAG
genomic: TGAAAGCGAGGTGTTG-AAGGAGCTGCGGATCGACGCTATTAAAATGGATgtgagtgttt ... ctggatgcagGTTTCTACACCTTTGATAAAGAATGTTCTGCTTCTAGATTCGGAAGGGAAG
EST: gi|208348631|gb|DC905868.1|DC905868
EST:     TTGAAAGCGAGGTGTTGAAGGAGCTGCGGATCGACGCTATTAAAATGGAT                         GTTTCTACACCTTTGATAAAGAATGTTCTGCTTCTAGATTCGGAAGGGAAG
genomic: TTGAAAGCGAGGTGTTGAAGGAGCTGCGGATCGACGCTATTAAAATGGATgtgagtgttt ... ctggatgcagGTTTCTACACCTTTGATAAAGAATGTTCTGCTTCTAGATTCGGAAGGGAAG
EST: gi|162221833|gb|FC398400.1|FC398400
EST:     TTGAAAGCGAGGTGTTGAAGGAGCTGCGGATCGACGCTATTAAAATGGAT                         GTTTCTACACCTTTGATAAAGAATGTTCTGCTTCTAGATTCGGAAGGGAAG
genomic: TTGAAAGCGAGGTGTTGAAGGAGCTGCGGATCGACGCTATTAAAATGGATgtgagtgttt ... ctggatgcagGTTTCTACACCTTTGATAAAGAATGTTCTGCTTCTAGATTCGGAAGGGAAG
EST: gi|18363484|gb|BJ195556.1|BJ195556
EST:     TTGAAAGCGAGGTGTTGAAGGAGCTGCGGATCGACGCTATTAAAATGGAT                         GTTTCTACACCTTTGATAAAGAATGTTCTGCTTCTAGATTCGGAAGGGAAG
genomic: TTGAAAGCGAGGTGTTGAAGGAGCTGCGGATCGACGCTATTAAAATGGATgtgagtgttt ... ctggatgcagGTTTCTACACCTTTGATAAAGAATGTTCTGCTTCTAGATTCGGAAGGGAAG
EST: gi|22492703|gb|BU052626.1|BU052626
EST:     TTGAAAGCGAGGTGTTGAAGGAGCTGCGGATCGACGCTATTAAAATGGAT                         GTTTCTACACCTTTGATAAAGAATGTTCTGCTTCTAGATTCGGAAGGGAAG
genomic: TTGAAAGCGAGGTGTTGAAGGAGCTGCGGATCGACGCTATTAAAATGGATgtgagtgttt ... ctggatgcagGTTTCTACACCTTTGATAAAGAATGTTCTGCTTCTAGATTCGGAAGGGAAG
EST: gi|162222859|gb|FC399321.1|FC399321
EST:     TTGAAAGCGAGGTGTTGAAGGAGCTGCGGATCGACGCTATTAAAATGGAT                         GTTTCTACACCTTTGATAAAGAATGTTCTGCTTCTAGATTCGGAAGGGAAG
genomic: TTGAAAGCGAGGTGTTGAAGGAGCTGCGGATCGACGCTATTAAAATGGATgtgagtgttt ... ctggatgcagGTTTCTACACCTTTGATAAAGAATGTTCTGCTTCTAGATTCGGAAGGGAAG
EST: gi|7286949|gb|AW599436.1|AW599436
EST:     TTGAAAGCGAGGTGTTGAAGGAGCTGCGGATCGACGCTATTAAAATGGAT                         GTTTCTACACCTTTGATAAAGAATGTTCTGCTTCTAGATTCGGAAGGGAAG
genomic: TTGAAAGCGAGGTGTTGAAGGAGCTGCGGATCGACGCTATTAAAATGGATgtgagtgttt ... ctggatgcagGTTTCTACACCTTTGATAAAGAATGTTCTGCTTCTAGATTCGGAAGGGAAG
EST: gi|67507871|gb|BJ940747.1|BJ940747
EST:     TTGAAAGCGAGGTGTTGAAGGAGCTGCGGATCGACGCTATTAAAATGGAT                         GTTTCTACACCTTTGATAAAGAATGTTCTGCTTCTAGATTCGGAAGGGAAG
genomic: TTGAAAGCGAGGTGTTGAAGGAGCTGCGGATCGACGCTATTAAAATGGATgtgagtgttt ... ctggatgcagGTTTCTACACCTTTGATAAAGAATGTTCTGCTTCTAGATTCGGAAGGGAAG
EST: gi|37835955|gb|BJ593967.1|BJ593967
EST:     TTGAAAGCGAGGTGTTGAAGGAGCTGCGGATCGACGCTATTAAAATGGAT                         GTTTCTACACCTTTGATAAAGAATGTTCTGCTTCTAGATTCGGAAGGGAAG
genomic: TTGAAAGCGAGGTGTTGAAGGAGCTGCGGATCGACGCTATTAAAATGGATgtgagtgttt ... ctggatgcagGTTTCTACACCTTTGATAAAGAATGTTCTGCTTCTAGATTCGGAAGGGAAG

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), 33 (downstream exon)
Score: 7

CGCAAGTCCCCCGGAAAGTGGGTCTGGGTTAGATCTGGTGGAAGCCGCATTTGAAAGCGAGGTGTTGAAGGAGCTGCGGATCGACGCTATTAAAATGGATgtgagtgttt ... ctggatgcagGTTTCTACACCTTTGATAAAGAATGTTCTGCTTCTAGATTCGGAAGGGAAGCGCGTAGCTGTTAAGTATTACTCGGATGACTGGCCTAAGCTTGCTGATA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acagagggtttagggttctgatgattggatcatgacattgcgattctggatgcagGTTTCTACACCTTTGATAAAGAATGTTCTGCTTCTAGATTCGGAAGGGAAGCGCGTAGCTGTTAAGTATTACTCGGATGACTGGCCTAAGCTTGCTGATA
               ttctgat  putative branch site (score: 7)
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aacgggcatcgaggctttgtactgttgcgaaggatgagtcggtagacagagggtttagggttctgatgattggatcatgacattgcgattctggatgcagGTTTCTACACCTTTGATAAAGAATGTTCTGCTTCTAGATTCGGAAGGGAAGCGCGTAGCTGTTAAGTATTACTCGGATGACTGGCCTAAGCTTGCTGATA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT