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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gaagcatgccttcgctctttcattgtctagtgccaagcgtgaaatctgtgatatcctctgtatagttgaaatcctggtcttctttgtttggtgatgacagGGTTGGAAAGACTTCTTTGATGAATCAGTATGTTAATAAGAAATTCAGCAATCAATATAAGGCCACTATTGGGGCAGACTTTCTAACTAAGGAAGTGCAG

Basic information

species Physcomitrella patens
transcript PP1S61_279V6.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S61_279V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: AT3G18820.1 (Arabidopsis thaliana), 3'ss of exon 1
---gaagcatgccttcgctctttcattgtctagtgccaagcgtgaaatctgtgatatcctctgtatagttgaaatcctggtcttctttgtttggtgatg--acagGGTTGGAAAGACTTCTTTGATGAATCAGTATGTTAATAAGAAATTCAGCAATCAATATAAGGCCACTATTGGGGCAGACTTTCTAACTAAGGAAGTGCAG
   ||||||     |     ||   || | |  || | | | ||||||  |||   |    ||  |      |||  ||  ||||| ||  | ||| |     ||||| ||||| || |||||||||||||||||||||||||| || |||||||| || || ||||| || ||||| || |||||  | || |||||||| |||
cctgaagcagaaaatg---tttgtgttatgtcatgacta-catgaaattggtgtctttacttgagtgaaactaattttga-cttctctgacttgtggttttgtagGGTGGGAAAAACCTCTTTGATGAATCAGTATGTTAATAAAAAGTTCAGCAACCAGTACAAGGCAACCATTGGAGCCGACTTCTTGACCAAGGAAGTACAG

upper sequence: PP1S61_279V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: AT1G49300.1 (Arabidopsis thaliana), 3'ss of exon 2
-----------------------------gaagcatgccttcgctctttcattgtctagtgccaagcgtga----aatctgtgatatcctctgtatagttgaaatcctggtcttcttt---gtttggtgatgacagGGTTG-GAAAGACTTCTTTGATGAATC----AGTATGTTAATAAGAAATTCAGCAATCAATATAAGGCCACTATTGGGGCAGACTTTCTAACTAAGGAAGTGCAG---------------------------
                               || ||||     |  | |  ||    |     |   ||||    | ||| || | ||   | |||   | | |  ||   ||| | |   ||| | |||      | ||  |    ||||     |     |      |||||||||||||| |||||||| || |||||||| ||||||||||| || ||  | ||||||||||| ||                            
gtatcctaaattttctgtgcatggagtcaagaggatgctactacaatgtttttaaaaaaaaatatatgtgaataaattctttggtctctgttttatgagtaacaatctttccttttgtcgagttagatgagtttgtgtttctgtttcactttaacaacacgcctttagATATGTTAATAAGAAGTTCAGCAACCAGTATAAGGCAACTATTGGGGCTGATTTCTTGACTAAGGAAGTTCAATTTGAAGACCGGCTTTTCACTTTACAG
















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|100359334|gb|BY965696.1|BY965696
EST:     TCGGCCCGCAAGAGGACGTTGTTGAAAGTTATCATCCTCGGTGATAGCGG                         GGTTGGAAAGACTTCTTTGATGAATCAGTATGTTAATAAGAAATTCAGCAA
genomic: TCGGCCCGCAAGAGGACGTTGTTGAAAGTTATCATCCTCGGTGATAGCGGgtatggtagt ... gtgatgacagGGTTGGAAAGACTTCTTTGATGAATCAGTATGTTAATAAGAAATTCAGCAA
EST: gi|100404323|gb|BY973519.1|BY973519
EST:     TCGGCCCGCAAGAGGACGTTGTTGAAAGTTATCATCCTCGGTGATAGCGG                         GGTTGGAAAGACTTCTTTGATGAATCAGTATGTTAATAAGAAATTCAGCAA
genomic: TCGGCCCGCAAGAGGACGTTGTTGAAAGTTATCATCCTCGGTGATAGCGGgtatggtagt ... gtgatgacagGGTTGGAAAGACTTCTTTGATGAATCAGTATGTTAATAAGAAATTCAGCAA
EST: gi|100411870|gb|BY992381.1|BY992381
EST:     TCGGCCCGCAAGAGGACGTTGTTGAAAGTTATCATCCTCGGTGATAGCGG                         GGTTGGAAAGACTTCTTTGATGAATCAGTATGTTAATAAGAAATTCAGCAA
genomic: TCGGCCCGCAAGAGGACGTTGTTGAAAGTTATCATCCTCGGTGATAGCGGgtatggtagt ... gtgatgacagGGTTGGAAAGACTTCTTTGATGAATCAGTATGTTAATAAGAAATTCAGCAA
EST: gi|100355333|gb|BY945882.1|BY945882
EST:     TCGGCCCGCAAGAGGACGTTGTTGAAAGTTATCATCCTCGGTGATAGCGG                         GGTTGGAAAGACTTCTTTGATGAATCAGTATGTTAATAAGAAATTCAGCAA
genomic: TCGGCCCGCAAGAGGACGTTGTTGAAAGTTATCATCCTCGGTGATAGCGGgtatggtagt ... gtgatgacagGGTTGGAAAGACTTCTTTGATGAATCAGTATGTTAATAAGAAATTCAGCAA
EST: gi|100442547|gb|BY963241.1|BY963241
EST:     TCGGCCCGCAAGAGGACGTTGTTGAAAGTTATCATCCTCGGTGATAGCGG                         GGTTGGAAAGACTTCTTTGATGAATCAGTATGTTAATAAGAAATTCAGCAA
genomic: TCGGCCCGCAAGAGGACGTTGTTGAAAGTTATCATCCTCGGTGATAGCGGgtatggtagt ... gtgatgacagGGTTGGAAAGACTTCTTTGATGAATCAGTATGTTAATAAGAAATTCAGCAA
EST: gi|100385743|gb|BY987808.1|BY987808
EST:     TCGGCCCGCAAGAGGACGTTGTTGAAAGTTATCATCCTCGGTGATAGCGG                         GGTTGGAAAGACTTCTTTGATGAATCAGTATGTTAATAAGAAATTCAGCAA
genomic: TCGGCCCGCAAGAGGACGTTGTTGAAAGTTATCATCCTCGGTGATAGCGGgtatggtagt ... gtgatgacagGGTTGGAAAGACTTCTTTGATGAATCAGTATGTTAATAAGAAATTCAGCAA
EST: gi|100392311|gb|BY953300.1|BY953300
EST:     TCGGCCCGCAAGAGGACGTTGTTGAAAGTTATCATCCTCGGTGATAGCGG                         GGTTGGAAAGACTTCTTTGATGAATCAGTATGTTAATAAGAAATTCAGCAA
genomic: TCGGCCCGCAAGAGGACGTTGTTGAAAGTTATCATCCTCGGTGATAGCGGgtatggtagt ... gtgatgacagGGTTGGAAAGACTTCTTTGATGAATCAGTATGTTAATAAGAAATTCAGCAA
EST: gi|100398316|gb|BY972543.1|BY972543
EST:     TCGGCCCGCAAGAGGACGTTGTTGAAAGTTATCACCCTCGGTGATAGCGG                         GGTTGGAAAGACTTCTTTGATGAATCAGTATGTTAATAAGAAATTCAGCAA
genomic: TCGGCCCGCAAGAGGACGTTGTTGAAAGTTATCATCCTCGGTGATAGCGGgtatggtagt ... gtgatgacagGGTTGGAAAGACTTCTTTGATGAATCAGTATGTTAATAAGAAATTCAGCAA
EST: gi|100444782|gb|BY982611.1|BY982611
EST:     TCGGCCCGCAAGAGGACGTTGTTGAAAGTTATCATCCTCGGTGATAGCGG                         GGTTGGAAAGACTTCTTTGATGAATCAGTATGTTAATAAGAAATTCAGCAA
genomic: TCGGCCCGCAAGAGGACGTTGTTGAAAGTTATCATCCTCGGTGATAGCGGgtatggtagt ... gtgatgacagGGTTGGAAAGACTTCTTTGATGAATCAGTATGTTAATAAGAAATTCAGCAA
EST: gi|162262619|gb|FC438440.1|FC438440
EST:     TCGGCCCGCAAGAGGACGTTGTTGAAAGTTATCATCCTCGGTGATAGCGG                         GGTTGGAAAGACTTCTTTGATGAATCAGTATGTTAATAAGAAATTCAGCAA
genomic: TCGGCCCGCAAGAGGACGTTGTTGAAAGTTATCATCCTCGGTGATAGCGGgtatggtagt ... gtgatgacagGGTTGGAAAGACTTCTTTGATGAATCAGTATGTTAATAAGAAATTCAGCAA
EST: gi|100443167|gb|BY981793.1|BY981793
EST:     TCGGCCCGCAAGAGGACGTTGTTGAAAGTTATCATCCTCGGTGATAGCGG                         GGTTGGAAAGACTTCTTTGATGAATCAGTATGTTAATAAGAAATTCAGCAA
genomic: TCGGCCCGCAAGAGGACGTTGTTGAAAGTTATCATCCTCGGTGATAGCGGgtatggtagt ... gtgatgacagGGTTGGAAAGACTTCTTTGATGAATCAGTATGTTAATAAGAAATTCAGCAA
EST: gi|100442275|gb|BY981299.1|BY981299
EST:     TCGGCCCGCAAGAGGACGTTGTTGAAAGTTATCATCCTCGGTGATAGCGG                         GGTTGGAAAGACTTCTTTGATGAATCAGTATGTTAATAAGAAATTCAGCAA
genomic: TCGGCCCGCAAGAGGACGTTGTTGAAAGTTATCATCCTCGGTGATAGCGGgtatggtagt ... gtgatgacagGGTTGGAAAGACTTCTTTGATGAATCAGTATGTTAATAAGAAATTCAGCAA
EST: gi|67572285|gb|BJ945109.1|BJ945109
EST:     TCGGCCCGCAAGAGGACGTTGTTGAAAGTTATCATCCTCGGTGATAGCGG                         GGTTGGAAAGACTTCTTTGATGAATCAGTATGTTAATAAGAAATTCAGCAA
genomic: TCGGCCCGCAAGAGGACGTTGTTGAAAGTTATCATCCTCGGTGATAGCGGgtatggtagt ... gtgatgacagGGTTGGAAAGACTTCTTTGATGAATCAGTATGTTAATAAGAAATTCAGCAA
EST: gi|208383813|gb|DC915152.1|DC915152
EST:     TCGGCCCGCAAGAGGACGTTGTTGAAAGTTATCATCCTCGGTGATAGCGG                         GGTTGGAAAGACTTCTTTGATGAATCAGTATGTTAATAAGAAATTCAGCAA
genomic: TCGGCCCGCAAGAGGACGTTGTTGAAAGTTATCATCCTCGGTGATAGCGGgtatggtagt ... gtgatgacagGGTTGGAAAGACTTCTTTGATGAATCAGTATGTTAATAAGAAATTCAGCAA
EST: gi|100383933|gb|BY987190.1|BY987190
EST:     TCGGCCCGCAAGAGGACGTTGTTGAAAGTTATCATCCTCGGTGATAGCGG                         GGTTGGAAAGACTTCTTTGATGAATCAGTATGTTAATAAGAAATTCAGCAA
genomic: TCGGCCCGCAAGAGGACGTTGTTGAAAGTTATCATCCTCGGTGATAGCGGgtatggtagt ... gtgatgacagGGTTGGAAAGACTTCTTTGATGAATCAGTATGTTAATAAGAAATTCAGCAA
EST: gi|100443114|gb|BY981740.1|BY981740
EST:     TCGGCCCGCAAGAGGACGTTGTTGAAAGTTATCATCCTCGGTGATAGCGG                         GGTTGGAAAGACTTCTTTGATGAATCAGTATGTTAATAAGAAATTCAGCAA
genomic: TCGGCCCGCAAGAGGACGTTGTTGAAAGTTATCATCCTCGGTGATAGCGGgtatggtagt ... gtgatgacagGGTTGGAAAGACTTCTTTGATGAATCAGTATGTTAATAAGAAATTCAGCAA
EST: gi|100374250|gb|BY985734.1|BY985734
EST:     TCGGCCCGCAAGAGGACGTTGTTGAAAGTTATCATCCTCGGTGATAGCGG                         GGTTGGAAAGACTTCTTTGATGAATCAGTATGTTAATAAGAAATTCAGCAA
genomic: TCGGCCCGCAAGAGGACGTTGTTGAAAGTTATCATCCTCGGTGATAGCGGgtatggtagt ... gtgatgacagGGTTGGAAAGACTTCTTTGATGAATCAGTATGTTAATAAGAAATTCAGCAA
EST: gi|100409462|gb|BY992023.1|BY992023
EST:     TCGGCCCGCAAGAGGACGTTGTTGAAAGTTATCATCCTCGGTGATAGCGG                         GGTTGGAAAGACTTCTTTGATGAATCAGTATGTTAATAAGAAATTCAGCAA
genomic: TCGGCCCGCAAGAGGACGTTGTTGAAAGTTATCATCCTCGGTGATAGCGGgtatggtagt ... gtgatgacagGGTTGGAAAGACTTCTTTGATGAATCAGTATGTTAATAAGAAATTCAGCAA
EST: gi|162162113|gb|FC338904.1|FC338904
EST:     TCGGCCCGCAAGAGGACGTTGTTGAAAGTTATCATCCTCGGTGATAGCGG                         GGTTGGAAAGACTTCTTTGATGAATCAGTATGTTAATAAGAAATTCAGCAA
genomic: TCGGCCCGCAAGAGGACGTTGTTGAAAGTTATCATCCTCGGTGATAGCGGgtatggtagt ... gtgatgacagGGTTGGAAAGACTTCTTTGATGAATCAGTATGTTAATAAGAAATTCAGCAA
EST: gi|208377828|gb|DC940940.1|DC940940
EST:     TCGGCCCGCAAGAGGACGTTGTTGAAAGTTATCATCCTCGGTGATAGCGG                         GGTTGGAAAGACTTCTTTGATGAATCAGTATGTTAATAAGAAATTCAGCAA
genomic: TCGGCCCGCAAGAGGACGTTGTTGAAAGTTATCATCCTCGGTGATAGCGGgtatggtagt ... gtgatgacagGGTTGGAAAGACTTCTTTGATGAATCAGTATGTTAATAAGAAATTCAGCAA
EST: gi|162263652|gb|FC438888.1|FC438888
EST:     TCGGCCCGCAAGAGGACGTTGTTGAAAGTTATCATCCTCGGTGATAGCGG                         GGTTGGAAAGACTTCTTTGATGAATCAGTATGTTAATAAGAAATTCAGCAA
genomic: TCGGCCCGCAAGAGGACGTTGTTGAAAGTTATCATCCTCGGTGATAGCGGgtatggtagt ... gtgatgacagGGTTGGAAAGACTTCTTTGATGAATCAGTATGTTAATAAGAAATTCAGCAA
EST: gi|100403295|gb|BY991132.1|BY991132
EST:     TCGGCCCGCAAGAGGACGTTGTTGAAAGTTATCATCCTCGGTGATAGCGG                         GGTTGGAAAGACTTCTTTGATGAATCAGTATGTTAATAAGAAATTCAGCAA
genomic: TCGGCCCGCAAGAGGACGTTGTTGAAAGTTATCATCCTCGGTGATAGCGGgtatggtagt ... gtgatgacagGGTTGGAAAGACTTCTTTGATGAATCAGTATGTTAATAAGAAATTCAGCAA
EST: gi|100371248|gb|BY986011.1|BY986011
EST:     TCGGCCCGCAAGAGGACGTTGTTGAAAGTTATCATCCTCGGTGATAGCGG                         GGTTGGAAAGACTTCTTTGATGAATCAGTATGTTAATAAGAAATTCAGCAA
genomic: TCGGCCCGCAAGAGGACGTTGTTGAAAGTTATCATCCTCGGTGATAGCGGgtatggtagt ... gtgatgacagGGTTGGAAAGACTTCTTTGATGAATCAGTATGTTAATAAGAAATTCAGCAA
EST: gi|100389472|gb|BY988950.1|BY988950
EST:     TCGGCCCGCAAGAGGACGTTGTTGAAAGTTATCATCCTCGGTGATAGCGG                         GGTTGGAAAGACTTCTTTGATGAATCAGTATGTTAATAAGAAATTCAGCAA
genomic: TCGGCCCGCAAGAGGACGTTGTTGAAAGTTATCATCCTCGGTGATAGCGGgtatggtagt ... gtgatgacagGGTTGGAAAGACTTCTTTGATGAATCAGTATGTTAATAAGAAATTCAGCAA
EST: gi|100424769|gb|BY976806.1|BY976806
EST:     TCGGCCCGCAAGAGGACGTTGTTGAAAGTTATCATCCTCGGTGATAGCGG                         GGTTGGAAAGACTTCTTTGATGAATCAGTATGTTAATAAGAAATTCAGCAA
genomic: TCGGCCCGCAAGAGGACGTTGTTGAAAGTTATCATCCTCGGTGATAGCGGgtatggtagt ... gtgatgacagGGTTGGAAAGACTTCTTTGATGAATCAGTATGTTAATAAGAAATTCAGCAA

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), 35 (downstream exon)
Score: 58

TGTGAGGGTTAAGAATTGGAAGCAGGAGATTGGAGAATCAGTCTGCGATGTCGGCCCGCAAGAGGACGTTGTTGAAAGTTATCATCCTCGGTGATAGCGGgtatggtagt ... gtgatgacagGGTTGGAAAGACTTCTTTGATGAATCAGTATGTTAATAAGAAATTCAGCAATCAATATAAGGCCACTATTGGGGCAGACTTTCTAACTAAGGAAGTGCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgtgatatcctctgtatagttgaaatcctggtcttctttgtttggtgatgacagGGTTGGAAAGACTTCTTTGATGAATCAGTATGTTAATAAGAAATTCAGCAATCAATATAAGGCCACTATTGGGGCAGACTTTCTAACTAAGGAAGTGCAG
               tatagtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gaagcatgccttcgctctttcattgtctagtgccaagcgtgaaatctgtgatatcctctgtatagttgaaatcctggtcttctttgtttggtgatgacagGGTTGGAAAGACTTCTTTGATGAATCAGTATGTTAATAAGAAATTCAGCAATCAATATAAGGCCACTATTGGGGCAGACTTTCTAACTAAGGAAGTGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA